diff --git a/docs/response_time_testing.md b/docs/response_time_testing.md new file mode 100644 index 00000000..1f78da85 --- /dev/null +++ b/docs/response_time_testing.md @@ -0,0 +1,24 @@ +# End-to-end and Response Time Testing + +The current state of the IGVF Catalog API can be evaluated by running the `response_times.py` script present at `tests/response_times`. + +The `urls.txt` file contains a list of API calls covering all available endpoints of the IGVF Catalog Production API with a combination of params. This file serves as input for the testing script. + +Each JSON response for each API call will be stored in a folder called `responses`. Each filename is an MD5 of the entire URL string, so we avoid very large filenames. If a conflicting response from a previous execution is already present in the folder, the script will compare values. Any differences in any response will be reported in the `differences.txt` file. + +In case any endpoint fails (HTTP response != 200), the error message will be printed on the screen and saved in the `responses` folder. + +Each response time will be stored in the `average_response_time.csv` file. If the same call has already been performed and stored in the CSV file, the script will compute the average between the response times and save in the same CSV file. It gives the feature of running the script multiple times to get fair response time values. + +Testing against our development environment is also available by running the same script and setting the global variable `TEST_DEV = True` at the top of the script. + +``` +$ tests/response_times> cd tests/response_times; python3 response_times.py +Fetching: https://api.catalog.igvf.org/api/variants?spdi=NC_000020.11%3A3658947%3AA%3AG&organism=Homo%20sapiens&page=0 +Fetching: https://api.catalog.igvf.org/api/variants?hgvs=NC_000020.11%3Ag.3658948A%3EG&organism=Homo%20sapiens&page=0 +Fetching: https://api.catalog.igvf.org/api/variants?region=chr1%3A1157520-1158189&organism=Homo%20sapiens&page=0 +Fetching: https://api.catalog.igvf.org/api/variants?mouse_strain=A_J&organism=Mus%20musculus&page=0 +... + +Saved responses in 'responses/', average times in 'average_response_time.csv', and differences in 'differences.txt' if any. +``` diff --git a/tests/acceptance_tests/api_test.py b/tests/acceptance_tests/api_test.py deleted file mode 100644 index eb37d681..00000000 --- a/tests/acceptance_tests/api_test.py +++ /dev/null @@ -1,131 +0,0 @@ -# execute with: $ pytest -# check catalog_api_response_times.txt file for report on response times - -import requests -import logging -import http.client as http_client -from datetime import datetime -import pytest - -from regulatory_regions import regulatory_regions -from genes import genes -from transcripts import transcripts -from proteins import proteins -from gene_transcripts import genes_transcripts -from transcripts_genes import transcripts_genes -from genes_proteins import genes_proteins -from proteins_genes import proteins_genes -from transcripts_proteins import transcripts_proteins -from proteins_transcripts import proteins_transcripts -from genes_genes import genes_genes -from variants import variants -from eqtls import eqtls -from sqtls import sqtls -from variants_genes import variants_genes -from genes_variants import genes_variants -from phenotypes_variants import phenotypes_variants -from variants_phenotypes import variants_phenotypes -from variants_ld import variants_ld -from motifs import motifs -from diseases_genes import diseases_genes -from genes_diseases import genes_diseases -from ontology_terms import ontology_terms -from complexes import complexes -from complexes_proteins import complexes_proteins -from proteins_complexes import proteins_complexes -from motifs_proteins import motifs_proteins -from proteins_motifs import proteins_motifs -from regulatory_regions_genes import regulatory_regions_genes -from genes_regulatory_regions import genes_regulatory_regions -from drugs import drugs -from drugs_variants import drugs_variants -from variants_drugs import variants_drugs -from studies import studies -from proteins_proteins import proteins_proteins -from regulatory_regions_biosamples import regulatory_regions_biosamples -from biosamples_regulatory_regions import biosamples_regulatory_regions -from coding_variants import coding_variants - -API = 'http://localhost:2023/api' - -http_client.HTTPConnection.debuglevel = 1 - -logging.basicConfig() -logging.getLogger().setLevel(logging.DEBUG) - -requests_log = logging.getLogger('requests.packages.urllib3') -requests_log.setLevel(logging.DEBUG) -requests_log.propagate = True - -requests_report = logging.getLogger('response_times') -requests_report.setLevel(logging.INFO) -requests_report.propagate = True - - -TESTS = { - **regulatory_regions, - **genes, - **transcripts, - **proteins, - **genes_transcripts, - **transcripts_genes, - **genes_proteins, - **proteins_genes, - **transcripts_proteins, - **proteins_transcripts, - **genes_genes, - **variants, - **eqtls, - **sqtls, - **variants_genes, - **genes_variants, - **phenotypes_variants, - **variants_phenotypes, - **variants_ld, - **motifs, - **diseases_genes, - **genes_diseases, - **ontology_terms, - **complexes, - **complexes_proteins, - **proteins_complexes, - **motifs_proteins, - **proteins_motifs, - **regulatory_regions_genes, - **genes_regulatory_regions, - **drugs, - **drugs_variants, - **variants_drugs, - **studies, - **proteins_proteins, - **regulatory_regions_biosamples, - **biosamples_regulatory_regions, - **coding_variants -} - - -@pytest.mark.parametrize('endpoint', TESTS.keys()) -class TestAPI(object): - response_times = {} - - def teardown_class(self): - with open('catalog_api_response_times.txt', 'w') as output: - output.write(API + '\n') - output.write(datetime.now().strftime('%d/%m/%Y %H:%M:%S') + '\n') - for key in TestAPI.response_times.keys(): - output.write( - key + '\t' + str(TestAPI.response_times[key]) + 's\n') - - def test_endpoints(self, endpoint): - url = API + endpoint - - for test in TESTS[endpoint]: - if test.get('params_url'): - url = API + endpoint.format(**test['params_url']) - - response = requests.get(url, params=test.get('params')) - - assert response.status_code == 200 - assert response.json() == test['response'] - TestAPI.response_times[response.url] = response.elapsed.total_seconds( - ) diff --git a/tests/acceptance_tests/biosamples_regulatory_regions.py b/tests/acceptance_tests/biosamples_regulatory_regions.py deleted file mode 100644 index 7f6c65a3..00000000 --- a/tests/acceptance_tests/biosamples_regulatory_regions.py +++ /dev/null @@ -1,570 +0,0 @@ -biosamples_regulatory_regions = { - '/biosamples/regulatory_regions': [{ - 'params': { - 'type': 'MPRA_expression_tested', - 'term_id': 'EFO_0001187', - 'term_name': 'hepg2', - 'verbose': 'false' - }, - 'response': [ - { - 'regulatory region': 'regulatory_regions/MPRA_chr1_100219984_100220184_GRCh38', - 'activity_score': 0.032, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - { - 'regulatory region': 'regulatory_regions/MPRA_chr1_100323595_100323795_GRCh38', - 'activity_score': -0.823, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - { - 'regulatory region': 'regulatory_regions/MPRA_chr1_100362940_100363140_GRCh38', - 'activity_score': 1.652, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - { - 'regulatory region': 'regulatory_regions/MPRA_chr1_100362973_100363173_GRCh38', - 'activity_score': 1.087, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - { - 'regulatory region': 'regulatory_regions/MPRA_chr1_100396066_100396266_GRCh38', - 'activity_score': -1.397, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - { - 'regulatory region': 'regulatory_regions/MPRA_chr1_100400441_100400641_GRCh38', - 'activity_score': 0.196, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - { - 'regulatory region': 'regulatory_regions/MPRA_chr1_100413104_100413304_GRCh38', - 'activity_score': -0.773, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - { - 'regulatory region': 'regulatory_regions/MPRA_chr1_100463785_100463985_GRCh38', - 'activity_score': 0.3, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - { - 'regulatory region': 'regulatory_regions/MPRA_chr1_100463814_100464014_GRCh38', - 'activity_score': 0.043, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - { - 'regulatory region': 'regulatory_regions/MPRA_chr1_100485894_100486094_GRCh38', - 'activity_score': -0.106, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - { - 'regulatory region': 'regulatory_regions/MPRA_chr1_100597374_100597574_GRCh38', - 'activity_score': -0.873, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - { - 'regulatory region': 'regulatory_regions/MPRA_chr1_10065440_10065640_GRCh38', - 'activity_score': -0.134, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - { - 'regulatory region': 'regulatory_regions/MPRA_chr1_10065472_10065672_GRCh38', - 'activity_score': -0.202, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - { - 'regulatory region': 'regulatory_regions/MPRA_chr1_100760579_100760779_GRCh38', - 'activity_score': -1.207, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - { - 'regulatory region': 'regulatory_regions/MPRA_chr1_100775574_100775774_GRCh38', - 'activity_score': 0.131, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - { - 'regulatory region': 'regulatory_regions/MPRA_chr1_100794809_100795009_GRCh38', - 'activity_score': -1.128, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - { - 'regulatory region': 'regulatory_regions/MPRA_chr1_100810477_100810677_GRCh38', - 'activity_score': -0.693, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - { - 'regulatory region': 'regulatory_regions/MPRA_chr1_100820306_100820506_GRCh38', - 'activity_score': -0.473, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - { - 'regulatory region': 'regulatory_regions/MPRA_chr1_100820330_100820530_GRCh38', - 'activity_score': 0.047, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - { - 'regulatory region': 'regulatory_regions/MPRA_chr1_100823534_100823734_GRCh38', - 'activity_score': -0.597, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - { - 'regulatory region': 'regulatory_regions/MPRA_chr1_10085242_10085442_GRCh38', - 'activity_score': -0.736, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - { - 'regulatory region': 'regulatory_regions/MPRA_chr1_100928230_100928430_GRCh38', - 'activity_score': -0.422, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - { - 'regulatory region': 'regulatory_regions/MPRA_chr1_100949583_100949783_GRCh38', - 'activity_score': 0.539, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - { - 'regulatory region': 'regulatory_regions/MPRA_chr1_100949595_100949795_GRCh38', - 'activity_score': 0.6, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - { - 'regulatory region': 'regulatory_regions/MPRA_chr1_101003084_101003284_GRCh38', - 'activity_score': -1.316, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - } - ]}, { - 'params': { - 'type': 'MPRA_expression_tested', - 'term_id': 'EFO_0001187', - 'term_name': 'hepg2', - 'verbose': 'true' - }, - 'response': [ - { - 'regulatory region': { - 'chr': 'chr1', - 'start': 100219984, - 'end': 100220184, - 'name': 'MPRA_chr1_100219984_100220184_GRCh38', - 'biochemical_activity': None, - 'biochemical_activity_description': None, - 'type': 'MPRA_tested_regulatory_element', - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - 'activity_score': 0.032, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - { - 'regulatory region': { - 'chr': 'chr1', - 'start': 100323595, - 'end': 100323795, - 'name': 'MPRA_chr1_100323595_100323795_GRCh38', - 'biochemical_activity': None, - 'biochemical_activity_description': None, - 'type': 'MPRA_tested_regulatory_element', - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - 'activity_score': -0.823, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - { - 'regulatory region': { - 'chr': 'chr1', - 'start': 100362940, - 'end': 100363140, - 'name': 'MPRA_chr1_100362940_100363140_GRCh38', - 'biochemical_activity': None, - 'biochemical_activity_description': None, - 'type': 'MPRA_tested_regulatory_element', - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - 'activity_score': 1.652, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - { - 'regulatory region': { - 'chr': 'chr1', - 'start': 100362973, - 'end': 100363173, - 'name': 'MPRA_chr1_100362973_100363173_GRCh38', - 'biochemical_activity': None, - 'biochemical_activity_description': None, - 'type': 'MPRA_tested_regulatory_element', - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - 'activity_score': 1.087, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - { - 'regulatory region': { - 'chr': 'chr1', - 'start': 100396066, - 'end': 100396266, - 'name': 'MPRA_chr1_100396066_100396266_GRCh38', - 'biochemical_activity': None, - 'biochemical_activity_description': None, - 'type': 'MPRA_tested_regulatory_element', - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - 'activity_score': -1.397, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - { - 'regulatory region': { - 'chr': 'chr1', - 'start': 100400441, - 'end': 100400641, - 'name': 'MPRA_chr1_100400441_100400641_GRCh38', - 'biochemical_activity': None, - 'biochemical_activity_description': None, - 'type': 'MPRA_tested_regulatory_element', - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - 'activity_score': 0.196, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - { - 'regulatory region': { - 'chr': 'chr1', - 'start': 100413104, - 'end': 100413304, - 'name': 'MPRA_chr1_100413104_100413304_GRCh38', - 'biochemical_activity': None, - 'biochemical_activity_description': None, - 'type': 'MPRA_tested_regulatory_element', - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - 'activity_score': -0.773, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - { - 'regulatory region': { - 'chr': 'chr1', - 'start': 100463785, - 'end': 100463985, - 'name': 'MPRA_chr1_100463785_100463985_GRCh38', - 'biochemical_activity': None, - 'biochemical_activity_description': None, - 'type': 'MPRA_tested_regulatory_element', - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - 'activity_score': 0.3, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - { - 'regulatory region': { - 'chr': 'chr1', - 'start': 100463814, - 'end': 100464014, - 'name': 'MPRA_chr1_100463814_100464014_GRCh38', - 'biochemical_activity': None, - 'biochemical_activity_description': None, - 'type': 'MPRA_tested_regulatory_element', - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - 'activity_score': 0.043, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - { - 'regulatory region': { - 'chr': 'chr1', - 'start': 100485894, - 'end': 100486094, - 'name': 'MPRA_chr1_100485894_100486094_GRCh38', - 'biochemical_activity': None, - 'biochemical_activity_description': None, - 'type': 'MPRA_tested_regulatory_element', - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - 'activity_score': -0.106, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - { - 'regulatory region': { - 'chr': 'chr1', - 'start': 100597374, - 'end': 100597574, - 'name': 'MPRA_chr1_100597374_100597574_GRCh38', - 'biochemical_activity': None, - 'biochemical_activity_description': None, - 'type': 'MPRA_tested_regulatory_element', - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - 'activity_score': -0.873, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - { - 'regulatory region': { - 'chr': 'chr1', - 'start': 10065440, - 'end': 10065640, - 'name': 'MPRA_chr1_10065440_10065640_GRCh38', - 'biochemical_activity': None, - 'biochemical_activity_description': None, - 'type': 'MPRA_tested_regulatory_element', - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - 'activity_score': -0.134, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - { - 'regulatory region': { - 'chr': 'chr1', - 'start': 10065472, - 'end': 10065672, - 'name': 'MPRA_chr1_10065472_10065672_GRCh38', - 'biochemical_activity': None, - 'biochemical_activity_description': None, - 'type': 'MPRA_tested_regulatory_element', - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - 'activity_score': -0.202, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - { - 'regulatory region': { - 'chr': 'chr1', - 'start': 100760579, - 'end': 100760779, - 'name': 'MPRA_chr1_100760579_100760779_GRCh38', - 'biochemical_activity': None, - 'biochemical_activity_description': None, - 'type': 'MPRA_tested_regulatory_element', - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - 'activity_score': -1.207, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - { - 'regulatory region': { - 'chr': 'chr1', - 'start': 100775574, - 'end': 100775774, - 'name': 'MPRA_chr1_100775574_100775774_GRCh38', - 'biochemical_activity': None, - 'biochemical_activity_description': None, - 'type': 'MPRA_tested_regulatory_element', - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - 'activity_score': 0.131, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - { - 'regulatory region': { - 'chr': 'chr1', - 'start': 100794809, - 'end': 100795009, - 'name': 'MPRA_chr1_100794809_100795009_GRCh38', - 'biochemical_activity': None, - 'biochemical_activity_description': None, - 'type': 'MPRA_tested_regulatory_element', - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - 'activity_score': -1.128, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - { - 'regulatory region': { - 'chr': 'chr1', - 'start': 100810477, - 'end': 100810677, - 'name': 'MPRA_chr1_100810477_100810677_GRCh38', - 'biochemical_activity': None, - 'biochemical_activity_description': None, - 'type': 'MPRA_tested_regulatory_element', - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - 'activity_score': -0.693, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - { - 'regulatory region': { - 'chr': 'chr1', - 'start': 100820306, - 'end': 100820506, - 'name': 'MPRA_chr1_100820306_100820506_GRCh38', - 'biochemical_activity': None, - 'biochemical_activity_description': None, - 'type': 'MPRA_tested_regulatory_element', - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - 'activity_score': -0.473, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - { - 'regulatory region': { - 'chr': 'chr1', - 'start': 100820330, - 'end': 100820530, - 'name': 'MPRA_chr1_100820330_100820530_GRCh38', - 'biochemical_activity': None, - 'biochemical_activity_description': None, - 'type': 'MPRA_tested_regulatory_element', - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - 'activity_score': 0.047, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - { - 'regulatory region': { - 'chr': 'chr1', - 'start': 100823534, - 'end': 100823734, - 'name': 'MPRA_chr1_100823534_100823734_GRCh38', - 'biochemical_activity': None, - 'biochemical_activity_description': None, - 'type': 'MPRA_tested_regulatory_element', - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - 'activity_score': -0.597, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - { - 'regulatory region': { - 'chr': 'chr1', - 'start': 10085242, - 'end': 10085442, - 'name': 'MPRA_chr1_10085242_10085442_GRCh38', - 'biochemical_activity': None, - 'biochemical_activity_description': None, - 'type': 'MPRA_tested_regulatory_element', - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - 'activity_score': -0.736, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - { - 'regulatory region': { - 'chr': 'chr1', - 'start': 100928230, - 'end': 100928430, - 'name': 'MPRA_chr1_100928230_100928430_GRCh38', - 'biochemical_activity': None, - 'biochemical_activity_description': None, - 'type': 'MPRA_tested_regulatory_element', - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - 'activity_score': -0.422, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - { - 'regulatory region': { - 'chr': 'chr1', - 'start': 100949583, - 'end': 100949783, - 'name': 'MPRA_chr1_100949583_100949783_GRCh38', - 'biochemical_activity': None, - 'biochemical_activity_description': None, - 'type': 'MPRA_tested_regulatory_element', - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - 'activity_score': 0.539, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - { - 'regulatory region': { - 'chr': 'chr1', - 'start': 100949595, - 'end': 100949795, - 'name': 'MPRA_chr1_100949595_100949795_GRCh38', - 'biochemical_activity': None, - 'biochemical_activity_description': None, - 'type': 'MPRA_tested_regulatory_element', - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - 'activity_score': 0.6, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - { - 'regulatory region': { - 'chr': 'chr1', - 'start': 101003084, - 'end': 101003284, - 'name': 'MPRA_chr1_101003084_101003284_GRCh38', - 'biochemical_activity': None, - 'biochemical_activity_description': None, - 'type': 'MPRA_tested_regulatory_element', - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - }, - 'activity_score': -1.316, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/' - } - ] - }] -} diff --git a/tests/acceptance_tests/coding_variants.py b/tests/acceptance_tests/coding_variants.py deleted file mode 100644 index 20ab6dc7..00000000 --- a/tests/acceptance_tests/coding_variants.py +++ /dev/null @@ -1,572 +0,0 @@ -coding_variants = { - '/coding_variants': [{ - 'params': { - 'gene_mame': 'CPX-6163', - 'position': 'range:0-2', - 'transcript_id': 'ENST00000641515' - }, - 'response': [ - { - 'id': '0b46cd82904e6c35986745140f32ad1e2bf7032ab1158770a2d4f6c43ee37741', - 'name': 'OR4F5_c.1A>G', - 'ref': 'M', - 'alt': 'V', - 'protein_name': None, - 'gene_name': 'OR4F5', - 'transcript_id': 'ENST00000641515', - 'aapos': 1, - 'hgvs': None, - 'refcodon': 'ATG', - 'codonpos': None, - 'SIFT_score': None, - 'SIFT4G_score': None, - 'Polyphen2_HDIV_score': None, - 'Polyphen2_HVAR_score': None, - 'VEST4_score': None, - 'Mcap_score': None, - 'REVEL_score': None, - 'MutPred_score': None, - 'BayesDel_addAF_score': None, - 'BayesDel_noAF_score': None, - 'VARITY_R_score': None, - 'VARITY_ER_score': None, - 'VARITY_R_LOO_score': None, - 'VARITY_ER_LOO_score': None, - 'ESM1b_score': None, - 'EVE_score': None, - 'AlphaMissense_score': None, - 'CADD_raw_score': 1.885325, - 'source': 'dbSNFP 4.5a', - 'source_url': 'http://database.liulab.science/dbNSFP' - }, - { - 'id': '1da95eddb53c644399be6839958647bc8587f087a51504a5e6ac51011d7bec31', - 'name': 'OR4F5_c.4A>C', - 'ref': 'K', - 'alt': 'Q', - 'protein_name': None, - 'gene_name': 'OR4F5', - 'transcript_id': 'ENST00000641515', - 'aapos': 2, - 'hgvs': None, - 'refcodon': 'AAG', - 'codonpos': None, - 'SIFT_score': None, - 'SIFT4G_score': None, - 'Polyphen2_HDIV_score': None, - 'Polyphen2_HVAR_score': None, - 'VEST4_score': None, - 'Mcap_score': None, - 'REVEL_score': None, - 'MutPred_score': None, - 'BayesDel_addAF_score': None, - 'BayesDel_noAF_score': None, - 'VARITY_R_score': None, - 'VARITY_ER_score': None, - 'VARITY_R_LOO_score': None, - 'VARITY_ER_LOO_score': None, - 'ESM1b_score': None, - 'EVE_score': None, - 'AlphaMissense_score': 0.0938, - 'CADD_raw_score': 1.964888, - 'source': 'dbSNFP 4.5a', - 'source_url': 'http://database.liulab.science/dbNSFP' - }, - { - 'id': '22c9b96e0d2438cfd8d186ed610f155f478dce2aa34dcbec07dd8c2af6302c23', - 'name': 'OR4F5_c.4A>G', - 'ref': 'K', - 'alt': 'E', - 'protein_name': None, - 'gene_name': 'OR4F5', - 'transcript_id': 'ENST00000641515', - 'aapos': 2, - 'hgvs': None, - 'refcodon': 'AAG', - 'codonpos': None, - 'SIFT_score': None, - 'SIFT4G_score': None, - 'Polyphen2_HDIV_score': None, - 'Polyphen2_HVAR_score': None, - 'VEST4_score': None, - 'Mcap_score': None, - 'REVEL_score': None, - 'MutPred_score': None, - 'BayesDel_addAF_score': None, - 'BayesDel_noAF_score': None, - 'VARITY_R_score': None, - 'VARITY_ER_score': None, - 'VARITY_R_LOO_score': None, - 'VARITY_ER_LOO_score': None, - 'ESM1b_score': None, - 'EVE_score': None, - 'AlphaMissense_score': 0.0766, - 'CADD_raw_score': 1.994556, - 'source': 'dbSNFP 4.5a', - 'source_url': 'http://database.liulab.science/dbNSFP' - }, - { - 'id': '281bdc888e740f1da3a69a59b83735a23a6ee819417d35a05ead83cdd4cae6e9', - 'name': 'OR4F5_c.4A>T', - 'ref': 'K', - 'alt': 'X', - 'protein_name': None, - 'gene_name': 'OR4F5', - 'transcript_id': 'ENST00000641515', - 'aapos': 2, - 'hgvs': None, - 'refcodon': 'AAG', - 'codonpos': None, - 'SIFT_score': None, - 'SIFT4G_score': None, - 'Polyphen2_HDIV_score': None, - 'Polyphen2_HVAR_score': None, - 'VEST4_score': None, - 'Mcap_score': None, - 'REVEL_score': None, - 'MutPred_score': None, - 'BayesDel_addAF_score': None, - 'BayesDel_noAF_score': None, - 'VARITY_R_score': None, - 'VARITY_ER_score': None, - 'VARITY_R_LOO_score': None, - 'VARITY_ER_LOO_score': None, - 'ESM1b_score': None, - 'EVE_score': None, - 'AlphaMissense_score': None, - 'CADD_raw_score': 1.951402, - 'source': 'dbSNFP 4.5a', - 'source_url': 'http://database.liulab.science/dbNSFP' - }, - { - 'id': '3f6c915bd9fd97fb15cc71847a278cf94b05eaf3b9f3432fa8a0d863f12594f8', - 'name': 'OR4F5_c.5A>G', - 'ref': 'K', - 'alt': 'R', - 'protein_name': None, - 'gene_name': 'OR4F5', - 'transcript_id': 'ENST00000641515', - 'aapos': 2, - 'hgvs': None, - 'refcodon': 'AAG', - 'codonpos': None, - 'SIFT_score': None, - 'SIFT4G_score': None, - 'Polyphen2_HDIV_score': None, - 'Polyphen2_HVAR_score': None, - 'VEST4_score': None, - 'Mcap_score': None, - 'REVEL_score': None, - 'MutPred_score': None, - 'BayesDel_addAF_score': None, - 'BayesDel_noAF_score': None, - 'VARITY_R_score': None, - 'VARITY_ER_score': None, - 'VARITY_R_LOO_score': None, - 'VARITY_ER_LOO_score': None, - 'ESM1b_score': None, - 'EVE_score': None, - 'AlphaMissense_score': 0.0756, - 'CADD_raw_score': 1.891145, - 'source': 'dbSNFP 4.5a', - 'source_url': 'http://database.liulab.science/dbNSFP' - }, - { - 'id': '65b4d2052dd48f5d038712f37d268b66a480339165b4b1c6b2ea04d182a75482', - 'name': 'OR4F5_c.3G>C', - 'ref': 'M', - 'alt': 'I', - 'protein_name': None, - 'gene_name': 'OR4F5', - 'transcript_id': 'ENST00000641515', - 'aapos': 1, - 'hgvs': None, - 'refcodon': 'ATG', - 'codonpos': None, - 'SIFT_score': None, - 'SIFT4G_score': None, - 'Polyphen2_HDIV_score': None, - 'Polyphen2_HVAR_score': None, - 'VEST4_score': None, - 'Mcap_score': None, - 'REVEL_score': None, - 'MutPred_score': None, - 'BayesDel_addAF_score': None, - 'BayesDel_noAF_score': None, - 'VARITY_R_score': None, - 'VARITY_ER_score': None, - 'VARITY_R_LOO_score': None, - 'VARITY_ER_LOO_score': None, - 'ESM1b_score': None, - 'EVE_score': None, - 'AlphaMissense_score': None, - 'CADD_raw_score': 1.846542, - 'source': 'dbSNFP 4.5a', - 'source_url': 'http://database.liulab.science/dbNSFP' - }, - { - 'id': '68f3083fd8e73095a54fa027d878078bf3998f63509758248f1cab56cab4cc08', - 'name': 'OR4F5_c.2T>G', - 'ref': 'M', - 'alt': 'R', - 'protein_name': None, - 'gene_name': 'OR4F5', - 'transcript_id': 'ENST00000641515', - 'aapos': 1, - 'hgvs': None, - 'refcodon': 'ATG', - 'codonpos': None, - 'SIFT_score': None, - 'SIFT4G_score': None, - 'Polyphen2_HDIV_score': None, - 'Polyphen2_HVAR_score': None, - 'VEST4_score': None, - 'Mcap_score': None, - 'REVEL_score': None, - 'MutPred_score': None, - 'BayesDel_addAF_score': None, - 'BayesDel_noAF_score': None, - 'VARITY_R_score': None, - 'VARITY_ER_score': None, - 'VARITY_R_LOO_score': None, - 'VARITY_ER_LOO_score': None, - 'ESM1b_score': None, - 'EVE_score': None, - 'AlphaMissense_score': None, - 'CADD_raw_score': 1.877065, - 'source': 'dbSNFP 4.5a', - 'source_url': 'http://database.liulab.science/dbNSFP' - }, - { - 'id': '82a8e174691b3e629127d3d9f7aa6306088f71b240c1607644f5a695d5064938', - 'name': 'OR4F5_c.2T>A', - 'ref': 'M', - 'alt': 'K', - 'protein_name': None, - 'gene_name': 'OR4F5', - 'transcript_id': 'ENST00000641515', - 'aapos': 1, - 'hgvs': None, - 'refcodon': 'ATG', - 'codonpos': None, - 'SIFT_score': None, - 'SIFT4G_score': None, - 'Polyphen2_HDIV_score': None, - 'Polyphen2_HVAR_score': None, - 'VEST4_score': None, - 'Mcap_score': None, - 'REVEL_score': None, - 'MutPred_score': None, - 'BayesDel_addAF_score': None, - 'BayesDel_noAF_score': None, - 'VARITY_R_score': None, - 'VARITY_ER_score': None, - 'VARITY_R_LOO_score': None, - 'VARITY_ER_LOO_score': None, - 'ESM1b_score': None, - 'EVE_score': None, - 'AlphaMissense_score': None, - 'CADD_raw_score': 1.860056, - 'source': 'dbSNFP 4.5a', - 'source_url': 'http://database.liulab.science/dbNSFP' - }, - { - 'id': '90ba594c09d970cb10fe28e63776a60d6506c402b89102057b13eceb0457302b', - 'name': 'OR4F5_c.2T>C', - 'ref': 'M', - 'alt': 'T', - 'protein_name': None, - 'gene_name': 'OR4F5', - 'transcript_id': 'ENST00000641515', - 'aapos': 1, - 'hgvs': None, - 'refcodon': 'ATG', - 'codonpos': None, - 'SIFT_score': None, - 'SIFT4G_score': None, - 'Polyphen2_HDIV_score': None, - 'Polyphen2_HVAR_score': None, - 'VEST4_score': None, - 'Mcap_score': None, - 'REVEL_score': None, - 'MutPred_score': None, - 'BayesDel_addAF_score': None, - 'BayesDel_noAF_score': None, - 'VARITY_R_score': None, - 'VARITY_ER_score': None, - 'VARITY_R_LOO_score': None, - 'VARITY_ER_LOO_score': None, - 'ESM1b_score': None, - 'EVE_score': None, - 'AlphaMissense_score': None, - 'CADD_raw_score': 1.90847, - 'source': 'dbSNFP 4.5a', - 'source_url': 'http://database.liulab.science/dbNSFP' - }, - { - 'id': '90ced60fbd2417d3785c9f128f62f9db5ea4ad4c8d201340d38ea74a22d860b0', - 'name': 'OR4F5_c.3G>T', - 'ref': 'M', - 'alt': 'I', - 'protein_name': None, - 'gene_name': 'OR4F5', - 'transcript_id': 'ENST00000641515', - 'aapos': 1, - 'hgvs': None, - 'refcodon': 'ATG', - 'codonpos': None, - 'SIFT_score': None, - 'SIFT4G_score': None, - 'Polyphen2_HDIV_score': None, - 'Polyphen2_HVAR_score': None, - 'VEST4_score': None, - 'Mcap_score': None, - 'REVEL_score': None, - 'MutPred_score': None, - 'BayesDel_addAF_score': None, - 'BayesDel_noAF_score': None, - 'VARITY_R_score': None, - 'VARITY_ER_score': None, - 'VARITY_R_LOO_score': None, - 'VARITY_ER_LOO_score': None, - 'ESM1b_score': None, - 'EVE_score': None, - 'AlphaMissense_score': None, - 'CADD_raw_score': 1.834384, - 'source': 'dbSNFP 4.5a', - 'source_url': 'http://database.liulab.science/dbNSFP' - }, - { - 'id': '992678c0adc6e6e03ffece63714d09e95d12fea42c2589fe6ee130d5f2e2cfd9', - 'name': 'OR4F5_c.1A>T', - 'ref': 'M', - 'alt': 'L', - 'protein_name': None, - 'gene_name': 'OR4F5', - 'transcript_id': 'ENST00000641515', - 'aapos': 1, - 'hgvs': None, - 'refcodon': 'ATG', - 'codonpos': None, - 'SIFT_score': None, - 'SIFT4G_score': None, - 'Polyphen2_HDIV_score': None, - 'Polyphen2_HVAR_score': None, - 'VEST4_score': None, - 'Mcap_score': None, - 'REVEL_score': None, - 'MutPred_score': None, - 'BayesDel_addAF_score': None, - 'BayesDel_noAF_score': None, - 'VARITY_R_score': None, - 'VARITY_ER_score': None, - 'VARITY_R_LOO_score': None, - 'VARITY_ER_LOO_score': None, - 'ESM1b_score': None, - 'EVE_score': None, - 'AlphaMissense_score': None, - 'CADD_raw_score': 1.842172, - 'source': 'dbSNFP 4.5a', - 'source_url': 'http://database.liulab.science/dbNSFP' - }, - { - 'id': 'bea4a795cc0e646763cff04ed8eb782f26cb40f25e567e227ddef01b918ac830', - 'name': 'OR4F5_c.6G>T', - 'ref': 'K', - 'alt': 'N', - 'protein_name': None, - 'gene_name': 'OR4F5', - 'transcript_id': 'ENST00000641515', - 'aapos': 2, - 'hgvs': None, - 'refcodon': 'AAG', - 'codonpos': None, - 'SIFT_score': None, - 'SIFT4G_score': None, - 'Polyphen2_HDIV_score': None, - 'Polyphen2_HVAR_score': None, - 'VEST4_score': None, - 'Mcap_score': None, - 'REVEL_score': None, - 'MutPred_score': None, - 'BayesDel_addAF_score': None, - 'BayesDel_noAF_score': None, - 'VARITY_R_score': None, - 'VARITY_ER_score': None, - 'VARITY_R_LOO_score': None, - 'VARITY_ER_LOO_score': None, - 'ESM1b_score': None, - 'EVE_score': None, - 'AlphaMissense_score': 0.1432, - 'CADD_raw_score': 1.324232, - 'source': 'dbSNFP 4.5a', - 'source_url': 'http://database.liulab.science/dbNSFP' - }, - { - 'id': 'c0abc6e753b11dc6a0aba6efdd0e2f15e6f93685d5d284c5c5207a93210f92bc', - 'name': 'OR4F5_c.6G>C', - 'ref': 'K', - 'alt': 'N', - 'protein_name': None, - 'gene_name': 'OR4F5', - 'transcript_id': 'ENST00000641515', - 'aapos': 2, - 'hgvs': None, - 'refcodon': 'AAG', - 'codonpos': None, - 'SIFT_score': None, - 'SIFT4G_score': None, - 'Polyphen2_HDIV_score': None, - 'Polyphen2_HVAR_score': None, - 'VEST4_score': None, - 'Mcap_score': None, - 'REVEL_score': None, - 'MutPred_score': None, - 'BayesDel_addAF_score': None, - 'BayesDel_noAF_score': None, - 'VARITY_R_score': None, - 'VARITY_ER_score': None, - 'VARITY_R_LOO_score': None, - 'VARITY_ER_LOO_score': None, - 'ESM1b_score': None, - 'EVE_score': None, - 'AlphaMissense_score': 0.1432, - 'CADD_raw_score': 1.33639, - 'source': 'dbSNFP 4.5a', - 'source_url': 'http://database.liulab.science/dbNSFP' - }, - { - 'id': 'd2f1f57ea5442013a02705310fe572dde363ace5c094fe4b4a65f9468ff8e2f0', - 'name': 'OR4F5_c.1A>C', - 'ref': 'M', - 'alt': 'L', - 'protein_name': None, - 'gene_name': 'OR4F5', - 'transcript_id': 'ENST00000641515', - 'aapos': 1, - 'hgvs': None, - 'refcodon': 'ATG', - 'codonpos': None, - 'SIFT_score': None, - 'SIFT4G_score': None, - 'Polyphen2_HDIV_score': None, - 'Polyphen2_HVAR_score': None, - 'VEST4_score': None, - 'Mcap_score': None, - 'REVEL_score': None, - 'MutPred_score': None, - 'BayesDel_addAF_score': None, - 'BayesDel_noAF_score': None, - 'VARITY_R_score': None, - 'VARITY_ER_score': None, - 'VARITY_R_LOO_score': None, - 'VARITY_ER_LOO_score': None, - 'ESM1b_score': None, - 'EVE_score': None, - 'AlphaMissense_score': None, - 'CADD_raw_score': 1.855658, - 'source': 'dbSNFP 4.5a', - 'source_url': 'http://database.liulab.science/dbNSFP' - }, - { - 'id': 'df3bc9f4b368cd035b1de6c5fd5b7befa799bc9edb760736816dd37e3aac5e14', - 'name': 'OR4F5_c.5A>T', - 'ref': 'K', - 'alt': 'M', - 'protein_name': None, - 'gene_name': 'OR4F5', - 'transcript_id': 'ENST00000641515', - 'aapos': 2, - 'hgvs': None, - 'refcodon': 'AAG', - 'codonpos': None, - 'SIFT_score': None, - 'SIFT4G_score': None, - 'Polyphen2_HDIV_score': None, - 'Polyphen2_HVAR_score': None, - 'VEST4_score': None, - 'Mcap_score': None, - 'REVEL_score': None, - 'MutPred_score': None, - 'BayesDel_addAF_score': None, - 'BayesDel_noAF_score': None, - 'VARITY_R_score': None, - 'VARITY_ER_score': None, - 'VARITY_R_LOO_score': None, - 'VARITY_ER_LOO_score': None, - 'ESM1b_score': None, - 'EVE_score': None, - 'AlphaMissense_score': 0.1732, - 'CADD_raw_score': 1.847991, - 'source': 'dbSNFP 4.5a', - 'source_url': 'http://database.liulab.science/dbNSFP' - }, - { - 'id': 'e77df952e590de549fbbc47fb3656b1b89ddc0468d0ea8bcc44ff3adae4cf39f', - 'name': 'OR4F5_c.3G>A', - 'ref': 'M', - 'alt': 'I', - 'protein_name': None, - 'gene_name': 'OR4F5', - 'transcript_id': 'ENST00000641515', - 'aapos': 1, - 'hgvs': None, - 'refcodon': 'ATG', - 'codonpos': None, - 'SIFT_score': None, - 'SIFT4G_score': None, - 'Polyphen2_HDIV_score': None, - 'Polyphen2_HVAR_score': None, - 'VEST4_score': None, - 'Mcap_score': None, - 'REVEL_score': None, - 'MutPred_score': None, - 'BayesDel_addAF_score': None, - 'BayesDel_noAF_score': None, - 'VARITY_R_score': None, - 'VARITY_ER_score': None, - 'VARITY_R_LOO_score': None, - 'VARITY_ER_LOO_score': None, - 'ESM1b_score': None, - 'EVE_score': None, - 'AlphaMissense_score': None, - 'CADD_raw_score': 1.883237, - 'source': 'dbSNFP 4.5a', - 'source_url': 'http://database.liulab.science/dbNSFP' - }, - { - 'id': 'e7fbb1367f058f9ab2688ef725e90f93991e7fe69cb217530edfad8bef1d185d', - 'name': 'OR4F5_c.5A>C', - 'ref': 'K', - 'alt': 'T', - 'protein_name': None, - 'gene_name': 'OR4F5', - 'transcript_id': 'ENST00000641515', - 'aapos': 2, - 'hgvs': None, - 'refcodon': 'AAG', - 'codonpos': None, - 'SIFT_score': None, - 'SIFT4G_score': None, - 'Polyphen2_HDIV_score': None, - 'Polyphen2_HVAR_score': None, - 'VEST4_score': None, - 'Mcap_score': None, - 'REVEL_score': None, - 'MutPred_score': None, - 'BayesDel_addAF_score': None, - 'BayesDel_noAF_score': None, - 'VARITY_R_score': None, - 'VARITY_ER_score': None, - 'VARITY_R_LOO_score': None, - 'VARITY_ER_LOO_score': None, - 'ESM1b_score': None, - 'EVE_score': None, - 'AlphaMissense_score': 0.1186, - 'CADD_raw_score': 1.861477, - 'source': 'dbSNFP 4.5a', - 'source_url': 'http://database.liulab.science/dbNSFP' - } - ] - }] -} diff --git a/tests/acceptance_tests/complexes.py b/tests/acceptance_tests/complexes.py deleted file mode 100644 index e6e13a87..00000000 --- a/tests/acceptance_tests/complexes.py +++ /dev/null @@ -1,534 +0,0 @@ -complexes = { - '/complexes': [{ - 'params': { - 'complex_id': 'CPX-6163' - }, - 'response': { - '_id': 'CPX-6163', - 'name': 'Complement factor H complex', - 'alias': [], - 'molecules': [ - 'P08603(2)' - ], - 'evidence_code': 'ECO:0000353(physical interaction evidence used in manual assertion)', - 'experimental_evidence': 'intact:EBI-25828406', - 'description': 'Glycoprotein complex of the alternative pathway (AP) of complement activation that discriminate between self-structures and foreign structures to maintain a well-balanced immune response by modulating complement activation. Downregulates the AP by enhancing dissociation of the C3bBb (CPX-5601) complexes and by acting as a cofactor for factor I (P05156) in proteolytic inactivation of already-deposited C3b (CPX-973). It inactivates C3b by competitively binding it thereby reducing available C3b molecules for the next factor, factor B (P00751), of the cascade. Binds to self markers such as glycan structures to prevent complement activation and amplification on self-surfaces. ', - 'complex_assembly': 'Homodimer', - 'complex_source': "psi-mi:\"MI:0469\"(IntAct)", - 'reactome_xref': [], - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/' - } - }, { - 'params': { - 'name': 'factor' - }, - 'response': [ - { - '_id': 'CPX-1956', - 'name': 'CCAAT-binding factor complex', - 'alias': [ - 'Nuclear transcription factor Y complex', - 'NF-Y transcription factor complex', - 'CCAAT box DNA-binding factor complex', - 'CBF complex' - ], - 'molecules': [ - 'P23511(1)', - 'P25208(1)', - 'Q13952(1)' - ], - 'evidence_code': 'ECO:0000353(physical interaction evidence used in manual assertion)', - 'experimental_evidence': 'intact:EBI-6672292', - 'description': 'Transcription factor which binds to the CCAAT box, which occurs in 30% of eukaryotic promoters and appears to be crucial for promoter activity. May also play a role in histone methylation and some acetylation through recruitment of relevant enzymes to active promoters.', - 'complex_assembly': 'Heterotrimer', - 'complex_source': "psi-mi:\"MI:0469\"(IntAct)", - 'reactome_xref': [ - 'R-HSA-381204(identity)' - ], - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/' - }, - { - '_id': 'CPX-1971', - 'name': 'E2F1-DP1 transcription factor complex', - 'alias': [ - 'E2F1-DP1 complex', - 'E2F1:DP1' - ], - 'molecules': [ - 'Q01094(1)', - 'Q14186(1)' - ], - 'evidence_code': 'ECO:0000353(physical interaction evidence used in manual assertion)', - 'experimental_evidence': 'intact:EBI-6878536', - 'description': "Transcription factor complex which binds DNA through the E2 recognition site, 5'-TTTC[CG]CGC-3', typically associated with the promoters of genes active in S phase. Activates genes that stimulate DNA synthesis and cell cycle advancement.", - 'complex_assembly': 'Heterodimer', - 'complex_source': "psi-mi:\"MI:0469\"(IntAct)", - 'reactome_xref': [], - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/' - }, - { - '_id': 'CPX-1972', - 'name': 'E2F2-DP1 transcription factor complex', - 'alias': [ - 'E2F2:DP1', - 'E2F2-DP1 complex' - ], - 'molecules': [ - 'Q14186(1)', - 'Q14209(1)' - ], - 'evidence_code': 'ECO:0005546(biological system reconstruction evidence based on paralogy evidence used in manual assertion)', - 'experimental_evidence': None, - 'description': "Transcription factor complex which binds DNA through the E2 recognition site, 5'-TTTC[CG]CGC-3', typically associated with active promoters in S phase, activating genes that stimulate DNA synthesis and cell cycle advancement.", - 'complex_assembly': 'Heterodimer', - 'complex_source': "psi-mi:\"MI:0469\"(IntAct)", - 'reactome_xref': [ - 'R-HSA-9007512(see-also)' - ], - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/' - }, - { - '_id': 'CPX-1973', - 'name': 'E2F3-DP1 transcription factor complex', - 'alias': [ - 'E2F3:DP1', - 'E2F3-DP1' - ], - 'molecules': [ - 'O00716(0)', - 'Q14186(0)' - ], - 'evidence_code': 'ECO:0005546(biological system reconstruction evidence based on paralogy evidence used in manual assertion)', - 'experimental_evidence': None, - 'description': "Transcription factor which binds DNA through the E2 recognition site, 5'-TTTC[CG]CGC-3'. Typically associated with active promoters in S phase, activating genes that stimulate DNA synthesis and cell cycle advancement.", - 'complex_assembly': [], - 'complex_source': "psi-mi:\"MI:0469\"(IntAct)", - 'reactome_xref': [ - 'R-HSA-2248825(identity)', - 'R-HSA-1227905(identity)' - ], - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/' - }, - { - '_id': 'CPX-2373', - 'name': 'General transcription factor TFIIIC complex', - 'alias': [], - 'molecules': [ - 'Q12789(0)', - 'Q8WUA4(0)', - 'Q969F1(0)', - 'Q9UKN8(0)', - 'Q9Y5Q8(0)', - 'Q9Y5Q9(0)' - ], - 'evidence_code': 'ECO:0000353(physical interaction evidence used in manual assertion)', - 'experimental_evidence': 'intact:EBI-36480786', - 'description': 'Transcription factor required for Pol III transcription complex assembly. Mediates tRNA and 5S RNA gene activation by binding to intragenic promoter elements. Assembles the initiation complex TFIIIB (CPX-2396/CPX-2397)-TFIIIC-tDNA upstream of the transcription start site, which is sufficient for RNA polymerase III (CPX-2393/CPX-7482) recruitment and function.', - 'complex_assembly': [], - 'complex_source': "psi-mi:\"MI:0469\"(IntAct)", - 'reactome_xref': [ - 'R-HSA-83698(see-also)' - ], - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/' - }, - { - '_id': 'CPX-1074', - 'name': 'SF1-U2AF65 splicing factor complex', - 'alias': [], - 'molecules': [ - 'P26368(1)', - 'Q15637(1)' - ], - 'evidence_code': 'ECO:0000353(physical interaction evidence used in manual assertion)', - 'experimental_evidence': 'intact:EBI-11300976', - 'description': 'Spliceosome complexes that recognizes consensus sequences at the 3-prime splice sites of pre-mRNAs. Once bound to the pre-mRNA, U2AF2 recruits the U2 small nuclear ribonucleoprotein particle (snRNP) to the assembling spliceosome. Phosphorylation of SF1 by UHMK1 (Q8TAS1) enhances SF1-U2AF2 interactions and promotes assembly of the ternary complex of SF1, U2AF2, and the 3-prime splice site. ', - 'complex_assembly': 'Heterodimer', - 'complex_source': "psi-mi:\"-\"(ceitec)", - 'reactome_xref': [], - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/' - }, - { - '_id': 'CPX-2394', - 'name': 'General transcription factor TFIIE complex', - 'alias': [ - 'TF2E1-TF2E2 complex' - ], - 'molecules': [ - 'P29083(1)', - 'P29084(1)' - ], - 'evidence_code': 'ECO:0000353(physical interaction evidence used in manual assertion)', - 'experimental_evidence': 'intact:EBI-8182405', - 'description': 'General transcription factor complex which recruits TFIIH (CPX-2395) to complete the assembly of the preinitiation complex which forms on gene promoters during a transcription cycle and consists of Pol II (CPX-2387/CPX-7481), general transcription factors (TFIID, TFIIA, TFIIB, TFIIF, TFIIE, and TFIIH) and the mediator complex (CPX-3227). Both subunits of the complex act to anchor the TFIIH kinase module (CAK) within the preinitiation complex. The TFIIE complex appears to directly influence the transition from initiation to elongation during transcription.', - 'complex_assembly': 'Heterodimer', - 'complex_source': "psi-mi:\"MI:0469\"(IntAct)", - 'reactome_xref': [ - 'R-HSA-109633(identity)' - ], - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/' - }, - { - '_id': 'CPX-2385', - 'name': 'Hypoxia-inducible transcription factor complex, HIF2', - 'alias': [ - 'HIF2Alpha-HIF1Beta complex', - 'HIF2A-HIF1B complex' - ], - 'molecules': [ - 'P27540(1)', - 'Q99814(1)' - ], - 'evidence_code': 'ECO:0000353(physical interaction evidence used in manual assertion)', - 'experimental_evidence': 'intact:EBI-16038074', - 'description': "A basic helix-loop-helix-PER-ARNT-SIM (bHLH-PAS) family transcription factor complex composed of a constitutively expressed HIF-beta subunit and an oxygen-regulated HIF-alpha subunit which mediates hypoxia-dependent transcription. Binds to core DNA sequence 5'-[AG]CGTG-3' within the hypoxia response element of target gene promoters. HIF-dependent transcription is activated by insulin and mediated by the PI3K-AKT and TOR pathways and regulates the transcription of genes involved in a multitude of processes including angiogenesis, erythropoiesis, cell proliferation/survival, glucose metabolism, and iron metabolism.", - 'complex_assembly': 'Heterodimer', - 'complex_source': "psi-mi:\"MI:0469\"(IntAct)", - 'reactome_xref': [ - 'R-HSA-1234130(see-also)' - ], - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/' - }, - { - '_id': 'CPX-2483', - 'name': 'bZIP transcription factor complex, BACH2-MAF', - 'alias': [], - 'molecules': [ - 'O75444(1)', - 'Q9BYV9(1)' - ], - 'evidence_code': 'ECO:0005546(biological system reconstruction evidence based on paralogy evidence used in manual assertion)', - 'experimental_evidence': None, - 'description': 'Transcription factor complex which binds to a specific DNA consensus sequence to regulate transcription. The DNA recognition sequence depends on the composition of the bZIP dimer with the complex either binding to the preferred region of one of the partners or to a novel bZIP cognate site. Acts as a transcriptional repressor binding to the MARE (Maf recognition element) site in gene promoters during specific stages of B-cell development and in neuronal cells.', - 'complex_assembly': 'Heterodimer', - 'complex_source': "psi-mi:\"MI:0469\"(IntAct)", - 'reactome_xref': [], - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/' - }, - { - '_id': 'CPX-2482', - 'name': 'bZIP transcription factor complex, BACH2-MAFK', - 'alias': [], - 'molecules': [ - 'O60675(1)', - 'Q9BYV9(1)' - ], - 'evidence_code': 'ECO:0005546(biological system reconstruction evidence based on paralogy evidence used in manual assertion)', - 'experimental_evidence': None, - 'description': 'Transcription factor complex which binds to a specific DNA consensus sequence to regulate transcription. The DNA recognition sequence depends on the composition of the bZIP dimer with the complex either binding to the preferred region of one of the partners or to a novel bZIP cognate site. Acts as a transcriptional repressor binding to the MARE (Maf recognition element) site in gene promoters during specific stages of B-cell development and in neuronal cells.', - 'complex_assembly': 'Heterodimer', - 'complex_source': "psi-mi:\"MI:0469\"(IntAct)", - 'reactome_xref': [], - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/' - }, - { - '_id': 'CPX-2479', - 'name': 'bZIP transcription factor complex, BACH2-MAFB', - 'alias': [], - 'molecules': [ - 'Q9BYV9(1)', - 'Q9Y5Q3(1)' - ], - 'evidence_code': 'ECO:0005546(biological system reconstruction evidence based on paralogy evidence used in manual assertion)', - 'experimental_evidence': None, - 'description': 'Transcription factor complex which binds to a specific DNA consensus sequence to regulate transcription. The DNA recognition sequence depends on the composition of the bZIP dimer with the complex either binding to the preferred region of one of the partners or to a novel bZIP cognate site. Acts as a transcriptional repressor binding to the MARE (Maf recognition element) site in gene promoters during specific stages of B-cell development and in neuronal cells.', - 'complex_assembly': 'Heterodimer', - 'complex_source': "psi-mi:\"MI:0469\"(IntAct)", - 'reactome_xref': [], - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/' - }, - { - '_id': 'CPX-2473', - 'name': 'bZIP transcription factor complex, BACH2-NFE2L1', - 'alias': [], - 'molecules': [ - 'Q14494-PRO_0000443103(1)', - 'Q9BYV9(1)' - ], - 'evidence_code': 'ECO:0000353(physical interaction evidence used in manual assertion)', - 'experimental_evidence': 'intact:EBI-26590533', - 'description': 'Transcription factor complex which binds to a specific DNA consensus sequence to regulate transcription. The DNA recognition sequence depends on the composition of the bZIP dimer with the complex either binding to the preferred region of one of the partners or to a novel bZIP cognate site. ', - 'complex_assembly': 'Heterodimer', - 'complex_source': "psi-mi:\"MI:0469\"(IntAct)", - 'reactome_xref': [], - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/' - }, - { - '_id': 'CPX-2471', - 'name': 'bZIP transcription factor complex, BACH2-NFE2L3', - 'alias': [], - 'molecules': [ - 'Q9BYV9(1)', - 'Q9Y4A8(1)' - ], - 'evidence_code': 'ECO:0000353(physical interaction evidence used in manual assertion)', - 'experimental_evidence': 'intact:EBI-26590547', - 'description': 'Transcription factor complex which binds to a specific DNA consensus sequence to regulate transcription. The DNA recognition sequence depends on the composition of the bZIP dimer with the complex either binding to the preferred region of one of the partners or to a novel bZIP cognate site.', - 'complex_assembly': 'Heterodimer', - 'complex_source': "psi-mi:\"MI:0469\"(IntAct)", - 'reactome_xref': [], - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/' - }, - { - '_id': 'CPX-2435', - 'name': 'mRNA nuclear export factor NXF1-NXT2', - 'alias': [], - 'molecules': [ - 'Q9NPJ8(2)', - 'Q9UBU9(2)' - ], - 'evidence_code': 'ECO:0005546(biological system reconstruction evidence based on paralogy evidence used in manual assertion)', - 'experimental_evidence': None, - 'description': 'Mediates the export of bulk mRNA through direct interactions with both the mRNA cargo and nuclear pore proteins that contain characteristic phenylalanine-glycine repeating sequence motifs (FG-nucleoporins or FG-nups).', - 'complex_assembly': 'Heterotetramer', - 'complex_source': "psi-mi:\"MI:0469\"(IntAct)", - 'reactome_xref': [], - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/' - }, - { - '_id': 'CPX-2433', - 'name': 'mRNA nuclear export factor NXF5-NXT1', - 'alias': [], - 'molecules': [ - 'Q9H1B4(2)', - 'Q9UKK6(2)' - ], - 'evidence_code': 'ECO:0005546(biological system reconstruction evidence based on paralogy evidence used in manual assertion)', - 'experimental_evidence': None, - 'description': 'Mediates the export of bulk mRNA through direct interactions with both the mRNA cargo and nuclear pore proteins that contain characteristic phenylalanine-glycine repeating sequence motifs (FG-nucleoporins or FG-nups).', - 'complex_assembly': 'Heterotetramer', - 'complex_source': "psi-mi:\"MI:0469\"(IntAct)", - 'reactome_xref': [], - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/' - }, - { - '_id': 'CPX-2401', - 'name': 'mRNA nuclear export factor NXF2-NXT2', - 'alias': [], - 'molecules': [ - 'Q9GZY0(2)', - 'Q9NPJ8(2)' - ], - 'evidence_code': 'ECO:0000353(physical interaction evidence used in manual assertion)', - 'experimental_evidence': 'intact:EBI-24693079', - 'description': 'Mediates the export of bulk mRNA through direct interactions with both the mRNA cargo and nuclear pore proteins that contain characteristic phenylalanine-glycine repeating sequence motifs (FG-nucleoporins or FG-nups).', - 'complex_assembly': 'Heterotetramer', - 'complex_source': "psi-mi:\"MI:0469\"(IntAct)", - 'reactome_xref': [], - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/' - }, - { - '_id': 'CPX-1977', - 'name': 'Vascular endothelial growth factor A complex', - 'alias': [ - 'VEGF-A complex' - ], - 'molecules': [ - 'P15692(2)' - ], - 'evidence_code': 'ECO:0000353(physical interaction evidence used in manual assertion)', - 'experimental_evidence': 'intact:EBI-6902902', - 'description': 'Growth factor active in angiogenesis, vasculogenesis and endothelial cell growth. Induces endothelial cell proliferation, promotes cell migration, inhibits apoptosis and induces permeabilization of blood vessels. Can promote tumor vascularization. Ligand to vascular endothelial growth factor receptor (VGFR-1) complex. Has heparin-binding properties.', - 'complex_assembly': 'Homodimer', - 'complex_source': "psi-mi:\"MI:0469\"(IntAct)", - 'reactome_xref': [ - 'R-HSA-195364(identity)', - 'R-HSA-4420158(identity)' - ], - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/' - }, - { - '_id': 'CPX-1876', - 'name': 'Platelet-derived growth factor BB complex', - 'alias': [ - 'PDGFB complex', - 'PDGF-BB complex', - 'PDGF-BB homodimer', - 'Platelet-derived growth factor BB homodimer' - ], - 'molecules': [ - 'P01127(2)' - ], - 'evidence_code': 'ECO:0000353(physical interaction evidence used in manual assertion)', - 'experimental_evidence': 'intact:EBI-2881377', - 'description': 'A-chain of the platelet-derived growth factor (PDGF). Binds to and activates PDGF receptor alpha (PDGFRalpha, P16234) and beta (PDGFRbeta, P09619) subunits by inducing receptor dimerisation and tyrosine phosphorylation. Is a potent mitogen for cells of mesenchymal origin. Plays an essential role in the regulation of embryonic development, cell proliferation, cell migration, survival and chemotaxis. Required for normal proliferation and recruitment of pericytes and vascular smooth muscle cells in the central nervous system, skin, lung, heart and placenta. Required for normal blood vessel development, and for normal development of kidney glomeruli. Plays an important role in wound healing.', - 'complex_assembly': 'Homodimer', - 'complex_source': "psi-mi:\"MI:0469\"(IntAct)", - 'reactome_xref': [ - 'R-HSA-184206(identity)', - 'R-HSA-184204(identity)', - 'R-HSA-2426276(identity)', - 'R-HSA-380748(identity)', - 'R-HSA-381938(identity)' - ], - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/' - }, - { - '_id': 'CPX-1875', - 'name': 'Platelet-derived growth factor AB complex', - 'alias': [ - 'PDGF-AB heterodimer', - 'PDGF-AB complex', - 'Platelet-derived growth factor AB heterodimer' - ], - 'molecules': [ - 'P01127(1)', - 'P04085(1)' - ], - 'evidence_code': 'ECO:0000353(physical interaction evidence used in manual assertion)', - 'experimental_evidence': 'intact:EBI-9077995', - 'description': 'A- and B-chain of the platelet-derived growth factor (PDGF). Binds to and activates PDGF receptor alpha (PDGFRalpha, P16234) and beta (PDGFRbeta, P09619) subunits by inducing receptor dimerisation and tyrosine phosphorylation. Is a potent mitogen for cells of mesenchymal origin. Plays an essential role in the regulation of embryonic development, cell proliferation, cell migration, survival and chemotaxis. Plays an important role in wound healing.', - 'complex_assembly': 'Heterodimer', - 'complex_source': "psi-mi:\"MI:0469\"(IntAct)", - 'reactome_xref': [ - 'R-HSA-380759(identity)' - ], - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/' - }, - { - '_id': 'CPX-1874', - 'name': 'Platelet-derived growth factor AA complex', - 'alias': [ - 'PDGF-AA homodimer', - 'PDGF-AA complex', - 'PDGFA homodimer', - 'Platelet-derived growth factor AA homodimer' - ], - 'molecules': [ - 'P04085(2)' - ], - 'evidence_code': 'ECO:0000353(physical interaction evidence used in manual assertion)', - 'experimental_evidence': 'intact:EBI-15858879', - 'description': 'A-chain of the platelet-derived growth factor (PDGF). Binds to and activates PDGF receptor alpha subunit (PDGFRalpha, P16234) by inducing receptor dimerisation and tyrosine phosphorylation. Is a potent mitogen for cells of mesenchymal origin. Plays an essential role in the regulation of embryonic development, cell proliferation, cell migration, survival and chemotaxis. Required for normal lung alveolar septum formation during embryogenesis, normal development of the gastrointestinal tract, normal development of Leydig cells and spermatogenesis. Required for normal oligodendrocyte development and normal myelination in the spinal cord and cerebellum. Plays an important role in wound healing.', - 'complex_assembly': 'Homodimer', - 'complex_source': "psi-mi:\"MI:0469\"(IntAct)", - 'reactome_xref': [ - 'R-HSA-380761(identity)', - 'R-HSA-2426269(identity)' - ], - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/' - }, - { - '_id': 'CPX-2397', - 'name': 'General transcription factor TFIII3B complex, BRF2 variant', - 'alias': [], - 'molecules': [ - 'A6H8Y1(0)', - 'P20226(0)', - 'Q9HAW0(0)' - ], - 'evidence_code': 'ECO:0000353(physical interaction evidence used in manual assertion)', - 'experimental_evidence': 'wwpdb:5N9G', - 'description': 'Key RNA polymerase III (CPX-2393/CPX-7482) transcription factor which binds type 3 Pol III promoters. TFIIIB binds to DNA through recognition of the TATA box by TBP.The binding of TFIIIB to the promoter drives the recruitment of Pol III. TF3IIIB also plays a role in the opening of the transcription bubble.', - 'complex_assembly': [], - 'complex_source': "psi-mi:\"MI:0469\"(IntAct)", - 'reactome_xref': [ - 'R-HSA-83722(identity)' - ], - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/' - }, - { - '_id': 'CPX-2396', - 'name': 'General transcription factor TFIII3B complex, BRF1 variant', - 'alias': [], - 'molecules': [ - 'A6H8Y1(0)', - 'P20226(0)', - 'Q92994(0)' - ], - 'evidence_code': 'ECO:0005546(biological system reconstruction evidence based on paralogy evidence used in manual assertion)', - 'experimental_evidence': None, - 'description': 'Key RNA polymerase III (CPX-2393/CPX-7482) transcription factor which binds type 1 and 2 Pol III promoters. TFIIIB binds to DNA through recognition of the TATA box by TBP.The binding of TFIIIB to the promoter drives the recruitment of Pol III. TF3IIIB also plays a role in the opening of the transcription bubble. ', - 'complex_assembly': [], - 'complex_source': "psi-mi:\"MI:0469\"(IntAct)", - 'reactome_xref': [ - 'R-HSA-83719(identity)' - ], - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/' - }, - { - '_id': 'CPX-2436', - 'name': 'mRNA nuclear export factor complex, NXF3-NXT1', - 'alias': [], - 'molecules': [ - 'Q9H4D5(2)', - 'Q9UKK6(2)' - ], - 'evidence_code': 'ECO:0005546(biological system reconstruction evidence based on paralogy evidence used in manual assertion)', - 'experimental_evidence': None, - 'description': 'Mediates the export of bulk mRNA through direct interactions with both the mRNA cargo and nuclear pore proteins that contain characteristic phenylalanine-glycine repeating sequence motifs (FG-nucleoporins or FG-nups). ', - 'complex_assembly': 'Heterotetramer', - 'complex_source': "psi-mi:\"MI:0469\"(IntAct)", - 'reactome_xref': [], - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/' - }, - { - '_id': 'CPX-1921', - 'name': 'U2 small nuclear ribonucleoprotein auxiliary factor complex', - 'alias': [ - 'U2AF complex', - 'U2AF35-U2AF65 complex' - ], - 'molecules': [ - 'P26368(1)', - 'Q01081(1)' - ], - 'evidence_code': 'ECO:0000353(physical interaction evidence used in manual assertion)', - 'experimental_evidence': None, - 'description': "Ribonucleoprotein complex that recognizes an consensus AG-dinucleotide at the splice site junction and a preceding polypyrimidine tract and recruits the U2 small nuclear ribonucleoprotein particle (snRNP) of the spliceosome during the removal of intervening sequences (introns) separating protein-coding regions within pre-mRNAs. The 65-kDa subunit (U2AF2), contacts the polypyrimidine-tract, and the 35-kDa subunit (U2AF1), interacts with the AG dinucleotide at the 3' splice site. ", - 'complex_assembly': 'Heterodimer', - 'complex_source': "psi-mi:\"MI:0469\"(IntAct)", - 'reactome_xref': [], - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/' - }, - { - '_id': 'CPX-222', - 'name': 'Positive transcription elongation factor B, CDK9-cyclinT1 complex', - 'alias': [ - 'TAK complex', - 'Tat-associated kinase complex', - 'P-TEFb complex' - ], - 'molecules': [ - 'O60563(1)', - 'P50750(1)' - ], - 'evidence_code': 'ECO:0000353(physical interaction evidence used in manual assertion)', - 'experimental_evidence': 'intact:EBI-7977776', - 'description': "A serine kinase complex that phosphorylates elongation pausing factors such as DSIF (CPX-891) and NELF (CPX-6267) and Ser-2 and Ser-5 of RNA polymerase II (RNA Pol II), thus positively regulating productive mRNA elongation through the gene body after promoter-proximal pausing of RNA Pol II. Involved in cotranscriptional histone modification, mRNA processing and mRNA export. Potential target of anticancer drugs. Binds to the transactivation domain of the HIV-1, HIV-2 and SIV nuclear transcriptional activator, Tat, thereby increasing Tat's affinity for the transactivating response RNA element (TAR RNA) leading to RNA Pol II activation and transcription of viral genes.", - 'complex_assembly': 'Heterodimer', - 'complex_source': "psi-mi:\"-\"(ceitec)", - 'reactome_xref': [ - 'R-HSA-112431(identity)', - 'R-HSA-167183(identity)' - ], - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/' - } - ] - }] -} diff --git a/tests/acceptance_tests/complexes_proteins.py b/tests/acceptance_tests/complexes_proteins.py deleted file mode 100644 index f470daf4..00000000 --- a/tests/acceptance_tests/complexes_proteins.py +++ /dev/null @@ -1,21091 +0,0 @@ -complexes_proteins = { - '/complexes/proteins': [{ - 'params': { - 'name': 'factor', - 'verbose': 'false' - }, - 'response': [ - { - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/', - 'protein': 'proteins/P26368' - }, - { - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/', - 'protein': 'proteins/Q15637' - }, - { - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/', - 'protein': 'proteins/P04085' - }, - { - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/', - 'protein': 'proteins/P01127' - }, - { - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/', - 'protein': 'proteins/P04085' - }, - { - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/', - 'protein': 'proteins/P01127' - }, - { - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/', - 'protein': 'proteins/P26368' - }, - { - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/', - 'protein': 'proteins/Q01081' - }, - { - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/', - 'protein': 'proteins/P23511' - }, - { - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/', - 'protein': 'proteins/P25208' - }, - { - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/', - 'protein': 'proteins/Q13952' - }, - { - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/', - 'protein': 'proteins/Q01094' - }, - { - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/', - 'protein': 'proteins/Q14186' - }, - { - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/', - 'protein': 'proteins/Q14186' - }, - { - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/', - 'protein': 'proteins/Q14209' - }, - { - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/', - 'protein': 'proteins/O00716' - }, - { - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/', - 'protein': 'proteins/Q14186' - }, - { - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/', - 'protein': 'proteins/P15692' - }, - { - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/', - 'protein': 'proteins/O60563' - }, - { - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/', - 'protein': 'proteins/P50750' - }, - { - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/', - 'protein': 'proteins/Q12789' - }, - { - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/', - 'protein': 'proteins/Q8WUA4' - }, - { - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/', - 'protein': 'proteins/Q969F1' - }, - { - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/', - 'protein': 'proteins/Q9UKN8' - }, - { - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/', - 'protein': 'proteins/Q9Y5Q8' - } - ] - }, { - 'params': { - 'name': 'factor', - 'verbose': 'true' - }, - 'response': [ - { - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/', - 'protein': [ - { - '_id': 'P26368', - 'name': 'U2AF2_HUMAN', - 'full_name': 'Splicing factor U2AF 65 kDa subunit', - 'dbxrefs': [ - { - 'name': 'AGR', - 'id': 'HGNC:23156' - }, - { - 'name': 'AlphaFoldDB', - 'id': 'P26368' - }, - { - 'name': 'Antibodypedia', - 'id': '4399' - }, - { - 'name': 'BMRB', - 'id': 'P26368' - }, - { - 'name': 'Bgee', - 'id': 'ENSG00000063244' - }, - { - 'name': 'BioGRID', - 'id': '116466' - }, - { - 'name': 'BioGRID-ORCS', - 'id': '11338' - }, - { - 'name': 'BioMuta', - 'id': 'U2AF2' - }, - { - 'name': 'CCDS', - 'id': 'CCDS12933.1' - }, - { - 'name': 'CCDS', - 'id': 'CCDS46197.1' - }, - { - 'name': 'CDD', - 'id': 'cd12230' - }, - { - 'name': 'CDD', - 'id': 'cd12231' - }, - { - 'name': 'CDD', - 'id': 'cd12232' - }, - { - 'name': 'CORUM', - 'id': 'P26368' - }, - { - 'name': 'CTD', - 'id': '11338' - }, - { - 'name': 'ChiTaRS', - 'id': 'U2AF2' - }, - { - 'name': 'ComplexPortal', - 'id': 'CPX-1074' - }, - { - 'name': 'ComplexPortal', - 'id': 'CPX-1921' - }, - { - 'name': 'DIP', - 'id': 'DIP-2154N' - }, - { - 'name': 'DMDM', - 'id': '267188' - }, - { - 'name': 'DNASU', - 'id': '11338' - }, - { - 'name': 'DisGeNET', - 'id': '11338' - }, - { - 'name': 'DisProt', - 'id': 'DP02921' - }, - { - 'name': 'EMBL', - 'id': 'X64044' - }, - { - 'name': 'EMBL', - 'id': 'CAA45409.1' - }, - { - 'name': 'EMBL', - 'id': 'CH471135' - }, - { - 'name': 'EMBL', - 'id': 'EAW72404.1' - }, - { - 'name': 'EMBL', - 'id': 'BC008740' - }, - { - 'name': 'EMBL', - 'id': 'AAH08740.1' - }, - { - 'name': 'EMBL', - 'id': 'BC030574' - }, - { - 'name': 'EMBL', - 'id': 'AAH30574.1' - }, - { - 'name': 'EPD', - 'id': 'P26368' - }, - { - 'name': 'Ensembl', - 'id': 'ENST00000308924.9' - }, - { - 'name': 'Ensembl', - 'id': 'ENSP00000307863.3' - }, - { - 'name': 'Ensembl', - 'id': 'ENSG00000063244.14' - }, - { - 'name': 'Ensembl', - 'id': 'ENST00000450554.6' - }, - { - 'name': 'Ensembl', - 'id': 'ENSP00000388475.1' - }, - { - 'name': 'Ensembl', - 'id': 'ENSG00000063244.14' - }, - { - 'name': 'EvolutionaryTrace', - 'id': 'P26368' - }, - { - 'name': 'ExpressionAtlas', - 'id': 'P26368' - }, - { - 'name': 'GO', - 'id': 'GO:0000243' - }, - { - 'name': 'GO', - 'id': 'GO:0016607' - }, - { - 'name': 'GO', - 'id': 'GO:0005654' - }, - { - 'name': 'GO', - 'id': 'GO:0005634' - }, - { - 'name': 'GO', - 'id': 'GO:0005681' - }, - { - 'name': 'GO', - 'id': 'GO:0071004' - }, - { - 'name': 'GO', - 'id': 'GO:0089701' - }, - { - 'name': 'GO', - 'id': 'GO:0070742' - }, - { - 'name': 'GO', - 'id': 'GO:0019899' - }, - { - 'name': 'GO', - 'id': 'GO:0140678' - }, - { - 'name': 'GO', - 'id': 'GO:0008187' - }, - { - 'name': 'GO', - 'id': 'GO:0030628' - }, - { - 'name': 'GO', - 'id': 'GO:0003723' - }, - { - 'name': 'GO', - 'id': 'GO:0006397' - }, - { - 'name': 'GO', - 'id': 'GO:0000398' - }, - { - 'name': 'GO', - 'id': 'GO:0048025' - }, - { - 'name': 'GO', - 'id': 'GO:0031397' - }, - { - 'name': 'GO', - 'id': 'GO:0033120' - }, - { - 'name': 'Gene3D', - 'id': '3.30.70.330' - }, - { - 'name': 'GeneCards', - 'id': 'U2AF2' - }, - { - 'name': 'GeneID', - 'id': '11338' - }, - { - 'name': 'GeneTree', - 'id': 'ENSGT00940000155556' - }, - { - 'name': 'GeneWiki', - 'id': 'U2AF2' - }, - { - 'name': 'Genevisible', - 'id': 'P26368' - }, - { - 'name': 'GenomeRNAi', - 'id': '11338' - }, - { - 'name': 'GlyGen', - 'id': 'P26368' - }, - { - 'name': 'HGNC', - 'id': 'HGNC:23156' - }, - { - 'name': 'HPA', - 'id': 'ENSG00000063244' - }, - { - 'name': 'IDEAL', - 'id': 'IID00147' - }, - { - 'name': 'InParanoid', - 'id': 'P26368' - }, - { - 'name': 'IntAct', - 'id': 'P26368' - }, - { - 'name': 'InterPro', - 'id': 'IPR012677' - }, - { - 'name': 'InterPro', - 'id': 'IPR035979' - }, - { - 'name': 'InterPro', - 'id': 'IPR000504' - }, - { - 'name': 'InterPro', - 'id': 'IPR006529' - }, - { - 'name': 'KEGG', - 'id': 'hsa:11338' - }, - { - 'name': 'MANE-Select', - 'id': 'ENST00000308924.9' - }, - { - 'name': 'MANE-Select', - 'id': 'ENSP00000307863.3' - }, - { - 'name': 'MANE-Select', - 'id': 'NM_007279.3' - }, - { - 'name': 'MANE-Select', - 'id': 'NP_009210.1' - }, - { - 'name': 'MIM', - 'id': '191318' - }, - { - 'name': 'MINT', - 'id': 'P26368' - }, - { - 'name': 'MassIVE', - 'id': 'P26368' - }, - { - 'name': 'MaxQB', - 'id': 'P26368' - }, - { - 'name': 'OMA', - 'id': 'MTQWDIK' - }, - { - 'name': 'OpenTargets', - 'id': 'ENSG00000063244' - }, - { - 'name': 'OrthoDB', - 'id': '101932at2759' - }, - { - 'name': 'PANTHER', - 'id': 'PTHR23139' - }, - { - 'name': 'PANTHER', - 'id': 'PTHR23139:SF9' - }, - { - 'name': 'PDB', - 'id': '1JMT' - }, - { - 'name': 'PDB', - 'id': '1O0P' - }, - { - 'name': 'PDB', - 'id': '1OPI' - }, - { - 'name': 'PDB', - 'id': '1U2F' - }, - { - 'name': 'PDB', - 'id': '2G4B' - }, - { - 'name': 'PDB', - 'id': '2HZC' - }, - { - 'name': 'PDB', - 'id': '2M0G' - }, - { - 'name': 'PDB', - 'id': '2U2F' - }, - { - 'name': 'PDB', - 'id': '2YH0' - }, - { - 'name': 'PDB', - 'id': '2YH1' - }, - { - 'name': 'PDB', - 'id': '3VAF' - }, - { - 'name': 'PDB', - 'id': '3VAG' - }, - { - 'name': 'PDB', - 'id': '3VAH' - }, - { - 'name': 'PDB', - 'id': '3VAI' - }, - { - 'name': 'PDB', - 'id': '3VAJ' - }, - { - 'name': 'PDB', - 'id': '3VAK' - }, - { - 'name': 'PDB', - 'id': '3VAL' - }, - { - 'name': 'PDB', - 'id': '3VAM' - }, - { - 'name': 'PDB', - 'id': '4FXW' - }, - { - 'name': 'PDB', - 'id': '4TU7' - }, - { - 'name': 'PDB', - 'id': '4TU8' - }, - { - 'name': 'PDB', - 'id': '4TU9' - }, - { - 'name': 'PDB', - 'id': '5EV1' - }, - { - 'name': 'PDB', - 'id': '5EV2' - }, - { - 'name': 'PDB', - 'id': '5EV3' - }, - { - 'name': 'PDB', - 'id': '5EV4' - }, - { - 'name': 'PDB', - 'id': '5W0G' - }, - { - 'name': 'PDB', - 'id': '5W0H' - }, - { - 'name': 'PDB', - 'id': '6TR0' - }, - { - 'name': 'PDB', - 'id': '6XLV' - }, - { - 'name': 'PDB', - 'id': '6XLW' - }, - { - 'name': 'PDB', - 'id': '6XLX' - }, - { - 'name': 'PDB', - 'id': '7S3A' - }, - { - 'name': 'PDB', - 'id': '7S3B' - }, - { - 'name': 'PDB', - 'id': '7S3C' - }, - { - 'name': 'PDB', - 'id': '7SN6' - }, - { - 'name': 'PDBsum', - 'id': '1JMT' - }, - { - 'name': 'PDBsum', - 'id': '1O0P' - }, - { - 'name': 'PDBsum', - 'id': '1OPI' - }, - { - 'name': 'PDBsum', - 'id': '1U2F' - }, - { - 'name': 'PDBsum', - 'id': '2G4B' - }, - { - 'name': 'PDBsum', - 'id': '2HZC' - }, - { - 'name': 'PDBsum', - 'id': '2M0G' - }, - { - 'name': 'PDBsum', - 'id': '2U2F' - }, - { - 'name': 'PDBsum', - 'id': '2YH0' - }, - { - 'name': 'PDBsum', - 'id': '2YH1' - }, - { - 'name': 'PDBsum', - 'id': '3VAF' - }, - { - 'name': 'PDBsum', - 'id': '3VAG' - }, - { - 'name': 'PDBsum', - 'id': '3VAH' - }, - { - 'name': 'PDBsum', - 'id': '3VAI' - }, - { - 'name': 'PDBsum', - 'id': '3VAJ' - }, - { - 'name': 'PDBsum', - 'id': '3VAK' - }, - { - 'name': 'PDBsum', - 'id': '3VAL' - }, - { - 'name': 'PDBsum', - 'id': '3VAM' - }, - { - 'name': 'PDBsum', - 'id': '4FXW' - }, - { - 'name': 'PDBsum', - 'id': '4TU7' - }, - { - 'name': 'PDBsum', - 'id': '4TU8' - }, - { - 'name': 'PDBsum', - 'id': '4TU9' - }, - { - 'name': 'PDBsum', - 'id': '5EV1' - }, - { - 'name': 'PDBsum', - 'id': '5EV2' - }, - { - 'name': 'PDBsum', - 'id': '5EV3' - }, - { - 'name': 'PDBsum', - 'id': '5EV4' - }, - { - 'name': 'PDBsum', - 'id': '5W0G' - }, - { - 'name': 'PDBsum', - 'id': '5W0H' - }, - { - 'name': 'PDBsum', - 'id': '6TR0' - }, - { - 'name': 'PDBsum', - 'id': '6XLV' - }, - { - 'name': 'PDBsum', - 'id': '6XLW' - }, - { - 'name': 'PDBsum', - 'id': '6XLX' - }, - { - 'name': 'PDBsum', - 'id': '7S3A' - }, - { - 'name': 'PDBsum', - 'id': '7S3B' - }, - { - 'name': 'PDBsum', - 'id': '7S3C' - }, - { - 'name': 'PDBsum', - 'id': '7SN6' - }, - { - 'name': 'PIR', - 'id': 'S20250' - }, - { - 'name': 'PRO', - 'id': 'PR:P26368' - }, - { - 'name': 'PROSITE', - 'id': 'PS50102' - }, - { - 'name': 'PathwayCommons', - 'id': 'P26368' - }, - { - 'name': 'PaxDb', - 'id': 'P26368' - }, - { - 'name': 'PeptideAtlas', - 'id': 'P26368' - }, - { - 'name': 'Pfam', - 'id': 'PF00076' - }, - { - 'name': 'PharmGKB', - 'id': 'PA134908683' - }, - { - 'name': 'Pharos', - 'id': 'P26368' - }, - { - 'name': 'PhosphoSitePlus', - 'id': 'P26368' - }, - { - 'name': 'PhylomeDB', - 'id': 'P26368' - }, - { - 'name': 'Proteomes', - 'id': 'UP000005640' - }, - { - 'name': 'ProteomicsDB', - 'id': '54325' - }, - { - 'name': 'ProteomicsDB', - 'id': '54326' - }, - { - 'name': 'RNAct', - 'id': 'P26368' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-159236' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-72163' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-72187' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-73856' - }, - { - 'name': 'RefSeq', - 'id': 'NP_001012496.1' - }, - { - 'name': 'RefSeq', - 'id': 'NM_001012478.1' - }, - { - 'name': 'RefSeq', - 'id': 'NP_009210.1' - }, - { - 'name': 'RefSeq', - 'id': 'NM_007279.2' - }, - { - 'name': 'SIGNOR', - 'id': 'P26368' - }, - { - 'name': 'SMART', - 'id': 'SM00360' - }, - { - 'name': 'SMR', - 'id': 'P26368' - }, - { - 'name': 'STRING', - 'id': '9606.ENSP00000307863' - }, - { - 'name': 'SUPFAM', - 'id': 'SSF54928' - }, - { - 'name': 'SignaLink', - 'id': 'P26368' - }, - { - 'name': 'SwissPalm', - 'id': 'P26368' - }, - { - 'name': 'TIGRFAMs', - 'id': 'TIGR01642' - }, - { - 'name': 'TopDownProteomics', - 'id': 'P26368-1' - }, - { - 'name': 'TopDownProteomics', - 'id': 'P26368-2' - }, - { - 'name': 'TreeFam', - 'id': 'TF314111' - }, - { - 'name': 'UCSC', - 'id': 'uc002qlt.4' - }, - { - 'name': 'VEuPathDB', - 'id': 'HostDB:ENSG00000063244' - }, - { - 'name': 'eggNOG', - 'id': 'KOG0120' - }, - { - 'name': 'iPTMnet', - 'id': 'P26368' - }, - { - 'name': 'jPOST', - 'id': 'P26368' - }, - { - 'name': 'neXtProt', - 'id': 'NX_P26368' - } - ], - 'source': 'UniProtKB/Swiss-Prot', - 'source_url': 'https://www.uniprot.org/help/downloads' - } - ] - }, - { - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/', - 'protein': [ - { - '_id': 'Q15637', - 'name': 'SF01_HUMAN', - 'full_name': 'Splicing factor 1', - 'dbxrefs': [ - { - 'name': 'AGR', - 'id': 'HGNC:12950' - }, - { - 'name': 'AlphaFoldDB', - 'id': 'Q15637' - }, - { - 'name': 'Antibodypedia', - 'id': '15586' - }, - { - 'name': 'BMRB', - 'id': 'Q15637' - }, - { - 'name': 'Bgee', - 'id': 'ENSG00000168066' - }, - { - 'name': 'BioGRID', - 'id': '113368' - }, - { - 'name': 'BioGRID-ORCS', - 'id': '7536' - }, - { - 'name': 'BioMuta', - 'id': 'SF1' - }, - { - 'name': 'CCDS', - 'id': 'CCDS31599.1' - }, - { - 'name': 'CCDS', - 'id': 'CCDS44642.2' - }, - { - 'name': 'CCDS', - 'id': 'CCDS53660.1' - }, - { - 'name': 'CCDS', - 'id': 'CCDS53661.1' - }, - { - 'name': 'CCDS', - 'id': 'CCDS8080.1' - }, - { - 'name': 'CCDS', - 'id': 'CCDS8081.1' - }, - { - 'name': 'CDD', - 'id': 'cd22382' - }, - { - 'name': 'CORUM', - 'id': 'Q15637' - }, - { - 'name': 'CTD', - 'id': '7536' - }, - { - 'name': 'ChiTaRS', - 'id': 'SF1' - }, - { - 'name': 'ComplexPortal', - 'id': 'CPX-1074' - }, - { - 'name': 'DIP', - 'id': 'DIP-29410N' - }, - { - 'name': 'DMDM', - 'id': '38258418' - }, - { - 'name': 'DNASU', - 'id': '7536' - }, - { - 'name': 'DisGeNET', - 'id': '7536' - }, - { - 'name': 'DisProt', - 'id': 'DP01449' - }, - { - 'name': 'DrugBank', - 'id': 'DB11638' - }, - { - 'name': 'ELM', - 'id': 'Q15637' - }, - { - 'name': 'EMBL', - 'id': 'Y08765' - }, - { - 'name': 'EMBL', - 'id': 'CAA70018.1' - }, - { - 'name': 'EMBL', - 'id': 'Y08766' - }, - { - 'name': 'EMBL', - 'id': 'CAA70019.1' - }, - { - 'name': 'EMBL', - 'id': 'L49345' - }, - { - 'name': 'EMBL', - 'id': 'AAB03514.1' - }, - { - 'name': 'EMBL', - 'id': 'L49380' - }, - { - 'name': 'EMBL', - 'id': 'AAB04033.1' - }, - { - 'name': 'EMBL', - 'id': 'D26120' - }, - { - 'name': 'EMBL', - 'id': 'BAA05116.1' - }, - { - 'name': 'EMBL', - 'id': 'D26120' - }, - { - 'name': 'EMBL', - 'id': 'BAA05117.1' - }, - { - 'name': 'EMBL', - 'id': 'AK293753' - }, - { - 'name': 'EMBL', - 'id': 'BAH11587.1' - }, - { - 'name': 'EMBL', - 'id': 'AP001462' - }, - { - 'name': 'EMBL', - 'id': 'BC000773' - }, - { - 'name': 'EMBL', - 'id': 'AAH00773.1' - }, - { - 'name': 'EMBL', - 'id': 'BC008080' - }, - { - 'name': 'EMBL', - 'id': 'AAH08080.1' - }, - { - 'name': 'EMBL', - 'id': 'BC008724' - }, - { - 'name': 'EMBL', - 'id': 'AAH08724.1' - }, - { - 'name': 'EMBL', - 'id': 'BC011657' - }, - { - 'name': 'EMBL', - 'id': 'BC020217' - }, - { - 'name': 'EMBL', - 'id': 'AAH20217.1' - }, - { - 'name': 'EMBL', - 'id': 'BC038446' - }, - { - 'name': 'EMBL', - 'id': 'AAH38446.1' - }, - { - 'name': 'EMBL', - 'id': 'AJ000051' - }, - { - 'name': 'EMBL', - 'id': 'CAA03883.1' - }, - { - 'name': 'EMBL', - 'id': 'AJ000052' - }, - { - 'name': 'EMBL', - 'id': 'CAA03883.1' - }, - { - 'name': 'EPD', - 'id': 'Q15637' - }, - { - 'name': 'Ensembl', - 'id': 'ENST00000227503.13' - }, - { - 'name': 'Ensembl', - 'id': 'ENSP00000227503.9' - }, - { - 'name': 'Ensembl', - 'id': 'ENSG00000168066.21' - }, - { - 'name': 'Ensembl', - 'id': 'ENST00000334944.9' - }, - { - 'name': 'Ensembl', - 'id': 'ENSP00000334414.5' - }, - { - 'name': 'Ensembl', - 'id': 'ENSG00000168066.21' - }, - { - 'name': 'Ensembl', - 'id': 'ENST00000377387.5' - }, - { - 'name': 'Ensembl', - 'id': 'ENSP00000366604.1' - }, - { - 'name': 'Ensembl', - 'id': 'ENSG00000168066.21' - }, - { - 'name': 'Ensembl', - 'id': 'ENST00000377390.8' - }, - { - 'name': 'Ensembl', - 'id': 'ENSP00000366607.3' - }, - { - 'name': 'Ensembl', - 'id': 'ENSG00000168066.21' - }, - { - 'name': 'Ensembl', - 'id': 'ENST00000377394.7' - }, - { - 'name': 'Ensembl', - 'id': 'ENSP00000366611.3' - }, - { - 'name': 'Ensembl', - 'id': 'ENSG00000168066.21' - }, - { - 'name': 'Ensembl', - 'id': 'ENST00000433274.6' - }, - { - 'name': 'Ensembl', - 'id': 'ENSP00000396793.2' - }, - { - 'name': 'Ensembl', - 'id': 'ENSG00000168066.21' - }, - { - 'name': 'EvolutionaryTrace', - 'id': 'Q15637' - }, - { - 'name': 'ExpressionAtlas', - 'id': 'Q15637' - }, - { - 'name': 'GO', - 'id': 'GO:0016604' - }, - { - 'name': 'GO', - 'id': 'GO:0005654' - }, - { - 'name': 'GO', - 'id': 'GO:0005634' - }, - { - 'name': 'GO', - 'id': 'GO:0005840' - }, - { - 'name': 'GO', - 'id': 'GO:0005681' - }, - { - 'name': 'GO', - 'id': 'GO:0089701' - }, - { - 'name': 'GO', - 'id': 'GO:0042802' - }, - { - 'name': 'GO', - 'id': 'GO:0003729' - }, - { - 'name': 'GO', - 'id': 'GO:0003723' - }, - { - 'name': 'GO', - 'id': 'GO:0003714' - }, - { - 'name': 'GO', - 'id': 'GO:0008270' - }, - { - 'name': 'GO', - 'id': 'GO:0033327' - }, - { - 'name': 'GO', - 'id': 'GO:0030238' - }, - { - 'name': 'GO', - 'id': 'GO:0000389' - }, - { - 'name': 'GO', - 'id': 'GO:0000398' - }, - { - 'name': 'GO', - 'id': 'GO:0048662' - }, - { - 'name': 'GO', - 'id': 'GO:0030575' - }, - { - 'name': 'GO', - 'id': 'GO:0048024' - }, - { - 'name': 'GO', - 'id': 'GO:0050810' - }, - { - 'name': 'GO', - 'id': 'GO:0000245' - }, - { - 'name': 'Gene3D', - 'id': '6.10.140.1790' - }, - { - 'name': 'Gene3D', - 'id': '3.30.1370.10' - }, - { - 'name': 'GeneCards', - 'id': 'SF1' - }, - { - 'name': 'GeneID', - 'id': '7536' - }, - { - 'name': 'GeneTree', - 'id': 'ENSGT00940000157258' - }, - { - 'name': 'GeneWiki', - 'id': 'SF1_(gene)' - }, - { - 'name': 'Genevisible', - 'id': 'Q15637' - }, - { - 'name': 'GenomeRNAi', - 'id': '7536' - }, - { - 'name': 'GlyCosmos', - 'id': 'Q15637' - }, - { - 'name': 'GlyGen', - 'id': 'Q15637' - }, - { - 'name': 'HGNC', - 'id': 'HGNC:12950' - }, - { - 'name': 'HOGENOM', - 'id': 'CLU_016864_5_0_1' - }, - { - 'name': 'HPA', - 'id': 'ENSG00000168066' - }, - { - 'name': 'IDEAL', - 'id': 'IID00247' - }, - { - 'name': 'InParanoid', - 'id': 'Q15637' - }, - { - 'name': 'IntAct', - 'id': 'Q15637' - }, - { - 'name': 'InterPro', - 'id': 'IPR045071' - }, - { - 'name': 'InterPro', - 'id': 'IPR004087' - }, - { - 'name': 'InterPro', - 'id': 'IPR004088' - }, - { - 'name': 'InterPro', - 'id': 'IPR036612' - }, - { - 'name': 'InterPro', - 'id': 'IPR032570' - }, - { - 'name': 'InterPro', - 'id': 'IPR047086' - }, - { - 'name': 'InterPro', - 'id': 'IPR001878' - }, - { - 'name': 'KEGG', - 'id': 'hsa:7536' - }, - { - 'name': 'MANE-Select', - 'id': 'ENST00000377390.8' - }, - { - 'name': 'MANE-Select', - 'id': 'ENSP00000366607.3' - }, - { - 'name': 'MANE-Select', - 'id': 'NM_004630.4' - }, - { - 'name': 'MANE-Select', - 'id': 'NP_004621.2' - }, - { - 'name': 'MIM', - 'id': '601516' - }, - { - 'name': 'MINT', - 'id': 'Q15637' - }, - { - 'name': 'MassIVE', - 'id': 'Q15637' - }, - { - 'name': 'MaxQB', - 'id': 'Q15637' - }, - { - 'name': 'MetOSite', - 'id': 'Q15637' - }, - { - 'name': 'MoonDB', - 'id': 'Q15637' - }, - { - 'name': 'OMA', - 'id': 'GAAPWHQ' - }, - { - 'name': 'OpenTargets', - 'id': 'ENSG00000168066' - }, - { - 'name': 'OrthoDB', - 'id': '1397at2759' - }, - { - 'name': 'PANTHER', - 'id': 'PTHR11208' - }, - { - 'name': 'PANTHER', - 'id': 'PTHR11208:SF45' - }, - { - 'name': 'PDB', - 'id': '1K1G' - }, - { - 'name': 'PDB', - 'id': '1O0P' - }, - { - 'name': 'PDB', - 'id': '1OPI' - }, - { - 'name': 'PDB', - 'id': '2M09' - }, - { - 'name': 'PDB', - 'id': '2M0G' - }, - { - 'name': 'PDB', - 'id': '4FXW' - }, - { - 'name': 'PDB', - 'id': '4FXX' - }, - { - 'name': 'PDB', - 'id': '7VH9' - }, - { - 'name': 'PDBsum', - 'id': '1K1G' - }, - { - 'name': 'PDBsum', - 'id': '1O0P' - }, - { - 'name': 'PDBsum', - 'id': '1OPI' - }, - { - 'name': 'PDBsum', - 'id': '2M09' - }, - { - 'name': 'PDBsum', - 'id': '2M0G' - }, - { - 'name': 'PDBsum', - 'id': '4FXW' - }, - { - 'name': 'PDBsum', - 'id': '4FXX' - }, - { - 'name': 'PDBsum', - 'id': '7VH9' - }, - { - 'name': 'PIR', - 'id': 'G02919' - }, - { - 'name': 'PRO', - 'id': 'PR:Q15637' - }, - { - 'name': 'PROSITE', - 'id': 'PS50084' - }, - { - 'name': 'PROSITE', - 'id': 'PS50158' - }, - { - 'name': 'PathwayCommons', - 'id': 'Q15637' - }, - { - 'name': 'PaxDb', - 'id': 'Q15637' - }, - { - 'name': 'PeptideAtlas', - 'id': 'Q15637' - }, - { - 'name': 'Pfam', - 'id': 'PF00013' - }, - { - 'name': 'Pfam', - 'id': 'PF16275' - }, - { - 'name': 'Pfam', - 'id': 'PF00098' - }, - { - 'name': 'PharmGKB', - 'id': 'PA37533' - }, - { - 'name': 'Pharos', - 'id': 'Q15637' - }, - { - 'name': 'PhosphoSitePlus', - 'id': 'Q15637' - }, - { - 'name': 'PhylomeDB', - 'id': 'Q15637' - }, - { - 'name': 'Proteomes', - 'id': 'UP000005640' - }, - { - 'name': 'ProteomicsDB', - 'id': '10457' - }, - { - 'name': 'ProteomicsDB', - 'id': '60669' - }, - { - 'name': 'ProteomicsDB', - 'id': '60670' - }, - { - 'name': 'ProteomicsDB', - 'id': '60671' - }, - { - 'name': 'ProteomicsDB', - 'id': '60672' - }, - { - 'name': 'ProteomicsDB', - 'id': '60673' - }, - { - 'name': 'ProteomicsDB', - 'id': '60674' - }, - { - 'name': 'RNAct', - 'id': 'Q15637' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-72163' - }, - { - 'name': 'RefSeq', - 'id': 'NP_001171501.1' - }, - { - 'name': 'RefSeq', - 'id': 'NM_001178030.1' - }, - { - 'name': 'RefSeq', - 'id': 'NP_001171502.1' - }, - { - 'name': 'RefSeq', - 'id': 'NM_001178031.2' - }, - { - 'name': 'RefSeq', - 'id': 'NP_001333292.1' - }, - { - 'name': 'RefSeq', - 'id': 'NM_001346363.1' - }, - { - 'name': 'RefSeq', - 'id': 'NP_001333293.1' - }, - { - 'name': 'RefSeq', - 'id': 'NM_001346364.1' - }, - { - 'name': 'RefSeq', - 'id': 'NP_004621.2' - }, - { - 'name': 'RefSeq', - 'id': 'NM_004630.3' - }, - { - 'name': 'RefSeq', - 'id': 'NP_973724.1' - }, - { - 'name': 'RefSeq', - 'id': 'NM_201995.2' - }, - { - 'name': 'RefSeq', - 'id': 'NP_973727.1' - }, - { - 'name': 'RefSeq', - 'id': 'NM_201998.2' - }, - { - 'name': 'RefSeq', - 'id': 'XP_016873733.1' - }, - { - 'name': 'RefSeq', - 'id': 'XM_017018244.1' - }, - { - 'name': 'SIGNOR', - 'id': 'Q15637' - }, - { - 'name': 'SMART', - 'id': 'SM00322' - }, - { - 'name': 'SMART', - 'id': 'SM00343' - }, - { - 'name': 'SMR', - 'id': 'Q15637' - }, - { - 'name': 'STRING', - 'id': '9606.ENSP00000366604' - }, - { - 'name': 'SUPFAM', - 'id': 'SSF54791' - }, - { - 'name': 'SignaLink', - 'id': 'Q15637' - }, - { - 'name': 'SwissPalm', - 'id': 'Q15637' - }, - { - 'name': 'TopDownProteomics', - 'id': 'Q15637-4' - }, - { - 'name': 'TreeFam', - 'id': 'TF319159' - }, - { - 'name': 'UCSC', - 'id': 'uc001oaz.3' - }, - { - 'name': 'VEuPathDB', - 'id': 'HostDB:ENSG00000168066' - }, - { - 'name': 'eggNOG', - 'id': 'KOG0119' - }, - { - 'name': 'iPTMnet', - 'id': 'Q15637' - }, - { - 'name': 'jPOST', - 'id': 'Q15637' - }, - { - 'name': 'neXtProt', - 'id': 'NX_Q15637' - } - ], - 'source': 'UniProtKB/Swiss-Prot', - 'source_url': 'https://www.uniprot.org/help/downloads' - } - ] - }, - { - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/', - 'protein': [ - { - '_id': 'P04085', - 'name': 'PDGFA_HUMAN', - 'full_name': 'Platelet-derived growth factor subunit A', - 'dbxrefs': [ - { - 'name': 'AGR', - 'id': 'HGNC:8799' - }, - { - 'name': 'AlphaFoldDB', - 'id': 'P04085' - }, - { - 'name': 'Antibodypedia', - 'id': '3957' - }, - { - 'name': 'Bgee', - 'id': 'ENSG00000197461' - }, - { - 'name': 'BindingDB', - 'id': 'P04085' - }, - { - 'name': 'BioGRID', - 'id': '111180' - }, - { - 'name': 'BioGRID-ORCS', - 'id': '5154' - }, - { - 'name': 'BioMuta', - 'id': 'PDGFA' - }, - { - 'name': 'CCDS', - 'id': 'CCDS34578.1' - }, - { - 'name': 'CCDS', - 'id': 'CCDS47524.1' - }, - { - 'name': 'CDD', - 'id': 'cd00135' - }, - { - 'name': 'CTD', - 'id': '5154' - }, - { - 'name': 'ChEMBL', - 'id': 'CHEMBL3137294' - }, - { - 'name': 'ChiTaRS', - 'id': 'PDGFA' - }, - { - 'name': 'ComplexPortal', - 'id': 'CPX-1874' - }, - { - 'name': 'ComplexPortal', - 'id': 'CPX-1875' - }, - { - 'name': 'ComplexPortal', - 'id': 'CPX-2881' - }, - { - 'name': 'ComplexPortal', - 'id': 'CPX-2885' - }, - { - 'name': 'ComplexPortal', - 'id': 'CPX-2886' - }, - { - 'name': 'ComplexPortal', - 'id': 'CPX-2892' - }, - { - 'name': 'DIP', - 'id': 'DIP-5735N' - }, - { - 'name': 'DNASU', - 'id': '5154' - }, - { - 'name': 'DisGeNET', - 'id': '5154' - }, - { - 'name': 'EMBL', - 'id': 'X03795' - }, - { - 'name': 'EMBL', - 'id': 'CAA27421.1' - }, - { - 'name': 'EMBL', - 'id': 'X06374' - }, - { - 'name': 'EMBL', - 'id': 'CAA29677.1' - }, - { - 'name': 'EMBL', - 'id': 'M20494' - }, - { - 'name': 'EMBL', - 'id': 'AAA60045.1' - }, - { - 'name': 'EMBL', - 'id': 'M20488' - }, - { - 'name': 'EMBL', - 'id': 'AAA60045.1' - }, - { - 'name': 'EMBL', - 'id': 'M20489' - }, - { - 'name': 'EMBL', - 'id': 'AAA60045.1' - }, - { - 'name': 'EMBL', - 'id': 'M20490' - }, - { - 'name': 'EMBL', - 'id': 'AAA60045.1' - }, - { - 'name': 'EMBL', - 'id': 'M20491' - }, - { - 'name': 'EMBL', - 'id': 'AAA60045.1' - }, - { - 'name': 'EMBL', - 'id': 'M20492' - }, - { - 'name': 'EMBL', - 'id': 'AAA60045.1' - }, - { - 'name': 'EMBL', - 'id': 'M20493' - }, - { - 'name': 'EMBL', - 'id': 'AAA60045.1' - }, - { - 'name': 'EMBL', - 'id': 'M19988' - }, - { - 'name': 'EMBL', - 'id': 'AAA60046.1' - }, - { - 'name': 'EMBL', - 'id': 'M21571' - }, - { - 'name': 'EMBL', - 'id': 'AAA60046.1' - }, - { - 'name': 'EMBL', - 'id': 'M19984' - }, - { - 'name': 'EMBL', - 'id': 'AAA60046.1' - }, - { - 'name': 'EMBL', - 'id': 'M19985' - }, - { - 'name': 'EMBL', - 'id': 'AAA60046.1' - }, - { - 'name': 'EMBL', - 'id': 'M19986' - }, - { - 'name': 'EMBL', - 'id': 'AAA60046.1' - }, - { - 'name': 'EMBL', - 'id': 'M19987' - }, - { - 'name': 'EMBL', - 'id': 'AAA60046.1' - }, - { - 'name': 'EMBL', - 'id': 'M19989' - }, - { - 'name': 'EMBL', - 'id': 'AAA60047.1' - }, - { - 'name': 'EMBL', - 'id': 'M21571' - }, - { - 'name': 'EMBL', - 'id': 'AAA60047.1' - }, - { - 'name': 'EMBL', - 'id': 'M19984' - }, - { - 'name': 'EMBL', - 'id': 'AAA60047.1' - }, - { - 'name': 'EMBL', - 'id': 'M19985' - }, - { - 'name': 'EMBL', - 'id': 'AAA60047.1' - }, - { - 'name': 'EMBL', - 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}, - { - 'name': 'MassIVE', - 'id': 'P01127' - }, - { - 'name': 'OMA', - 'id': 'KHTHDKE' - }, - { - 'name': 'OpenTargets', - 'id': 'ENSG00000100311' - }, - { - 'name': 'Orphanet', - 'id': '1980' - }, - { - 'name': 'Orphanet', - 'id': '31112' - }, - { - 'name': 'Orphanet', - 'id': '263662' - }, - { - 'name': 'Orphanet', - 'id': '2495' - }, - { - 'name': 'OrthoDB', - 'id': '5348340at2759' - }, - { - 'name': 'PANTHER', - 'id': 'PTHR11633' - }, - { - 'name': 'PANTHER', - 'id': 'PTHR11633:SF2' - }, - { - 'name': 'PDB', - 'id': '1PDG' - }, - { - 'name': 'PDB', - 'id': '3MJG' - }, - { - 'name': 'PDB', - 'id': '4HQU' - }, - { - 'name': 'PDB', - 'id': '4HQX' - }, - { - 'name': 'PDB', - 'id': '4QCI' - }, - { - 'name': 'PDB', - 'id': '6T9E' - }, - { - 'name': 'PDBsum', - 'id': '1PDG' - }, - { - 'name': 'PDBsum', - 'id': '3MJG' - }, - { - 'name': 'PDBsum', - 'id': '4HQU' - }, - { - 'name': 'PDBsum', - 'id': '4HQX' - }, - { - 'name': 'PDBsum', - 'id': '4QCI' - }, - { - 'name': 'PDBsum', - 'id': '6T9E' - }, - { - 'name': 'PIR', - 'id': 'A94276' - }, - { - 'name': 'PRO', - 'id': 'PR:P01127' - }, - { - 'name': 'PROSITE', - 'id': 'PS00249' - }, - { - 'name': 'PROSITE', - 'id': 'PS50278' - }, - { - 'name': 'PathwayCommons', - 'id': 'P01127' - }, - { - 'name': 'PaxDb', - 'id': 'P01127' - }, - { - 'name': 'PeptideAtlas', - 'id': 'P01127' - }, - { - 'name': 'Pfam', - 'id': 'PF00341' - }, - { - 'name': 'Pfam', - 'id': 'PF04692' - }, - { - 'name': 'PharmGKB', - 'id': 'PA33145' - }, - { - 'name': 'Pharos', - 'id': 'P01127' - }, - { - 'name': 'PhosphoSitePlus', - 'id': 'P01127' - }, - { - 'name': 'PhylomeDB', - 'id': 'P01127' - }, - { - 'name': 'Proteomes', - 'id': 'UP000005640' - }, - { - 'name': 'ProteomicsDB', - 'id': '33745' - }, - { - 'name': 'ProteomicsDB', - 'id': '51325' - }, - { - 'name': 'RNAct', - 'id': 'P01127' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-114608' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-1257604' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-186763' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-186797' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-2219530' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-3000171' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-5673001' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-6811558' - }, - { - 'name': 'RefSeq', - 'id': 'NP_002599.1' - }, - { - 'name': 'RefSeq', - 'id': 'NM_002608.3' - }, - { - 'name': 'RefSeq', - 'id': 'NP_148937.1' - }, - { - 'name': 'RefSeq', - 'id': 'NM_033016.3' - }, - { - 'name': 'SIGNOR', - 'id': 'P01127' - }, - { - 'name': 'SMART', - 'id': 'SM00141' - }, - { - 'name': 'SMR', - 'id': 'P01127' - }, - { - 'name': 'STRING', - 'id': '9606.ENSP00000330382' - }, - { - 'name': 'SUPFAM', - 'id': 'SSF57501' - }, - { - 'name': 'SignaLink', - 'id': 'P01127' - }, - { - 'name': 'TopDownProteomics', - 'id': 'P01127-2' - }, - { - 'name': 'TreeFam', - 'id': 'TF319554' - }, - { - 'name': 'UCSC', - 'id': 'uc003axe.4' - }, - { - 'name': 'VEuPathDB', - 'id': 'HostDB:ENSG00000100311' - }, - { - 'name': 'eggNOG', - 'id': 'ENOG502S2VW' - }, - { - 'name': 'iPTMnet', - 'id': 'P01127' - }, - { - 'name': 'neXtProt', - 'id': 'NX_P01127' - } - ], - 'source': 'UniProtKB/Swiss-Prot', - 'source_url': 'https://www.uniprot.org/help/downloads' - } - ] - }, - { - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/', - 'protein': [ - { - '_id': 'P04085', - 'name': 'PDGFA_HUMAN', - 'full_name': 'Platelet-derived growth factor subunit A', - 'dbxrefs': [ - { - 'name': 'AGR', - 'id': 'HGNC:8799' - }, - { - 'name': 'AlphaFoldDB', - 'id': 'P04085' - }, - { - 'name': 'Antibodypedia', - 'id': '3957' - }, - { - 'name': 'Bgee', - 'id': 'ENSG00000197461' - }, - { - 'name': 'BindingDB', - 'id': 'P04085' - }, - { - 'name': 'BioGRID', - 'id': '111180' - }, - { - 'name': 'BioGRID-ORCS', - 'id': '5154' - }, - { - 'name': 'BioMuta', - 'id': 'PDGFA' - }, - { - 'name': 'CCDS', - 'id': 'CCDS34578.1' - }, - { - 'name': 'CCDS', - 'id': 'CCDS47524.1' - }, - { - 'name': 'CDD', - 'id': 'cd00135' - }, - { - 'name': 'CTD', - 'id': '5154' - }, - { - 'name': 'ChEMBL', - 'id': 'CHEMBL3137294' - }, - { - 'name': 'ChiTaRS', - 'id': 'PDGFA' - }, - { - 'name': 'ComplexPortal', - 'id': 'CPX-1874' - }, - { - 'name': 'ComplexPortal', - 'id': 'CPX-1875' - }, - { - 'name': 'ComplexPortal', - 'id': 'CPX-2881' - }, - { - 'name': 'ComplexPortal', - 'id': 'CPX-2885' - }, - { - 'name': 'ComplexPortal', - 'id': 'CPX-2886' - }, - { - 'name': 'ComplexPortal', - 'id': 'CPX-2892' - }, - { - 'name': 'DIP', - 'id': 'DIP-5735N' - }, - { - 'name': 'DNASU', - 'id': '5154' - }, - { - 'name': 'DisGeNET', - 'id': '5154' - }, - { - 'name': 'EMBL', - 'id': 'X03795' - }, - { - 'name': 'EMBL', - 'id': 'CAA27421.1' - }, - { - 'name': 'EMBL', - 'id': 'X06374' - }, - { - 'name': 'EMBL', - 'id': 'CAA29677.1' - }, - { - 'name': 'EMBL', - 'id': 'M20494' - }, - { - 'name': 'EMBL', - 'id': 'AAA60045.1' - }, - { - 'name': 'EMBL', - 'id': 'M20488' - }, - { - 'name': 'EMBL', - 'id': 'AAA60045.1' - }, - { - 'name': 'EMBL', - 'id': 'M20489' - }, - { - 'name': 'EMBL', - 'id': 'AAA60045.1' - }, - { - 'name': 'EMBL', - 'id': 'M20490' - }, - { - 'name': 'EMBL', - 'id': 'AAA60045.1' - }, - { - 'name': 'EMBL', - 'id': 'M20491' - }, - { - 'name': 'EMBL', - 'id': 'AAA60045.1' - }, - { - 'name': 'EMBL', - 'id': 'M20492' - }, - { - 'name': 'EMBL', - 'id': 'AAA60045.1' - }, - { - 'name': 'EMBL', - 'id': 'M20493' - }, - { - 'name': 'EMBL', - 'id': 'AAA60045.1' - }, - { - 'name': 'EMBL', - 'id': 'M19988' - }, - { - 'name': 'EMBL', - 'id': 'AAA60046.1' - }, - { - 'name': 'EMBL', - 'id': 'M21571' - }, - { - 'name': 'EMBL', - 'id': 'AAA60046.1' - }, - { - 'name': 'EMBL', - 'id': 'M19984' - }, - { - 'name': 'EMBL', - 'id': 'AAA60046.1' - }, - { - 'name': 'EMBL', - 'id': 'M19985' - }, - { - 'name': 'EMBL', - 'id': 'AAA60046.1' - }, - { - 'name': 'EMBL', - 'id': 'M19986' - }, - { - 'name': 'EMBL', - 'id': 'AAA60046.1' - }, - { - 'name': 'EMBL', - 'id': 'M19987' - }, - { - 'name': 'EMBL', - 'id': 'AAA60046.1' - }, - { - 'name': 'EMBL', - 'id': 'M19989' - }, - { - 'name': 'EMBL', - 'id': 'AAA60047.1' - }, - { - 'name': 'EMBL', - 'id': 'M21571' - }, - { - 'name': 'EMBL', - 'id': 'AAA60047.1' - }, - { - 'name': 'EMBL', - 'id': 'M19984' - }, - { - 'name': 'EMBL', - 'id': 'AAA60047.1' - }, - { - 'name': 'EMBL', - 'id': 'M19985' - }, - { - 'name': 'EMBL', - 'id': 'AAA60047.1' - }, - { - 'name': 'EMBL', - 'id': 'M19986' - }, - { - 'name': 'EMBL', - 'id': 'AAA60047.1' - }, - { - 'name': 'EMBL', - 'id': 'M19987' - }, - { - 'name': 'EMBL', - 'id': 'AAA60047.1' - }, - { - 'name': 'EMBL', - 'id': 'AB451309' - }, - { - 'name': 'EMBL', - 'id': 'BAG70123.1' - }, - { - 'name': 'EMBL', - 'id': 'AB451439' - }, - { - 'name': 'EMBL', - 'id': 'BAG70253.1' - }, - { - 'name': 'EMBL', - 'id': 'AC147651' - }, - { - 'name': 'EMBL', - 'id': 'S62078' - }, - { - 'name': 'EMBL', - 'id': 'AAB26566.1' - }, - { - 'name': 'EPD', - 'id': 'P04085' - }, - { - 'name': 'Ensembl', - 'id': 'ENST00000354513.9' - }, - { - 'name': 'Ensembl', - 'id': 'ENSP00000346508.5' - }, - { - 'name': 'Ensembl', - 'id': 'ENSG00000197461.13' - 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'id': 'GO:0042803' - }, - { - 'name': 'GO', - 'id': 'GO:0030036' - }, - { - 'name': 'GO', - 'id': 'GO:0001525' - }, - { - 'name': 'GO', - 'id': 'GO:0009887' - }, - { - 'name': 'GO', - 'id': 'GO:0001775' - }, - { - 'name': 'GO', - 'id': 'GO:0030031' - }, - { - 'name': 'GO', - 'id': 'GO:0007267' - }, - { - 'name': 'GO', - 'id': 'GO:0071560' - }, - { - 'name': 'GO', - 'id': 'GO:1990401' - }, - { - 'name': 'GO', - 'id': 'GO:0001942' - }, - { - 'name': 'GO', - 'id': 'GO:0048839' - }, - { - 'name': 'GO', - 'id': 'GO:0048286' - }, - { - 'name': 'GO', - 'id': 'GO:0008584' - }, - { - 'name': 'GO', - 'id': 'GO:0050919' - }, - { - 'name': 'GO', - 'id': 'GO:0010512' - }, - { - 'name': 'GO', - 'id': 'GO:0010544' - }, - { - 'name': 'GO', - 'id': 'GO:0048008' - }, - { - 'name': 'GO', - 'id': 'GO:0035790' - }, - { - 'name': 'GO', - 'id': 'GO:0051781' - }, - { - 'name': 'GO', - 'id': 'GO:0030335' - }, - { - 'name': 'GO', - 'id': 'GO:0008284' - }, - { - 'name': 'GO', - 'id': 'GO:0070374' - }, - { - 'name': 'GO', - 'id': 'GO:0048146' - }, - { - 'name': 'GO', - 'id': 'GO:0043406' - }, - { - 'name': 'GO', - 'id': 'GO:0043410' - }, - { - 'name': 'GO', - 'id': 'GO:0002053' - }, - { - 'name': 'GO', - 'id': 'GO:0035793' - }, - { - 'name': 'GO', - 'id': 'GO:0014068' - }, - { - 'name': 'GO', - 'id': 'GO:0031954' - }, - { - 'name': 'GO', - 'id': 'GO:0051897' - }, - { - 'name': 'GO', - 'id': 'GO:0032956' - }, - { - 'name': 'GO', - 'id': 'GO:0060683' - }, - { - 'name': 'GO', - 'id': 'GO:0050730' - }, - { - 'name': 'GO', - 'id': 'GO:0014910' - }, - { - 'name': 'GO', - 'id': 'GO:0032355' - }, - { - 'name': 'GO', - 'id': 'GO:0001666' - }, - { - 'name': 'GO', - 'id': 'GO:0010035' - }, - { - 'name': 'GO', - 'id': 'GO:0032526' - }, - { - 'name': 'GO', - 'id': 'GO:0009611' - }, - { - 'name': 'GO', - 'id': 'GO:0009410' - }, - { - 'name': 'GO', - 'id': 'GO:0043588' - }, - { - 'name': 'GO', - 'id': 'GO:0042060' - }, - { - 'name': 'Gene3D', - 'id': '2.10.90.10' - }, - { - 'name': 'GeneCards', - 'id': 'PDGFA' - }, - { - 'name': 'GeneID', - 'id': '5154' - }, - { - 'name': 'GeneTree', - 'id': 'ENSGT00940000159039' - }, - { - 'name': 'GeneWiki', - 'id': 'PDGFA' - }, - { - 'name': 'Genevisible', - 'id': 'P04085' - }, - { - 'name': 'GenomeRNAi', - 'id': '5154' - }, - { - 'name': 'GlyCosmos', - 'id': 'P04085' - }, - { - 'name': 'GlyGen', - 'id': 'P04085' - }, - { - 'name': 'HGNC', - 'id': 'HGNC:8799' - }, - { - 'name': 'HOGENOM', - 'id': 'CLU_094438_1_0_1' - }, - { - 'name': 'HPA', - 'id': 'ENSG00000197461' - }, - { - 'name': 'InParanoid', - 'id': 'P04085' - }, - { - 'name': 'IntAct', - 'id': 'P04085' - }, - { - 'name': 'InterPro', - 'id': 'IPR029034' - }, - { - 'name': 'InterPro', - 'id': 'IPR023581' - }, - { - 'name': 'InterPro', - 'id': 'IPR000072' - }, - { - 'name': 'InterPro', - 'id': 'IPR006782' - }, - { - 'name': 'KEGG', - 'id': 'hsa:5154' - }, - { - 'name': 'MANE-Select', - 'id': 'ENST00000402802.8' - }, - { - 'name': 'MANE-Select', - 'id': 'ENSP00000383889.3' - }, - { - 'name': 'MANE-Select', - 'id': 'NM_033023.5' - }, - { - 'name': 'MANE-Select', - 'id': 'NP_148983.1' - }, - { - 'name': 'MIM', - 'id': '173430' - }, - { - 'name': 'MassIVE', - 'id': 'P04085' - }, - { - 'name': 'OMA', - 'id': 'CTCTTSN' - }, - { - 'name': 'OpenTargets', - 'id': 'ENSG00000197461' - }, - { - 'name': 'OrthoDB', - 'id': '5310792at2759' - }, - { - 'name': 'PANTHER', - 'id': 'PTHR11633' - }, - { - 'name': 'PANTHER', - 'id': 'PTHR11633:SF3' - }, - { - 'name': 'PDB', - 'id': '3MJK' - }, - { - 'name': 'PDBsum', - 'id': '3MJK' - }, - { - 'name': 'PIR', - 'id': 'A28964' - }, - { - 'name': 'PIR', - 'id': 'B28964' - }, - { - 'name': 'PRO', - 'id': 'PR:P04085' - }, - { - 'name': 'PROSITE', - 'id': 'PS00249' - }, - { - 'name': 'PROSITE', - 'id': 'PS50278' - }, - { - 'name': 'PathwayCommons', - 'id': 'P04085' - }, - { - 'name': 'PaxDb', - 'id': 'P04085' - }, - { - 'name': 'PeptideAtlas', - 'id': 'P04085' - }, - { - 'name': 'Pfam', - 'id': 'PF00341' - }, - { - 'name': 'Pfam', - 'id': 'PF04692' - }, - { - 'name': 'PharmGKB', - 'id': 'PA33144' - }, - { - 'name': 'Pharos', - 'id': 'P04085' - }, - { - 'name': 'PhosphoSitePlus', - 'id': 'P04085' - }, - { - 'name': 'PhylomeDB', - 'id': 'P04085' - }, - { - 'name': 'Proteomes', - 'id': 'UP000005640' - }, - { - 'name': 'ProteomicsDB', - 'id': '51650' - }, - { - 'name': 'ProteomicsDB', - 'id': '51651' - }, - { - 'name': 'RNAct', - 'id': 'P04085' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-114608' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-1257604' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-186763' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-186797' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-2219530' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-3000171' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-5673001' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-6811558' - }, - { - 'name': 'RefSeq', - 'id': 'NP_002598.4' - }, - { - 'name': 'RefSeq', - 'id': 'NM_002607.5' - }, - { - 'name': 'RefSeq', - 'id': 'NP_148983.1' - }, - { - 'name': 'RefSeq', - 'id': 'NM_033023.4' - }, - { - 'name': 'SIGNOR', - 'id': 'P04085' - }, - { - 'name': 'SMART', - 'id': 'SM00141' - }, - { - 'name': 'SMR', - 'id': 'P04085' - }, - { - 'name': 'STRING', - 'id': '9606.ENSP00000346508' - }, - { - 'name': 'SUPFAM', - 'id': 'SSF57501' - }, - { - 'name': 'SignaLink', - 'id': 'P04085' - }, - { - 'name': 'TreeFam', - 'id': 'TF319554' - }, - { - 'name': 'UCSC', - 'id': 'uc003sir.4' - }, - { - 'name': 'VEuPathDB', - 'id': 'HostDB:ENSG00000197461' - }, - { - 'name': 'eggNOG', - 'id': 'ENOG502QVAU' - }, - { - 'name': 'iPTMnet', - 'id': 'P04085' - }, - { - 'name': 'jPOST', - 'id': 'P04085' - }, - { - 'name': 'neXtProt', - 'id': 'NX_P04085' - } - ], - 'source': 'UniProtKB/Swiss-Prot', - 'source_url': 'https://www.uniprot.org/help/downloads' - } - ] - }, - { - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/', - 'protein': [ - { - '_id': 'P01127', - 'name': 'PDGFB_HUMAN', - 'full_name': 'Platelet-derived growth factor subunit B', - 'dbxrefs': [ - { - 'name': 'ABCD', - 'id': 'P01127' - 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'id': 'ENSP00000330382.6' - }, - { - 'name': 'MANE-Select', - 'id': 'NM_002608.4' - }, - { - 'name': 'MANE-Select', - 'id': 'NP_002599.1' - }, - { - 'name': 'MIM', - 'id': '190040' - }, - { - 'name': 'MIM', - 'id': '607907' - }, - { - 'name': 'MIM', - 'id': '615483' - }, - { - 'name': 'MalaCards', - 'id': 'PDGFB' - }, - { - 'name': 'MassIVE', - 'id': 'P01127' - }, - { - 'name': 'OMA', - 'id': 'KHTHDKE' - }, - { - 'name': 'OpenTargets', - 'id': 'ENSG00000100311' - }, - { - 'name': 'Orphanet', - 'id': '1980' - }, - { - 'name': 'Orphanet', - 'id': '31112' - }, - { - 'name': 'Orphanet', - 'id': '263662' - }, - { - 'name': 'Orphanet', - 'id': '2495' - }, - { - 'name': 'OrthoDB', - 'id': '5348340at2759' - }, - { - 'name': 'PANTHER', - 'id': 'PTHR11633' - }, - { - 'name': 'PANTHER', - 'id': 'PTHR11633:SF2' - }, - { - 'name': 'PDB', - 'id': '1PDG' - }, - { - 'name': 'PDB', - 'id': '3MJG' - }, - { - 'name': 'PDB', - 'id': '4HQU' - }, - { - 'name': 'PDB', - 'id': '4HQX' - }, - { - 'name': 'PDB', - 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'id': 'SSF57501' - }, - { - 'name': 'SignaLink', - 'id': 'P01127' - }, - { - 'name': 'TopDownProteomics', - 'id': 'P01127-2' - }, - { - 'name': 'TreeFam', - 'id': 'TF319554' - }, - { - 'name': 'UCSC', - 'id': 'uc003axe.4' - }, - { - 'name': 'VEuPathDB', - 'id': 'HostDB:ENSG00000100311' - }, - { - 'name': 'eggNOG', - 'id': 'ENOG502S2VW' - }, - { - 'name': 'iPTMnet', - 'id': 'P01127' - }, - { - 'name': 'neXtProt', - 'id': 'NX_P01127' - } - ], - 'source': 'UniProtKB/Swiss-Prot', - 'source_url': 'https://www.uniprot.org/help/downloads' - } - ] - }, - { - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/', - 'protein': [ - { - '_id': 'P26368', - 'name': 'U2AF2_HUMAN', - 'full_name': 'Splicing factor U2AF 65 kDa subunit', - 'dbxrefs': [ - { - 'name': 'AGR', - 'id': 'HGNC:23156' - }, - { - 'name': 'AlphaFoldDB', - 'id': 'P26368' - }, - { - 'name': 'Antibodypedia', - 'id': '4399' - }, - { - 'name': 'BMRB', - 'id': 'P26368' - }, - { - 'name': 'Bgee', - 'id': 'ENSG00000063244' - 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}, - { - 'name': 'PDBsum', - 'id': '3VAG' - }, - { - 'name': 'PDBsum', - 'id': '3VAH' - }, - { - 'name': 'PDBsum', - 'id': '3VAI' - }, - { - 'name': 'PDBsum', - 'id': '3VAJ' - }, - { - 'name': 'PDBsum', - 'id': '3VAK' - }, - { - 'name': 'PDBsum', - 'id': '3VAL' - }, - { - 'name': 'PDBsum', - 'id': '3VAM' - }, - { - 'name': 'PDBsum', - 'id': '4FXW' - }, - { - 'name': 'PDBsum', - 'id': '4TU7' - }, - { - 'name': 'PDBsum', - 'id': '4TU8' - }, - { - 'name': 'PDBsum', - 'id': '4TU9' - }, - { - 'name': 'PDBsum', - 'id': '5EV1' - }, - { - 'name': 'PDBsum', - 'id': '5EV2' - }, - { - 'name': 'PDBsum', - 'id': '5EV3' - }, - { - 'name': 'PDBsum', - 'id': '5EV4' - }, - { - 'name': 'PDBsum', - 'id': '5W0G' - }, - { - 'name': 'PDBsum', - 'id': '5W0H' - }, - { - 'name': 'PDBsum', - 'id': '6TR0' - }, - { - 'name': 'PDBsum', - 'id': '6XLV' - }, - { - 'name': 'PDBsum', - 'id': '6XLW' - }, - { - 'name': 'PDBsum', - 'id': '6XLX' - }, - { - 'name': 'PDBsum', - 'id': '7S3A' - }, - { - 'name': 'PDBsum', - 'id': '7S3B' - 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'id': 'R-HSA-73856' - }, - { - 'name': 'RefSeq', - 'id': 'NP_001012496.1' - }, - { - 'name': 'RefSeq', - 'id': 'NM_001012478.1' - }, - { - 'name': 'RefSeq', - 'id': 'NP_009210.1' - }, - { - 'name': 'RefSeq', - 'id': 'NM_007279.2' - }, - { - 'name': 'SIGNOR', - 'id': 'P26368' - }, - { - 'name': 'SMART', - 'id': 'SM00360' - }, - { - 'name': 'SMR', - 'id': 'P26368' - }, - { - 'name': 'STRING', - 'id': '9606.ENSP00000307863' - }, - { - 'name': 'SUPFAM', - 'id': 'SSF54928' - }, - { - 'name': 'SignaLink', - 'id': 'P26368' - }, - { - 'name': 'SwissPalm', - 'id': 'P26368' - }, - { - 'name': 'TIGRFAMs', - 'id': 'TIGR01642' - }, - { - 'name': 'TopDownProteomics', - 'id': 'P26368-1' - }, - { - 'name': 'TopDownProteomics', - 'id': 'P26368-2' - }, - { - 'name': 'TreeFam', - 'id': 'TF314111' - }, - { - 'name': 'UCSC', - 'id': 'uc002qlt.4' - }, - { - 'name': 'VEuPathDB', - 'id': 'HostDB:ENSG00000063244' - }, - { - 'name': 'eggNOG', - 'id': 'KOG0120' - }, - { - 'name': 'iPTMnet', - 'id': 'P26368' - }, - { - 'name': 'jPOST', - 'id': 'P26368' - }, - { - 'name': 'neXtProt', - 'id': 'NX_P26368' - } - ], - 'source': 'UniProtKB/Swiss-Prot', - 'source_url': 'https://www.uniprot.org/help/downloads' - } - ] - }, - { - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/', - 'protein': [ - { - '_id': 'Q01081', - 'name': 'U2AF1_HUMAN', - 'full_name': 'Splicing factor U2AF 35 kDa subunit', - 'dbxrefs': [ - { - 'name': 'AGR', - 'id': 'HGNC:12453' - }, - { - 'name': 'AlphaFoldDB', - 'id': 'Q01081' - }, - { - 'name': 'Antibodypedia', - 'id': '23951' - }, - { - 'name': 'Bgee', - 'id': 'ENSG00000160201' - }, - { - 'name': 'BioGRID', - 'id': '113157' - }, - { - 'name': 'BioGRID', - 'id': '3195698' - }, - { - 'name': 'BioGRID-ORCS', - 'id': '102724594' - }, - { - 'name': 'BioGRID-ORCS', - 'id': '7307' - }, - { - 'name': 'BioMuta', - 'id': 'U2AF1' - }, - { - 'name': 'CCDS', - 'id': 'CCDS13694.1' - }, - { - 'name': 'CCDS', - 'id': 'CCDS33574.1' - }, - { - 'name': 'CCDS', - 'id': 'CCDS42948.1' - 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'name': 'Reactome', - 'id': 'R-HSA-9614657' - }, - { - 'name': 'RefSeq', - 'id': 'NP_006157.1' - }, - { - 'name': 'RefSeq', - 'id': 'NM_006166.3' - }, - { - 'name': 'SASBDB', - 'id': 'P25208' - }, - { - 'name': 'SIGNOR', - 'id': 'P25208' - }, - { - 'name': 'SMR', - 'id': 'P25208' - }, - { - 'name': 'STRING', - 'id': '9606.ENSP00000240055' - }, - { - 'name': 'SUPFAM', - 'id': 'SSF47113' - }, - { - 'name': 'SignaLink', - 'id': 'P25208' - }, - { - 'name': 'TreeFam', - 'id': 'TF314521' - }, - { - 'name': 'UCSC', - 'id': 'uc001tkl.2' - }, - { - 'name': 'VEuPathDB', - 'id': 'HostDB:ENSG00000120837' - }, - { - 'name': 'eggNOG', - 'id': 'KOG0869' - }, - { - 'name': 'iPTMnet', - 'id': 'P25208' - }, - { - 'name': 'jPOST', - 'id': 'P25208' - }, - { - 'name': 'neXtProt', - 'id': 'NX_P25208' - } - ], - 'source': 'UniProtKB/Swiss-Prot', - 'source_url': 'https://www.uniprot.org/help/downloads' - } - ] - }, - { - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/', - 'protein': [ - 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'name': 'GO', - 'id': 'GO:0006357' - }, - { - 'name': 'GO', - 'id': 'GO:0000083' - }, - { - 'name': 'GO', - 'id': 'GO:0006366' - }, - { - 'name': 'Gene3D', - 'id': '1.20.140.80' - }, - { - 'name': 'Gene3D', - 'id': '1.10.10.10' - }, - { - 'name': 'GeneCards', - 'id': 'TFDP1' - }, - { - 'name': 'GeneID', - 'id': '7027' - }, - { - 'name': 'GeneTree', - 'id': 'ENSGT00940000154652' - }, - { - 'name': 'GeneWiki', - 'id': 'TFDP1' - }, - { - 'name': 'Genevisible', - 'id': 'Q14186' - }, - { - 'name': 'GenomeRNAi', - 'id': '7027' - }, - { - 'name': 'HGNC', - 'id': 'HGNC:11749' - }, - { - 'name': 'HOGENOM', - 'id': 'CLU_039874_3_1_1' - }, - { - 'name': 'HPA', - 'id': 'ENSG00000198176' - }, - { - 'name': 'IDEAL', - 'id': 'IID00076' - }, - { - 'name': 'InParanoid', - 'id': 'Q14186' - }, - { - 'name': 'IntAct', - 'id': 'Q14186' - }, - { - 'name': 'InterPro', - 'id': 'IPR037241' - }, - { - 'name': 'InterPro', - 'id': 'IPR003316' - }, - { - 'name': 'InterPro', - 'id': 'IPR038168' - }, - { - 'name': 'InterPro', - 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'id': '5TUU' - }, - { - 'name': 'PDB', - 'id': '5TUV' - }, - { - 'name': 'PDBsum', - 'id': '2AZE' - }, - { - 'name': 'PDBsum', - 'id': '5GOW' - }, - { - 'name': 'PDBsum', - 'id': '5TUU' - }, - { - 'name': 'PDBsum', - 'id': '5TUV' - }, - { - 'name': 'PIR', - 'id': 'A48585' - }, - { - 'name': 'PIRSF', - 'id': 'PIRSF009404' - }, - { - 'name': 'PRO', - 'id': 'PR:Q14186' - }, - { - 'name': 'PathwayCommons', - 'id': 'Q14186' - }, - { - 'name': 'PaxDb', - 'id': 'Q14186' - }, - { - 'name': 'PeptideAtlas', - 'id': 'Q14186' - }, - { - 'name': 'Pfam', - 'id': 'PF08781' - }, - { - 'name': 'Pfam', - 'id': 'PF02319' - }, - { - 'name': 'PharmGKB', - 'id': 'PA36464' - }, - { - 'name': 'Pharos', - 'id': 'Q14186' - }, - { - 'name': 'PhosphoSitePlus', - 'id': 'Q14186' - }, - { - 'name': 'PhylomeDB', - 'id': 'Q14186' - }, - { - 'name': 'Proteomes', - 'id': 'UP000005640' - }, - { - 'name': 'ProteomicsDB', - 'id': '4551' - }, - { - 'name': 'ProteomicsDB', - 'id': '59904' - }, - { - 'name': 'RNAct', - 'id': 'Q14186' - 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'id': 'NP_009042.1' - }, - { - 'name': 'RefSeq', - 'id': 'NM_007111.4' - }, - { - 'name': 'RefSeq', - 'id': 'XP_005268384.1' - }, - { - 'name': 'RefSeq', - 'id': 'XM_005268327.1' - }, - { - 'name': 'RefSeq', - 'id': 'XP_005268388.1' - }, - { - 'name': 'RefSeq', - 'id': 'XM_005268331.1' - }, - { - 'name': 'SASBDB', - 'id': 'Q14186' - }, - { - 'name': 'SIGNOR', - 'id': 'Q14186' - }, - { - 'name': 'SMART', - 'id': 'SM01138' - }, - { - 'name': 'SMART', - 'id': 'SM01372' - }, - { - 'name': 'SMR', - 'id': 'Q14186' - }, - { - 'name': 'STRING', - 'id': '9606.ENSP00000364519' - }, - { - 'name': 'SUPFAM', - 'id': 'SSF144074' - }, - { - 'name': 'SUPFAM', - 'id': 'SSF46785' - }, - { - 'name': 'SignaLink', - 'id': 'Q14186' - }, - { - 'name': 'TreeFam', - 'id': 'TF314396' - }, - { - 'name': 'UCSC', - 'id': 'uc001vtw.4' - }, - { - 'name': 'VEuPathDB', - 'id': 'HostDB:ENSG00000198176' - }, - { - 'name': 'eggNOG', - 'id': 'KOG2829' - }, - { - 'name': 'iPTMnet', - 'id': 'Q14186' - }, - { - 'name': 'jPOST', - 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}, - { - 'name': 'PeptideAtlas', - 'id': 'Q14209' - }, - { - 'name': 'Pfam', - 'id': 'PF16421' - }, - { - 'name': 'Pfam', - 'id': 'PF02319' - }, - { - 'name': 'PharmGKB', - 'id': 'PA27572' - }, - { - 'name': 'Pharos', - 'id': 'Q14209' - }, - { - 'name': 'PhosphoSitePlus', - 'id': 'Q14209' - }, - { - 'name': 'PhylomeDB', - 'id': 'Q14209' - }, - { - 'name': 'Proteomes', - 'id': 'UP000005640' - }, - { - 'name': 'ProteomicsDB', - 'id': '59931' - }, - { - 'name': 'RNAct', - 'id': 'Q14209' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-2559580' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-2559585' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-69231' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-9661069' - }, - { - 'name': 'RefSeq', - 'id': 'NP_004082.1' - }, - { - 'name': 'RefSeq', - 'id': 'NM_004091.3' - }, - { - 'name': 'SIGNOR', - 'id': 'Q14209' - }, - { - 'name': 'SMART', - 'id': 'SM01372' - }, - { - 'name': 'SMR', - 'id': 'Q14209' - }, - { - 'name': 'STRING', - 'id': '9606.ENSP00000355249' - 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'id': 'O00716' - }, - { - 'name': 'IntAct', - 'id': 'O00716' - }, - { - 'name': 'InterPro', - 'id': 'IPR015633' - }, - { - 'name': 'InterPro', - 'id': 'IPR037241' - }, - { - 'name': 'InterPro', - 'id': 'IPR032198' - }, - { - 'name': 'InterPro', - 'id': 'IPR003316' - }, - { - 'name': 'InterPro', - 'id': 'IPR036388' - }, - { - 'name': 'InterPro', - 'id': 'IPR036390' - }, - { - 'name': 'KEGG', - 'id': 'hsa:1871' - }, - { - 'name': 'MANE-Select', - 'id': 'ENST00000346618.8' - }, - { - 'name': 'MANE-Select', - 'id': 'ENSP00000262904.4' - }, - { - 'name': 'MANE-Select', - 'id': 'NM_001949.5' - }, - { - 'name': 'MANE-Select', - 'id': 'NP_001940.1' - }, - { - 'name': 'MIM', - 'id': '600427' - }, - { - 'name': 'MINT', - 'id': 'O00716' - }, - { - 'name': 'MassIVE', - 'id': 'O00716' - }, - { - 'name': 'MaxQB', - 'id': 'O00716' - }, - { - 'name': 'OMA', - 'id': 'WMGCNLS' - }, - { - 'name': 'OpenTargets', - 'id': 'ENSG00000112242' - }, - { - 'name': 'OrthoDB', - 'id': '1761at2759' - }, - { - 'name': 'PANTHER', - 'id': 'PTHR12081' - }, - { - 'name': 'PANTHER', - 'id': 'PTHR12081:SF44' - }, - { - 'name': 'PRO', - 'id': 'PR:O00716' - }, - { - 'name': 'PathwayCommons', - 'id': 'O00716' - }, - { - 'name': 'PaxDb', - 'id': 'O00716' - }, - { - 'name': 'PeptideAtlas', - 'id': 'O00716' - }, - { - 'name': 'Pfam', - 'id': 'PF16421' - }, - { - 'name': 'Pfam', - 'id': 'PF02319' - }, - { - 'name': 'PharmGKB', - 'id': 'PA27573' - }, - { - 'name': 'Pharos', - 'id': 'O00716' - }, - { - 'name': 'PhosphoSitePlus', - 'id': 'O00716' - }, - { - 'name': 'PhylomeDB', - 'id': 'O00716' - }, - { - 'name': 'Proteomes', - 'id': 'UP000005640' - }, - { - 'name': 'ProteomicsDB', - 'id': '48008' - }, - { - 'name': 'ProteomicsDB', - 'id': '66100' - }, - { - 'name': 'RNAct', - 'id': 'O00716' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-1912408' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-2559580' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-2559585' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-68911' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-69231' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-9661069' - }, - { - 'name': 'RefSeq', - 'id': 'NP_001230005.1' - }, - { - 'name': 'RefSeq', - 'id': 'NM_001243076.2' - }, - { - 'name': 'RefSeq', - 'id': 'NP_001940.1' - }, - { - 'name': 'RefSeq', - 'id': 'NM_001949.4' - }, - { - 'name': 'SIGNOR', - 'id': 'O00716' - }, - { - 'name': 'SMART', - 'id': 'SM01372' - }, - { - 'name': 'SMR', - 'id': 'O00716' - }, - { - 'name': 'STRING', - 'id': '9606.ENSP00000262904' - }, - { - 'name': 'SUPFAM', - 'id': 'SSF144074' - }, - { - 'name': 'SUPFAM', - 'id': 'SSF46785' - }, - { - 'name': 'SignaLink', - 'id': 'O00716' - }, - { - 'name': 'TreeFam', - 'id': 'TF105566' - }, - { - 'name': 'UCSC', - 'id': 'uc003nda.3' - }, - { - 'name': 'VEuPathDB', - 'id': 'HostDB:ENSG00000112242' - }, - { - 'name': 'eggNOG', - 'id': 'KOG2577' - }, - { - 'name': 'iPTMnet', - 'id': 'O00716' - }, - { - 'name': 'jPOST', - 'id': 'O00716' - }, - { - 'name': 'neXtProt', - 'id': 'NX_O00716' - } - ], - 'source': 'UniProtKB/Swiss-Prot', - 'source_url': 'https://www.uniprot.org/help/downloads' - } - ] - }, - { - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/', - 'protein': [ - { - '_id': 'Q14186', - 'name': 'TFDP1_HUMAN', - 'full_name': 'Transcription factor Dp-1', - 'dbxrefs': [ - { - 'name': 'AGR', - 'id': 'HGNC:11749' - }, - { - 'name': 'AlphaFoldDB', - 'id': 'Q14186' - }, - { - 'name': 'Antibodypedia', - 'id': '11828' - }, - { - 'name': 'Bgee', - 'id': 'ENSG00000198176' - }, - { - 'name': 'BioGRID', - 'id': '112885' - }, - { - 'name': 'BioGRID-ORCS', - 'id': '7027' - }, - { - 'name': 'BioMuta', - 'id': 'TFDP1' - }, - { - 'name': 'CCDS', - 'id': 'CCDS9538.1' - }, - { - 'name': 'CDD', - 'id': 'cd14458' - }, - { - 'name': 'CORUM', - 'id': 'Q14186' - }, - { - 'name': 'CTD', - 'id': '7027' - }, - { - 'name': 'ChEMBL', - 'id': 'CHEMBL4523289' - }, - { - 'name': 'ChiTaRS', - 'id': 'TFDP1' - }, - { - 'name': 'ComplexPortal', - 'id': 'CPX-155' - }, - { - 'name': 'ComplexPortal', - 'id': 'CPX-175' - }, - 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}, - { - 'name': 'PDB', - 'id': '5TUU' - }, - { - 'name': 'PDB', - 'id': '5TUV' - }, - { - 'name': 'PDBsum', - 'id': '2AZE' - }, - { - 'name': 'PDBsum', - 'id': '5GOW' - }, - { - 'name': 'PDBsum', - 'id': '5TUU' - }, - { - 'name': 'PDBsum', - 'id': '5TUV' - }, - { - 'name': 'PIR', - 'id': 'A48585' - }, - { - 'name': 'PIRSF', - 'id': 'PIRSF009404' - }, - { - 'name': 'PRO', - 'id': 'PR:Q14186' - }, - { - 'name': 'PathwayCommons', - 'id': 'Q14186' - }, - { - 'name': 'PaxDb', - 'id': 'Q14186' - }, - { - 'name': 'PeptideAtlas', - 'id': 'Q14186' - }, - { - 'name': 'Pfam', - 'id': 'PF08781' - }, - { - 'name': 'Pfam', - 'id': 'PF02319' - }, - { - 'name': 'PharmGKB', - 'id': 'PA36464' - }, - { - 'name': 'Pharos', - 'id': 'Q14186' - }, - { - 'name': 'PhosphoSitePlus', - 'id': 'Q14186' - }, - { - 'name': 'PhylomeDB', - 'id': 'Q14186' - }, - { - 'name': 'Proteomes', - 'id': 'UP000005640' - }, - { - 'name': 'ProteomicsDB', - 'id': '4551' - }, - { - 'name': 'ProteomicsDB', - 'id': '59904' - }, - { - 'name': 'RNAct', - 'id': 'Q14186' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-111448' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-113501' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-1362277' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-1362300' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-139915' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-1538133' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-1912408' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-2173796' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-2559580' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-2559585' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-6804114' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-69202' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-69205' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-69231' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-69656' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-8953750' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-9616222' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-9661069' - }, - { - 'name': 'RefSeq', - 'id': 'NP_009042.1' - }, - { - 'name': 'RefSeq', - 'id': 'NM_007111.4' - }, - { - 'name': 'RefSeq', - 'id': 'XP_005268384.1' - }, - { - 'name': 'RefSeq', - 'id': 'XM_005268327.1' - }, - { - 'name': 'RefSeq', - 'id': 'XP_005268388.1' - }, - { - 'name': 'RefSeq', - 'id': 'XM_005268331.1' - }, - { - 'name': 'SASBDB', - 'id': 'Q14186' - }, - { - 'name': 'SIGNOR', - 'id': 'Q14186' - }, - { - 'name': 'SMART', - 'id': 'SM01138' - }, - { - 'name': 'SMART', - 'id': 'SM01372' - }, - { - 'name': 'SMR', - 'id': 'Q14186' - }, - { - 'name': 'STRING', - 'id': '9606.ENSP00000364519' - }, - { - 'name': 'SUPFAM', - 'id': 'SSF144074' - }, - { - 'name': 'SUPFAM', - 'id': 'SSF46785' - }, - { - 'name': 'SignaLink', - 'id': 'Q14186' - }, - { - 'name': 'TreeFam', - 'id': 'TF314396' - }, - { - 'name': 'UCSC', - 'id': 'uc001vtw.4' - }, - { - 'name': 'VEuPathDB', - 'id': 'HostDB:ENSG00000198176' - }, - { - 'name': 'eggNOG', - 'id': 'KOG2829' - }, - { - 'name': 'iPTMnet', - 'id': 'Q14186' - }, - { - 'name': 'jPOST', - 'id': 'Q14186' - }, - { - 'name': 'neXtProt', - 'id': 'NX_Q14186' - } - ], - 'source': 'UniProtKB/Swiss-Prot', - 'source_url': 'https://www.uniprot.org/help/downloads' - } - ] - }, - { - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/', - 'protein': [ - { - '_id': 'P15692', - 'name': 'VEGFA_HUMAN', - 'full_name': 'Vascular endothelial growth factor A', - 'dbxrefs': [ - { - 'name': 'ABCD', - 'id': 'P15692' - }, - { - 'name': 'AGR', - 'id': 'HGNC:12680' - }, - { - 'name': 'AlphaFoldDB', - 'id': 'P15692' - }, - { - 'name': 'Antibodypedia', - 'id': '3956' - }, - { - 'name': 'BMRB', - 'id': 'P15692' - }, - { - 'name': 'Bgee', - 'id': 'ENSG00000112715' - }, - { - 'name': 'BindingDB', - 'id': 'P15692' - }, - { - 'name': 'BioGRID', - 'id': '113265' - }, - { - 'name': 'BioGRID-ORCS', - 'id': '7422' - }, - { - 'name': 'BioMuta', - 'id': 'VEGFA' - }, - { - 'name': 'CCDS', - 'id': 'CCDS34457.1' - }, - { - 'name': 'CCDS', - 'id': 'CCDS34458.1' - }, - { - 'name': 'CCDS', - 'id': 'CCDS47432.1' - }, - { - 'name': 'CCDS', - 'id': 'CCDS47433.1' - }, - { - 'name': 'CCDS', - 'id': 'CCDS47434.1' - }, - { - 'name': 'CCDS', - 'id': 'CCDS47435.1' - }, - { - 'name': 'CCDS', - 'id': 'CCDS4907.2' - }, - { - 'name': 'CCDS', - 'id': 'CCDS55007.1' - }, - { - 'name': 'CCDS', - 'id': 'CCDS55008.1' - }, - { - 'name': 'CCDS', - 'id': 'CCDS55009.1' - }, - { - 'name': 'CCDS', - 'id': 'CCDS55010.1' - }, - { - 'name': 'CCDS', - 'id': 'CCDS55011.1' - }, - { - 'name': 'CCDS', - 'id': 'CCDS55012.1' - }, - { - 'name': 'CCDS', - 'id': 'CCDS55013.1' - }, - { - 'name': 'CCDS', - 'id': 'CCDS55014.1' - }, - { - 'name': 'CCDS', - 'id': 'CCDS55015.1' - }, - { - 'name': 'CDD', - 'id': 'cd00135' - }, - { - 'name': 'CORUM', - 'id': 'P15692' - }, - { - 'name': 'CPTC', - 'id': 'P15692' - }, - { - 'name': 'CTD', - 'id': '7422' - }, - { - 'name': 'ChEMBL', - 'id': 'CHEMBL1783' - }, - { - 'name': 'ChiTaRS', - 'id': 'VEGFA' - }, - { - 'name': 'ComplexPortal', - 'id': 'CPX-1977' - 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'name': 'PDBsum', - 'id': '4BCG' - }, - { - 'name': 'PDBsum', - 'id': '4BCH' - }, - { - 'name': 'PDBsum', - 'id': '4BCI' - }, - { - 'name': 'PDBsum', - 'id': '4BCJ' - }, - { - 'name': 'PDBsum', - 'id': '4EC8' - }, - { - 'name': 'PDBsum', - 'id': '4EC9' - }, - { - 'name': 'PDBsum', - 'id': '4IMY' - }, - { - 'name': 'PDBsum', - 'id': '4OGR' - }, - { - 'name': 'PDBsum', - 'id': '4OR5' - }, - { - 'name': 'PDBsum', - 'id': '5L1Z' - }, - { - 'name': 'PDBsum', - 'id': '6CYT' - }, - { - 'name': 'PDBsum', - 'id': '6GZH' - }, - { - 'name': 'PDBsum', - 'id': '6W9E' - }, - { - 'name': 'PDBsum', - 'id': '6Z45' - }, - { - 'name': 'PDBsum', - 'id': '7NWK' - }, - { - 'name': 'PRO', - 'id': 'PR:O60563' - }, - { - 'name': 'PathwayCommons', - 'id': 'O60563' - }, - { - 'name': 'PaxDb', - 'id': 'O60563' - }, - { - 'name': 'PeptideAtlas', - 'id': 'O60563' - }, - { - 'name': 'Pfam', - 'id': 'PF00134' - }, - { - 'name': 'PharmGKB', - 'id': 'PA26163' - }, - { - 'name': 'Pharos', - 'id': 'O60563' - }, - { - 'name': 'PhosphoSitePlus', - 'id': 'O60563' - }, - { - 'name': 'PhylomeDB', - 'id': 'O60563' - }, - { - 'name': 'Proteomes', - 'id': 'UP000005640' - }, - { - 'name': 'ProteomicsDB', - 'id': '2517' - }, - { - 'name': 'ProteomicsDB', - 'id': '49468' - }, - { - 'name': 'RNAct', - 'id': 'O60563' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-112382' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-167152' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-167200' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-167238' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-167243' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-167246' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-167287' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-167290' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-176034' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-2173796' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-674695' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-6796648' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-6807505' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-75955' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-9018519' - }, - { - 'name': 'RefSeq', - 'id': 'NP_001231.2' - }, - { - 'name': 'RefSeq', - 'id': 'NM_001240.3' - }, - { - 'name': 'RefSeq', - 'id': 'NP_001264771.1' - }, - { - 'name': 'RefSeq', - 'id': 'NM_001277842.1' - }, - { - 'name': 'SIGNOR', - 'id': 'O60563' - }, - { - 'name': 'SMART', - 'id': 'SM00385' - }, - { - 'name': 'SMR', - 'id': 'O60563' - }, - { - 'name': 'STRING', - 'id': '9606.ENSP00000261900' - }, - { - 'name': 'SUPFAM', - 'id': 'SSF47954' - }, - { - 'name': 'SignaLink', - 'id': 'O60563' - }, - { - 'name': 'TreeFam', - 'id': 'TF101014' - }, - { - 'name': 'UCSC', - 'id': 'uc001rsd.5' - }, - { - 'name': 'VEuPathDB', - 'id': 'HostDB:ENSG00000129315' - }, - { - 'name': 'eggNOG', - 'id': 'KOG0834' - }, - { - 'name': 'iPTMnet', - 'id': 'O60563' - }, - { - 'name': 'jPOST', - 'id': 'O60563' - }, - { - 'name': 'neXtProt', - 'id': 'NX_O60563' - } - ], - 'source': 'UniProtKB/Swiss-Prot', - 'source_url': 'https://www.uniprot.org/help/downloads' - } - ] - }, - { - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/', - 'protein': [ - { - '_id': 'P50750', - 'name': 'CDK9_HUMAN', - 'full_name': 'Cyclin-dependent kinase 9', - 'dbxrefs': [ - { - 'name': 'AGR', - 'id': 'HGNC:1780' - }, - { - 'name': 'AlphaFoldDB', - 'id': 'P50750' - }, - { - 'name': 'Antibodypedia', - 'id': '1447' - }, - { - 'name': 'BRENDA', - 'id': '2.7.11.22' - }, - { - 'name': 'BRENDA', - 'id': '2.7.11.23' - }, - { - 'name': 'Bgee', - 'id': 'ENSG00000136807' - }, - { - 'name': 'BindingDB', - 'id': 'P50750' - }, - { - 'name': 'BioGRID', - 'id': '107459' - }, - { - 'name': 'BioGRID-ORCS', - 'id': '1025' - }, - { - 'name': 'BioMuta', - 'id': 'CDK9' - }, - { - 'name': 'CCDS', - 'id': 'CCDS6879.1' - }, - { - 'name': 'CDD', - 'id': 'cd07865' - }, - { - 'name': 'CORUM', - 'id': 'P50750' - }, - { - 'name': 'CPTAC', - 'id': 'CPTAC-1602' - }, - { - 'name': 'CTD', - 'id': '1025' - }, - { - 'name': 'ChEMBL', - 'id': 'CHEMBL3116' - }, - { - 'name': 'ChiTaRS', - 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'id': 'BT019903' - }, - { - 'name': 'EMBL', - 'id': 'AAV38706.1' - }, - { - 'name': 'EMBL', - 'id': 'AF517840' - }, - { - 'name': 'EMBL', - 'id': 'AAM54039.1' - }, - { - 'name': 'EMBL', - 'id': 'AL162586' - }, - { - 'name': 'EMBL', - 'id': 'BC001968' - }, - { - 'name': 'EMBL', - 'id': 'AAH01968.1' - }, - { - 'name': 'EPD', - 'id': 'P50750' - }, - { - 'name': 'Ensembl', - 'id': 'ENST00000373264.5' - }, - { - 'name': 'Ensembl', - 'id': 'ENSP00000362361.4' - }, - { - 'name': 'Ensembl', - 'id': 'ENSG00000136807.14' - }, - { - 'name': 'EvolutionaryTrace', - 'id': 'P50750' - }, - { - 'name': 'ExpressionAtlas', - 'id': 'P50750' - }, - { - 'name': 'GO', - 'id': 'GO:0008024' - }, - { - 'name': 'GO', - 'id': 'GO:0036464' - }, - { - 'name': 'GO', - 'id': 'GO:0016020' - }, - { - 'name': 'GO', - 'id': 'GO:0005654' - }, - { - 'name': 'GO', - 'id': 'GO:0005634' - }, - { - 'name': 'GO', - 'id': 'GO:0070691' - }, - { - 'name': 'GO', - 'id': 'GO:0016605' - }, - { - 'name': 'GO', - 'id': 'GO:0008023' - }, - 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}, - { - 'name': 'GO', - 'id': 'GO:0032968' - }, - { - 'name': 'GO', - 'id': 'GO:0006468' - }, - { - 'name': 'GO', - 'id': 'GO:0051726' - }, - { - 'name': 'GO', - 'id': 'GO:0006282' - }, - { - 'name': 'GO', - 'id': 'GO:0031056' - }, - { - 'name': 'GO', - 'id': 'GO:0031440' - }, - { - 'name': 'GO', - 'id': 'GO:0051147' - }, - { - 'name': 'GO', - 'id': 'GO:0031297' - }, - { - 'name': 'GO', - 'id': 'GO:0009410' - }, - { - 'name': 'GO', - 'id': 'GO:0006366' - }, - { - 'name': 'GO', - 'id': 'GO:0006368' - }, - { - 'name': 'GO', - 'id': 'GO:0006367' - }, - { - 'name': 'Gene3D', - 'id': '1.10.510.10' - }, - { - 'name': 'GeneCards', - 'id': 'CDK9' - }, - { - 'name': 'GeneID', - 'id': '1025' - }, - { - 'name': 'GeneTree', - 'id': 'ENSGT00940000155373' - }, - { - 'name': 'GeneWiki', - 'id': 'CDK9' - }, - { - 'name': 'GeneWiki', - 'id': 'Cyclin-dependent_kinase_9' - }, - { - 'name': 'Genevisible', - 'id': 'P50750' - }, - { - 'name': 'GenomeRNAi', - 'id': '1025' - }, - { - 'name': 'GlyGen', - 'id': 'P50750' - }, - { - 'name': 'GuidetoPHARMACOLOGY', - 'id': '1981' - }, - { - 'name': 'HGNC', - 'id': 'HGNC:1780' - }, - { - 'name': 'HOGENOM', - 'id': 'CLU_000288_181_1_1' - }, - { - 'name': 'HPA', - 'id': 'ENSG00000136807' - }, - { - 'name': 'InParanoid', - 'id': 'P50750' - }, - { - 'name': 'IntAct', - 'id': 'P50750' - }, - { - 'name': 'InterPro', - 'id': 'IPR011009' - }, - { - 'name': 'InterPro', - 'id': 'IPR000719' - }, - { - 'name': 'InterPro', - 'id': 'IPR017441' - }, - { - 'name': 'InterPro', - 'id': 'IPR008271' - }, - { - 'name': 'KEGG', - 'id': 'hsa:1025' - }, - { - 'name': 'MANE-Select', - 'id': 'ENST00000373264.5' - }, - { - 'name': 'MANE-Select', - 'id': 'ENSP00000362361.4' - }, - { - 'name': 'MANE-Select', - 'id': 'NM_001261.4' - }, - { - 'name': 'MANE-Select', - 'id': 'NP_001252.1' - }, - { - 'name': 'MIM', - 'id': '603251' - }, - { - 'name': 'MINT', - 'id': 'P50750' - }, - { - 'name': 'MassIVE', - 'id': 'P50750' - }, - { - 'name': 'MaxQB', - 'id': 'P50750' - }, - { - 'name': 'OMA', - 'id': 'YIEEFDF' - }, - { - 'name': 'OpenTargets', - 'id': 'ENSG00000136807' - }, - { - 'name': 'OrthoDB', - 'id': '244018at2759' - }, - { - 'name': 'PANTHER', - 'id': 'PTHR24056' - }, - { - 'name': 'PANTHER', - 'id': 'PTHR24056:SF233' - }, - { - 'name': 'PDB', - 'id': '3BLH' - }, - { - 'name': 'PDB', - 'id': '3BLQ' - }, - { - 'name': 'PDB', - 'id': '3BLR' - }, - { - 'name': 'PDB', - 'id': '3LQ5' - }, - { - 'name': 'PDB', - 'id': '3MI9' - }, - { - 'name': 'PDB', - 'id': '3MIA' - }, - { - 'name': 'PDB', - 'id': '3MY1' - }, - { - 'name': 'PDB', - 'id': '3TN8' - }, - { - 'name': 'PDB', - 'id': '3TNH' - }, - { - 'name': 'PDB', - 'id': '3TNI' - }, - { - 'name': 'PDB', - 'id': '4BCF' - }, - { - 'name': 'PDB', - 'id': '4BCG' - }, - { - 'name': 'PDB', - 'id': '4BCH' - }, - { - 'name': 'PDB', - 'id': '4BCI' - }, - { - 'name': 'PDB', - 'id': '4BCJ' - }, - { - 'name': 'PDB', - 'id': '4EC8' - }, - { - 'name': 'PDB', - 'id': '4EC9' - }, - { - 'name': 'PDB', - 'id': '4IMY' - }, - { - 'name': 'PDB', - 'id': '4OGR' - }, - { - 'name': 'PDB', - 'id': '4OR5' - }, - { - 'name': 'PDB', - 'id': '5L1Z' - }, - { - 'name': 'PDB', - 'id': '6CYT' - }, - { - 'name': 'PDB', - 'id': '6GZH' - }, - { - 'name': 'PDB', - 'id': '6W9E' - }, - { - 'name': 'PDB', - 'id': '6Z45' - }, - { - 'name': 'PDB', - 'id': '7NWK' - }, - { - 'name': 'PDBsum', - 'id': '3BLH' - }, - { - 'name': 'PDBsum', - 'id': '3BLQ' - }, - { - 'name': 'PDBsum', - 'id': '3BLR' - }, - { - 'name': 'PDBsum', - 'id': '3LQ5' - }, - { - 'name': 'PDBsum', - 'id': '3MI9' - }, - { - 'name': 'PDBsum', - 'id': '3MIA' - }, - { - 'name': 'PDBsum', - 'id': '3MY1' - }, - { - 'name': 'PDBsum', - 'id': '3TN8' - }, - { - 'name': 'PDBsum', - 'id': '3TNH' - }, - { - 'name': 'PDBsum', - 'id': '3TNI' - }, - { - 'name': 'PDBsum', - 'id': '4BCF' - }, - { - 'name': 'PDBsum', - 'id': '4BCG' - }, - { - 'name': 'PDBsum', - 'id': '4BCH' - }, - { - 'name': 'PDBsum', - 'id': '4BCI' - }, - { - 'name': 'PDBsum', - 'id': '4BCJ' - }, - { - 'name': 'PDBsum', - 'id': '4EC8' - }, - { - 'name': 'PDBsum', - 'id': '4EC9' - }, - { - 'name': 'PDBsum', - 'id': '4IMY' - }, - { - 'name': 'PDBsum', - 'id': '4OGR' - }, - { - 'name': 'PDBsum', - 'id': '4OR5' - }, - { - 'name': 'PDBsum', - 'id': '5L1Z' - }, - { - 'name': 'PDBsum', - 'id': '6CYT' - }, - { - 'name': 'PDBsum', - 'id': '6GZH' - }, - { - 'name': 'PDBsum', - 'id': '6W9E' - }, - { - 'name': 'PDBsum', - 'id': '6Z45' - }, - { - 'name': 'PDBsum', - 'id': '7NWK' - }, - { - 'name': 'PIR', - 'id': 'A55262' - }, - { - 'name': 'PRO', - 'id': 'PR:P50750' - }, - { - 'name': 'PROSITE', - 'id': 'PS00107' - }, - { - 'name': 'PROSITE', - 'id': 'PS50011' - }, - { - 'name': 'PROSITE', - 'id': 'PS00108' - }, - { - 'name': 'PathwayCommons', - 'id': 'P50750' - }, - { - 'name': 'PaxDb', - 'id': 'P50750' - }, - { - 'name': 'PeptideAtlas', - 'id': 'P50750' - }, - { - 'name': 'Pfam', - 'id': 'PF00069' - }, - { - 'name': 'PharmGKB', - 'id': 'PA26316' - }, - { - 'name': 'Pharos', - 'id': 'P50750' - }, - { - 'name': 'PhosphoSitePlus', - 'id': 'P50750' - }, - { - 'name': 'PhylomeDB', - 'id': 'P50750' - }, - { - 'name': 'Proteomes', - 'id': 'UP000005640' - }, - { - 'name': 'ProteomicsDB', - 'id': '56263' - }, - { - 'name': 'ProteomicsDB', - 'id': '56264' - }, - { - 'name': 'RNAct', - 'id': 'P50750' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-112382' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-167152' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-167200' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-167238' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-167243' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-167246' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-167287' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-167290' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-176034' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-2173796' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-674695' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-6796648' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-6807505' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-75955' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-9018519' - }, - { - 'name': 'RefSeq', - 'id': 'NP_001252.1' - }, - { - 'name': 'RefSeq', - 'id': 'NM_001261.3' - }, - { - 'name': 'SIGNOR', - 'id': 'P50750' - }, - { - 'name': 'SMART', - 'id': 'SM00220' - }, - { - 'name': 'SMR', - 'id': 'P50750' - }, - { - 'name': 'STRING', - 'id': '9606.ENSP00000362361' - }, - { - 'name': 'SUPFAM', - 'id': 'SSF56112' - }, - { - 'name': 'SignaLink', - 'id': 'P50750' - }, - { - 'name': 'SwissPalm', - 'id': 'P50750' - }, - { - 'name': 'TreeFam', - 'id': 'TF101039' - }, - { - 'name': 'UCSC', - 'id': 'uc004bse.3' - }, - { - 'name': 'VEuPathDB', - 'id': 'HostDB:ENSG00000136807' - }, - { - 'name': 'eggNOG', - 'id': 'KOG0669' - }, - { - 'name': 'iPTMnet', - 'id': 'P50750' - }, - { - 'name': 'jPOST', - 'id': 'P50750' - }, - { - 'name': 'neXtProt', - 'id': 'NX_P50750' - } - ], - 'source': 'UniProtKB/Swiss-Prot', - 'source_url': 'https://www.uniprot.org/help/downloads' - } - ] - }, - { - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/', - 'protein': [ - { - '_id': 'Q12789', - 'name': 'TF3C1_HUMAN', - 'full_name': 'General transcription factor 3C polypeptide 1', - 'dbxrefs': [ - { - 'name': 'AGR', - 'id': 'HGNC:4664' - }, - { - 'name': 'AlphaFoldDB', - 'id': 'Q12789' - }, - { - 'name': 'Antibodypedia', - 'id': '26269' - }, - { - 'name': 'Bgee', - 'id': 'ENSG00000077235' - }, - { - 'name': 'BioGRID', - 'id': '109230' - }, - { - 'name': 'BioGRID-ORCS', - 'id': '2975' - }, - { - 'name': 'BioMuta', - 'id': 'GTF3C1' - }, - { - 'name': 'CCDS', - 'id': 'CCDS32414.1' - }, - { - 'name': 'CCDS', - 'id': 'CCDS66988.1' - }, - { - 'name': 'CDD', - 'id': 'cd16169' - }, - { - 'name': 'CORUM', - 'id': 'Q12789' - }, - { - 'name': 'CTD', - 'id': '2975' - }, - { - 'name': 'ChiTaRS', - 'id': 'GTF3C1' - }, - { - 'name': 'DIP', - 'id': 'DIP-38212N' - }, - { - 'name': 'DMDM', - 'id': '215274233' - }, - { - 'name': 'DNASU', - 'id': '2975' - }, - { - 'name': 'DisGeNET', - 'id': '2975' - }, - { - 'name': 'EMBL', - 'id': 'U02619' - }, - { - 'name': 'EMBL', - 'id': 'AAA17985.1' - }, - { - 'name': 'EMBL', - 'id': 'AC002303' - }, - { - 'name': 'EMBL', - 'id': 'AAB67637.1' - }, - { - 'name': 'EMBL', - 'id': 'AC025275' - }, - { - 'name': 'EMBL', - 'id': 'AC002551' - }, - { - 'name': 'EMBL', - 'id': 'AAC05811.1' - }, - { - 'name': 'EMBL', - 'id': 'BC044857' - }, - { - 'name': 'EMBL', - 'id': 'AAH44857.1' - }, - { - 'name': 'EMBL', - 'id': 'BC137229' - }, - { - 'name': 'EMBL', - 'id': 'AAI37230.1' - }, - { - 'name': 'EMBL', - 'id': 'U06485' - }, - { - 'name': 'EMBL', - 'id': 'AAA85638.1' - }, - { - 'name': 'EPD', - 'id': 'Q12789' - }, - { - 'name': 'Ensembl', - 'id': 'ENST00000356183.9' - }, - { - 'name': 'Ensembl', - 'id': 'ENSP00000348510.4' - }, - { - 'name': 'Ensembl', - 'id': 'ENSG00000077235.18' - }, - { - 'name': 'Ensembl', - 'id': 'ENST00000561623.5' - }, - { - 'name': 'Ensembl', - 'id': 'ENSP00000455417.1' - }, - { - 'name': 'Ensembl', - 'id': 'ENSG00000077235.18' - }, - { - 'name': 'ExpressionAtlas', - 'id': 'Q12789' - }, - { - 'name': 'GO', - 'id': 'GO:0016020' - }, - { - 'name': 'GO', - 'id': 'GO:0005730' - }, - { - 'name': 'GO', - 'id': 'GO:0005654' - }, - { - 'name': 'GO', - 'id': 'GO:1990904' - }, - { - 'name': 'GO', - 'id': 'GO:0000127' - }, - { - 'name': 'GO', - 'id': 'GO:0003677' - }, - { - 'name': 'GO', - 'id': 'GO:0000995' - }, - { - 'name': 'GO', - 'id': 'GO:0042791' - }, - { - 'name': 'GO', - 'id': 'GO:0009303' - }, - { - 'name': 'GO', - 'id': 'GO:0006383' - }, - { - 'name': 'GO', - 'id': 'GO:0006384' - }, - { - 'name': 'GO', - 'id': 'GO:0009304' - }, - { - 'name': 'GO', - 'id': 'GO:0042797' - }, - { - 'name': 'GeneCards', - 'id': 'GTF3C1' - }, - { - 'name': 'GeneID', - 'id': '2975' - }, - { - 'name': 'GeneTree', - 'id': 'ENSGT00390000008664' - }, - { - 'name': 'GeneWiki', - 'id': 'GTF3C1' - }, - { - 'name': 'Genevisible', - 'id': 'Q12789' - }, - { - 'name': 'GenomeRNAi', - 'id': '2975' - }, - { - 'name': 'GlyCosmos', - 'id': 'Q12789' - }, - { - 'name': 'GlyGen', - 'id': 'Q12789' - }, - { - 'name': 'HGNC', - 'id': 'HGNC:4664' - }, - { - 'name': 'HOGENOM', - 'id': 'CLU_001556_1_0_1' - }, - { - 'name': 'HPA', - 'id': 'ENSG00000077235' - }, - { - 'name': 'InParanoid', - 'id': 'Q12789' - }, - { - 'name': 'IntAct', - 'id': 'Q12789' - }, - { - 'name': 'InterPro', - 'id': 'IPR044210' - }, - { - 'name': 'InterPro', - 'id': 'IPR035625' - }, - { - 'name': 'InterPro', - 'id': 'IPR007309' - }, - { - 'name': 'KEGG', - 'id': 'hsa:2975' - }, - { - 'name': 'MANE-Select', - 'id': 'ENST00000356183.9' - }, - { - 'name': 'MANE-Select', - 'id': 'ENSP00000348510.4' - }, - { - 'name': 'MANE-Select', - 'id': 'NM_001520.4' - }, - { - 'name': 'MANE-Select', - 'id': 'NP_001511.2' - }, - { - 'name': 'MIM', - 'id': '603246' - }, - { - 'name': 'MINT', - 'id': 'Q12789' - }, - { - 'name': 'MassIVE', - 'id': 'Q12789' - }, - { - 'name': 'MaxQB', - 'id': 'Q12789' - }, - { - 'name': 'MetOSite', - 'id': 'Q12789' - }, - { - 'name': 'OMA', - 'id': 'PHKVHVE' - }, - 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'name': 'Reactome', - 'id': 'R-HSA-76061' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-76066' - }, - { - 'name': 'RefSeq', - 'id': 'NP_001273171.1' - }, - { - 'name': 'RefSeq', - 'id': 'NM_001286242.1' - }, - { - 'name': 'RefSeq', - 'id': 'NP_001511.2' - }, - { - 'name': 'RefSeq', - 'id': 'NM_001520.3' - }, - { - 'name': 'SIGNOR', - 'id': 'Q12789' - }, - { - 'name': 'STRING', - 'id': '9606.ENSP00000348510' - }, - { - 'name': 'SignaLink', - 'id': 'Q12789' - }, - { - 'name': 'SwissPalm', - 'id': 'Q12789' - }, - { - 'name': 'TreeFam', - 'id': 'TF351624' - }, - { - 'name': 'UCSC', - 'id': 'uc002dou.4' - }, - { - 'name': 'VEuPathDB', - 'id': 'HostDB:ENSG00000077235' - }, - { - 'name': 'eggNOG', - 'id': 'KOG4560' - }, - { - 'name': 'iPTMnet', - 'id': 'Q12789' - }, - { - 'name': 'jPOST', - 'id': 'Q12789' - }, - { - 'name': 'neXtProt', - 'id': 'NX_Q12789' - } - ], - 'source': 'UniProtKB/Swiss-Prot', - 'source_url': 'https://www.uniprot.org/help/downloads' - } - ] - }, - { - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/', - 'protein': [ - { - '_id': 'Q8WUA4', - 'name': 'TF3C2_HUMAN', - 'full_name': 'General transcription factor 3C polypeptide 2', - 'dbxrefs': [ - { - 'name': 'AGR', - 'id': 'HGNC:4665' - }, - { - 'name': 'AlphaFoldDB', - 'id': 'Q8WUA4' - }, - { - 'name': 'Antibodypedia', - 'id': '13626' - }, - { - 'name': 'Bgee', - 'id': 'ENSG00000115207' - }, - { - 'name': 'BioGRID', - 'id': '109231' - }, - { - 'name': 'BioGRID-ORCS', - 'id': '2976' - }, - { - 'name': 'BioMuta', - 'id': 'GTF3C2' - }, - { - 'name': 'CCDS', - 'id': 'CCDS1749.1' - }, - { - 'name': 'CORUM', - 'id': 'Q8WUA4' - }, - { - 'name': 'CTD', - 'id': '2976' - }, - { - 'name': 'ChiTaRS', - 'id': 'GTF3C2' - }, - { - 'name': 'DIP', - 'id': 'DIP-38213N' - }, - { - 'name': 'DMDM', - 'id': '48428661' - }, - { - 'name': 'DNASU', - 'id': '2976' - }, - { - 'name': 'DisGeNET', - 'id': '2976' - }, - { - 'name': 'EMBL', - 'id': 'D13636' - }, - { - 'name': 'EMBL', - 'id': 'BAA02800.1' - }, - { - 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'id': 'PS00678' - }, - { - 'name': 'PROSITE', - 'id': 'PS50082' - }, - { - 'name': 'PROSITE', - 'id': 'PS50294' - }, - { - 'name': 'PathwayCommons', - 'id': 'Q8WUA4' - }, - { - 'name': 'PaxDb', - 'id': 'Q8WUA4' - }, - { - 'name': 'PeptideAtlas', - 'id': 'Q8WUA4' - }, - { - 'name': 'Pfam', - 'id': 'PF00400' - }, - { - 'name': 'PharmGKB', - 'id': 'PA29053' - }, - { - 'name': 'Pharos', - 'id': 'Q8WUA4' - }, - { - 'name': 'PhosphoSitePlus', - 'id': 'Q8WUA4' - }, - { - 'name': 'PhylomeDB', - 'id': 'Q8WUA4' - }, - { - 'name': 'Proteomes', - 'id': 'UP000005640' - }, - { - 'name': 'ProteomicsDB', - 'id': '74647' - }, - { - 'name': 'ProteomicsDB', - 'id': '74648' - }, - { - 'name': 'RNAct', - 'id': 'Q8WUA4' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-749476' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-76061' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-76066' - }, - { - 'name': 'RefSeq', - 'id': 'NP_001030598.1' - }, - { - 'name': 'RefSeq', - 'id': 'NM_001035521.2' - }, - { - 'name': 'RefSeq', - 'id': 'NP_001305838.1' - }, - { - 'name': 'RefSeq', - 'id': 'NM_001318909.1' - }, - { - 'name': 'RefSeq', - 'id': 'NP_001512.1' - }, - { - 'name': 'RefSeq', - 'id': 'NM_001521.3' - }, - { - 'name': 'SIGNOR', - 'id': 'Q8WUA4' - }, - { - 'name': 'SMART', - 'id': 'SM00320' - }, - { - 'name': 'STRING', - 'id': '9606.ENSP00000352536' - }, - { - 'name': 'SUPFAM', - 'id': 'SSF50978' - }, - { - 'name': 'SignaLink', - 'id': 'Q8WUA4' - }, - { - 'name': 'SwissPalm', - 'id': 'Q8WUA4' - }, - { - 'name': 'TreeFam', - 'id': 'TF314779' - }, - { - 'name': 'UCSC', - 'id': 'uc002rju.3' - }, - { - 'name': 'VEuPathDB', - 'id': 'HostDB:ENSG00000115207' - }, - { - 'name': 'eggNOG', - 'id': 'ENOG502RAA6' - }, - { - 'name': 'iPTMnet', - 'id': 'Q8WUA4' - }, - { - 'name': 'jPOST', - 'id': 'Q8WUA4' - }, - { - 'name': 'neXtProt', - 'id': 'NX_Q8WUA4' - } - ], - 'source': 'UniProtKB/Swiss-Prot', - 'source_url': 'https://www.uniprot.org/help/downloads' - } - ] - }, - { - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/', - 'protein': [ - { - '_id': 'Q969F1', - 'name': 'TF3C6_HUMAN', - 'full_name': 'General transcription factor 3C polypeptide 6', - 'dbxrefs': [ - { - 'name': 'AGR', - 'id': 'HGNC:20872' - }, - { - 'name': 'AlphaFoldDB', - 'id': 'Q969F1' - }, - { - 'name': 'Antibodypedia', - 'id': '54521' - }, - { - 'name': 'Bgee', - 'id': 'ENSG00000155115' - }, - { - 'name': 'BioGRID', - 'id': '125192' - }, - { - 'name': 'BioGRID-ORCS', - 'id': '112495' - }, - { - 'name': 'BioMuta', - 'id': 'GTF3C6' - }, - { - 'name': 'CCDS', - 'id': 'CCDS5087.1' - }, - { - 'name': 'CTD', - 'id': '112495' - }, - { - 'name': 'ChiTaRS', - 'id': 'GTF3C6' - }, - { - 'name': 'DMDM', - 'id': '30580360' - }, - { - 'name': 'DNASU', - 'id': '112495' - }, - { - 'name': 'EMBL', - 'id': 'EF137904' - }, - { - 'name': 'EMBL', - 'id': 'ABO33431.1' - }, - { - 'name': 'EMBL', - 'id': 'AF361492' - }, - { - 'name': 'EMBL', - 'id': 'AAL57217.1' - }, - { - 'name': 'EMBL', - 'id': 'AF361496' - }, - { - 'name': 'EMBL', - 'id': 'AAL57221.1' - }, - { - 'name': 'EMBL', - 'id': 'AK057977' - }, - { - 'name': 'EMBL', - 'id': 'BAB71624.1' - }, - { - 'name': 'EMBL', - 'id': 'AL357515' - }, - { - 'name': 'EMBL', - 'id': 'CH471051' - }, - { - 'name': 'EMBL', - 'id': 'EAW48305.1' - }, - { - 'name': 'EMBL', - 'id': 'BC011593' - }, - { - 'name': 'EMBL', - 'id': 'AAH11593.1' - }, - { - 'name': 'EPD', - 'id': 'Q969F1' - }, - { - 'name': 'Ensembl', - 'id': 'ENST00000329970.8' - }, - { - 'name': 'Ensembl', - 'id': 'ENSP00000357863.4' - }, - { - 'name': 'Ensembl', - 'id': 'ENSG00000155115.7' - }, - { - 'name': 'GO', - 'id': 'GO:0016604' - }, - { - 'name': 'GO', - 'id': 'GO:0005654' - }, - { - 'name': 'GO', - 'id': 'GO:0000127' - }, - { - 'name': 'GO', - 'id': 'GO:0003677' - }, - { - 'name': 'GO', - 'id': 'GO:0000995' - }, - { - 'name': 'GO', - 'id': 'GO:0042791' - }, - { - 'name': 'GO', - 'id': 'GO:0006383' - }, - { - 'name': 'GO', - 'id': 'GO:0042797' - }, - { - 'name': 'Gene3D', - 'id': '2.60.40.4370' - }, - { - 'name': 'GeneCards', - 'id': 'GTF3C6' - 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'id': 'FMETQDA' - }, - { - 'name': 'OpenTargets', - 'id': 'ENSG00000155115' - }, - { - 'name': 'OrthoDB', - 'id': '5399811at2759' - }, - { - 'name': 'PANTHER', - 'id': 'PTHR21860:SF2' - }, - { - 'name': 'PANTHER', - 'id': 'PTHR21860' - }, - { - 'name': 'PRO', - 'id': 'PR:Q969F1' - }, - { - 'name': 'PathwayCommons', - 'id': 'Q969F1' - }, - { - 'name': 'PaxDb', - 'id': 'Q969F1' - }, - { - 'name': 'PeptideAtlas', - 'id': 'Q969F1' - }, - { - 'name': 'Pfam', - 'id': 'PF10419' - }, - { - 'name': 'PharmGKB', - 'id': 'PA162390481' - }, - { - 'name': 'Pharos', - 'id': 'Q969F1' - }, - { - 'name': 'PhosphoSitePlus', - 'id': 'Q969F1' - }, - { - 'name': 'PhylomeDB', - 'id': 'Q969F1' - }, - { - 'name': 'Proteomes', - 'id': 'UP000005640' - }, - { - 'name': 'ProteomicsDB', - 'id': '75747' - }, - { - 'name': 'RNAct', - 'id': 'Q969F1' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-749476' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-76061' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-76066' - }, - { - 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{ - 'name': 'RefSeq', - 'id': 'XM_017001369.1' - }, - { - 'name': 'SASBDB', - 'id': 'Q13952' - }, - { - 'name': 'SIGNOR', - 'id': 'Q13952' - }, - { - 'name': 'SMR', - 'id': 'Q13952' - }, - { - 'name': 'SUPFAM', - 'id': 'SSF47113' - }, - { - 'name': 'SignaLink', - 'id': 'Q13952' - }, - { - 'name': 'TreeFam', - 'id': 'TF354207' - }, - { - 'name': 'UCSC', - 'id': 'uc001cfx.6' - }, - { - 'name': 'VEuPathDB', - 'id': 'HostDB:ENSG00000066136' - }, - { - 'name': 'eggNOG', - 'id': 'KOG1657' - }, - { - 'name': 'iPTMnet', - 'id': 'Q13952' - }, - { - 'name': 'jPOST', - 'id': 'Q13952' - }, - { - 'name': 'neXtProt', - 'id': 'NX_Q13952' - } - ], - 'source': 'UniProtKB/Swiss-Prot', - 'source_url': 'https://www.uniprot.org/help/downloads' - } - ] - } - ] - }] -} diff --git a/tests/acceptance_tests/diseases_genes.py b/tests/acceptance_tests/diseases_genes.py deleted file mode 100644 index 779667a6..00000000 --- a/tests/acceptance_tests/diseases_genes.py +++ /dev/null @@ -1,2017 +0,0 @@ -diseases_genes = { - '/diseases/genes': [{ - 'params': { - 'disease_id': 'Orphanet_586', - 'verbose': 'false' - }, - 'response': [ - { - 'pmid': [ - '16690975' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'GCLC', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': 'genes/ENSG00000001084', - 'ontology term': 'ontology_terms/Orphanet_586' - }, - { - 'pmid': [ - '22214395' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'CFTR', - 'association_type': 'Disease-causing germline mutation(s) (loss of function) in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': 'genes/ENSG00000001626', - 'ontology term': 'ontology_terms/Orphanet_586' - }, - { - 'pmid': [ - '30291871' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'HFE', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': 'genes/ENSG00000010704', - 'ontology term': 'ontology_terms/Orphanet_586' - }, - { - 'pmid': [ - '23073314' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'CLCA4', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': 'genes/ENSG00000016602', - 'ontology term': 'ontology_terms/Orphanet_586' - }, - { - 'pmid': [ - '28756021' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'SLC11A1', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': 'genes/ENSG00000018280', - 'ontology term': 'ontology_terms/Orphanet_586' - }, - { - 'pmid': [ - '28756021' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'SLC9A3', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': 'genes/ENSG00000066230', - 'ontology term': 'ontology_terms/Orphanet_586' - }, - { - 'pmid': [ - '20047061' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'CEACAM6', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': 'genes/ENSG00000086548', - 'ontology term': 'ontology_terms/Orphanet_586' - }, - { - 'pmid': [ - '28289476' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'HMOX1', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': 'genes/ENSG00000100292', - 'ontology term': 'ontology_terms/Orphanet_586' - }, - { - 'pmid': [ - '29915289' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'KCNN4', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': 'genes/ENSG00000104783', - 'ontology term': 'ontology_terms/Orphanet_586' - }, - { - 'pmid': [ - '18424453' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'TGFB1', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': 'genes/ENSG00000105329', - 'ontology term': 'ontology_terms/Orphanet_586' - }, - { - 'pmid': [ - '23572023' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'STX1A', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': 'genes/ENSG00000106089', - 'ontology term': 'ontology_terms/Orphanet_586' - }, - { - 'pmid': [ - '22772370' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'DCTN4', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': 'genes/ENSG00000132912', - 'ontology term': 'ontology_terms/Orphanet_586' - }, - { - 'pmid': [ - '28289476' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'GSTM3', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': 'genes/ENSG00000134202', - 'ontology term': 'ontology_terms/Orphanet_586' - }, - { - 'pmid': [ - '20028935' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'EDNRA', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': 'genes/ENSG00000151617', - 'ontology term': 'ontology_terms/Orphanet_586' - }, - { - 'pmid': [ - '20047061' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'CEACAM3', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': 'genes/ENSG00000170956', - 'ontology term': 'ontology_terms/Orphanet_586' - }, - { - 'pmid': [ - '28756021' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'SLC26A9', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': 'genes/ENSG00000174502', - 'ontology term': 'ontology_terms/Orphanet_586' - }, - { - 'pmid': [ - '19738092' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'SERPINA1', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': 'genes/ENSG00000197249', - 'ontology term': 'ontology_terms/Orphanet_586' - }, - { - 'pmid': [ - '16179637' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'MIF', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': 'genes/ENSG00000240972', - 'ontology term': 'ontology_terms/Orphanet_586' - }, - { - 'pmid': [ - '28756021' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'SLC6A14', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': 'genes/ENSG00000268104', - 'ontology term': 'ontology_terms/Orphanet_586' - } - ] - }, { - 'params': { - 'disease_id': 'Orphanet_586', - 'verbose': 'true' - }, - 'response': [ - { - 'pmid': [ - '16690975' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'GCLC', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': { - '_id': 'ENSG00000001084', - 'chr': 'chr6', - 'start': 53497340, - 'end': 53616970, - 'gene_type': 'protein_coding', - 'name': 'GCLC', - 'hgnc': 'HGNC:4311', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'GLCLC', - 'GLCL', - 'GCS', - 'gamma-ECS', - 'gamma-glutamylcysteine synthetase', - 'GCL', - 'GCS heavy chain', - 'GCLC', - 'glutamate-cysteine ligase catalytic subunit', - 'glutamate--cysteine ligase catalytic subunit' - ] - }, - 'ontology term': { - 'uri': 'http://www.orpha.net/ORDO/Orphanet_586', - 'term_id': 'Orphanet_586', - 'name': 'cystic fibrosis', - 'description': '', - 'source': 'ORPHANET', - 'subontology': None - } - }, - { - 'pmid': [ - '22214395' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'CFTR', - 'association_type': 'Disease-causing germline mutation(s) (loss of function) in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': { - '_id': 'ENSG00000001626', - 'chr': 'chr7', - 'start': 117287119, - 'end': 117715971, - 'gene_type': 'protein_coding', - 'name': 'CFTR', - 'hgnc': 'HGNC:1884', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'CF', - 'channel conductance-controlling ATPase', - 'cystic fibrosis transmembrane conductance regulator', - 'ABCC7', - 'cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)', - 'CFTR/MRP', - 'MRP7', - 'CF transmembrane conductance regulator', - 'cAMP-dependent chloride channel', - 'dJ760C5.1', - 'ABC35', - 'cystic fibrosis transmembrane conductance regulating', - 'CFTR', - 'TNR-CFTR' - ] - }, - 'ontology term': { - 'uri': 'http://www.orpha.net/ORDO/Orphanet_586', - 'term_id': 'Orphanet_586', - 'name': 'cystic fibrosis', - 'description': '', - 'source': 'ORPHANET', - 'subontology': None - } - }, - { - 'pmid': [ - '30291871' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'HFE', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': { - '_id': 'ENSG00000010704', - 'chr': 'chr6', - 'start': 26087280, - 'end': 26098343, - 'gene_type': 'protein_coding', - 'name': 'HFE', - 'hgnc': 'HGNC:4886', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'high Fe', - 'hereditary hemochromatosis protein HLA-H', - 'hereditary hemochromatosis protein', - 'homeostatic iron regulator', - 'TFQTL2', - 'MVCD7', - 'HH', - 'HFE', - 'MHC class I-like protein HFE', - 'HFE1', - 'HLA-H' - ] - }, - 'ontology term': { - 'uri': 'http://www.orpha.net/ORDO/Orphanet_586', - 'term_id': 'Orphanet_586', - 'name': 'cystic fibrosis', - 'description': '', - 'source': 'ORPHANET', - 'subontology': None - } - }, - { - 'pmid': [ - '23073314' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'CLCA4', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': { - '_id': 'ENSG00000016602', - 'chr': 'chr1', - 'start': 86547077, - 'end': 86580754, - 'gene_type': 'protein_coding', - 'name': 'CLCA4', - 'hgnc': 'HGNC:2018', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'CaCC', - 'CLCA4', - 'calcium-activated chloride channel regulator 4', - 'calcium-activated chloride channel family member 4', - 'caCC-2', - 'chloride channel regulator 4', - 'chloride channel, calcium activated, family member 4', - 'hCaCC-2', - 'calcium-activated chloride channel protein 2', - 'CaCC2', - 'hCLCA4', - 'chloride channel accessory 4' - ] - }, - 'ontology term': { - 'uri': 'http://www.orpha.net/ORDO/Orphanet_586', - 'term_id': 'Orphanet_586', - 'name': 'cystic fibrosis', - 'description': '', - 'source': 'ORPHANET', - 'subontology': None - } - }, - { - 'pmid': [ - '28756021' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'SLC11A1', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': { - '_id': 'ENSG00000018280', - 'chr': 'chr2', - 'start': 218382028, - 'end': 218396894, - 'gene_type': 'protein_coding', - 'name': 'SLC11A1', - 'hgnc': 'HGNC:10907', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'solute carrier family 11 member 1', - 'SLC11A1', - 'LSH', - 'NRAMP', - 'solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1', - 'solute carrier family 11 (proton-coupled divalent metal ion transporter), member 1', - 'Leishmaniasis resistance', - 'solute carrier family 11 (sodium/phosphate symporters), member 1', - 'NRAMP1', - 'NRAMP 1', - 'natural resistance-associated macrophage protein 1' - ] - }, - 'ontology term': { - 'uri': 'http://www.orpha.net/ORDO/Orphanet_586', - 'term_id': 'Orphanet_586', - 'name': 'cystic fibrosis', - 'description': '', - 'source': 'ORPHANET', - 'subontology': None - } - }, - { - 'pmid': [ - '28756021' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'SLC9A3', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': { - '_id': 'ENSG00000066230', - 'chr': 'chr5', - 'start': 470455, - 'end': 524449, - 'gene_type': 'protein_coding', - 'name': 'SLC9A3', - 'hgnc': 'HGNC:11073', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'NHE3', - 'sodium/hydrogen exchanger 3', - 'solute carrier family 9 member A3', - 'DIAR8', - 'Na(+)/H(+) exchanger 3', - 'NHE-3', - 'solute carrier family 9, subfamily A (NHE3, cation proton antiporter 3), member 3', - 'solute carrier family 9 (sodium/hydrogen exchanger), member 3', - 'SLC9A3' - ] - }, - 'ontology term': { - 'uri': 'http://www.orpha.net/ORDO/Orphanet_586', - 'term_id': 'Orphanet_586', - 'name': 'cystic fibrosis', - 'description': '', - 'source': 'ORPHANET', - 'subontology': None - } - }, - { - 'pmid': [ - '20047061' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'CEACAM6', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': { - '_id': 'ENSG00000086548', - 'chr': 'chr19', - 'start': 41750976, - 'end': 41772211, - 'gene_type': 'protein_coding', - 'name': 'CEACAM6', - 'hgnc': 'HGNC:1818', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'CEA cell adhesion molecule 6', - 'CD66c', - 'CEACAM6', - 'normal cross-reacting antigen', - 'carcinoembryonic antigen-related cell adhesion molecule 6', - 'Cluster of Differentiation 66c', - 'carcinoembryonic antigen related cell adhesion molecule 6', - 'carcinoembryonic antigen-related cell adhesion molecule 6 (non-specific cross reacting antigen)', - 'NCA', - 'CEAL' - ] - }, - 'ontology term': { - 'uri': 'http://www.orpha.net/ORDO/Orphanet_586', - 'term_id': 'Orphanet_586', - 'name': 'cystic fibrosis', - 'description': '', - 'source': 'ORPHANET', - 'subontology': None - } - }, - { - 'pmid': [ - '28289476' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'HMOX1', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': { - '_id': 'ENSG00000100292', - 'chr': 'chr22', - 'start': 35380360, - 'end': 35394214, - 'gene_type': 'protein_coding', - 'name': 'HMOX1', - 'hgnc': 'HGNC:5013', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'bK286B10', - 'HSP32', - 'heat shock protein, 32-kD', - 'HMOX1', - 'heme oxygenase (decycling) 1', - 'heme oxygenase 1', - 'HMOX1D', - 'HO-1' - ] - }, - 'ontology term': { - 'uri': 'http://www.orpha.net/ORDO/Orphanet_586', - 'term_id': 'Orphanet_586', - 'name': 'cystic fibrosis', - 'description': '', - 'source': 'ORPHANET', - 'subontology': None - } - }, - { - 'pmid': [ - '29915289' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'KCNN4', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': { - '_id': 'ENSG00000104783', - 'chr': 'chr19', - 'start': 43766532, - 'end': 43780976, - 'gene_type': 'protein_coding', - 'name': 'KCNN4', - 'hgnc': 'HGNC:6293', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'putative erythrocyte intermediate conductance calcium-activated potassium Gardos channel', - 'potassium channel, calcium activated intermediate/small conductance subfamily N alpha, member 4', - 'SK4', - 'hIKCa1', - 'SKCa 4', - 'potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4', - 'IK1', - 'SKCa4', - 'KCa3.1', - 'IK', - 'DHS2', - 'intermediate-conductance Ca2+-activated K+ channel, KCa3.1', - 'small conductance calcium-activated potassium channel 4', - 'potassium calcium-activated channel subfamily N member 4', - 'intermediate conductance calcium-activated potassium channel protein 4', - 'KCNN4', - 'IKCA1', - 'hKCa4', - 'putative Gardos channel', - 'KCA4', - 'hSK4' - ] - }, - 'ontology term': { - 'uri': 'http://www.orpha.net/ORDO/Orphanet_586', - 'term_id': 'Orphanet_586', - 'name': 'cystic fibrosis', - 'description': '', - 'source': 'ORPHANET', - 'subontology': None - } - }, - { - 'pmid': [ - '18424453' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'TGFB1', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': { - '_id': 'ENSG00000105329', - 'chr': 'chr19', - 'start': 41301586, - 'end': 41353922, - 'gene_type': 'protein_coding', - 'name': 'TGFB1', - 'hgnc': 'HGNC:11766', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'transforming growth factor beta-1 proprotein', - 'DPD1', - 'transforming growth factor beta 1', - 'TGF-beta-1', - 'transforming growth factor beta1', - 'TGFbeta', - 'IBDIMDE', - 'latency-associated peptide', - 'CED', - 'prepro-transforming growth factor beta-1', - 'TGFB', - 'TGFB1', - 'LAP', - 'TGF-beta1' - ] - }, - 'ontology term': { - 'uri': 'http://www.orpha.net/ORDO/Orphanet_586', - 'term_id': 'Orphanet_586', - 'name': 'cystic fibrosis', - 'description': '', - 'source': 'ORPHANET', - 'subontology': None - } - }, - { - 'pmid': [ - '23572023' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'STX1A', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': { - '_id': 'ENSG00000106089', - 'chr': 'chr7', - 'start': 73699205, - 'end': 73719672, - 'gene_type': 'protein_coding', - 'name': 'STX1A', - 'hgnc': 'HGNC:11433', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'syntaxin 1A (brain)', - 'P35-1', - 'syntaxin-1A', - 'HPC-1', - 'SYN1A', - 'syntaxin 1A', - 'STX1', - 'neuron-specific antigen HPC-1', - 'STX1A' - ] - }, - 'ontology term': { - 'uri': 'http://www.orpha.net/ORDO/Orphanet_586', - 'term_id': 'Orphanet_586', - 'name': 'cystic fibrosis', - 'description': '', - 'source': 'ORPHANET', - 'subontology': None - } - }, - { - 'pmid': [ - '22772370' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'DCTN4', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': { - '_id': 'ENSG00000132912', - 'chr': 'chr5', - 'start': 150708439, - 'end': 150759095, - 'gene_type': 'protein_coding', - 'name': 'DCTN4', - 'hgnc': 'HGNC:15518', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'dynactin 4 (p62)', - 'DCTN4', - 'P62', - 'dynactin p62 subunit', - 'dynactin subunit p62', - 'dynactin subunit 4', - 'DYN4' - ] - }, - 'ontology term': { - 'uri': 'http://www.orpha.net/ORDO/Orphanet_586', - 'term_id': 'Orphanet_586', - 'name': 'cystic fibrosis', - 'description': '', - 'source': 'ORPHANET', - 'subontology': None - } - }, - { - 'pmid': [ - '28289476' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'GSTM3', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': { - '_id': 'ENSG00000134202', - 'chr': 'chr1', - 'start': 109733931, - 'end': 109741038, - 'gene_type': 'protein_coding', - 'name': 'GSTM3', - 'hgnc': 'HGNC:4635', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'GST class-mu 3', - 'GTM3', - 'GSTM3-3', - 'glutathione S-aralkyltransferase M3', - 'glutathione S-transferase, Mu-3', - 'glutathione S-transferase mu 3 (brain)', - 'glutathione S-transferase mu 3', - 'hGSTM3-3', - 'glutathione S-aryltransferase M3', - 'glutathione S-transferase Mu 3', - 'GSTB', - 'GSTM3TV2', - 'epididymis secretory sperm binding protein', - 'brain GST', - 'GSTM3', - 'glutathione S-alkyltransferase M3', - 'GST5', - 'brain type mu-glutathione S-transferase', - 'S-(hydroxyalkyl)glutathione lyase M3', - 'glutathione S-transferase M3 (brain)' - ] - }, - 'ontology term': { - 'uri': 'http://www.orpha.net/ORDO/Orphanet_586', - 'term_id': 'Orphanet_586', - 'name': 'cystic fibrosis', - 'description': '', - 'source': 'ORPHANET', - 'subontology': None - } - }, - { - 'pmid': [ - '20028935' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'EDNRA', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': { - '_id': 'ENSG00000151617', - 'chr': 'chr4', - 'start': 147480916, - 'end': 147544954, - 'gene_type': 'protein_coding', - 'name': 'EDNRA', - 'hgnc': 'HGNC:3179', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'EDNRA', - 'MFDA', - 'hET-AR', - 'ET-A', - 'endothelin-1 receptor', - 'endothelin receptor subtype A', - 'endothelin-1-specific receptor', - 'ETAR', - 'ETA-R', - 'ETA', - 'G protein-coupled receptor', - 'ETRA', - 'endothelin receptor type A' - ] - }, - 'ontology term': { - 'uri': 'http://www.orpha.net/ORDO/Orphanet_586', - 'term_id': 'Orphanet_586', - 'name': 'cystic fibrosis', - 'description': '', - 'source': 'ORPHANET', - 'subontology': None - } - }, - { - 'pmid': [ - '20047061' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'CEACAM3', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': { - '_id': 'ENSG00000170956', - 'chr': 'chr19', - 'start': 41796586, - 'end': 41811554, - 'gene_type': 'protein_coding', - 'name': 'CEACAM3', - 'hgnc': 'HGNC:1815', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'CGM1', - 'CEACAM3', - 'CD66D', - 'carcinoembryonic antigen related cell adhesion molecule 3', - 'CEA cell adhesion molecule 3', - 'CEA', - 'W264', - 'W282', - 'CD66d antigen', - 'carcinoembryonic antigen gene family member 1', - 'carcinoembryonic antigen CGM1', - 'carcinoembryonic antigen-related cell adhesion molecule 3', - 'nonspecific cross-reacting antigen' - ] - }, - 'ontology term': { - 'uri': 'http://www.orpha.net/ORDO/Orphanet_586', - 'term_id': 'Orphanet_586', - 'name': 'cystic fibrosis', - 'description': '', - 'source': 'ORPHANET', - 'subontology': None - } - }, - { - 'pmid': [ - '28756021' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'SLC26A9', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': { - '_id': 'ENSG00000174502', - 'chr': 'chr1', - 'start': 205913047, - 'end': 205943460, - 'gene_type': 'protein_coding', - 'name': 'SLC26A9', - 'hgnc': 'HGNC:14469', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'solute carrier family 26 member 9', - 'solute carrier family 26 (anion exchanger), member 9', - 'anion transporter/exchanger protein 9', - 'SLC26A9', - 'anion transporter/exchanger-9' - ] - }, - 'ontology term': { - 'uri': 'http://www.orpha.net/ORDO/Orphanet_586', - 'term_id': 'Orphanet_586', - 'name': 'cystic fibrosis', - 'description': '', - 'source': 'ORPHANET', - 'subontology': None - } - }, - { - 'pmid': [ - '19738092' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'SERPINA1', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': { - '_id': 'ENSG00000197249', - 'chr': 'chr14', - 'start': 94376746, - 'end': 94390693, - 'gene_type': 'protein_coding', - 'name': 'SERPINA1', - 'hgnc': 'HGNC:8941', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'SERPINA1', - 'alpha-1-antiproteinase', - 'nNIF', - 'serpin A1', - 'AAT', - 'PI', - 'alpha-1 antitrypsin', - 'protease inhibitor 1 (anti-elastase), alpha-1-antitrypsin', - 'serpin peptidase inhibitor clade A member 1', - 'anti-elastase', - 'serpin family A member 1', - 'serine (or cysteine) proteinase inhibitor, clade A, member 1', - 'A1AT', - 'epididymis secretory sperm binding protein', - 'alpha-1-antitrypsin', - 'alpha-1 proteinase inhibitor', - 'alpha-1 protease inhibitor', - 'PI1', - 'serpin peptidase inhibitor clade A (alpha-1antiproteinase, antitrypsin) member 1', - 'A1A', - 'alpha1AT', - 'serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1', - 'PRO2275' - ] - }, - 'ontology term': { - 'uri': 'http://www.orpha.net/ORDO/Orphanet_586', - 'term_id': 'Orphanet_586', - 'name': 'cystic fibrosis', - 'description': '', - 'source': 'ORPHANET', - 'subontology': None - } - }, - { - 'pmid': [ - '16179637' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'MIF', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': { - '_id': 'ENSG00000240972', - 'chr': 'chr22', - 'start': 23894382, - 'end': 23895227, - 'gene_type': 'protein_coding', - 'name': 'MIF', - 'hgnc': 'HGNC:7097', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'MMIF', - 'GIF', - 'macrophage migration inhibitory factor', - 'macrophage migration inhibitory factor (glycosylation-inhibiting factor)', - 'phenylpyruvate tautomerase', - 'epididymis secretory sperm binding protein', - 'GLIF', - 'MIF', - 'L-dopachrome isomerase', - 'L-dopachrome tautomerase' - ] - }, - 'ontology term': { - 'uri': 'http://www.orpha.net/ORDO/Orphanet_586', - 'term_id': 'Orphanet_586', - 'name': 'cystic fibrosis', - 'description': '', - 'source': 'ORPHANET', - 'subontology': None - } - }, - { - 'pmid': [ - '28756021' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'SLC6A14', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': { - '_id': 'ENSG00000268104', - 'chr': 'chrX', - 'start': 116436605, - 'end': 116461458, - 'gene_type': 'protein_coding', - 'name': 'SLC6A14', - 'hgnc': 'HGNC:11047', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'solute carrier family 6 (amino acid transporter), member 14', - 'BMIQ11', - 'solute carrier family 6 (neurotransmitter transporter), member 14', - 'sodium- and chloride-dependent neutral and basic amino acid transporter B(0+)', - 'solute carrier family 6 member 14', - 'amino acid transporter ATB0+', - 'amino acid transporter B0+', - 'SLC6A14' - ] - }, - 'ontology term': { - 'uri': 'http://www.orpha.net/ORDO/Orphanet_586', - 'term_id': 'Orphanet_586', - 'name': 'cystic fibrosis', - 'description': '', - 'source': 'ORPHANET', - 'subontology': None - } - } - ] - }, { - 'params': { - 'term_name': 'fibrosis', - 'association_type': 'Modifying germline mutation in', - 'source': 'Orphanet', - 'verbose': 'false' - }, - 'response': [ - { - 'pmid': [ - '16690975' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'GCLC', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': 'genes/ENSG00000001084' - }, - { - 'pmid': [ - '28756021' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'SLC11A1', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': 'genes/ENSG00000018280' - }, - { - 'pmid': [ - '16179637' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'MIF', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': 'genes/ENSG00000240972' - }, - { - 'pmid': [ - '29915289' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'KCNN4', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': 'genes/ENSG00000104783' - }, - { - 'pmid': [ - '23572023' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'STX1A', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': 'genes/ENSG00000106089' - }, - { - 'pmid': [ - '23073314' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'CLCA4', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': 'genes/ENSG00000016602' - }, - { - 'pmid': [ - '22772370' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'DCTN4', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': 'genes/ENSG00000132912' - }, - { - 'pmid': [ - '18424453' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'TGFB1', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': 'genes/ENSG00000105329' - }, - { - 'pmid': [ - '30291871' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'HFE', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': 'genes/ENSG00000010704' - }, - { - 'pmid': [ - '19738092' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'SERPINA1', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': 'genes/ENSG00000197249' - }, - { - 'pmid': [ - '28289476' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'HMOX1', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': 'genes/ENSG00000100292' - }, - { - 'pmid': [ - '28289476' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'GSTM3', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': 'genes/ENSG00000134202' - }, - { - 'pmid': [ - '20028935' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'EDNRA', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': 'genes/ENSG00000151617' - }, - { - 'pmid': [ - '20047061' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'CEACAM6', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': 'genes/ENSG00000086548' - }, - { - 'pmid': [ - '20047061' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'CEACAM3', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': 'genes/ENSG00000170956' - }, - { - 'pmid': [ - '28756021' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'SLC9A3', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': 'genes/ENSG00000066230' - }, - { - 'pmid': [ - '28756021' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'SLC6A14', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': 'genes/ENSG00000268104' - }, - { - 'pmid': [ - '28756021' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'SLC26A9', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': 'genes/ENSG00000174502' - } - ] - }, { - 'params': { - 'term_name': 'fibrosis', - 'association_type': 'Modifying germline mutation in', - 'source': 'Orphanet', - 'verbose': 'true' - }, - 'response': [ - { - 'pmid': [ - '16690975' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'GCLC', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': { - '_id': 'ENSG00000001084', - 'chr': 'chr6', - 'start': 53497340, - 'end': 53616970, - 'gene_type': 'protein_coding', - 'name': 'GCLC', - 'hgnc': 'HGNC:4311', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'GLCLC', - 'GLCL', - 'GCS', - 'gamma-ECS', - 'gamma-glutamylcysteine synthetase', - 'GCL', - 'GCS heavy chain', - 'GCLC', - 'glutamate-cysteine ligase catalytic subunit', - 'glutamate--cysteine ligase catalytic subunit' - ] - } - }, - { - 'pmid': [ - '28756021' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'SLC11A1', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': { - '_id': 'ENSG00000018280', - 'chr': 'chr2', - 'start': 218382028, - 'end': 218396894, - 'gene_type': 'protein_coding', - 'name': 'SLC11A1', - 'hgnc': 'HGNC:10907', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'solute carrier family 11 member 1', - 'SLC11A1', - 'LSH', - 'NRAMP', - 'solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1', - 'solute carrier family 11 (proton-coupled divalent metal ion transporter), member 1', - 'Leishmaniasis resistance', - 'solute carrier family 11 (sodium/phosphate symporters), member 1', - 'NRAMP1', - 'NRAMP 1', - 'natural resistance-associated macrophage protein 1' - ] - } - }, - { - 'pmid': [ - '16179637' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'MIF', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': { - '_id': 'ENSG00000240972', - 'chr': 'chr22', - 'start': 23894382, - 'end': 23895227, - 'gene_type': 'protein_coding', - 'name': 'MIF', - 'hgnc': 'HGNC:7097', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'MMIF', - 'GIF', - 'macrophage migration inhibitory factor', - 'macrophage migration inhibitory factor (glycosylation-inhibiting factor)', - 'phenylpyruvate tautomerase', - 'epididymis secretory sperm binding protein', - 'GLIF', - 'MIF', - 'L-dopachrome isomerase', - 'L-dopachrome tautomerase' - ] - } - }, - { - 'pmid': [ - '29915289' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'KCNN4', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': { - '_id': 'ENSG00000104783', - 'chr': 'chr19', - 'start': 43766532, - 'end': 43780976, - 'gene_type': 'protein_coding', - 'name': 'KCNN4', - 'hgnc': 'HGNC:6293', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'putative erythrocyte intermediate conductance calcium-activated potassium Gardos channel', - 'potassium channel, calcium activated intermediate/small conductance subfamily N alpha, member 4', - 'SK4', - 'hIKCa1', - 'SKCa 4', - 'potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4', - 'IK1', - 'SKCa4', - 'KCa3.1', - 'IK', - 'DHS2', - 'intermediate-conductance Ca2+-activated K+ channel, KCa3.1', - 'small conductance calcium-activated potassium channel 4', - 'potassium calcium-activated channel subfamily N member 4', - 'intermediate conductance calcium-activated potassium channel protein 4', - 'KCNN4', - 'IKCA1', - 'hKCa4', - 'putative Gardos channel', - 'KCA4', - 'hSK4' - ] - } - }, - { - 'pmid': [ - '23572023' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'STX1A', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': { - '_id': 'ENSG00000106089', - 'chr': 'chr7', - 'start': 73699205, - 'end': 73719672, - 'gene_type': 'protein_coding', - 'name': 'STX1A', - 'hgnc': 'HGNC:11433', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'syntaxin 1A (brain)', - 'P35-1', - 'syntaxin-1A', - 'HPC-1', - 'SYN1A', - 'syntaxin 1A', - 'STX1', - 'neuron-specific antigen HPC-1', - 'STX1A' - ] - } - }, - { - 'pmid': [ - '23073314' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'CLCA4', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': { - '_id': 'ENSG00000016602', - 'chr': 'chr1', - 'start': 86547077, - 'end': 86580754, - 'gene_type': 'protein_coding', - 'name': 'CLCA4', - 'hgnc': 'HGNC:2018', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'CaCC', - 'CLCA4', - 'calcium-activated chloride channel regulator 4', - 'calcium-activated chloride channel family member 4', - 'caCC-2', - 'chloride channel regulator 4', - 'chloride channel, calcium activated, family member 4', - 'hCaCC-2', - 'calcium-activated chloride channel protein 2', - 'CaCC2', - 'hCLCA4', - 'chloride channel accessory 4' - ] - } - }, - { - 'pmid': [ - '22772370' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'DCTN4', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': { - '_id': 'ENSG00000132912', - 'chr': 'chr5', - 'start': 150708439, - 'end': 150759095, - 'gene_type': 'protein_coding', - 'name': 'DCTN4', - 'hgnc': 'HGNC:15518', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'dynactin 4 (p62)', - 'DCTN4', - 'P62', - 'dynactin p62 subunit', - 'dynactin subunit p62', - 'dynactin subunit 4', - 'DYN4' - ] - } - }, - { - 'pmid': [ - '18424453' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'TGFB1', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': { - '_id': 'ENSG00000105329', - 'chr': 'chr19', - 'start': 41301586, - 'end': 41353922, - 'gene_type': 'protein_coding', - 'name': 'TGFB1', - 'hgnc': 'HGNC:11766', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'transforming growth factor beta-1 proprotein', - 'DPD1', - 'transforming growth factor beta 1', - 'TGF-beta-1', - 'transforming growth factor beta1', - 'TGFbeta', - 'IBDIMDE', - 'latency-associated peptide', - 'CED', - 'prepro-transforming growth factor beta-1', - 'TGFB', - 'TGFB1', - 'LAP', - 'TGF-beta1' - ] - } - }, - { - 'pmid': [ - '30291871' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'HFE', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': { - '_id': 'ENSG00000010704', - 'chr': 'chr6', - 'start': 26087280, - 'end': 26098343, - 'gene_type': 'protein_coding', - 'name': 'HFE', - 'hgnc': 'HGNC:4886', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'high Fe', - 'hereditary hemochromatosis protein HLA-H', - 'hereditary hemochromatosis protein', - 'homeostatic iron regulator', - 'TFQTL2', - 'MVCD7', - 'HH', - 'HFE', - 'MHC class I-like protein HFE', - 'HFE1', - 'HLA-H' - ] - } - }, - { - 'pmid': [ - '19738092' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'SERPINA1', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': { - '_id': 'ENSG00000197249', - 'chr': 'chr14', - 'start': 94376746, - 'end': 94390693, - 'gene_type': 'protein_coding', - 'name': 'SERPINA1', - 'hgnc': 'HGNC:8941', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'SERPINA1', - 'alpha-1-antiproteinase', - 'nNIF', - 'serpin A1', - 'AAT', - 'PI', - 'alpha-1 antitrypsin', - 'protease inhibitor 1 (anti-elastase), alpha-1-antitrypsin', - 'serpin peptidase inhibitor clade A member 1', - 'anti-elastase', - 'serpin family A member 1', - 'serine (or cysteine) proteinase inhibitor, clade A, member 1', - 'A1AT', - 'epididymis secretory sperm binding protein', - 'alpha-1-antitrypsin', - 'alpha-1 proteinase inhibitor', - 'alpha-1 protease inhibitor', - 'PI1', - 'serpin peptidase inhibitor clade A (alpha-1antiproteinase, antitrypsin) member 1', - 'A1A', - 'alpha1AT', - 'serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1', - 'PRO2275' - ] - } - }, - { - 'pmid': [ - '28289476' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'HMOX1', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': { - '_id': 'ENSG00000100292', - 'chr': 'chr22', - 'start': 35380360, - 'end': 35394214, - 'gene_type': 'protein_coding', - 'name': 'HMOX1', - 'hgnc': 'HGNC:5013', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'bK286B10', - 'HSP32', - 'heat shock protein, 32-kD', - 'HMOX1', - 'heme oxygenase (decycling) 1', - 'heme oxygenase 1', - 'HMOX1D', - 'HO-1' - ] - } - }, - { - 'pmid': [ - '28289476' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'GSTM3', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': { - '_id': 'ENSG00000134202', - 'chr': 'chr1', - 'start': 109733931, - 'end': 109741038, - 'gene_type': 'protein_coding', - 'name': 'GSTM3', - 'hgnc': 'HGNC:4635', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'GST class-mu 3', - 'GTM3', - 'GSTM3-3', - 'glutathione S-aralkyltransferase M3', - 'glutathione S-transferase, Mu-3', - 'glutathione S-transferase mu 3 (brain)', - 'glutathione S-transferase mu 3', - 'hGSTM3-3', - 'glutathione S-aryltransferase M3', - 'glutathione S-transferase Mu 3', - 'GSTB', - 'GSTM3TV2', - 'epididymis secretory sperm binding protein', - 'brain GST', - 'GSTM3', - 'glutathione S-alkyltransferase M3', - 'GST5', - 'brain type mu-glutathione S-transferase', - 'S-(hydroxyalkyl)glutathione lyase M3', - 'glutathione S-transferase M3 (brain)' - ] - } - }, - { - 'pmid': [ - '20028935' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'EDNRA', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': { - '_id': 'ENSG00000151617', - 'chr': 'chr4', - 'start': 147480916, - 'end': 147544954, - 'gene_type': 'protein_coding', - 'name': 'EDNRA', - 'hgnc': 'HGNC:3179', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'EDNRA', - 'MFDA', - 'hET-AR', - 'ET-A', - 'endothelin-1 receptor', - 'endothelin receptor subtype A', - 'endothelin-1-specific receptor', - 'ETAR', - 'ETA-R', - 'ETA', - 'G protein-coupled receptor', - 'ETRA', - 'endothelin receptor type A' - ] - } - }, - { - 'pmid': [ - '20047061' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'CEACAM6', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': { - '_id': 'ENSG00000086548', - 'chr': 'chr19', - 'start': 41750976, - 'end': 41772211, - 'gene_type': 'protein_coding', - 'name': 'CEACAM6', - 'hgnc': 'HGNC:1818', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'CEA cell adhesion molecule 6', - 'CD66c', - 'CEACAM6', - 'normal cross-reacting antigen', - 'carcinoembryonic antigen-related cell adhesion molecule 6', - 'Cluster of Differentiation 66c', - 'carcinoembryonic antigen related cell adhesion molecule 6', - 'carcinoembryonic antigen-related cell adhesion molecule 6 (non-specific cross reacting antigen)', - 'NCA', - 'CEAL' - ] - } - }, - { - 'pmid': [ - '20047061' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'CEACAM3', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': { - '_id': 'ENSG00000170956', - 'chr': 'chr19', - 'start': 41796586, - 'end': 41811554, - 'gene_type': 'protein_coding', - 'name': 'CEACAM3', - 'hgnc': 'HGNC:1815', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'CGM1', - 'CEACAM3', - 'CD66D', - 'carcinoembryonic antigen related cell adhesion molecule 3', - 'CEA cell adhesion molecule 3', - 'CEA', - 'W264', - 'W282', - 'CD66d antigen', - 'carcinoembryonic antigen gene family member 1', - 'carcinoembryonic antigen CGM1', - 'carcinoembryonic antigen-related cell adhesion molecule 3', - 'nonspecific cross-reacting antigen' - ] - } - }, - { - 'pmid': [ - '28756021' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'SLC9A3', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': { - '_id': 'ENSG00000066230', - 'chr': 'chr5', - 'start': 470455, - 'end': 524449, - 'gene_type': 'protein_coding', - 'name': 'SLC9A3', - 'hgnc': 'HGNC:11073', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'NHE3', - 'sodium/hydrogen exchanger 3', - 'solute carrier family 9 member A3', - 'DIAR8', - 'Na(+)/H(+) exchanger 3', - 'NHE-3', - 'solute carrier family 9, subfamily A (NHE3, cation proton antiporter 3), member 3', - 'solute carrier family 9 (sodium/hydrogen exchanger), member 3', - 'SLC9A3' - ] - } - }, - { - 'pmid': [ - '28756021' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'SLC6A14', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': { - '_id': 'ENSG00000268104', - 'chr': 'chrX', - 'start': 116436605, - 'end': 116461458, - 'gene_type': 'protein_coding', - 'name': 'SLC6A14', - 'hgnc': 'HGNC:11047', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'solute carrier family 6 (amino acid transporter), member 14', - 'BMIQ11', - 'solute carrier family 6 (neurotransmitter transporter), member 14', - 'sodium- and chloride-dependent neutral and basic amino acid transporter B(0+)', - 'solute carrier family 6 member 14', - 'amino acid transporter ATB0+', - 'amino acid transporter B0+', - 'SLC6A14' - ] - } - }, - { - 'pmid': [ - '28756021' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'SLC26A9', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'gene': { - '_id': 'ENSG00000174502', - 'chr': 'chr1', - 'start': 205913047, - 'end': 205943460, - 'gene_type': 'protein_coding', - 'name': 'SLC26A9', - 'hgnc': 'HGNC:14469', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'solute carrier family 26 member 9', - 'solute carrier family 26 (anion exchanger), member 9', - 'anion transporter/exchanger protein 9', - 'SLC26A9', - 'anion transporter/exchanger-9' - ] - } - } - ] - }] -} diff --git a/tests/acceptance_tests/drugs.py b/tests/acceptance_tests/drugs.py deleted file mode 100644 index 96e955e7..00000000 --- a/tests/acceptance_tests/drugs.py +++ /dev/null @@ -1,15 +0,0 @@ -drugs = { - '/drugs': [{ - 'params': { - 'drug_id': 'PA448497', - 'name': 'aspirin' - }, - 'response': { - '_id': 'PA448497', - 'name': 'aspirin', - 'drug_ontology_terms': [], - 'source': 'pharmGKB', - 'source_url': 'https://www.pharmgkb.org/chemical/PA448497' - } - }] -} diff --git a/tests/acceptance_tests/drugs_variants.py b/tests/acceptance_tests/drugs_variants.py deleted file mode 100644 index 864605df..00000000 --- a/tests/acceptance_tests/drugs_variants.py +++ /dev/null @@ -1,237 +0,0 @@ -drugs_variants = { - '/drugs/variants': [{ - 'params': { - 'drug_id': 'PA448497', - 'drug_name': 'aspirin', - 'pmid': '20824505', - 'phenotype_categories': 'Toxicity', - 'verbose': 'false' - }, - 'response': [ - { - 'drug': 'drugs/PA448497', - 'sequence variant': 'variants/b8d8a33facd5b62cb7f1004ae38419b8d914082ea9b217bef008a6a7f0218687', - 'gene_symbol': [ - 'AGT' - ], - 'pmid': '20824505', - 'study_parameters': [ - { - 'study_parameter_id': '1009568432', - 'study_type': 'cohort', - 'study_cases': '68', - 'study_controls': '357', - 'p-value': '< 0.05', - 'biogeographical_groups': 'East Asian' - } - ], - 'phenotype_categories': [ - 'Toxicity' - ], - 'source': 'pharmGKB', - 'source_url': 'https://www.pharmgkb.org/variantAnnotation/1009360953' - } - ] - }, { - 'params': { - 'drug_id': 'PA448497', - 'drug_name': 'aspirin', - 'pmid': '20824505', - 'phenotype_categories': 'Toxicity', - 'verbose': 'true' - }, - 'response': [ - { - 'drug': 'drugs/PA448497', - 'sequence variant': { - '_id': 'b8d8a33facd5b62cb7f1004ae38419b8d914082ea9b217bef008a6a7f0218687', - 'chr': 'chr1', - 'pos': 230714139, - 'rsid': [ - 'rs5050' - ], - 'ref': 'T', - 'alt': 'G', - 'spdi': 'NC_000001.11:230714139:T:G', - 'hgvs': 'NC_000001.11:g.230714140T>G', - 'qual': '.', - 'filter': None, - 'annotations': { - 'freq': { - '1000genomes': { - 'ref:long': 0.8241, - 'alt:long': 0 - }, - 'alspac': { - 'ref:long': 0.8441, - 'alt:long': 0 - }, - 'estonian': { - 'ref:long': 0.8107, - 'alt:long': 0 - }, - 'genome_dk': { - 'ref:long': 0.85, - 'alt:long': 0 - }, - 'gonl': { - 'ref:long': 0.8377, - 'alt:long': 0 - }, - 'hgdp_stanford': { - 'ref:long': 0.8272, - 'alt:long': 0 - }, - 'hapmap': { - 'ref:long': 0.84, - 'alt:long': 0 - }, - 'korean': { - 'ref:long': 0.8164, - 'alt:long': 0 - }, - 'northernsweden': { - 'ref:long': 0.8433, - 'alt:long': 0 - }, - 'page_study': { - 'ref:long': 0.8311, - 'alt:long': 0 - }, - 'prjeb36033': { - 'ref:long': 0.8857, - 'alt:long': 0 - }, - 'pharmgkb': { - 'ref:long': 0.883, - 'alt:long': 0 - }, - 'qatari': { - 'ref:long': 0.8796, - 'alt:long': 0 - }, - 'sgdp_prj': { - 'ref:long': 0.4595, - 'alt:long': 0.006757 - }, - 'siberian': { - 'ref:long': 0.3571, - 'alt:long': 0 - }, - 'tommo': { - 'ref:long': 0.7589, - 'alt:long': 0 - }, - 'topmed': { - 'ref:long': 0.8342, - 'alt:long': 0 - }, - 'twinsuk': { - 'ref:long': 0.836, - 'alt:long': 0 - }, - 'dbgap_popfreq': { - 'ref:long': 0.8768, - 'alt:long': 0 - } - }, - 'varinfo': '1-230714140-T-G', - 'vid': '6.36746e+08', - 'variant_vcf': '1-230714140-T-G', - 'variant_annovar': '1-230714140-230714140-T-G', - 'start_position': '2.30714e+08', - 'end_position': '2.30714e+08', - 'ref_annovar': 'T', - 'alt_annovar': 'G', - 'ref_vcf': 'T', - 'alt_vcf': 'G', - 'apc_conservation': 2.37719, - 'apc_conservation_v2': 4.1684, - 'apc_epigenetics_active': 19.8025, - 'apc_epigenetics': 20.9484, - 'apc_epigenetics_repressed': 3.93328, - 'apc_epigenetics_transcription': 2.35907, - 'apc_local_nucleotide_diversity': 1.30443, - 'apc_local_nucleotide_diversity_v2': 0.177866, - 'apc_local_nucleotide_diversity_v3': 0.16922, - 'apc_mappability': 17.0936, - 'apc_micro_rna': 99.4512, - 'apc_mutation_density': 0.183242, - 'apc_protein_function': 20.2494, - 'apc_protein_function_v2': 4.92793e-10, - 'apc_protein_function_v3': 2.96949, - 'apc_proximity_to_coding': 10.3211, - 'apc_proximity_to_coding_v2': 15.1786, - 'apc_proximity_to_tsstes': 14.2933, - 'apc_transcription_factor': 21.409, - 'bravo_an': '264690', - 'bravo_af': '0.165779', - 'filter_status': 'PASS', - 'origin': None, - 'fathmm_xf': '6.60508', - 'funseq_description': 'noncoding', - 'af_total': 0.168579, - 'af_asj_female': 0.174485, - 'af_eas_female': 0.174515, - 'af_afr_male': 0.146568, - 'af_female': 0.166875, - 'af_fin_male': 0.216127, - 'af_oth_female': 0.196364, - 'af_ami': 0.282366, - 'af_oth': 0.183892, - 'af_male': 0.170393, - 'af_ami_female': 0.273504, - 'af_afr': 0.148104, - 'af_eas_male': 0.150179, - 'af_sas': 0.176684, - 'af_nfe_female': 0.169528, - 'af_asj_male': 0.17545, - 'af_raw': 0.168736, - 'af_oth_male': 0.170802, - 'af_nfe_male': 0.168105, - 'af_asj': 0.174939, - 'af_amr_male': 0.186368, - 'af_amr_female': 0.181664, - 'af_fin': 0.213523, - 'af_afr_female': 0.149413, - 'af_sas_male': 0.175731, - 'af_amr': 0.184334, - 'af_nfe': 0.168929, - 'af_eas': 0.161435, - 'af_ami_male': 0.292056, - 'af_fin_female': 0.205263, - 'cadd_rawscore': '0.530047', - 'cadd_phred': '7.596', - 'tg_afr': '0.1634', - 'tg_all': '0.175919', - 'tg_amr': '0.2104', - 'tg_eas': '0.1597', - 'tg_eur': '0.1779', - 'tg_sas': '0.183' - }, - 'source': 'FAVOR', - 'source_url': 'http://favor.genohub.org/' - }, - 'gene_symbol': [ - 'AGT' - ], - 'pmid': '20824505', - 'study_parameters': [ - { - 'study_parameter_id': '1009568432', - 'study_type': 'cohort', - 'study_cases': '68', - 'study_controls': '357', - 'p-value': '< 0.05', - 'biogeographical_groups': 'East Asian' - } - ], - 'phenotype_categories': [ - 'Toxicity' - ], - 'source': 'pharmGKB', - 'source_url': 'https://www.pharmgkb.org/variantAnnotation/1009360953' - } - ] - }] -} diff --git a/tests/acceptance_tests/eqtls.py b/tests/acceptance_tests/eqtls.py deleted file mode 100644 index 713fc37c..00000000 --- a/tests/acceptance_tests/eqtls.py +++ /dev/null @@ -1,5024 +0,0 @@ -eqtls = { - '/variants/genes': [{ - 'params': { - 'p_value': 'lte:0.01', - 'label': 'eQTL', - 'verbose': 'false' - }, - 'response': [ - { - 'sequence variant': 'variants/990edb6dfac2bd1c1643f66e26807fb4c75a538d05934529a84c4be177c47b75', - 'gene': 'genes/ENSG00000204623', - 'beta': 5.92148e-24, - 'label': 'eQTL', - 'log10pvalue': 9.19000822584648, - 'slope': -0.285369, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'thyroid gland', - 'chr': 'chr6', - 'intron_chr': None, - 'intron_start': None, - 'intron_end': None - }, - { - 'sequence variant': 'variants/75186c95284121bf757cc5d43b63a093b7cc7506498edcc7ae9fda46ff171ba9', - 'gene': 'genes/ENSG00000245937', - 'beta': 2.70587e-31, - 'label': 'eQTL', - 'log10pvalue': 4.988484533867433, - 'slope': 0.1708, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'lower leg skin', - 'chr': 'chr5', - 'intron_chr': None, - 'intron_start': None, - 'intron_end': None - }, - { - 'sequence variant': 'variants/3a976b04856698b15850c1da6676500b4e08f34fdbfce56778816a4ccf786bf6', - 'gene': 'genes/ENSG00000224272', - 'beta': 1.99947e-51, - 'label': 'eQTL', - 'log10pvalue': 5.68681427092834, - 'slope': -0.268048, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'thyroid gland', - 'chr': 'chr2', - 'intron_chr': None, - 'intron_start': None, - 'intron_end': None - }, - { - 'sequence variant': 'variants/167702881c58bd973a19fdfc1f550397c0dcef2d203b2414b296db60833a10da', - 'gene': 'genes/ENSG00000205659', - 'beta': 3.9557e-22, - 'label': 'eQTL', - 'log10pvalue': 13.018177317092114, - 'slope': -0.216265, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'subcutaneous adipose tissue', - 'chr': 'chr14', - 'intron_chr': None, - 'intron_start': None, - 'intron_end': None - }, - { - 'sequence variant': 'variants/7d49eb680179e891cbb9bcd5fc5cbd805bd21b81803e24554398037e7ecfe0bc', - 'gene': 'genes/ENSG00000244731', - 'beta': 1.3965e-36, - 'label': 'eQTL', - 'log10pvalue': 6.515506551193956, - 'slope': -0.233573, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'tibial nerve', - 'chr': 'chr6', - 'intron_chr': None, - 'intron_start': None, - 'intron_end': None - }, - { - 'sequence variant': 'variants/6e6ab0223433ae7375ff2c4dbd98615f9a8fd2bb7cb72dea76e8439021aa67e5', - 'gene': 'genes/ENSG00000132780', - 'beta': 0.0000217928, - 'label': 'eQTL', - 'log10pvalue': 5.150926562438678, - 'slope': -0.117136, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'tibial nerve', - 'chr': 'chr1', - 'intron_chr': None, - 'intron_start': None, - 'intron_end': None - }, - { - 'sequence variant': 'variants/6b3f2a0292c4ef743e0f484f5dc833c1da33bad0cf2f8fe364d4a8320c3b78f7', - 'gene': 'genes/ENSG00000196126', - 'beta': 5.43412e-7, - 'label': 'eQTL', - 'log10pvalue': 7.052230148612905, - 'slope': -0.326603, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'amygdala', - 'chr': 'chr6', - 'intron_chr': None, - 'intron_start': None, - 'intron_end': None - }, - { - 'sequence variant': 'variants/6ac165d8d6a3cb4d2c4cda1a818925bc0aa58cf9fad991479702291fb38c9959', - 'gene': 'genes/ENSG00000204301', - 'beta': 2.59001e-92, - 'label': 'eQTL', - 'log10pvalue': 3.9828539258054874, - 'slope': 0.214847, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'venous blood', - 'chr': 'chr6', - 'intron_chr': None, - 'intron_start': None, - 'intron_end': None - }, - { - 'sequence variant': 'variants/6ac69bceaf532230689baf43731abb4af12e28c0a73aadd0461e4695110f6b91', - 'gene': 'genes/ENSG00000140575', - 'beta': 2.15345e-28, - 'label': 'eQTL', - 'log10pvalue': 27.778403214259736, - 'slope': 0.509341, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'spleen', - 'chr': 'chr15', - 'intron_chr': None, - 'intron_start': None, - 'intron_end': None - }, - { - 'sequence variant': 'variants/cf860003a8c7b41b1031acaac29e19ad223d1f5cde30fcdf562333aca25e42ce', - 'gene': 'genes/ENSG00000108588', - 'beta': 0.00008871, - 'label': 'eQTL', - 'log10pvalue': 5.410089475771274, - 'slope': -0.0901586, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'testis', - 'chr': 'chr17', - 'intron_chr': None, - 'intron_start': None, - 'intron_end': None - }, - { - 'sequence variant': 'variants/91c00814ae7ceb37a5e59782405c7735c79164e9944dbca4dab32645b687e338', - 'gene': 'genes/ENSG00000234327', - 'beta': 3.27471e-20, - 'label': 'eQTL', - 'log10pvalue': 10.994986886204508, - 'slope': -0.664311, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'ascending aorta', - 'chr': 'chr17', - 'intron_chr': None, - 'intron_start': None, - 'intron_end': None - }, - { - 'sequence variant': 'variants/09bff5657eb79da05f08523652cbf6998135d4659da2a87cf1d0333b1ece62d7', - 'gene': 'genes/ENSG00000230563', - 'beta': 5.62723e-71, - 'label': 'eQTL', - 'log10pvalue': 15.938796406761966, - 'slope': 0.64163, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'esophagus muscularis mucosa', - 'chr': 'chr20', - 'intron_chr': None, - 'intron_start': None, - 'intron_end': None - }, - { - 'sequence variant': 'variants/d740ef79a9b77a42e49a27e4a21f970b81a8235d80a13403e1d5157325c12197', - 'gene': 'genes/ENSG00000125618', - 'beta': 7.59477e-72, - 'label': 'eQTL', - 'log10pvalue': 14.075975160944276, - 'slope': -0.476235, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'subcutaneous adipose tissue', - 'chr': 'chr2', - 'intron_chr': None, - 'intron_start': None, - 'intron_end': None - }, - { - 'sequence variant': 'variants/1a0d470031db7fc0af1b2d36bc95821729bc8dc429cf90f648a6c93f16386ecc', - 'gene': 'genes/ENSG00000186281', - 'beta': 2.68366e-8, - 'label': 'eQTL', - 'log10pvalue': 4.4111223848876495, - 'slope': -0.865461, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'thyroid gland', - 'chr': 'chr2', - 'intron_chr': None, - 'intron_start': None, - 'intron_end': None - }, - { - 'sequence variant': 'variants/98129504502a811d601d4a616578cc348827e898a618a4cfce286fe1ec09c0ea', - 'gene': 'genes/ENSG00000214189', - 'beta': 9.19512e-72, - 'label': 'eQTL', - 'log10pvalue': 45.29519852953061, - 'slope': -0.795968, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'suprapubic skin', - 'chr': 'chr19', - 'intron_chr': None, - 'intron_start': None, - 'intron_end': None - }, - { - 'sequence variant': 'variants/2be92484f4ebf3cb8a9b9b761574b157f7c50f6b0a3eb9fa15f8a286a4550b42', - 'gene': 'genes/ENSG00000279170', - 'beta': 0.000153916, - 'label': 'eQTL', - 'log10pvalue': 4.778851897962264, - 'slope': -0.511334, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'putamen', - 'chr': 'chr6', - 'intron_chr': None, - 'intron_start': None, - 'intron_end': None - }, - { - 'sequence variant': 'variants/2c67069d7fe13a673e2aaec5aa15db24d9e3ab195c35c69c9c6f2769c50a0f7a', - 'gene': 'genes/ENSG00000026103', - 'beta': 2.49992e-23, - 'label': 'eQTL', - 'log10pvalue': 14.372586004941663, - 'slope': -0.224334, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'lower leg skin', - 'chr': 'chr10', - 'intron_chr': None, - 'intron_start': None, - 'intron_end': None - }, - { - 'sequence variant': 'variants/899f24f4be5d022fcd7b0ee349a594d1806b9ef955fcb7e0a22d453ea712bba4', - 'gene': 'genes/ENSG00000189014', - 'beta': 0.000368857, - 'label': 'eQTL', - 'log10pvalue': 4.920641453235365, - 'slope': -0.277984, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'esophagus squamous epithelium', - 'chr': 'chr10', - 'intron_chr': None, - 'intron_start': None, - 'intron_end': None - }, - { - 'sequence variant': 'variants/6ddd059d1eee891231e1edef657e13d95892c15a94214e387e8a9cf9978863c3', - 'gene': 'genes/ENSG00000143951', - 'beta': 3.53107e-32, - 'label': 'eQTL', - 'log10pvalue': 21.493077109507322, - 'slope': -0.360554, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'subcutaneous adipose tissue', - 'chr': 'chr2', - 'intron_chr': None, - 'intron_start': None, - 'intron_end': None - }, - { - 'sequence variant': 'variants/f9837bce771a5c2a7f52b09ddc52c388a9ad643323adc8788a3bd86b7bb020ac', - 'gene': 'genes/ENSG00000237276', - 'beta': 3.23274e-9, - 'label': 'eQTL', - 'log10pvalue': 4.898545073590217, - 'slope': 0.234929, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'omental fat pad', - 'chr': 'chr1', - 'intron_chr': None, - 'intron_start': None, - 'intron_end': None - }, - { - 'sequence variant': 'variants/59ac4faaf3e6e51cabc3ecfa43d5f9b78684064378a13f16214c556ee9291576', - 'gene': 'genes/ENSG00000179344', - 'beta': 2.68353e-20, - 'label': 'eQTL', - 'log10pvalue': 4.5243128345804955, - 'slope': -0.488403, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'hypothalamus', - 'chr': 'chr6', - 'intron_chr': None, - 'intron_start': None, - 'intron_end': None - }, - { - 'sequence variant': 'variants/1fd8e189360cb33ebd0e349e026cbe9e4484d2d3234d2b2b3791ff077255cecd', - 'gene': 'genes/ENSG00000129484', - 'beta': 1.02281e-13, - 'label': 'eQTL', - 'log10pvalue': 8.35730009461348, - 'slope': -0.126144, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'lower leg skin', - 'chr': 'chr14', - 'intron_chr': None, - 'intron_start': None, - 'intron_end': None - }, - { - 'sequence variant': 'variants/20896812f9b918fc2809b8a03a87f316ebd242b19cce0f999c33b1c0fe222ca6', - 'gene': 'genes/ENSG00000242353', - 'beta': 0.000138426, - 'label': 'eQTL', - 'log10pvalue': 5.005355160054925, - 'slope': -0.365255, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'testis', - 'chr': 'chr11', - 'intron_chr': None, - 'intron_start': None, - 'intron_end': None - }, - { - 'sequence variant': 'variants/07789c75456565f4dc37f1cc995b19fe5c81610e6805e356a838f9285c443aae', - 'gene': 'genes/ENSG00000124302', - 'beta': 0.0000321999, - 'label': 'eQTL', - 'log10pvalue': 4.352838145969047, - 'slope': 0.246652, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'thyroid gland', - 'chr': 'chr19', - 'intron_chr': None, - 'intron_start': None, - 'intron_end': None - }, - { - 'sequence variant': 'variants/82d593ddaa22d709dbed6444e5966f72abfbf465790491c5da6a15c1fc79f631', - 'gene': 'genes/ENSG00000071967', - 'beta': 4.60592e-10, - 'label': 'eQTL', - 'log10pvalue': 5.671520499931029, - 'slope': 0.25207, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'ovary', - 'chr': 'chr2', - 'intron_chr': None, - 'intron_start': None, - 'intron_end': None - } - ] - }, { - 'params': { - 'p_value': 'lte:0.01', - 'label': 'eQTL', - 'verbose': 'true' - }, - 'response': [ - { - 'sequence variant': { - '_id': '990edb6dfac2bd1c1643f66e26807fb4c75a538d05934529a84c4be177c47b75', - 'chr': 'chr6', - 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'sequence variant': { - '_id': '6ddd059d1eee891231e1edef657e13d95892c15a94214e387e8a9cf9978863c3', - 'chr': 'chr2', - 'pos': 63373364, - 'rsid': [ - 'rs12713489' - ], - 'ref': 'C', - 'alt': 'T', - 'spdi': 'NC_000002.12:63373364:C:T', - 'hgvs': 'NC_000002.12:g.63373365C>T', - 'qual': '.', - 'filter': '.', - 'format': None, - 'source': 'FAVOR', - 'source_url': 'http://favor.genohub.org/', - 'annotations': { - 'freq': { - '1000genomes': { - 'ref:long': 0.503, - 'alt:long': 0 - }, - 'alspac': { - 'ref:long': 0.4403, - 'alt:long': 0 - }, - 'estonian': { - 'ref:long': 0.4488, - 'alt:long': 0 - }, - 'genome_dk': { - 'ref:long': 0.425, - 'alt:long': 0 - }, - 'gnomad': { - 'ref:long': 0.4299, - 'alt:long': 0 - }, - 'gonl': { - 'ref:long': 0.4339, - 'alt:long': 0 - }, - 'korean': { - 'ref:long': 0.6444, - 'alt:long': 0 - }, - 'korea1k': { - 'ref:long': 0.6393, - 'alt:long': 0 - }, - 'northernsweden': { - 'ref:long': 0.3552, - 'alt:long': 0 - }, - 'qatari': { - 'ref:long': 0.4028, - 'alt:long': 0 - 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}, - 'topmed': { - 'ref:long': 0.7383, - 'alt:long': 0.2617 - }, - 'dbgap_popfreq': { - 'ref:long': 0.7605, - 'alt:long': 0.2395 - } - }, - 'varinfo': '6-32683840-A-G', - 'vid': '6.58004e+09', - 'variant_vcf': '6-32683840-A-G', - 'variant_annovar': '6-32683840-32683840-A-G', - 'start_position': '3.26838e+07', - 'end_position': '3.26838e+07', - 'ref_annovar': 'A', - 'alt_annovar': 'G', - 'ref_vcf': 'A', - 'alt_vcf': 'G', - 'apc_conservation': 0.495227, - 'apc_conservation_v2': 0.398166, - 'apc_epigenetics_active': 2.9021, - 'apc_epigenetics': 3.78216, - 'apc_epigenetics_repressed': 10.2619, - 'apc_epigenetics_transcription': 5.04727, - 'apc_local_nucleotide_diversity': 1.15872, - 'apc_local_nucleotide_diversity_v2': 0.00221746, - 'apc_local_nucleotide_diversity_v3': 0.000312647, - 'apc_mappability': 2.59407, - 'apc_micro_rna': 99.4512, - 'apc_mutation_density': 0.00235739, - 'apc_protein_function': 20.2494, - 'apc_protein_function_v2': 4.92793e-10, - 'apc_protein_function_v3': 2.96949, - 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'ARTD2', - 'poly (ADP-ribosyl) transferase-like 2', - 'protein poly-ADP-ribosyltransferase PARP2', - 'ADPRTL3', - 'poly[ADP-ribose] synthase 2', - 'hPARP-2', - 'PARP2', - 'DNA ADP-ribosyltransferase PARP2', - 'PARP-2' - ] - }, - 'beta': 1.02281e-13, - 'label': 'eQTL', - 'log10pvalue': 8.35730009461348, - 'slope': -0.126144, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'lower leg skin', - 'chr': 'chr14', - 'intron_chr': None, - 'intron_start': None, - 'intron_end': None - }, - { - 'sequence variant': { - '_id': '20896812f9b918fc2809b8a03a87f316ebd242b19cce0f999c33b1c0fe222ca6', - 'chr': 'chr11', - 'pos': 30355150, - 'rsid': [ - 'rs1717779' - ], - 'ref': 'A', - 'alt': 'T', - 'spdi': 'NC_000011.10:30355150:A:T', - 'hgvs': 'NC_000011.10:g.30355151A>T', - 'qual': '.', - 'filter': None, - 'format': '.', - 'source': 'FAVOR', - 'source_url': 'http://favor.genohub.org/', - 'annotations': { - 'freq': { - '1000genomes': { - 'ref:long': 0.8452, - 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'_id': '82d593ddaa22d709dbed6444e5966f72abfbf465790491c5da6a15c1fc79f631', - 'chr': 'chr2', - 'pos': 171524204, - 'rsid': [ - 'rs58368144' - ], - 'ref': 'CGGCATCAG', - 'alt': 'C', - 'spdi': 'NC_000002.12:171524205:GGCATCAGGG:GG', - 'hgvs': 'NC_000002.12:g.171524208_171524215del', - 'qual': '.', - 'filter': '.', - 'format': None, - 'source': 'FAVOR', - 'source_url': 'http://favor.genohub.org/', - 'annotations': { - 'freq': { - 'genome_dk': { - 'ref:long': 0.65, - 'alt:long': 0.35 - }, - 'gnomad': { - 'ref:long': 0.6277, - 'alt:long': 0.3723 - }, - 'korea1k': { - 'ref:long': 0.8035, - 'alt:long': 0.1965 - }, - 'northernsweden': { - 'ref:long': 0.6117, - 'alt:long': 0.3883 - }, - 'tommo': { - 'ref:long': 0.7412, - 'alt:long': 0.2588 - }, - 'dbgap_popfreq': { - 'ref:long': 0.6022, - 'alt:long': 0.3978 - } - }, - 'varinfo': '2-171524205-CGGCATCAG-C', - 'vid': '8.85175e+09', - 'variant_vcf': '2-171524205-CGGCATCAG-C', - 'variant_annovar': '2-171524206-171524213-GGCATCAG--', - 'start_position': '1.71524e+08', - 'end_position': '1.71524e+08', - 'ref_annovar': 'GGCATCAG', - 'alt_annovar': '-', - 'ref_vcf': 'CGGCATCAG', - 'alt_vcf': 'C', - 'af_total': 0.373228, - 'af_asj_female': 0.441477, - 'af_eas_female': 0.202909, - 'af_afr_male': 0.401703, - 'af_female': 0.374145, - 'af_fin_male': 0.25562, - 'af_oth_female': 0.364717, - 'af_ami': 0.34375, - 'af_oth': 0.375116, - 'af_male': 0.372252, - 'af_ami_female': 0.333333, - 'af_afr': 0.396246, - 'af_eas_male': 0.204545, - 'af_sas': 0.41453, - 'af_nfe_female': 0.367539, - 'af_asj_male': 0.419231, - 'af_raw': 0.373357, - 'af_oth_male': 0.385932, - 'af_nfe_male': 0.37372, - 'af_asj': 0.431024, - 'af_amr_male': 0.428109, - 'af_amr_female': 0.40889, - 'af_fin': 0.26137, - 'af_afr_female': 0.3916, - 'af_sas_male': 0.406704, - 'af_amr': 0.419788, - 'af_nfe': 0.37014, - 'af_eas': 0.203787, - 'af_ami_male': 0.35514, - 'af_fin_female': 0.279553, - 'cadd_rawscore': '1.20257', - 'cadd_phred': '13.87' - } - }, - 'gene': { - '_id': 'ENSG00000071967', - 'chr': 'chr2', - 'start': 171522246, - 'end': 171558129, - 'gene_id': 'ENSG00000071967.12', - 'hgnc': 'HGNC:20797', - 'name': 'CYBRD1', - 'gene_type': 'protein_coding', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'ferric-chelate reductase 3', - 'cytochrome b561 family, member A2', - 'duodenal cytochrome b', - 'CYBRD1', - 'FRRS3', - 'plasma membrane ascorbate-dependent reductase CYBRD1', - 'cytochrome b reductase 1', - 'DCYTB', - 'CYB561A2' - ] - }, - 'beta': 4.60592e-10, - 'label': 'eQTL', - 'log10pvalue': 5.671520499931029, - 'slope': 0.25207, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'ovary', - 'chr': 'chr2', - 'intron_chr': None, - 'intron_start': None, - 'intron_end': None - } - ] - }] -} diff --git a/tests/acceptance_tests/gene_transcripts.py b/tests/acceptance_tests/gene_transcripts.py deleted file mode 100644 index 759c2ab0..00000000 --- a/tests/acceptance_tests/gene_transcripts.py +++ /dev/null @@ -1,413 +0,0 @@ -genes_transcripts = { - '/genes/transcripts': [{ - 'params': { - 'gene_name': 'ATF3', - 'gene_region': 'chr1:212565300-212620800', - 'alias': 'ATF3', - 'gene_type': 'protein_coding', - 'verbose': 'false' - }, - 'response': [ - { - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'version': 'v43', - 'transcript': 'transcripts/ENST00000366981' - }, - { - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'version': 'v43', - 'transcript': 'transcripts/ENST00000366987' - }, - { - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'version': 'v43', - 'transcript': 'transcripts/ENST00000613954' - }, - { - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'version': 'v43', - 'transcript': 'transcripts/ENST00000465155' - }, - { - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'version': 'v43', - 'transcript': 'transcripts/ENST00000341491' - }, - { - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'version': 'v43', - 'transcript': 'transcripts/ENST00000366985' - }, - { - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'version': 'v43', - 'transcript': 'transcripts/ENST00000492118' - }, - { - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'version': 'v43', - 'transcript': 'transcripts/ENST00000336937' - }, - { - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'version': 'v43', - 'transcript': 'transcripts/ENST00000464547' - }, - { - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'version': 'v43', - 'transcript': 'transcripts/ENST00000366983' - }, - { - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'version': 'v43', - 'transcript': 'transcripts/ENST00000613104' - } - ] - }, { - 'params': { - 'gene_name': 'ATF3', - 'gene_region': 'chr1:212565300-212620800', - 'alias': 'ATF3', - 'gene_type': 'protein_coding', - 'verbose': 'true' - }, - 'response': [ - { - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'version': 'v43', - 'transcript': [ - { - '_id': 'ENST00000366981', - 'transcript_type': 'protein_coding', - 'chr': 'chr1', - 'start': 212565333, - 'end': 212619535, - 'name': 'ATF3-203', - 'gene_name': 'ATF3', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/' - } - ] - }, - { - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'version': 'v43', - 'transcript': [ - { - '_id': 'ENST00000366987', - 'transcript_type': 'protein_coding', - 'chr': 'chr1', - 'start': 212565333, - 'end': 212620772, - 'name': 'ATF3-206', - 'gene_name': 'ATF3', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/' - } - ] - }, - { - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'version': 'v43', - 'transcript': [ - { - '_id': 'ENST00000613954', - 'transcript_type': 'protein_coding', - 'chr': 'chr1', - 'start': 212608627, - 'end': 212620772, - 'name': 'ATF3-211', - 'gene_name': 'ATF3', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/' - } - ] - }, - { - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'version': 'v43', - 'transcript': [ - { - '_id': 'ENST00000465155', - 'transcript_type': 'retained_intron', - 'chr': 'chr1', - 'start': 212608669, - 'end': 212619247, - 'name': 'ATF3-208', - 'gene_name': 'ATF3', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/' - } - ] - }, - { - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'version': 'v43', - 'transcript': [ - { - '_id': 'ENST00000341491', - 'transcript_type': 'protein_coding', - 'chr': 'chr1', - 'start': 212608760, - 'end': 212620775, - 'name': 'ATF3-202', - 'gene_name': 'ATF3', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/' - } - ] - }, - { - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'version': 'v43', - 'transcript': [ - { - '_id': 'ENST00000366985', - 'transcript_type': 'protein_coding', - 'chr': 'chr1', - 'start': 212608914, - 'end': 212619611, - 'name': 'ATF3-205', - 'gene_name': 'ATF3', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/' - } - ] - }, - { - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'version': 'v43', - 'transcript': [ - { - '_id': 'ENST00000492118', - 'transcript_type': 'protein_coding_CDS_not_defined', - 'chr': 'chr1', - 'start': 212613435, - 'end': 212620777, - 'name': 'ATF3-209', - 'gene_name': 'ATF3', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/' - } - ] - }, - { - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'version': 'v43', - 'transcript': [ - { - '_id': 'ENST00000336937', - 'transcript_type': 'protein_coding', - 'chr': 'chr1', - 'start': 212615021, - 'end': 212619266, - 'name': 'ATF3-201', - 'gene_name': 'ATF3', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/' - } - ] - }, - { - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'version': 'v43', - 'transcript': [ - { - '_id': 'ENST00000464547', - 'transcript_type': 'nonsense_mediated_decay', - 'chr': 'chr1', - 'start': 212615021, - 'end': 212619555, - 'name': 'ATF3-207', - 'gene_name': 'ATF3', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/' - } - ] - }, - { - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'version': 'v43', - 'transcript': [ - { - '_id': 'ENST00000366983', - 'transcript_type': 'protein_coding', - 'chr': 'chr1', - 'start': 212615021, - 'end': 212619555, - 'name': 'ATF3-204', - 'gene_name': 'ATF3', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/' - } - ] - }, - { - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'version': 'v43', - 'transcript': [ - { - '_id': 'ENST00000613104', - 'transcript_type': 'protein_coding', - 'chr': 'chr1', - 'start': 212615177, - 'end': 212619746, - 'name': 'ATF3-210', - 'gene_name': 'ATF3', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/' - } - ] - } - ] - - }, { - 'params': { - 'gene_id': 'ENSG00000187642', - 'verbose': 'false' - }, - 'response': [ - { - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'version': 'v43', - 'transcript': 'transcripts/ENST00000433179' - }, - { - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'version': 'v43', - 'transcript': 'transcripts/ENST00000341290' - }, - { - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'version': 'v43', - 'transcript': 'transcripts/ENST00000479361' - }, - { - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'version': 'v43', - 'transcript': 'transcripts/ENST00000694917' - } - ] - }, { - 'params': { - 'gene_id': 'ENSG00000187642', - 'verbose': 'true' - }, - 'response': [ - { - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'version': 'v43', - 'transcript': [ - { - '_id': 'ENST00000433179', - 'transcript_type': 'protein_coding', - 'chr': 'chr1', - 'start': 975197, - 'end': 982093, - 'name': 'PERM1-202', - 'gene_name': 'PERM1', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/' - } - ] - }, - { - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'version': 'v43', - 'transcript': [ - { - '_id': 'ENST00000341290', - 'transcript_type': 'protein_coding', - 'chr': 'chr1', - 'start': 975203, - 'end': 982093, - 'name': 'PERM1-201', - 'gene_name': 'PERM1', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/' - } - ] - }, - { - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'version': 'v43', - 'transcript': [ - { - '_id': 'ENST00000479361', - 'transcript_type': 'retained_intron', - 'chr': 'chr1', - 'start': 975204, - 'end': 976641, - 'name': 'PERM1-203', - 'gene_name': 'PERM1', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/' - } - ] - }, - { - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'version': 'v43', - 'transcript': [ - { - '_id': 'ENST00000694917', - 'transcript_type': 'protein_coding', - 'chr': 'chr1', - 'start': 976120, - 'end': 982117, - 'name': 'PERM1-204', - 'gene_name': 'PERM1', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/' - } - ] - } - ] - }] -} diff --git a/tests/acceptance_tests/genes.py b/tests/acceptance_tests/genes.py deleted file mode 100644 index 93dc02d9..00000000 --- a/tests/acceptance_tests/genes.py +++ /dev/null @@ -1,54 +0,0 @@ -genes = { - '/genes': [{ - 'params': { - 'name': 'ATF3', - 'region': 'chr1:212565300-212620800', - 'alias': 'ATF3', - 'gene_type': 'protein_coding' - }, - 'response': [{ - '_id': 'ENSG00000162772', - 'chr': 'chr1', - 'start': 212565333, - 'end': 212620777, - 'gene_type': 'protein_coding', - 'name': 'ATF3', - 'hgnc': 'HGNC:785', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'ATF3', - 'cAMP-dependent transcription factor ATF-3', - 'activating transcription factor 3', - 'cyclic AMP-dependent transcription factor ATF-3' - ] - }] - }, { - 'params': { - 'gene_id': 'ENSG00000187642' - }, - 'response': { - '_id': 'ENSG00000187642', - 'chr': 'chr1', - 'start': 975197, - 'end': 982117, - 'gene_type': 'protein_coding', - 'name': 'PERM1', - 'hgnc': 'HGNC:28208', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'PGC-1 and ERR-induced regulator in muscle 1', - 'PGC-1 and ERR-induced regulator in muscle protein 1', - 'PPARGC1 and ESRR induced regulator, muscle 1', - 'C1orf170', - 'PPARGC1 and ESRR-induced regulator in muscle 1', - 'PERM1', - 'peroxisome proliferator-activated receptor gamma coactivator 1 and estrogen-related receptor-induced regulator in muscle 1', - 'pGC-1 and ERR-induced regulator in muscle protein 1' - ] - } - }] -} diff --git a/tests/acceptance_tests/genes_diseases.py b/tests/acceptance_tests/genes_diseases.py deleted file mode 100644 index 1a99b6c0..00000000 --- a/tests/acceptance_tests/genes_diseases.py +++ /dev/null @@ -1,138 +0,0 @@ -genes_diseases = { - '/genes/diseases': [{ - 'params': { - 'gene_id': 'ENSG00000104783', - 'verbose': 'false' - }, - 'response': [ - { - 'pmid': [ - '26148990', - '26198474' - ], - 'term_name': 'Dehydrated hereditary stomatocytosis', - 'gene_symbol': 'KCNN4', - 'association_type': 'Disease-causing germline mutation(s) in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'ontology term': 'ontology_terms/Orphanet_3202' - }, - { - 'pmid': [ - '29915289' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'KCNN4', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'ontology term': 'ontology_terms/Orphanet_586' - } - ] - }, { - 'params': { - 'gene_id': 'ENSG00000104783', - 'verbose': 'true' - }, - 'response': [ - { - 'pmid': [ - '26148990', - '26198474' - ], - 'term_name': 'Dehydrated hereditary stomatocytosis', - 'gene_symbol': 'KCNN4', - 'association_type': 'Disease-causing germline mutation(s) in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'ontology term': { - 'uri': 'http://www.orpha.net/ORDO/Orphanet_3202', - 'term_id': 'Orphanet_3202', - 'name': 'dehydrated hereditary stomatocytosis', - 'description': '', - 'source': 'ORPHANET', - 'subontology': None - } - }, - { - 'pmid': [ - '29915289' - ], - 'term_name': 'Cystic fibrosis', - 'gene_symbol': 'KCNN4', - 'association_type': 'Modifying germline mutation in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'ontology term': { - 'uri': 'http://www.orpha.net/ORDO/Orphanet_586', - 'term_id': 'Orphanet_586', - 'name': 'cystic fibrosis', - 'description': '', - 'source': 'ORPHANET', - 'subontology': None - } - } - ] - }, { - 'params': { - 'gene_name': 'KCNN4', - 'region': 'chr19:43764000-43784000', - 'gene_type': 'protein_coding', - 'alias': 'DHS2', - 'association_type': 'Disease-causing germline mutation(s) in', - 'source': 'Orphanet', - 'verbose': 'false' - }, - 'response': [ - { - 'pmid': [ - '26148990', - '26198474' - ], - 'term_name': 'Dehydrated hereditary stomatocytosis', - 'gene_symbol': 'KCNN4', - 'association_type': 'Disease-causing germline mutation(s) in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'ontology term': 'ontology_terms/Orphanet_3202' - } - ] - }, { - 'params': { - 'gene_name': 'KCNN4', - 'region': 'chr19:43764000-43784000', - 'gene_type': 'protein_coding', - 'alias': 'DHS2', - 'association_type': 'Disease-causing germline mutation(s) in', - 'source': 'Orphanet', - 'verbose': 'true' - }, - 'response': [ - { - 'pmid': [ - '26148990', - '26198474' - ], - 'term_name': 'Dehydrated hereditary stomatocytosis', - 'gene_symbol': 'KCNN4', - 'association_type': 'Disease-causing germline mutation(s) in', - 'association_status': 'Assessed', - 'source': 'Orphanet', - 'source_url': 'https://www.orphadata.com/genes/', - 'ontology term': { - 'uri': 'http://www.orpha.net/ORDO/Orphanet_3202', - 'term_id': 'Orphanet_3202', - 'name': 'dehydrated hereditary stomatocytosis', - 'description': '', - 'source': 'ORPHANET', - 'subontology': None - } - } - ] - }] -} diff --git a/tests/acceptance_tests/genes_genes.py b/tests/acceptance_tests/genes_genes.py deleted file mode 100644 index 3792196a..00000000 --- a/tests/acceptance_tests/genes_genes.py +++ /dev/null @@ -1,498 +0,0 @@ -genes_genes = { - '/genes/genes': [{ - 'params': { - 'gene_id': 'ENSG00000170558', - 'source': 'CoXPresdb', - 'logit_score': 'gt:0.1', - }, - 'response': [{ - 'gene': { - '_key': 'ENSG00000121410', - 'alias': ['alpha-1-B glycoprotein', - 'GAB', - 'HEL-S-163pA', - 'A1BG', - 'HYST2477', - 'alpha-1B-glycoprotein', - 'ABG', - 'A1B', - 'epididymis secretory sperm binding protein Li 163pA'], - 'chr': 'chr19', - 'end:long': 58353492, - 'entrez': '1', - 'gene_id': 'ENSG00000121410.12', - 'gene_type': 'protein_coding', - 'hgnc': 'HGNC:5', - 'name': 'A1BG', - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'start:long': 58345177, - 'version': 'v43'}, - 'logit_score': 0.13, - 'source': 'CoXPresdb', - 'source_url': 'https://coxpresdb.jp/'}, - { - 'gene': { - '_key': 'ENSG00000121410', - 'alias': ['alpha-1-B glycoprotein', - 'GAB', - 'HEL-S-163pA', - 'A1BG', - 'HYST2477', - 'alpha-1B-glycoprotein', - 'ABG', - 'A1B', - 'epididymis secretory sperm binding protein Li 163pA'], - 'chr': 'chr19', - 'end:long': 58353492, - 'entrez': '1', - 'gene_id': 'ENSG00000121410.12', - 'gene_type': 'protein_coding', - 'hgnc': 'HGNC:5', - 'name': 'A1BG', - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'start:long': 58345177, - 'version': 'v43'}, - 'logit_score': 0.13, - 'source': 'CoXPresdb', - 'source_url': 'https://coxpresdb.jp/'}, - {'gene': {'_key': 'ENSG00000077616', - 'alias': ['GCP3', - 'N-acetylated-alpha-linked acidic dipeptidase 2', - 'NAALADase II', - 'N-acetylated alpha-linked acidic dipeptidase 2', - 'NAALADASE2', - 'glutamate carboxypeptidase III', - 'GCPIII', - 'NAALAD2', - 'N-acetylated alpha-linked acidic dipeptidase II', - 'GPCIII'], - 'chr': 'chr11', - 'end:long': 90192894, - 'entrez': '10003', - 'gene_id': 'ENSG00000077616.11', - 'gene_type': 'protein_coding', - 'hgnc': 'HGNC:14526', - 'name': 'NAALAD2', - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'start:long': 90131514, - 'version': 'v43'}, - 'logit_score': 1.01, - 'source': 'CoXPresdb', - 'source_url': 'https://coxpresdb.jp/'}, - {'gene': {'_key': 'ENSG00000233369', - 'alias': ['GTF2I', - 'GTF2IP4', - 'general transcription factor IIi pseudogene 4', - 'general transcription factor II, i, pseudogene'], - 'chr': 'chr7', - 'end:long': 73207283, - 'entrez': '100093631', - 'gene_id': 'ENSG00000233369.7', - 'gene_type': 'transcribed_processed_pseudogene', - 'hgnc': 'HGNC:51716', - 'name': 'GTF2IP4', - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'start:long': 73154937, - 'version': 'v43'}, - 'logit_score': 1.34, - 'source': 'CoXPresdb', - 'source_url': 'https://coxpresdb.jp/'}, - {'gene': {'_key': 'ENSG00000213523', - 'alias': ['SRAP', - 'STRAA1', - 'SRA1', - 'pp7684', - 'SRA', - 'steroid receptor RNA activator protein', - 'steroid receptor RNA activator 1 (complexes with NCOA1)', - 'steroid receptor RNA activator 1', - 'steroid receptor coactivator'], - 'chr': 'chr5', - 'end:long': 140557677, - 'entrez': '10011', - 'gene_id': 'ENSG00000213523.12', - 'gene_type': 'protein_coding', - 'hgnc': 'HGNC:11281', - 'name': 'SRA1', - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'start:long': 140537339, - 'version': 'v43'}, - 'logit_score': 0.43, - 'source': 'CoXPresdb', - 'source_url': 'https://coxpresdb.jp/'}, - {'gene': {'_key': 'ENSG00000205269', - 'alias': ['TMEM170B', 'transmembrane protein 170B'], - 'chr': 'chr6', - 'end:long': 11583524, - 'entrez': '100113407', - 'gene_id': 'ENSG00000205269.6', - 'gene_type': 'protein_coding', - 'hgnc': 'HGNC:34244', - 'name': 'TMEM170B', - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'start:long': 11537748, - 'version': 'v43'}, - 'logit_score': 0.26, - 'source': 'CoXPresdb', - 'source_url': 'https://coxpresdb.jp/'}, - {'gene': {'_key': 'ENSG00000291071', - 'alias': ['FAM86JP', - 'family with sequence similarity 86 member J, pseudogene'], - 'chr': 'chr3', - 'end:long': 125930056, - 'entrez': '100125556', - 'gene_id': 'ENSG00000291071.1', - 'gene_type': 'lncRNA', - 'hgnc': 'HGNC:44097', - 'name': 'FAM86JP', - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'start:long': 125916608, - 'version': 'v43'}, - 'logit_score': 0.19, - 'source': 'CoXPresdb', - 'source_url': 'https://coxpresdb.jp/'}, - {'gene': {'_key': 'ENSG00000270607', - 'alias': ['LEISA', - 'NAV2-AS6', - 'LEISA1', - 'lncRNA enhancing IL-6/STAT3 signaling activation 1', - 'lncRNA enhancing IL-6/STAT3 signaling activation', - 'NAV2 antisense RNA 6'], - 'chr': 'chr11', - 'end:long': 19712619, - 'entrez': '100126784', - 'gene_id': 'ENSG00000270607.1', - 'gene_type': 'lncRNA', - 'hgnc': 'HGNC:55264', - 'name': 'NAV2-AS6', - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'start:long': 19710933, - 'version': 'v43'}, - 'logit_score': 0.44, - 'source': 'CoXPresdb', - 'source_url': 'https://coxpresdb.jp/'}, - {'gene': {'_key': 'ENSG00000253250', - 'alias': ['chromosome 8 open reading frame 88', - 'C8orf88', - 'uncharacterized protein C8orf88'], - 'chr': 'chr8', - 'end:long': 90985238, - 'entrez': '100127983', - 'gene_id': 'ENSG00000253250.3', - 'gene_type': 'protein_coding', - 'hgnc': 'HGNC:44672', - 'name': 'C8orf88', - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'start:long': 90958470, - 'version': 'v43'}, - 'logit_score': 1.57, - 'source': 'CoXPresdb', - 'source_url': 'https://coxpresdb.jp/'}, - {'gene': {'_key': 'ENSG00000166770', - 'alias': ['Mortal Obligate RNA Transcript', - 'ZNF667-AS1', - 'MORT', - 'ZNF667 antisense RNA 1 (head to head)'], - 'chr': 'chr19', - 'end:long': 56504362, - 'entrez': '100128252', - 'gene_id': 'ENSG00000166770.12', - 'gene_type': 'lncRNA', - 'hgnc': 'HGNC:44321', - 'name': 'ZNF667-AS1', - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'start:long': 56477249, - 'version': 'v43'}, - 'logit_score': 0.26, - 'source': 'CoXPresdb', - 'source_url': 'https://coxpresdb.jp/'}, - {'gene': {'_key': 'ENSG00000176593', - 'alias': ['ZNF606-AS1', 'ZNF606 antisense RNA 1'], - 'chr': 'chr19', - 'end:long': 58011232, - 'entrez': '100128398', - 'gene_id': 'ENSG00000176593.8', - 'gene_type': 'lncRNA', - 'hgnc': 'HGNC:44322', - 'name': 'ENSG00000176593', - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'start:long': 58002060, - 'version': 'v43'}, - 'logit_score': 0.84, - 'source': 'CoXPresdb', - 'source_url': 'https://coxpresdb.jp/'}, - {'gene': {'_key': 'ENSG00000183397', - 'alias': ['tektin bundle-interacting protein 1', - 'uncharacterized protein C19orf71', - 'tektin bundle interacting protein 1', - 'TEKTIP1', - 'C19orf71'], - 'chr': 'chr19', - 'end:long': 3544030, - 'entrez': '100128569', - 'gene_id': 'ENSG00000183397.6', - 'gene_type': 'protein_coding', - 'hgnc': 'HGNC:34496', - 'name': 'TEKTIP1', - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'start:long': 3539170, - 'version': 'v43'}, - 'logit_score': 0.49, - 'source': 'CoXPresdb', - 'source_url': 'https://coxpresdb.jp/'}, - {'gene': {'_key': 'ENSG00000266010', - 'alias': ['GATA6 antisense RNA 1 (head to head)', - 'locus 5689', - 'locus5689', - 'BM742401', - 'GATA6-AS1'], - 'chr': 'chr18', - 'end:long': 22169878, - 'entrez': '100128893', - 'gene_id': 'ENSG00000266010.4', - 'gene_type': 'lncRNA', - 'hgnc': 'HGNC:48840', - 'name': 'GATA6-AS1', - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'start:long': 22164885, - 'version': 'v43'}, - 'logit_score': 1.84, - 'source': 'CoXPresdb', - 'source_url': 'https://coxpresdb.jp/'}, - {'gene': {'_key': 'ENSG00000179627', - 'alias': ['zinc finger and BTB domain containing 42', - 'zinc finger and BTB domain-containing protein 42', - 'ZNF925', - 'LCCS6', - 'ZBTB42'], - 'chr': 'chr14', - 'end:long': 104804712, - 'entrez': '100128927', - 'gene_id': 'ENSG00000179627.10', - 'gene_type': 'protein_coding', - 'hgnc': 'HGNC:32550', - 'name': 'ZBTB42', - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'start:long': 104800595, - 'version': 'v43'}, - 'logit_score': 0.12, - 'source': 'CoXPresdb', - 'source_url': 'https://coxpresdb.jp/'}, - {'gene': {'_key': 'ENSG00000235016', - 'alias': ['SEMA3F antisense RNA 1', 'RBM5-AS1', 'SEMA3F-AS1'], - 'chr': 'chr3', - 'end:long': 50156085, - 'entrez': '100129060', - 'gene_id': 'ENSG00000235016.1', - 'gene_type': 'lncRNA', - 'hgnc': 'HGNC:40518', - 'name': 'SEMA3F-AS1', - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'start:long': 50116021, - 'version': 'v43'}, - 'logit_score': 0.13, - 'source': 'CoXPresdb', - 'source_url': 'https://coxpresdb.jp/'}, - {'gene': {'_key': 'ENSG00000256537', - 'alias': ['chromosome X open reading frame 69-like', - 'small integral membrane protein 10 like 1', - 'Small integral membrane protein 10-like protein 1', - 'SMIM10L1', - 'small integral membrane protein 10-like protein 1'], - 'chr': 'chr12', - 'end:long': 11176016, - 'entrez': '100129361', - 'gene_id': 'ENSG00000256537.5', - 'gene_type': 'protein_coding', - 'hgnc': 'HGNC:49847', - 'name': 'SMIM10L1', - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'start:long': 11171193, - 'version': 'v43'}, - 'logit_score': 0.22, - 'source': 'CoXPresdb', - 'source_url': 'https://coxpresdb.jp/'}, - {'gene': {'_key': 'ENSG00000233251', - 'alias': ['LOC100129434'], - 'chr': 'chr2', - 'end:long': 56185870, - 'entrez': '100129434', - 'gene_id': 'ENSG00000233251.8', - 'gene_type': 'lncRNA', - 'name': 'ENSG00000233251', - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'start:long': 56173533, - 'version': 'v43'}, - 'logit_score': 0.29, - 'source': 'CoXPresdb', - 'source_url': 'https://coxpresdb.jp/'}, - {'gene': {'_key': 'ENSG00000234432', - 'alias': ['LINC02983', - 'long intergenic non-protein coding RNA 2983'], - 'chr': 'chr7', - 'end:long': 5428927, - 'entrez': '100129484', - 'gene_id': 'ENSG00000234432.4', - 'gene_type': 'lncRNA', - 'hgnc': 'HGNC:56060', - 'name': 'LINC02983', - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'start:long': 5426276, - 'version': 'v43'}, - 'logit_score': 1.25, - 'source': 'CoXPresdb', - 'source_url': 'https://coxpresdb.jp/'}, - {'gene': {'_key': 'ENSG00000262454', - 'alias': ['linc noncoding oxygen-sensitive regulator of sterol ' - 'homeostasis', - 'MIR193BHG', - 'lincNORS', - 'MIR193b-365a host gene', - 'noncoding oxygen-sensitive regulator of sterol ' - 'homeostasis', - 'HypERlnc', - 'MIR193B host', - 'hypoxia-induced endoplasmic reticulum stress regulating ' - 'long noncoding RNA'], - 'chr': 'chr16', - 'end:long': 14331067, - 'entrez': '100129781', - 'gene_id': 'ENSG00000262454.4', - 'gene_type': 'lncRNA', - 'hgnc': 'HGNC:51945', - 'name': 'MIR193BHG', - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'start:long': 14301388, - 'version': 'v43'}, - 'logit_score': 0.49, - 'source': 'CoXPresdb', - 'source_url': 'https://coxpresdb.jp/'}, - {'gene': {'_key': 'ENSG00000237440', - 'alias': ['ZNF737', - 'zinc finger protein 737', - 'ZNF102', - 'zinc finger protein 102 (Y3)'], - 'chr': 'chr19', - 'end:long': 20565809, - 'entrez': '100129842', - 'gene_id': 'ENSG00000237440.9', - 'gene_type': 'protein_coding', - 'hgnc': 'HGNC:32468', - 'name': 'ZNF737', - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'start:long': 20535824, - 'version': 'v43'}, - 'logit_score': 0.68, - 'source': 'CoXPresdb', - 'source_url': 'https://coxpresdb.jp/'}, - {'gene': {'_key': 'ENSG00000224043', - 'alias': ['CCNT2 antisense RNA 1', 'CCNT2-AS1'], - 'chr': 'chr2', - 'end:long': 134918712, - 'entrez': '100129961', - 'gene_id': 'ENSG00000224043.9', - 'gene_type': 'lncRNA', - 'hgnc': 'HGNC:40130', - 'name': 'CCNT2-AS1', - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'start:long': 134735463, - 'version': 'v43'}, - 'logit_score': 0.69, - 'source': 'CoXPresdb', - 'source_url': 'https://coxpresdb.jp/'}, - {'gene': {'_key': 'ENSG00000094631', - 'alias': ['HD6', - 'histone deacetylase 6', - 'protein phosphatase 1, regulatory subunit 90', - 'PPP1R90', - 'HDAC6', - 'JM21', - 'CPBHM', - 'tubulin-lysine deacetylase HDAC6'], - 'chr': 'chrX', - 'end:long': 48824982, - 'entrez': '10013', - 'gene_id': 'ENSG00000094631.22', - 'gene_type': 'protein_coding', - 'hgnc': 'HGNC:14064', - 'name': 'HDAC6', - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'start:long': 48801376, - 'version': 'v43'}, - 'logit_score': 0.12, - 'source': 'CoXPresdb', - 'source_url': 'https://coxpresdb.jp/'}, - {'gene': {'_key': 'ENSG00000256802', - 'alias': ['LCIIAR', - 'lung cancer immune cell infiltration associated lncRNA'], - 'chr': 'chr15', - 'end:long': 29680957, - 'entrez': '100130111', - 'gene_id': 'ENSG00000256802.3', - 'gene_type': 'lncRNA', - 'hgnc': 'HGNC:56346', - 'name': 'ENSG00000256802', - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'start:long': 29674931, - 'version': 'v43'}, - 'logit_score': 0.77, - 'source': 'CoXPresdb', - 'source_url': 'https://coxpresdb.jp/'}, - {'gene': {'_key': 'ENSG00000223764', - 'alias': ['LINC02593', - 'long intergenic non-protein coding RNA 2593'], - 'chr': 'chr1', - 'end:long': 921016, - 'entrez': '100130417', - 'gene_id': 'ENSG00000223764.2', - 'gene_type': 'lncRNA', - 'hgnc': 'HGNC:53933', - 'name': 'LINC02593', - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'start:long': 916864, - 'version': 'v43'}, - 'logit_score': 0.67, - 'source': 'CoXPresdb', - 'source_url': 'https://coxpresdb.jp/'}, - {'gene': {'_key': 'ENSG00000213963', - 'alias': ['LOC100130691'], - 'chr': 'chr2', - 'end:long': 177392699, - 'entrez': '100130691', - 'gene_id': 'ENSG00000213963.7', - 'gene_type': 'lncRNA', - 'name': 'ENSG00000213963', - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'start:long': 177271124, - 'version': 'v43'}, - 'logit_score': 0.4, - 'source': 'CoXPresdb', - 'source_url': 'https://coxpresdb.jp/' - }] - }] -} diff --git a/tests/acceptance_tests/genes_proteins.py b/tests/acceptance_tests/genes_proteins.py deleted file mode 100644 index 7b1fbcd9..00000000 --- a/tests/acceptance_tests/genes_proteins.py +++ /dev/null @@ -1,234 +0,0 @@ -genes_proteins = { - '/genes/proteins': [{ - 'params': { - 'gene_name': 'ATF3', - 'gene_region': 'chr1:212565300-212620800', - 'alias': 'HGNC:785', - 'gene_type': 'protein_coding', - 'verbose': 'false' - }, - 'response': [ - { - '_id': 'P18847', - 'name': 'ATF3_HUMAN', - 'dbxrefs': [ - 'AGR:HGNC:785', - 'AlphaFoldDB:P18847', - 'Antibodypedia:658', - 'Bgee:ENSG00000162772', - 'BioGRID-ORCS:467', - 'BioGRID:106957', - 'BioMuta:ATF3', - 'CCDS:CCDS1506.1', - 'CCDS:CCDS41464.1', - 'CCDS:CCDS55688.1', - 'CCDS:CCDS58059.1', - 'CDD:cd14722', - 'ChiTaRS:ATF3', - 'ComplexPortal:CPX-6385', - 'ComplexPortal:CPX-6407', - 'ComplexPortal:CPX-6465', - 'ComplexPortal:CPX-6466', - 'ComplexPortal:CPX-6467', - 'ComplexPortal:CPX-6468', - 'ComplexPortal:CPX-6469', - 'ComplexPortal:CPX-6470', - 'ComplexPortal:CPX-6471', - 'ComplexPortal:CPX-6472', - 'ComplexPortal:CPX-6473', - 'ComplexPortal:CPX-6474', - 'ComplexPortal:CPX-6476', - 'ComplexPortal:CPX-6477', - 'ComplexPortal:CPX-6478', - 'ComplexPortal:CPX-6479', - 'ComplexPortal:CPX-6480', - 'ComplexPortal:CPX-6481', - 'CORUM:P18847', - 'CPTAC:CPTAC-1755', - 'CTD:467', - 'DIP:DIP-344N', - 'DisGeNET:467', - 'DMDM:1168543', - 'DNASU:467', - 'DrugBank:DB00852', - 'eggNOG:KOG1414', - 'EMBL:AAA20506.1', - 'EMBL:AAH06322.1', - 'EMBL:AAP35642.1', - 'EMBL:AAP93896.1', - 'EMBL:AAQ93358.1', - 'EMBL:AB066566', - 'EMBL:AB078026', - 'EMBL:AB078027', - 'EMBL:AC092803', - 'EMBL:AK312998', - 'EMBL:AL590648', - 'EMBL:AL606913', - 'EMBL:AY313927', - 'EMBL:AY426987', - 'EMBL:BAB84092.1', - 'EMBL:BAC00495.1', - 'EMBL:BAC00496.1', - 'EMBL:BAG35834.1', - 'EMBL:BC006322', - 'EMBL:BT006996', - 'EMBL:CAG29330.1', - 'EMBL:CH471100', - 'EMBL:CR450334', - 'EMBL:DA589280', - 'EMBL:EAW93385.1', - 'EMBL:EAW93386.1', - 'EMBL:EAW93387.1', - 'EMBL:EAW93388.1', - 'EMBL:L19871', - 'Ensembl:ENSG00000162772.17', - 'Ensembl:ENSP00000336908.4', - 'Ensembl:ENSP00000344352.4', - 'Ensembl:ENSP00000355950.1', - 'Ensembl:ENSP00000355954.2', - 'Ensembl:ENSP00000432208.1', - 'Ensembl:ENSP00000480606.1', - 'Ensembl:ENSP00000483576.1', - 'Ensembl:ENST00000336937.8', - 'Ensembl:ENST00000341491.9', - 'Ensembl:ENST00000366983.5', - 'Ensembl:ENST00000366987.6', - 'Ensembl:ENST00000464547.5', - 'Ensembl:ENST00000613104.1', - 'Ensembl:ENST00000613954.4', - 'EPD:P18847', - 'ExpressionAtlas:P18847', - 'Gene3D:1.20.5.170', - 'GeneCards:ATF3', - 'GeneID:467', - 'GeneTree:ENSGT00940000156376', - 'Genevisible:P18847', - 'GeneWiki:ATF3', - 'GenomeRNAi:467', - 'GlyGen:P18847', - 'GO:GO:0000122', - 'GO:GO:0000785', - 'GO:GO:0000976', - 'GO:GO:0000977', - 'GO:GO:0000978', - 'GO:GO:0000981', - 'GO:GO:0001227', - 'GO:GO:0001228', - 'GO:GO:0003700', - 'GO:GO:0005634', - 'GO:GO:0005654', - 'GO:GO:0005730', - 'GO:GO:0006094', - 'GO:GO:0006357', - 'GO:GO:0008284', - 'GO:GO:0010628', - 'GO:GO:0030968', - 'GO:GO:0034198', - 'GO:GO:0035914', - 'GO:GO:0042802', - 'GO:GO:0042803', - 'GO:GO:0045944', - 'GO:GO:0046982', - 'GO:GO:0061394', - 'GO:GO:0070373', - 'GO:GO:0090575', - 'GO:GO:1903984', - 'GO:GO:1990440', - 'GO:GO:1990622', - 'GO:GO:1990837', - 'HGNC:HGNC:785', - 'HOGENOM:CLU_088612_0_2_1', - 'HPA:ENSG00000162772', - 'InParanoid:P18847', - 'IntAct:P18847', - 'InterPro:IPR000837', - 'InterPro:IPR004827', - 'InterPro:IPR046347', - 'iPTMnet:P18847', - 'jPOST:P18847', - 'KEGG:hsa:467', - 'MANE-Select:ENSP00000344352.4', - 'MANE-Select:ENST00000341491.9', - 'MANE-Select:NM_001674.4', - 'MANE-Select:NP_001665.1', - 'MassIVE:P18847', - 'MaxQB:P18847', - 'MIM:603148', - 'MINT:P18847', - 'neXtProt:NX_P18847', - 'OMA:LEMSVMK', - 'OpenTargets:ENSG00000162772', - 'OrthoDB:5354319at2759', - 'PANTHER:PTHR23351', - 'PANTHER:PTHR23351:SF23', - 'PathwayCommons:P18847', - 'PaxDb:P18847', - 'PeptideAtlas:P18847', - 'Pfam:PF00170', - 'PharmGKB:PA25085', - 'Pharos:P18847', - 'PhosphoSitePlus:P18847', - 'PhylomeDB:P18847', - 'PIR:A54025', - 'PIR:B54025', - 'PIR:C34223', - 'PRINTS:PR00042', - 'PRO:PR:P18847', - 'PROSITE:PS00036', - 'PROSITE:PS50217', - 'Proteomes:UP000005640', - 'ProteomicsDB:53611', - 'ProteomicsDB:53612', - 'ProteomicsDB:53613', - 'ProteomicsDB:53614', - 'ProteomicsDB:65367', - 'Reactome:R-HSA-380994', - 'Reactome:R-HSA-9633012', - 'Reactome:R-HSA-9648895', - 'RefSeq:NM_001030287.3', - 'RefSeq:NM_001040619.2', - 'RefSeq:NM_001206484.2', - 'RefSeq:NM_001206486.2', - 'RefSeq:NM_001206488.2', - 'RefSeq:NM_001674.3', - 'RefSeq:NP_001025458.1', - 'RefSeq:NP_001035709.1', - 'RefSeq:NP_001193413.2', - 'RefSeq:NP_001193415.1', - 'RefSeq:NP_001193417.2', - 'RefSeq:NP_001665.1', - 'RefSeq:XM_005273146.1', - 'RefSeq:XM_011509579.1', - 'RefSeq:XP_005273203.1', - 'RefSeq:XP_011507881.1', - 'RNAct:P18847', - 'SignaLink:P18847', - 'SIGNOR:P18847', - 'SMART:SM00338', - 'SMR:P18847', - 'STRING:9606.ENSP00000344352', - 'SUPFAM:SSF57959', - 'TopDownProteomics:P18847-1', - 'TreeFam:TF326301', - 'UCSC:uc001hjf.4', - 'VEuPathDB:HostDB:ENSG00000162772' - ], - 'source': 'UniProtKB/Swiss-Prot', - 'source_url': 'https://www.uniprot.org/help/downloads' - } - ] - }], - '/genes/proteins': [{ - 'params': { - 'gene_id': 'ENSG00000187642' - }, - 'response': [{ - '_id': 'Q5SV97', - 'name': 'PERM1_HUMAN', - 'full_name': 'PGC-1 and ERR-induced regulator in muscle protein 1', - 'dbxrefs': [{'name': 'AGR', 'id': 'HGNC:28208'}, {'name': 'AlphaFoldDB', 'id': 'Q5SV97'}, {'name': 'Antibodypedia', 'id': '51128'}, {'name': 'Bgee', 'id': 'ENSG00000187642'}, {'name': 'BioGRID', 'id': '124270'}, {'name': 'BioGRID-ORCS', 'id': '84808'}, {'name': 'BioMuta', 'id': 'PERM1'}, {'name': 'CCDS', 'id': 'CCDS76083.1'}, {'name': 'CCDS', 'id': 'CCDS90836.1'}, {'name': 'CTD', 'id': '84808'}, {'name': 'ChiTaRS', 'id': 'PERM1'}, {'name': 'DMDM', 'id': '158563938'}, {'name': 'DNASU', 'id': '84808'}, {'name': 'DisGeNET', 'id': '84808'}, {'name': 'EMBL', 'id': 'KF150175'}, {'name': 'EMBL', 'id': 'AGQ48858.1'}, {'name': 'EMBL', 'id': 'AK123855'}, {'name': 'EMBL', 'id': 'BAC85711.1'}, {'name': 'EMBL', 'id': 'AL645608'}, {'name': 'EMBL', 'id': 'BC006300'}, {'name': 'EMBL', 'id': 'AAH06300.1'}, {'name': 'Ensembl', 'id': 'ENST00000341290.6'}, {'name': 'Ensembl', 'id': 'ENSP00000343864.2'}, {'name': 'Ensembl', 'id': 'ENSG00000187642.10'}, {'name': 'Ensembl', 'id': 'ENST00000433179.4'}, {'name': 'Ensembl', 'id': 'ENSP00000414022.3'}, {'name': 'Ensembl', 'id': 'ENSG00000187642.10'}, {'name': 'Ensembl', 'id': 'ENST00000694917.1'}, {'name': 'Ensembl', 'id': 'ENSP00000511592.1'}, {'name': 'Ensembl', 'id': 'ENSG00000187642.10'}, {'name': 'GO', 'id': 'GO:0005737'}, {'name': 'GO', 'id': 'GO:0005634'}, {'name': 'GO', 'id': 'GO:0006355'}, {'name': 'GO', 'id': 'GO:0014850'}, {'name': 'GeneCards', 'id': 'PERM1'}, {'name': 'GeneID', 'id': '84808'}, {'name': 'GeneTree', 'id': 'ENSGT00390000017652'}, {'name': 'Genevisible', 'id': 'Q5SV97'}, {'name': 'GenomeRNAi', 'id': '84808'}, {'name': 'HGNC', 'id': 'HGNC:28208'}, {'name': 'HOGENOM', 'id': 'CLU_015049_1_0_1'}, {'name': 'HPA', 'id': 'ENSG00000187642'}, {'name': 'InParanoid', 'id': 'Q5SV97'}, {'name': 'IntAct', 'id': 'Q5SV97'}, {'name': 'InterPro', 'id': 'IPR043442'}, {'name': 'KEGG', 'id': 'hsa:84808'}, {'name': 'MANE-Select', 'id': 'ENST00000433179.4'}, {'name': 'MANE-Select', 'id': 'ENSP00000414022.3'}, {'name': 'MANE-Select', 'id': 'NM_001394713.1'}, {'name': 'MANE-Select', 'id': 'NP_001381642.1'}, {'name': 'MIM', 'id': '615921'}, {'name': 'MassIVE', 'id': 'Q5SV97'}, {'name': 'OMA', 'id': 'EVQWPDT'}, {'name': 'OpenTargets', 'id': 'ENSG00000187642'}, {'name': 'OrthoDB', 'id': '4268376at2759'}, {'name': 'PANTHER', 'id': 'PTHR47282'}, {'name': 'PANTHER', 'id': 'PTHR47282:SF1'}, {'name': 'PRO', 'id': 'PR:Q5SV97'}, {'name': 'PathwayCommons', 'id': 'Q5SV97'}, {'name': 'PaxDb', 'id': 'Q5SV97'}, {'name': 'PeptideAtlas', 'id': 'Q5SV97'}, {'name': 'Pharos', 'id': 'Q5SV97'}, {'name': 'PhosphoSitePlus', 'id': 'Q5SV97'}, {'name': 'Proteomes', 'id': 'UP000005640'}, {'name': 'ProteomicsDB', 'id': '63932'}, {'name': 'ProteomicsDB', 'id': '63933'}, {'name': 'RNAct', 'id': 'Q5SV97'}, {'name': 'Reactome', 'id': 'R-HSA-2151201'}, {'name': 'RefSeq', 'id': 'NP_001278295.1'}, {'name': 'RefSeq', 'id': 'NM_001291366.1'}, {'name': 'RefSeq', 'id': 'NP_001278296.1'}, {'name': 'RefSeq', 'id': 'NM_001291367.1'}, {'name': 'RefSeq', 'id': 'XP_016858072.1'}, {'name': 'RefSeq', 'id': 'XM_017002583.1'}, {'name': 'RefSeq', 'id': 'XP_016858073.1'}, {'name': 'RefSeq', 'id': 'XM_017002584.1'}, {'name': 'STRING', 'id': '9606.ENSP00000414022'}, {'name': 'TreeFam', 'id': 'TF338365'}, {'name': 'UCSC', 'id': 'uc001ach.3'}, {'name': 'VEuPathDB', 'id': 'HostDB:ENSG00000187642'}, {'name': 'eggNOG', 'id': 'ENOG502RYI7'}, {'name': 'iPTMnet', 'id': 'Q5SV97'}, {'name': 'neXtProt', 'id': 'NX_Q5SV97'}], - 'source': 'UniProtKB/Swiss-Prot', - 'source_url': 'https://www.uniprot.org/help/downloads' - }] - }] -} diff --git a/tests/acceptance_tests/genes_regulatory_regions.py b/tests/acceptance_tests/genes_regulatory_regions.py deleted file mode 100644 index c83504b8..00000000 --- a/tests/acceptance_tests/genes_regulatory_regions.py +++ /dev/null @@ -1,677 +0,0 @@ -genes_regulatory_regions = { - '/genes/regulatory_regions': [{ - 'params': { - 'gene_id': 'ENSG00000187634', - 'gene_name': 'SAMD11', - 'region': 'chr1:923900-924900', - 'gene_type': 'protein_coding', - 'alias': 'MRS', - 'source': 'ENCODE-E2G-DNaseOnly', - 'verbose': 'true' - }, - 'response': [ - { - 'term_name': 'nci-h226', - 'score': 0.25304072686060236, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF712UPR/', - 'regulatory region': [ - { - 'chr': 'chr1', - 'start': 1023573, - 'end': 1025047, - 'name': 'genic_chr1_1023573_1025047_GRCh38', - 'biochemical_activity': 'ENH', - 'biochemical_activity_description': 'genic enhancer', - 'type': 'candidate_cis_regulatory_element', - 'source': 'ENCODE-E2G', - 'source_url': 'https://www.encodeproject.org/annotations/ENCSR361ATY/' - } - ] - }, - { - 'term_name': 'ht-29', - 'score': 0.2850190760899295, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF693AEC/', - 'regulatory region': [ - { - 'chr': 'chr1', - 'start': 1023587, - 'end': 1025020, - 'name': 'genic_chr1_1023587_1025020_GRCh38', - 'biochemical_activity': 'ENH', - 'biochemical_activity_description': 'genic enhancer', - 'type': 'candidate_cis_regulatory_element', - 'source': 'ENCODE-E2G', - 'source_url': 'https://www.encodeproject.org/annotations/ENCSR602YDS/' - } - ] - }, - { - 'term_name': None, - 'score': 0.2041189148997833, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF462MWS/', - 'regulatory region': [ - { - 'chr': 'chr1', - 'start': 1032165, - 'end': 1034368, - 'name': 'genic_chr1_1032165_1034368_GRCh38', - 'biochemical_activity': 'ENH', - 'biochemical_activity_description': 'genic enhancer', - 'type': 'candidate_cis_regulatory_element', - 'source': 'ENCODE-E2G', - 'source_url': 'https://www.encodeproject.org/annotations/ENCSR295YAP/' - } - ] - }, - { - 'term_name': 'gm25256', - 'score': 0.20927402267574963, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF011LTM/', - 'regulatory region': [ - { - 'chr': 'chr1', - 'start': 1032856, - 'end': 1035584, - 'name': 'genic_chr1_1032856_1035584_GRCh38', - 'biochemical_activity': 'ENH', - 'biochemical_activity_description': 'genic enhancer', - 'type': 'candidate_cis_regulatory_element', - 'source': 'ENCODE-E2G', - 'source_url': 'https://www.encodeproject.org/annotations/ENCSR109MQQ/' - } - ] - }, - { - 'term_name': 'gm20000', - 'score': 0.20842470474832037, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF160KXF/', - 'regulatory region': [ - { - 'chr': 'chr1', - 'start': 1032905, - 'end': 1033405, - 'name': 'genic_chr1_1032905_1033405_GRCh38', - 'biochemical_activity': 'ENH', - 'biochemical_activity_description': 'genic enhancer', - 'type': 'candidate_cis_regulatory_element', - 'source': 'ENCODE-E2G', - 'source_url': 'https://www.encodeproject.org/annotations/ENCSR644SVV/' - } - ] - }, - { - 'term_name': None, - 'score': 0.21031952107886565, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF881UNU/', - 'regulatory region': [ - { - 'chr': 'chr1', - 'start': 1032924, - 'end': 1033761, - 'name': 'genic_chr1_1032924_1033761_GRCh38', - 'biochemical_activity': 'ENH', - 'biochemical_activity_description': 'genic enhancer', - 'type': 'candidate_cis_regulatory_element', - 'source': 'ENCODE-E2G', - 'source_url': 'https://www.encodeproject.org/annotations/ENCSR863DXW/' - } - ] - }, - { - 'term_name': None, - 'score': 0.21310100557076692, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF403AVZ/', - 'regulatory region': [ - { - 'chr': 'chr1', - 'start': 1032932, - 'end': 1033432, - 'name': 'genic_chr1_1032932_1033432_GRCh38', - 'biochemical_activity': 'ENH', - 'biochemical_activity_description': 'genic enhancer', - 'type': 'candidate_cis_regulatory_element', - 'source': 'ENCODE-E2G', - 'source_url': 'https://www.encodeproject.org/annotations/ENCSR305UEE/' - } - ] - }, - { - 'term_name': 'gm20000', - 'score': 0.21467353312732756, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF160KXF/', - 'regulatory region': [ - { - 'chr': 'chr1', - 'start': 1040665, - 'end': 1041165, - 'name': 'genic_chr1_1040665_1041165_GRCh38', - 'biochemical_activity': 'ENH', - 'biochemical_activity_description': 'genic enhancer', - 'type': 'candidate_cis_regulatory_element', - 'source': 'ENCODE-E2G', - 'source_url': 'https://www.encodeproject.org/annotations/ENCSR644SVV/' - } - ] - }, - { - 'term_name': 'gm13977', - 'score': 0.219349147066961, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF867ZSX/', - 'regulatory region': [ - { - 'chr': 'chr1', - 'start': 1040665, - 'end': 1041165, - 'name': 'genic_chr1_1040665_1041165_GRCh38', - 'biochemical_activity': 'ENH', - 'biochemical_activity_description': 'genic enhancer', - 'type': 'candidate_cis_regulatory_element', - 'source': 'ENCODE-E2G', - 'source_url': 'https://www.encodeproject.org/annotations/ENCSR644SVV/' - } - ] - }, - { - 'term_name': 'chondrocyte', - 'score': 0.21673271109623832, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF891XJU/', - 'regulatory region': [ - { - 'chr': 'chr1', - 'start': 1079259, - 'end': 1083327, - 'name': 'genic_chr1_1079259_1083327_GRCh38', - 'biochemical_activity': 'ENH', - 'biochemical_activity_description': 'genic enhancer', - 'type': 'candidate_cis_regulatory_element', - 'source': 'ENCODE-E2G', - 'source_url': 'https://www.encodeproject.org/annotations/ENCSR886VNW/' - } - ] - }, - { - 'term_name': None, - 'score': 0.28577423069253277, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF281GMW/', - 'regulatory region': [ - { - 'chr': 'chr1', - 'start': 869491, - 'end': 870177, - 'name': 'genic_chr1_869491_870177_GRCh38', - 'biochemical_activity': 'ENH', - 'biochemical_activity_description': 'genic enhancer', - 'type': 'candidate_cis_regulatory_element', - 'source': 'ENCODE-E2G', - 'source_url': 'https://www.encodeproject.org/annotations/ENCSR929SQR/' - } - ] - }, - { - 'term_name': 't-helper 22 cell', - 'score': 0.20220709734346864, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF109SPE/', - 'regulatory region': [ - { - 'chr': 'chr1', - 'start': 869594, - 'end': 870094, - 'name': 'genic_chr1_869594_870094_GRCh38', - 'biochemical_activity': 'ENH', - 'biochemical_activity_description': 'genic enhancer', - 'type': 'candidate_cis_regulatory_element', - 'source': 'ENCODE-E2G', - 'source_url': 'https://www.encodeproject.org/annotations/ENCSR284CNU/' - } - ] - }, - { - 'term_name': None, - 'score': 0.2118945661827181, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF616RIA/', - 'regulatory region': [ - { - 'chr': 'chr1', - 'start': 869594, - 'end': 870094, - 'name': 'genic_chr1_869594_870094_GRCh38', - 'biochemical_activity': 'ENH', - 'biochemical_activity_description': 'genic enhancer', - 'type': 'candidate_cis_regulatory_element', - 'source': 'ENCODE-E2G', - 'source_url': 'https://www.encodeproject.org/annotations/ENCSR284CNU/' - } - ] - }, - { - 'term_name': None, - 'score': 0.22262478068252856, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF071HFX/', - 'regulatory region': [ - { - 'chr': 'chr1', - 'start': 869596, - 'end': 870413, - 'name': 'genic_chr1_869596_870413_GRCh38', - 'biochemical_activity': 'ENH', - 'biochemical_activity_description': 'genic enhancer', - 'type': 'candidate_cis_regulatory_element', - 'source': 'ENCODE-E2G', - 'source_url': 'https://www.encodeproject.org/annotations/ENCSR028HBN/' - } - ] - }, - { - 'term_name': 'naive b cell', - 'score': 0.35623470301452503, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF283NCL/', - 'regulatory region': [ - { - 'chr': 'chr1', - 'start': 869625, - 'end': 870125, - 'name': 'genic_chr1_869625_870125_GRCh38', - 'biochemical_activity': 'ENH', - 'biochemical_activity_description': 'genic enhancer', - 'type': 'candidate_cis_regulatory_element', - 'source': 'ENCODE-E2G', - 'source_url': 'https://www.encodeproject.org/annotations/ENCSR926IPQ/' - } - ] - }, - { - 'term_name': 'germinal center', - 'score': 0.29426311002068933, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF803JTD/', - 'regulatory region': [ - { - 'chr': 'chr1', - 'start': 869625, - 'end': 870125, - 'name': 'genic_chr1_869625_870125_GRCh38', - 'biochemical_activity': 'ENH', - 'biochemical_activity_description': 'genic enhancer', - 'type': 'candidate_cis_regulatory_element', - 'source': 'ENCODE-E2G', - 'source_url': 'https://www.encodeproject.org/annotations/ENCSR926IPQ/' - } - ] - }, - { - 'term_name': 'memory b cell', - 'score': 0.22153772383222073, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF023QMI/', - 'regulatory region': [ - { - 'chr': 'chr1', - 'start': 869673, - 'end': 870173, - 'name': 'genic_chr1_869673_870173_GRCh38', - 'biochemical_activity': 'ENH', - 'biochemical_activity_description': 'genic enhancer', - 'type': 'candidate_cis_regulatory_element', - 'source': 'ENCODE-E2G', - 'source_url': 'https://www.encodeproject.org/annotations/ENCSR633LTE/' - } - ] - }, - { - 'term_name': 'gm12892', - 'score': 0.3835596404476509, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF374TXD/', - 'regulatory region': [ - { - 'chr': 'chr1', - 'start': 915988, - 'end': 916951, - 'name': 'genic_chr1_915988_916951_GRCh38', - 'biochemical_activity': 'ENH', - 'biochemical_activity_description': 'genic enhancer', - 'type': 'candidate_cis_regulatory_element', - 'source': 'ENCODE-E2G', - 'source_url': 'https://www.encodeproject.org/annotations/ENCSR524HTB/' - } - ] - }, - { - 'term_name': 'posterior vena cava', - 'score': 0.6098183765709317, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF151KHP/', - 'regulatory region': [ - { - 'chr': 'chr1', - 'start': 915993, - 'end': 917206, - 'name': 'genic_chr1_915993_917206_GRCh38', - 'biochemical_activity': 'ENH', - 'biochemical_activity_description': 'genic enhancer', - 'type': 'candidate_cis_regulatory_element', - 'source': 'ENCODE-E2G', - 'source_url': 'https://www.encodeproject.org/annotations/ENCSR163EFB/' - } - ] - }, - { - 'term_name': 'limb', - 'score': 0.6935212963919393, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF302WSW/', - 'regulatory region': [ - { - 'chr': 'chr1', - 'start': 916041, - 'end': 917553, - 'name': 'genic_chr1_916041_917553_GRCh38', - 'biochemical_activity': 'ENH', - 'biochemical_activity_description': 'genic enhancer', - 'type': 'candidate_cis_regulatory_element', - 'source': 'ENCODE-E2G', - 'source_url': 'https://www.encodeproject.org/annotations/ENCSR866MNS/' - } - ] - }, - { - 'term_name': 'ascending aorta', - 'score': 0.6101957581060062, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF409CKM/', - 'regulatory region': [ - { - 'chr': 'chr1', - 'start': 916133, - 'end': 916882, - 'name': 'genic_chr1_916133_916882_GRCh38', - 'biochemical_activity': 'ENH', - 'biochemical_activity_description': 'genic enhancer', - 'type': 'candidate_cis_regulatory_element', - 'source': 'ENCODE-E2G', - 'source_url': 'https://www.encodeproject.org/annotations/ENCSR011QXR/' - } - ] - }, - { - 'term_name': 'kidney', - 'score': 0.8538844756859066, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF122CVV/', - 'regulatory region': [ - { - 'chr': 'chr1', - 'start': 916157, - 'end': 917905, - 'name': 'genic_chr1_916157_917905_GRCh38', - 'biochemical_activity': 'ENH', - 'biochemical_activity_description': 'genic enhancer', - 'type': 'candidate_cis_regulatory_element', - 'source': 'ENCODE-E2G', - 'source_url': 'https://www.encodeproject.org/annotations/ENCSR820LHU/' - } - ] - }, - { - 'term_name': 'be(2)-c', - 'score': 0.886270288216963, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF031XQO/', - 'regulatory region': [ - { - 'chr': 'chr1', - 'start': 916271, - 'end': 917582, - 'name': 'genic_chr1_916271_917582_GRCh38', - 'biochemical_activity': 'ENH', - 'biochemical_activity_description': 'genic enhancer', - 'type': 'candidate_cis_regulatory_element', - 'source': 'ENCODE-E2G', - 'source_url': 'https://www.encodeproject.org/annotations/ENCSR783XUD/' - } - ] - }, - { - 'term_name': 'right kidney', - 'score': 0.874505811202448, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF651NOZ/', - 'regulatory region': [ - { - 'chr': 'chr1', - 'start': 916328, - 'end': 917441, - 'name': 'genic_chr1_916328_917441_GRCh38', - 'biochemical_activity': 'ENH', - 'biochemical_activity_description': 'genic enhancer', - 'type': 'candidate_cis_regulatory_element', - 'source': 'ENCODE-E2G', - 'source_url': 'https://www.encodeproject.org/annotations/ENCSR071DLS/' - } - ] - }, - { - 'term_name': 'left renal cortex interstitium', - 'score': 0.9428891883369912, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF346PHP/', - 'regulatory region': [ - { - 'chr': 'chr1', - 'start': 916339, - 'end': 917814, - 'name': 'genic_chr1_916339_917814_GRCh38', - 'biochemical_activity': 'ENH', - 'biochemical_activity_description': 'genic enhancer', - 'type': 'candidate_cis_regulatory_element', - 'source': 'ENCODE-E2G', - 'source_url': 'https://www.encodeproject.org/annotations/ENCSR355KXS/' - } - ] - } - ] - }, { - 'params': { - 'gene_id': 'ENSG00000187634', - 'gene_name': 'SAMD11', - 'region': 'chr1:923900-924900', - 'gene_type': 'protein_coding', - 'alias': 'MRS', - 'source': 'ENCODE-E2G-DNaseOnly', - 'verbose': 'false' - }, - 'response': [ - { - 'term_name': 'nci-h226', - 'score': 0.25304072686060236, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF712UPR/', - 'regulatory region': 'regulatory_regions/genic_chr1_1023573_1025047_GRCh38' - }, - { - 'term_name': 'ht-29', - 'score': 0.2850190760899295, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF693AEC/', - 'regulatory region': 'regulatory_regions/genic_chr1_1023587_1025020_GRCh38' - }, - { - 'term_name': None, - 'score': 0.2041189148997833, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF462MWS/', - 'regulatory region': 'regulatory_regions/genic_chr1_1032165_1034368_GRCh38' - }, - { - 'term_name': 'gm25256', - 'score': 0.20927402267574963, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF011LTM/', - 'regulatory region': 'regulatory_regions/genic_chr1_1032856_1035584_GRCh38' - }, - { - 'term_name': 'gm20000', - 'score': 0.20842470474832037, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF160KXF/', - 'regulatory region': 'regulatory_regions/genic_chr1_1032905_1033405_GRCh38' - }, - { - 'term_name': None, - 'score': 0.21031952107886565, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF881UNU/', - 'regulatory region': 'regulatory_regions/genic_chr1_1032924_1033761_GRCh38' - }, - { - 'term_name': None, - 'score': 0.21310100557076692, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF403AVZ/', - 'regulatory region': 'regulatory_regions/genic_chr1_1032932_1033432_GRCh38' - }, - { - 'term_name': 'gm20000', - 'score': 0.21467353312732756, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF160KXF/', - 'regulatory region': 'regulatory_regions/genic_chr1_1040665_1041165_GRCh38' - }, - { - 'term_name': 'gm13977', - 'score': 0.219349147066961, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF867ZSX/', - 'regulatory region': 'regulatory_regions/genic_chr1_1040665_1041165_GRCh38' - }, - { - 'term_name': 'chondrocyte', - 'score': 0.21673271109623832, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF891XJU/', - 'regulatory region': 'regulatory_regions/genic_chr1_1079259_1083327_GRCh38' - }, - { - 'term_name': None, - 'score': 0.28577423069253277, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF281GMW/', - 'regulatory region': 'regulatory_regions/genic_chr1_869491_870177_GRCh38' - }, - { - 'term_name': 't-helper 22 cell', - 'score': 0.20220709734346864, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF109SPE/', - 'regulatory region': 'regulatory_regions/genic_chr1_869594_870094_GRCh38' - }, - { - 'term_name': None, - 'score': 0.2118945661827181, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF616RIA/', - 'regulatory region': 'regulatory_regions/genic_chr1_869594_870094_GRCh38' - }, - { - 'term_name': None, - 'score': 0.22262478068252856, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF071HFX/', - 'regulatory region': 'regulatory_regions/genic_chr1_869596_870413_GRCh38' - }, - { - 'term_name': 'naive b cell', - 'score': 0.35623470301452503, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF283NCL/', - 'regulatory region': 'regulatory_regions/genic_chr1_869625_870125_GRCh38' - }, - { - 'term_name': 'germinal center', - 'score': 0.29426311002068933, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF803JTD/', - 'regulatory region': 'regulatory_regions/genic_chr1_869625_870125_GRCh38' - }, - { - 'term_name': 'memory b cell', - 'score': 0.22153772383222073, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF023QMI/', - 'regulatory region': 'regulatory_regions/genic_chr1_869673_870173_GRCh38' - }, - { - 'term_name': 'gm12892', - 'score': 0.3835596404476509, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF374TXD/', - 'regulatory region': 'regulatory_regions/genic_chr1_915988_916951_GRCh38' - }, - { - 'term_name': 'posterior vena cava', - 'score': 0.6098183765709317, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF151KHP/', - 'regulatory region': 'regulatory_regions/genic_chr1_915993_917206_GRCh38' - }, - { - 'term_name': 'limb', - 'score': 0.6935212963919393, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF302WSW/', - 'regulatory region': 'regulatory_regions/genic_chr1_916041_917553_GRCh38' - }, - { - 'term_name': 'ascending aorta', - 'score': 0.6101957581060062, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF409CKM/', - 'regulatory region': 'regulatory_regions/genic_chr1_916133_916882_GRCh38' - }, - { - 'term_name': 'kidney', - 'score': 0.8538844756859066, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF122CVV/', - 'regulatory region': 'regulatory_regions/genic_chr1_916157_917905_GRCh38' - }, - { - 'term_name': 'be(2)-c', - 'score': 0.886270288216963, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF031XQO/', - 'regulatory region': 'regulatory_regions/genic_chr1_916271_917582_GRCh38' - }, - { - 'term_name': 'right kidney', - 'score': 0.874505811202448, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF651NOZ/', - 'regulatory region': 'regulatory_regions/genic_chr1_916328_917441_GRCh38' - }, - { - 'term_name': 'left renal cortex interstitium', - 'score': 0.9428891883369912, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF346PHP/', - 'regulatory region': 'regulatory_regions/genic_chr1_916339_917814_GRCh38' - } - ] - }] -} diff --git a/tests/acceptance_tests/genes_variants.py b/tests/acceptance_tests/genes_variants.py deleted file mode 100644 index f233cf39..00000000 --- a/tests/acceptance_tests/genes_variants.py +++ /dev/null @@ -1,4862 +0,0 @@ -genes_variants = { - '/genes/variants': [{ - 'params': { - 'gene_id': 'ENSG00000187642', - 'p_value': 'lt:0.00001', - 'verbose': 'false' - }, - 'response': [ - { - 'sequence variant': 'variants/9386dd3a5b27f4631a7ad5e464d2e64947ebc71d241c73ffc34251f9940ea231', - 'gene': 'genes/ENSG00000187642', - 'beta': 9.59363e-9, - 'label': 'splice_QTL', - 'log10pvalue': 5.125459623174361, - 'slope': 0.369677, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'right atrium auricular region', - 'chr': 'chr1' - }, - { - 'sequence variant': 'variants/1600f5f4534ca9b49fc32656e238d33035b488450e85fc9b08b0007be96c1761', - 'gene': 'genes/ENSG00000187642', - 'beta': 1.88772e-11, - 'label': 'eQTL', - 'log10pvalue': 7.942794294438085, - 'slope': -0.513867, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'sigmoid colon', - 'chr': 'chr1' - }, - { - 'sequence variant': 'variants/b33df1a4583e39d388ab082341f0d7ec80553ad11f2a8ce207e1216279c10271', - 'gene': 'genes/ENSG00000187642', - 'beta': 3.21634e-32, - 'label': 'splice_QTL', - 'log10pvalue': 8.41357024003359, - 'slope': 0.282577, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'gastrocnemius medialis', - 'chr': 'chr1' - }, - { - 'sequence variant': 'variants/789de7331f2bec144e8f5e033fe6130dfdf21cebabaf49bf6e42013eede0945c', - 'gene': 'genes/ENSG00000187642', - 'beta': 0.00178975, - 'label': 'eQTL', - 'log10pvalue': 4.4849478556355855, - 'slope': 1.62954, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'caudate nucleus', - 'chr': 'chr1' - }, - { - 'sequence variant': 'variants/28bd5b04dbc9665c81462e94b63650ce25d41b13f3f519a62e3986dacceaaa44', - 'gene': 'genes/ENSG00000187642', - 'beta': 1.92358e-18, - 'label': 'eQTL', - 'log10pvalue': 8.09172359980412, - 'slope': 0.414658, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'gastroesophageal sphincter', - 'chr': 'chr1' - }, - { - 'sequence variant': 'variants/8265a41dcf836fc0b6b506a93b4d1c171339384db0a08122891360150f637d2a', - 'gene': 'genes/ENSG00000187642', - 'beta': 6.21017e-16, - 'label': 'eQTL', - 'log10pvalue': 4.581211643823275, - 'slope': 0.26558, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'esophagus muscularis mucosa', - 'chr': 'chr1' - }, - { - 'sequence variant': 'variants/dcaa5f2b3204d178c6295716e9373cc37b0eb9e69dc0d1ac1a295fc896105530', - 'gene': 'genes/ENSG00000187642', - 'beta': 8.02765e-24, - 'label': 'eQTL', - 'log10pvalue': 7.606251113671948, - 'slope': -0.608183, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'testis', - 'chr': 'chr1' - }, - { - 'sequence variant': 'variants/8b83112e918c4408b9499561d72573b0c54f9deaf4a37bb5e6cd763d8a86d07a', - 'gene': 'genes/ENSG00000187642', - 'beta': 3.21634e-32, - 'label': 'splice_QTL', - 'log10pvalue': 17.562904542779403, - 'slope': 0.543051, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'gastrocnemius medialis', - 'chr': 'chr1' - }, - { - 'sequence variant': 'variants/3c9aeef0562f70801a1f3e262c8e48603c0927fda6241e58d9852d71cdec0285', - 'gene': 'genes/ENSG00000187642', - 'beta': 0.00000761937, - 'label': 'splice_QTL', - 'log10pvalue': 6.31760850208729, - 'slope': 0.224428, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'left ventricle myocardium', - 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'chr': 'chr1' - }, - { - 'sequence variant': { - '_id': 'def9b31b7df14de99deeac209cee089e92107d6489d75c3b2f153276503bb186', - 'chr': 'chr1', - 'pos': 962357, - 'rsid': [ - 'rs6696971' - ], - 'ref': 'C', - 'alt': 'T', - 'spdi': 'NC_000001.11:962357:C:T', - 'hgvs': 'NC_000001.11:g.962358C>T', - 'qual': '.', - 'filter': None, - 'format': 'SNV;FAVORFullDB/genecode_comprehensive_exonic_info=KLHL17:ENST00000338591.8:exon5:c.C715T:p.L239L,;FAVORFullDB/af_total=0.102297;FAVORFullDB/af_asj_female=0.0756542;FAVORFullDB/af_eas_female=0.0759669;FAVORFullDB/af_afr_male=0.182878;FAVORFullDB/af_female=0.102454;FAVORFullDB/af_fin_male=0.060241;FAVORFullDB/af_oth_female=0.107273;FAVORFullDB/af_ami=0.12;FAVORFullDB/af_oth=0.0979573;FAVORFullDB/af_male=0.10213;FAVORFullDB/af_ami_female=0.110638;FAVORFullDB/af_afr=0.183228;FAVORFullDB/af_eas_male=0.0832342;FAVORFullDB/af_sas=0.0804334;FAVORFullDB/af_nfe_female=0.0627173;FAVORFullDB/af_asj_male=0.0864277;FAVORFullDB/af_raw=0.102486;FAVORFullDB/af_oth_male=0.0882353;FAVORFullDB/af_nfe_male=0.0658079;FAVORFullDB/af_asj=0.0807229;FAVORFullDB/af_amr_male=0.086109;FAVORFullDB/af_amr_female=0.0772743;FAVORFullDB/af_sas_female=0.0833333;FAVORFullDB/af_fin=0.0591942;FAVORFullDB/af_afr_female=0.183526;FAVORFullDB/af_sas_male=0.0797744;FAVORFullDB/af_amr=0.082284;FAVORFullDB/af_nfe=0.064018;FAVORFullDB/af_eas=0.0798722;FAVORFullDB/af_ami_male=0.130233;FAVORFullDB/af_fin_female=0.0558659;FAVORFullDB/linsight=0.214926;FAVORFullDB/gc=0.616;FAVORFullDB/cpg=0.053;FAVORFullDB/min_dist_tss=370;FAVORFullDB/min_dist_tse=121;FAVORFullDB/priphcons=0.4;FAVORFullDB/mamphcons=1;FAVORFullDB/verphcons=1;FAVORFullDB/priphylop=0.418;FAVORFullDB/mamphylop=2.859;FAVORFullDB/verphylop=2.912;FAVORFullDB/bstatistic=923;FAVORFullDB/chmm_e1=1;FAVORFullDB/chmm_e2=0;FAVORFullDB/chmm_e3=0;FAVORFullDB/chmm_e4=0;FAVORFullDB/chmm_e5=0;FAVORFullDB/chmm_e6=3;FAVORFullDB/chmm_e7=9;FAVORFullDB/chmm_e8=10;FAVORFullDB/chmm_e9=1;FAVORFullDB/chmm_e10=0;FAVORFullDB/chmm_e11=3;FAVORFullDB/chmm_e12=1;FAVORFullDB/chmm_e13=0;FAVORFullDB/chmm_e14=0;FAVORFullDB/chmm_e15=11;FAVORFullDB/chmm_e16=0;FAVORFullDB/chmm_e17=0;FAVORFullDB/chmm_e18=0;FAVORFullDB/chmm_e19=0;FAVORFullDB/chmm_e20=1;FAVORFullDB/chmm_e21=2;FAVORFullDB/chmm_e22=0;FAVORFullDB/chmm_e23=4;FAVORFullDB/chmm_e24=2;FAVORFullDB/chmm_e25=0;FAVORFullDB/gerp_rs=379.698;FAVORFullDB/gerp_rs_pval=0;FAVORFullDB/gerp_n=19.5;FAVORFullDB/gerp_s=3.8;FAVORFullDB/encodeh3k4me1_sum=11.05;FAVORFullDB/encodeh3k4me2_sum=14.07;FAVORFullDB/encodeh3k4me3_sum=15.8;FAVORFullDB/encodeh3k9ac_sum=7.46;FAVORFullDB/encodeh3k9me3_sum=3.48;FAVORFullDB/encodeh3k27ac_sum=5.2;FAVORFullDB/encodeh3k27me3_sum=4.99;FAVORFullDB/encodeh3k36me3_sum=38.71;FAVORFullDB/encodeh3k79me2_sum=10.45;FAVORFullDB/encodeh4k20me1_sum=10.14;FAVORFullDB/encodeh2afz_sum=5.68;FAVORFullDB/encode_dnase_sum=1.05;FAVORFullDB/encodetotal_rna_sum=2.28;FAVORFullDB/freq100bp=2;FAVORFullDB/rare100bp=1;FAVORFullDB/sngl100bp=32;FAVORFullDB/freq1000bp=4;FAVORFullDB/rare1000bp=7;FAVORFullDB/sngl1000bp=284;FAVORFullDB/freq10000bp=26;FAVORFullDB/rare10000bp=93;FAVORFullDB/sngl10000bp=2577;FAVORFullDB/remap_overlap_tf=6;FAVORFullDB/remap_overlap_cl=6;FAVORFullDB/cadd_rawscore=1.72604;FAVORFullDB/cadd_phred=17.02;FAVORFullDB/k24_bismap=0.542;FAVORFullDB/k24_umap=1;FAVORFullDB/k36_bismap=1;FAVORFullDB/k36_umap=1;FAVORFullDB/k50_bismap=1;FAVORFullDB/k50_umap=1;FAVORFullDB/k100_bismap=1;FAVORFullDB/k100_umap=1;FAVORFullDB/nucdiv=5.55;FAVORFullDB/recombination_rate=2.059;FAVORFullDB/refseq_category=exonic;FAVORFullDB/refseq_info=KLHL17;FAVORFullDB/refseq_exonic_category=synonymous', - 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'tg_all': '0.374201', - 'tg_amr': '0.2997', - 'tg_eas': '0.1597', - 'tg_eur': '0.3877', - 'tg_sas': '0.3548' - } - }, - 'gene': { - '_id': 'ENSG00000187642', - 'chr': 'chr1', - 'start': 975197, - 'end': 982117, - 'gene_id': 'ENSG00000187642.10', - 'hgnc': 'HGNC:28208', - 'name': 'PERM1', - 'gene_type': 'protein_coding', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'PGC-1 and ERR-induced regulator in muscle 1', - 'PGC-1 and ERR-induced regulator in muscle protein 1', - 'PPARGC1 and ESRR induced regulator, muscle 1', - 'C1orf170', - 'PPARGC1 and ESRR-induced regulator in muscle 1', - 'PERM1', - 'peroxisome proliferator-activated receptor gamma coactivator 1 and estrogen-related receptor-induced regulator in muscle 1', - 'pGC-1 and ERR-induced regulator in muscle protein 1' - ] - }, - 'beta': 0.00281122, - 'label': 'eQTL', - 'log10pvalue': 4.502099117025656, - 'slope': -0.324043, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'prostate gland', - 'chr': 'chr1' - }, - { - 'sequence variant': { - '_id': '7d973d5396c4b888ca2c598b751f1a37692744d47a96a9cce33981a075802e9d', - 'chr': 'chr1', - 'pos': 912709, - 'rsid': [ - 'rs4246505' - ], - 'ref': 'G', - 'alt': 'A', - 'spdi': 'NC_000001.11:912709:G:A', - 'hgvs': 'NC_000001.11:g.912710G>A', - 'qual': '.', - 'filter': None, - 'format': '.', - 'source': 'FAVOR', - 'source_url': 'http://favor.genohub.org/', - 'annotations': { - 'freq': { - '1000genomes': { - 'ref:long': 0.8289, - 'alt:long': 0.1711 - }, - 'alspac': { - 'ref:long': 0.7761, - 'alt:long': 0.2239 - }, - 'estonian': { - 'ref:long': 0.8103, - 'alt:long': 0.1897 - }, - 'genome_dk': { - 'ref:long': 0.775, - 'alt:long': 0.225 - }, - 'gonl': { - 'ref:long': 0.7846, - 'alt:long': 0.2154 - }, - 'korean': { - 'ref:long': 0.9072, - 'alt:long': 0.09283 - }, - 'korea1k': { - 'ref:long': 0.8892, - 'alt:long': 0.1108 - }, - 'northernsweden': { - 'ref:long': 0.8483, - 'alt:long': 0.1517 - }, - 'qatari': { - 'ref:long': 0.7639, - 'alt:long': 0.2361 - }, - 'sgdp_prj': { - 'ref:long': 0.4568, - 'alt:long': 0.5432 - }, - 'siberian': { - 'ref:long': 0.4545, - 'alt:long': 0.5455 - }, - 'tommo': { - 'ref:long': 0.8619, - 'alt:long': 0.1381 - }, - 'topmed': { - 'ref:long': 0.8202, - 'alt:long': 0.1798 - }, - 'twinsuk': { - 'ref:long': 0.7894, - 'alt:long': 0.2106 - }, - 'vietnamese': { - 'ref:long': 0.8942, - 'alt:long': 0.1058 - }, - 'dbgap_popfreq': { - 'ref:long': 0.8976, - 'alt:long': 0.1024 - } - }, - 'varinfo': '1-912710-G-A', - 'vid': '2.25813e+06', - 'variant_vcf': '1-912710-G-A', - 'variant_annovar': '1-912710-912710-G-A', - 'start_position': '912710', - 'end_position': '912710', - 'ref_annovar': 'G', - 'alt_annovar': 'A', - 'ref_vcf': 'G', - 'alt_vcf': 'A', - 'apc_conservation': 0.0933592, - 'apc_conservation_v2': 0.0976708, - 'apc_epigenetics_active': 14.7563, - 'apc_epigenetics': 16.2908, - 'apc_epigenetics_repressed': 11.5151, - 'apc_epigenetics_transcription': 5.07044, - 'apc_local_nucleotide_diversity': 1.30443, - 'apc_local_nucleotide_diversity_v2': 0.399165, - 'apc_local_nucleotide_diversity_v3': 0.36347, - 'apc_mappability': 7.36474, - 'apc_micro_rna': 0.0411083, - 'apc_mutation_density': 0.413919, - 'apc_protein_function': 20.2494, - 'apc_protein_function_v2': 4.92793e-10, - 'apc_protein_function_v3': 2.96949, - 'apc_proximity_to_coding': 15.7112, - 'apc_proximity_to_coding_v2': 15.7958, - 'apc_proximity_to_tsstes': 10.9811, - 'apc_transcription_factor': 15.5889, - 'bravo_an': '264690', - 'bravo_af': '0.179844', - 'filter_status': 'PASS', - 'fathmm_xf': '0.718013', - 'funseq_description': 'noncoding', - 'af_total': 0.181937, - 'af_asj_female': 0.209989, - 'af_eas_female': 0.0987569, - 'af_afr_male': 0.120437, - 'af_female': 0.181194, - 'af_fin_male': 0.18621, - 'af_oth_female': 0.193934, - 'af_ami': 0.358259, - 'af_oth': 0.184977, - 'af_male': 0.182726, - 'af_ami_female': 0.346154, - 'af_afr': 0.120135, - 'af_eas_male': 0.0766033, - 'af_sas': 0.250656, - 'af_nfe_female': 0.207887, - 'af_asj_male': 0.194872, - 'af_raw': 0.1815, - 'af_oth_male': 0.175624, - 'af_nfe_male': 0.210887, - 'af_asj': 0.20289, - 'af_amr_male': 0.221776, - 'af_amr_female': 0.227969, - 'af_fin': 0.187177, - 'af_afr_female': 0.119877, - 'af_sas_male': 0.249799, - 'af_amr': 0.224452, - 'af_nfe': 0.20915, - 'af_eas': 0.0868455, - 'af_ami_male': 0.371495, - 'af_fin_female': 0.190248, - 'cadd_rawscore': '-0.154267', - 'cadd_phred': '0.723', - 'refseq_category': 'intergenic', - 'tg_afr': '0.1021', - 'tg_all': '0.171126', - 'tg_amr': '0.2349', - 'tg_eas': '0.1062', - 'tg_eur': '0.1899', - 'tg_sas': '0.2669' - } - }, - 'gene': { - '_id': 'ENSG00000187642', - 'chr': 'chr1', - 'start': 975197, - 'end': 982117, - 'gene_id': 'ENSG00000187642.10', - 'hgnc': 'HGNC:28208', - 'name': 'PERM1', - 'gene_type': 'protein_coding', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'PGC-1 and ERR-induced regulator in muscle 1', - 'PGC-1 and ERR-induced regulator in muscle protein 1', - 'PPARGC1 and ESRR induced regulator, muscle 1', - 'C1orf170', - 'PPARGC1 and ESRR-induced regulator in muscle 1', - 'PERM1', - 'peroxisome proliferator-activated receptor gamma coactivator 1 and estrogen-related receptor-induced regulator in muscle 1', - 'pGC-1 and ERR-induced regulator in muscle protein 1' - ] - }, - 'beta': 1.92358e-18, - 'label': 'eQTL', - 'log10pvalue': 6.834275039685489, - 'slope': -0.459021, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'gastroesophageal sphincter', - 'chr': 'chr1' - } - ] - }], - '/variants/nearest-genes': [{ - 'params': { - 'region': 'chr1:11868-14409' - }, - 'response': [ - { - 'chr': 'chr1', - 'start': 11868, - 'end': 14409, - 'gene_type': 'lncRNA', - 'name': 'DDX11L2', - 'hgnc': 'HGNC:37102', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 1', - 'DEAD/H box polypeptide 11 like 1', - 'DEAD/H-box helicase 11 like 1 (pseudogene)', - 'DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 like 1', - 'DDX11L1' - ], - 'id': 'ENSG00000290825' - }, - { - 'chr': 'chr1', - 'start': 12009, - 'end': 13670, - 'gene_type': 'transcribed_unprocessed_pseudogene', - 'name': 'DDX11L1', - 'hgnc': 'HGNC:37102', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11 like 1', - 'DEAD/H box polypeptide 11 like 1', - 'DEAD/H-box helicase 11 like 1 (pseudogene)', - 'DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 like 1', - 'DDX11L1' - ], - 'id': 'ENSG00000223972' - }, - { - 'chr': 'chr1', - 'start': 14403, - 'end': 29570, - 'gene_type': 'unprocessed_pseudogene', - 'name': 'WASH7P', - 'hgnc': 'HGNC:38034', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'WAS protein family homolog 5 pseudogene', - 'WASP family homolog 7, pseudogene', - 'WASH5P', - 'FAM39F', - 'family with sequence similarity 39, member F', - 'WASH7P', - 'WAS protein family homolog 7, pseudogene' - ], - 'id': 'ENSG00000227232' - } - ] - }, { - 'params': { - 'region': 'chr1:1157520-1158189' - }, - 'response': [ - { - 'chr': 'chr1', - 'start': 1137016, - 'end': 1144056, - 'gene_type': 'lncRNA', - 'name': 'LINC01342', - 'hgnc': 'HGNC:50551', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'long intergenic non-protein coding RNA 1342', - 'LINC01342' - ], - 'id': 'ENSG00000223823' - } - ] - }] -} diff --git a/tests/acceptance_tests/motifs.py b/tests/acceptance_tests/motifs.py deleted file mode 100644 index 91022932..00000000 --- a/tests/acceptance_tests/motifs.py +++ /dev/null @@ -1,91 +0,0 @@ -motifs = { - '/motifs': [{ - 'params': { - 'tf_name': 'STAT3_HUMAN', - 'source': 'HOCOMOCOv11' - }, - 'response': [ - { - 'name': 'STAT3_HUMAN_HOCOMOCOv11', - 'tf_name': 'STAT3_HUMAN', - 'length': 12, - 'pwm': [ - [ - '-0.39152265672705855', - '0.5232217537098749', - '-0.09093140312847327', - '-0.323741183564272' - ], - [ - '0.5867196987339434', - '-0.2602638410957252', - '-0.23996962976064704', - '-0.4394052342198476' - ], - [ - '-0.7707228823699511', - '0.30422971254744535', - '-0.8599823519543183', - '0.564501860305333' - ], - [ - '-2.2340103118057417', - '-3.324736791140142', - '-3.903141843818025', - '1.3446234455022716' - ], - [ - '-2.694308015795771', - '-3.903141843818025', - '-1.113680932793377', - '1.276447224188738' - ], - [ - '-1.0439722185100666', - '1.258651325763289', - '-3.324736791140142', - '-2.3936647653320064' - ], - [ - '-3.903141843818025', - '1.2382449369440467', - '-4.400058040447161', - '-0.6577974226988328' - ], - [ - '0.5778917104362213', - '0.7853479101998049', - '-4.400058040447161', - '-4.400058040447161' - ], - [ - '0.3272783608001891', - '-2.5837428525823363', - '0.891229395855903', - '-2.310654723705371' - ], - [ - '-1.524531258237574', - '-2.8186351867496584', - '1.0662029549727963', - '-0.20057648948421875' - ], - [ - '1.142145001052313', - '-0.3684145734784018', - '-3.572690530904845', - '-1.9199997006100191' - ], - [ - '1.276447224188738', - '-1.9199997006100191', - '-2.1628243845506163', - '-1.8675042716147343' - ] - ], - 'source': 'HOCOMOCOv11', - 'source_url': 'hocomoco11.autosome.org/motif/STAT3_HUMAN.H11MO.0.A' - } - ] - }] -} diff --git a/tests/acceptance_tests/motifs_proteins.py b/tests/acceptance_tests/motifs_proteins.py deleted file mode 100644 index c5ad931f..00000000 --- a/tests/acceptance_tests/motifs_proteins.py +++ /dev/null @@ -1,593 +0,0 @@ -motifs_proteins = { - '/motifs/proteins': [{ - 'params': { - 'tf_name': 'ATF1_HUMAN', - 'source': 'HOCOMOCOv11', - 'verbose': 'false' - }, - 'response': [ - { - 'source': 'HOCOMOCOv11', - 'protein': 'proteins/P18846' - } - ] - }, { - 'params': { - 'tf_name': 'ATF1_HUMAN', - 'source': 'HOCOMOCOv11', - 'verbose': 'true' - }, - 'response': [ - { - 'source': 'HOCOMOCOv11', - 'protein': [ - { - '_id': 'P18846', - 'name': 'ATF1_HUMAN', - 'full_name': 'Cyclic AMP-dependent transcription factor ATF-1', - 'dbxrefs': [ - { - 'name': 'ABCD', - 'id': 'P18846' - }, - { - 'name': 'AGR', - 'id': 'HGNC:783' - }, - { - 'name': 'AlphaFoldDB', - 'id': 'P18846' - }, - { - 'name': 'Antibodypedia', - 'id': '4260' - }, - { - 'name': 'Bgee', - 'id': 'ENSG00000123268' - }, - { - 'name': 'BindingDB', - 'id': 'P18846' - }, - { - 'name': 'BioGRID', - 'id': '106956' - }, - { - 'name': 'BioGRID-ORCS', - 'id': '466' - }, - { - 'name': 'BioMuta', - 'id': 'ATF1' - }, - { - 'name': 'CCDS', - 'id': 'CCDS8803.1' - }, - { - 'name': 'CDD', - 'id': 'cd14690' - }, - { - 'name': 'CTD', - 'id': '466' - }, - { - 'name': 'ChEMBL', - 'id': 'CHEMBL3255' - }, - { - 'name': 'ChiTaRS', - 'id': 'ATF1' - }, - { - 'name': 'ComplexPortal', - 'id': 'CPX-6401' - }, - { - 'name': 'ComplexPortal', - 'id': 'CPX-6402' - }, - { - 'name': 'ComplexPortal', - 'id': 'CPX-6404' - }, - { - 'name': 'ComplexPortal', - 'id': 'CPX-6405' - }, - { - 'name': 'ComplexPortal', - 'id': 'CPX-9' - }, - { - 'name': 'DIP', - 'id': 'DIP-652N' - }, - { - 'name': 'DMDM', - 'id': '1168542' - }, - { - 'name': 'DNASU', - 'id': '466' - }, - { - 'name': 'DisGeNET', - 'id': '466' - }, - { - 'name': 'DrugBank', - 'id': 'DB00852' - }, - { - 'name': 'EMBL', - 'id': 'X55544' - }, - { - 'name': 'EMBL', - 'id': 'CAA39150.1' - }, - { - 'name': 'EMBL', - 'id': 'AK299240' - }, - { - 'name': 'EMBL', - 'id': 'BAG61271.1' - }, - { - 'name': 'EMBL', - 'id': 'AC013244' - }, - { - 'name': 'EMBL', - 'id': 'BC029619' - }, - { - 'name': 'EMBL', - 'id': 'AAH29619.1' - }, - { - 'name': 'EMBL', - 'id': 'AJ295163' - }, - { - 'name': 'EMBL', - 'id': 'CAC15058.1' - }, - { - 'name': 'EPD', - 'id': 'P18846' - }, - { - 'name': 'Ensembl', - 'id': 'ENST00000262053.8' - }, - { - 'name': 'Ensembl', - 'id': 'ENSP00000262053.3' - }, - { - 'name': 'Ensembl', - 'id': 'ENSG00000123268.9' - }, - { - 'name': 'ExpressionAtlas', - 'id': 'P18846' - }, - { - 'name': 'GO', - 'id': 'GO:1990590' - }, - { - 'name': 'GO', - 'id': 'GO:1990589' - }, - { - 'name': 'GO', - 'id': 'GO:0000785' - }, - { - 'name': 'GO', - 'id': 'GO:0005654' - }, - { - 'name': 'GO', - 'id': 'GO:0005634' - }, - { - 'name': 'GO', - 'id': 'GO:0090575' - }, - { - 'name': 'GO', - 'id': 'GO:0001228' - }, - { - 'name': 'GO', - 'id': 'GO:0003700' - }, - { - 'name': 'GO', - 'id': 'GO:0000981' - }, - { - 'name': 'GO', - 'id': 'GO:0042802' - }, - { - 'name': 'GO', - 'id': 'GO:0044877' - }, - { - 'name': 'GO', - 'id': 'GO:0000978' - }, - { - 'name': 'GO', - 'id': 'GO:0000977' - }, - { - 'name': 'GO', - 'id': 'GO:0019933' - }, - { - 'name': 'GO', - 'id': 'GO:0045740' - }, - { - 'name': 'GO', - 'id': 'GO:0010976' - }, - { - 'name': 'GO', - 'id': 'GO:0045944' - }, - { - 'name': 'GO', - 'id': 'GO:0065003' - }, - { - 'name': 'GO', - 'id': 'GO:0006357' - }, - { - 'name': 'GO', - 'id': 'GO:0032025' - }, - { - 'name': 'GO', - 'id': 'GO:0014074' - }, - { - 'name': 'Gene3D', - 'id': '1.20.5.170' - }, - { - 'name': 'GeneCards', - 'id': 'ATF1' - }, - { - 'name': 'GeneID', - 'id': '466' - }, - { - 'name': 'GeneTree', - 'id': 'ENSGT00940000158200' - }, - { - 'name': 'GeneWiki', - 'id': 'ATF1' - }, - { - 'name': 'Genevisible', - 'id': 'P18846' - }, - { - 'name': 'GenomeRNAi', - 'id': '466' - }, - { - 'name': 'GlyCosmos', - 'id': 'P18846' - }, - { - 'name': 'GlyGen', - 'id': 'P18846' - }, - { - 'name': 'HGNC', - 'id': 'HGNC:783' - }, - { - 'name': 'HOGENOM', - 'id': 'CLU_042675_1_0_1' - }, - { - 'name': 'HPA', - 'id': 'ENSG00000123268' - }, - { - 'name': 'InParanoid', - 'id': 'P18846' - }, - { - 'name': 'IntAct', - 'id': 'P18846' - }, - { - 'name': 'InterPro', - 'id': 'IPR004827' - }, - { - 'name': 'InterPro', - 'id': 'IPR046347' - }, - { - 'name': 'InterPro', - 'id': 'IPR003102' - }, - { - 'name': 'InterPro', - 'id': 'IPR001630' - }, - { - 'name': 'KEGG', - 'id': 'hsa:466' - }, - { - 'name': 'MANE-Select', - 'id': 'ENST00000262053.8' - }, - { - 'name': 'MANE-Select', - 'id': 'ENSP00000262053.3' - }, - { - 'name': 'MANE-Select', - 'id': 'NM_005171.5' - }, - { - 'name': 'MANE-Select', - 'id': 'NP_005162.1' - }, - { - 'name': 'MIM', - 'id': '123803' - }, - { - 'name': 'MIM', - 'id': '612160' - }, - { - 'name': 'MINT', - 'id': 'P18846' - }, - { - 'name': 'MalaCards', - 'id': 'ATF1' - }, - { - 'name': 'MassIVE', - 'id': 'P18846' - }, - { - 'name': 'MaxQB', - 'id': 'P18846' - }, - { - 'name': 'OMA', - 'id': 'THISHIA' - }, - { - 'name': 'OpenTargets', - 'id': 'ENSG00000123268' - }, - { - 'name': 'Orphanet', - 'id': '97338' - }, - { - 'name': 'OrthoDB', - 'id': '3137625at2759' - }, - { - 'name': 'PANTHER', - 'id': 'PTHR45879' - }, - { - 'name': 'PANTHER', - 'id': 'PTHR45879:SF2' - }, - { - 'name': 'PIR', - 'id': 'S12560' - }, - { - 'name': 'PRINTS', - 'id': 'PR00041' - }, - { - 'name': 'PRO', - 'id': 'PR:P18846' - }, - { - 'name': 'PROSITE', - 'id': 'PS50217' - }, - { - 'name': 'PROSITE', - 'id': 'PS00036' - }, - { - 'name': 'PROSITE', - 'id': 'PS50953' - }, - { - 'name': 'PathwayCommons', - 'id': 'P18846' - }, - { - 'name': 'PaxDb', - 'id': 'P18846' - }, - { - 'name': 'PeptideAtlas', - 'id': 'P18846' - }, - { - 'name': 'Pfam', - 'id': 'PF00170' - }, - { - 'name': 'Pfam', - 'id': 'PF02173' - }, - { - 'name': 'PharmGKB', - 'id': 'PA25083' - }, - { - 'name': 'Pharos', - 'id': 'P18846' - }, - { - 'name': 'PhosphoSitePlus', - 'id': 'P18846' - }, - { - 'name': 'PhylomeDB', - 'id': 'P18846' - }, - { - 'name': 'Proteomes', - 'id': 'UP000005640' - }, - { - 'name': 'ProteomicsDB', - 'id': '4950' - }, - { - 'name': 'ProteomicsDB', - 'id': '53610' - }, - { - 'name': 'RNAct', - 'id': 'P18846' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-199920' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-9031628' - }, - { - 'name': 'RefSeq', - 'id': 'NP_005162.1' - }, - { - 'name': 'RefSeq', - 'id': 'NM_005171.4' - }, - { - 'name': 'RefSeq', - 'id': 'XP_011536688.1' - }, - { - 'name': 'RefSeq', - 'id': 'XM_011538386.2' - }, - { - 'name': 'RefSeq', - 'id': 'XP_011536689.1' - }, - { - 'name': 'RefSeq', - 'id': 'XM_011538387.2' - }, - { - 'name': 'RefSeq', - 'id': 'XP_016874821.1' - }, - { - 'name': 'RefSeq', - 'id': 'XM_017019332.1' - }, - { - 'name': 'RefSeq', - 'id': 'XP_016874822.1' - }, - { - 'name': 'RefSeq', - 'id': 'XM_017019333.1' - }, - { - 'name': 'RefSeq', - 'id': 'XP_016874823.1' - }, - { - 'name': 'RefSeq', - 'id': 'XM_017019334.1' - }, - { - 'name': 'SIGNOR', - 'id': 'P18846' - }, - { - 'name': 'SMART', - 'id': 'SM00338' - }, - { - 'name': 'STRING', - 'id': '9606.ENSP00000262053' - }, - { - 'name': 'SUPFAM', - 'id': 'SSF57959' - }, - { - 'name': 'SignaLink', - 'id': 'P18846' - }, - { - 'name': 'TreeFam', - 'id': 'TF106464' - }, - { - 'name': 'UCSC', - 'id': 'uc001rww.5' - }, - { - 'name': 'VEuPathDB', - 'id': 'HostDB:ENSG00000123268' - }, - { - 'name': 'eggNOG', - 'id': 'KOG3584' - }, - { - 'name': 'iPTMnet', - 'id': 'P18846' - }, - { - 'name': 'jPOST', - 'id': 'P18846' - }, - { - 'name': 'neXtProt', - 'id': 'NX_P18846' - } - ], - 'source': 'UniProtKB/Swiss-Prot', - 'source_url': 'https://www.uniprot.org/help/downloads' - } - ] - } - ] - }] -} diff --git a/tests/acceptance_tests/ontology_terms.py b/tests/acceptance_tests/ontology_terms.py deleted file mode 100644 index a3dbf479..00000000 --- a/tests/acceptance_tests/ontology_terms.py +++ /dev/null @@ -1,378 +0,0 @@ -ontology_terms = { - '/ontology_terms': [{ - 'params': { - 'term_id': 'Orphanet_101435', - 'name': 'Rare genetic eye disease', - 'source': 'ORPHANET' - }, - 'response': [ - { - 'uri': 'http://www.orpha.net/ORDO/Orphanet_101435', - 'term_id': 'Orphanet_101435', - 'name': 'rare genetic eye disease', - 'description': '', - 'source': 'ORPHANET', - 'subontology': None - } - ] - }, { - 'params': { - 'name': 'liver' - }, - 'response': [ - { - 'uri': 'http://purl.obolibrary.org/obo/NCIT_C12392', - 'term_id': 'NCIT_C12392', - 'name': 'liver', - 'description': 'A triangular-shaped organ located under the diaphragm in the right hypochondrium. It is the largest internal organ of the body, weighting up to 2 kg. Metabolism and bile secretion are its main functions. It is composed of cells which have the ability to regenerate.', - 'source': 'NCIT', - 'subontology': None - }, - { - 'uri': 'http://purl.obolibrary.org/obo/UBERON_0002107', - 'term_id': 'UBERON_0002107', - 'name': 'liver', - 'description': 'An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO].', - 'source': 'UBERON', - 'subontology': None - } - ] - }], - '/ontology_terms/{term_id}/parents': [{ - 'params_url': { - 'term_id': 'UBERON_0003661', - 'page': 0 - }, - 'response': [ - { - 'term': { - 'uri': 'http://purl.obolibrary.org/obo/UBERON_0014892', - 'term_id': 'UBERON_0014892', - 'name': 'skeletal muscle organ', - 'description': 'A muscle organ that consists of skeletal muscle tissue ensheathed in epimysium, that develops from myotome and that is innervated by some somatic motor neuron. Skeletal muscles are typically attached (via a tendon) to a bone but there are exceptions (e.g. intrinsic tongue muscles).', - 'source': 'UBERON', - 'subontology': None - }, - 'relationship_type': 'subclass' - } - ] - }], - '/ontology_terms/{term_id}/children': [{ - 'params_url': { - 'term_id': 'UBERON_0014892', - 'page': 0 - }, - 'response': [ - { - 'term': { - 'uri': 'http://www.ebi.ac.uk/efo/EFO_0003067', - 'term_id': 'EFO_0003067', - 'name': 'latissimus dorsi', - 'description': '', - 'source': 'EFO', - 'subontology': None - }, - 'relationship_type': 'subclass' - }, - { - 'term': { - 'uri': 'http://purl.obolibrary.org/obo/UBERON_0000311', - 'term_id': 'UBERON_0000311', - 'name': 'extensor muscle', - 'description': 'A skeletal muscle whose contraction extends or stretches a body part.', - 'source': 'UBERON', - 'subontology': None - }, - 'relationship_type': 'subclass' - }, - { - 'term': { - 'uri': 'http://purl.obolibrary.org/obo/UBERON_0000366', - 'term_id': 'UBERON_0000366', - 'name': 'flexor muscle', - 'description': 'A skeletal muscle whose contraction bends a joint.', - 'source': 'UBERON', - 'subontology': None - }, - 'relationship_type': 'subclass' - }, - { - 'term': { - 'uri': 'http://purl.obolibrary.org/obo/UBERON_0000378', - 'term_id': 'UBERON_0000378', - 'name': 'tongue muscle', - 'description': 'The muscular portion of the tongue.', - 'source': 'UBERON', - 'subontology': None - }, - 'relationship_type': 'subclass' - }, - { - 'term': { - 'uri': 'http://purl.obolibrary.org/obo/UBERON_0001401', - 'term_id': 'UBERON_0001401', - 'name': 'longissimus thoracis muscle', - 'description': 'The longissimus thoracis is the intermediate and largest of the continuations of the sacrospinalis.[WP]. intermediate erector spinae muscle of back; origin, with iliocostalis and from transverse processes of lower thoracic vertebrae; insertion, by lateral slips into most or all of the ribs between angles and tubercles and into tips of transverse processes of upper lumbar vertebrae, and by medial slips into accessory processes of upper lumbar and transverse processes of thoracic vertebrae; action, extends vertebral column; nerve supply, dorsal primary rami of thoracic and lumbar spinal nerves[Stedmans].', - 'source': 'UBERON', - 'subontology': None - }, - 'relationship_type': 'subclass' - }, - { - 'term': { - 'uri': 'http://purl.obolibrary.org/obo/UBERON_0001476', - 'term_id': 'UBERON_0001476', - 'name': 'deltoid', - 'description': 'A muscle of shoulder which attaches to the scapula, clavicle and humerus.[FMA,generalized].', - 'source': 'UBERON', - 'subontology': None - }, - 'relationship_type': 'subclass' - }, - { - 'term': { - 'uri': 'http://purl.obolibrary.org/obo/UBERON_0001482', - 'term_id': 'UBERON_0001482', - 'name': 'muscle of shoulder', - 'description': 'Any muscle organ that is part of a shoulder [Automatically generated definition].', - 'source': 'UBERON', - 'subontology': None - }, - 'relationship_type': 'subclass' - }, - { - 'term': { - 'uri': 'http://purl.obolibrary.org/obo/UBERON_0001507', - 'term_id': 'UBERON_0001507', - 'name': 'biceps brachii', - 'description': 'A muscle in the forelimb stylopod which in humans has several functions, the most important being to rotate the forearm and to flex the elbow. [WP,unvetted].', - 'source': 'UBERON', - 'subontology': None - }, - 'relationship_type': 'subclass' - }, - { - 'term': { - 'uri': 'http://purl.obolibrary.org/obo/UBERON_0001601', - 'term_id': 'UBERON_0001601', - 'name': 'extra-ocular muscle', - 'description': 'Skeletal muscle derived from cranial mesoderm and controls eye movements.', - 'source': 'UBERON', - 'subontology': None - }, - 'relationship_type': 'subclass' - }, - { - 'term': { - 'uri': 'http://purl.obolibrary.org/obo/UBERON_0001774', - 'term_id': 'UBERON_0001774', - 'name': 'skeletal muscle of trunk', - 'description': 'A skeletal muscle organ that is part of the trunk region.', - 'source': 'UBERON', - 'subontology': None - }, - 'relationship_type': 'subclass' - }, - { - 'term': { - 'uri': 'http://purl.obolibrary.org/obo/UBERON_0002376', - 'term_id': 'UBERON_0002376', - 'name': 'cranial muscle', - 'description': 'Any skeletal muscle that is part of the head region.', - 'source': 'UBERON', - 'subontology': None - }, - 'relationship_type': 'subclass' - }, - { - 'term': { - 'uri': 'http://purl.obolibrary.org/obo/UBERON_0003661', - 'term_id': 'UBERON_0003661', - 'name': 'limb muscle', - 'description': 'Any muscle organ that is part of a limb [Automatically generated definition].', - 'source': 'UBERON', - 'subontology': None - }, - 'relationship_type': 'subclass' - }, - { - 'term': { - 'uri': 'http://purl.obolibrary.org/obo/UBERON_0003663', - 'term_id': 'UBERON_0003663', - 'name': 'hindlimb muscle', - 'description': 'Any muscle organ that is part of a hindlimb [Automatically generated definition].', - 'source': 'UBERON', - 'subontology': None - }, - 'relationship_type': 'subclass' - }, - { - 'term': { - 'uri': 'http://purl.obolibrary.org/obo/UBERON_0003897', - 'term_id': 'UBERON_0003897', - 'name': 'axial muscle', - 'description': 'One of the skeletal muscles of the head and neck, spine, and ribs.', - 'source': 'UBERON', - 'subontology': None - }, - 'relationship_type': 'subclass' - }, - { - 'term': { - 'uri': 'http://purl.obolibrary.org/obo/UBERON_0004518', - 'term_id': 'UBERON_0004518', - 'name': 'muscle of vertebral column', - 'description': 'A muscle that is attached to a vertebra of the vertebral column.', - 'source': 'UBERON', - 'subontology': None - }, - 'relationship_type': 'subclass' - }, - { - 'term': { - 'uri': 'http://purl.obolibrary.org/obo/UBERON_0006845', - 'term_id': 'UBERON_0006845', - 'name': 'abductor muscle', - 'description': 'A muscle that moves a body part away from the sagittal plane/midline of the body[ZFA]. For example, the abductor muscles of the legs spread the legs away from the midline and away from one another. An abductor muscle opposes an adductor muscle[BTO].', - 'source': 'UBERON', - 'subontology': None - }, - 'relationship_type': 'subclass' - }, - { - 'term': { - 'uri': 'http://purl.obolibrary.org/obo/UBERON_0008876', - 'term_id': 'UBERON_0008876', - 'name': 'hypodermis skeletal muscle layer', - 'description': 'Any skeletal muscle organ in the hypodermis / superficial fascia.', - 'source': 'UBERON', - 'subontology': None - }, - 'relationship_type': 'subclass' - }, - { - 'term': { - 'uri': 'http://purl.obolibrary.org/obo/UBERON_0010890', - 'term_id': 'UBERON_0010890', - 'name': 'pelvic complex muscle', - 'description': 'Muscles of the pelvic girdle, hindlimb or pelvic fin.', - 'source': 'UBERON', - 'subontology': None - }, - 'relationship_type': 'subclass' - }, - { - 'term': { - 'uri': 'http://purl.obolibrary.org/obo/UBERON_0010891', - 'term_id': 'UBERON_0010891', - 'name': 'pectoral complex muscle', - 'description': 'A muscle of a pectoral girdle, pectoral fin or anterior limb.', - 'source': 'UBERON', - 'subontology': None - }, - 'relationship_type': 'subclass' - }, - { - 'term': { - 'uri': 'http://purl.obolibrary.org/obo/UBERON_0010940', - 'term_id': 'UBERON_0010940', - 'name': 'muscle of digastric group', - 'description': 'Either of the two muscles that comprise the digastric group (anterior or posterior).', - 'source': 'UBERON', - 'subontology': None - }, - 'relationship_type': 'subclass' - }, - { - 'term': { - 'uri': 'http://purl.obolibrary.org/obo/UBERON_0010948', - 'term_id': 'UBERON_0010948', - 'name': 'cleidooccipital muscle', - 'description': 'A muscle organ that attaches_to a clavicle and attaches_to a occipital bone.', - 'source': 'UBERON', - 'subontology': None - }, - 'relationship_type': 'subclass' - }, - { - 'term': { - 'uri': 'http://purl.obolibrary.org/obo/UBERON_0010959', - 'term_id': 'UBERON_0010959', - 'name': 'craniocervical muscle', - 'description': 'Any muscle organ that is part of either the head or the neck.', - 'source': 'UBERON', - 'subontology': None - }, - 'relationship_type': 'subclass' - }, - { - 'term': { - 'uri': 'http://purl.obolibrary.org/obo/UBERON_0011145', - 'term_id': 'UBERON_0011145', - 'name': 'adductor muscle', - 'description': 'A muscle capable of adduction. Adduction is a movement which brings a part of the anatomy closer to the middle sagittal plane of the body. It is opposed to abduction.', - 'source': 'UBERON', - 'subontology': None - }, - 'relationship_type': 'subclass' - }, - { - 'term': { - 'uri': 'http://purl.obolibrary.org/obo/UBERON_0011364', - 'term_id': 'UBERON_0011364', - 'name': 'cleidocephalicus muscle', - 'description': 'The cleidomastoideus is a thick, strap-like muscle that together with the cleidocervicalis forms the proximal part of the brachiocephalicus. It lies beneath the cleidocervicalis. Its origin is the clavicular tendon with its insertion being at the mastoid process of the temporal bone. It is distinctly narrow and is united with the cleidocervicalis and cleidobrachialis by the clavicular tendon. Together with the other two components of the brachiocephalicus muscle, its primary function is to advance the free limb, however, it can also act as an shoulder extensor. Acting bilaterally, it fixes and depresses the neck, while by its unilateral action, it allows the head and neck to be drawn to the side. Its blood supply is the inferior cervical, carotid and vertebral arteries and its nerve supply is the spinal accessory, cervical and axillary nerves.', - 'source': 'UBERON', - 'subontology': None - }, - 'relationship_type': 'subclass' - }, - { - 'term': { - 'uri': 'http://purl.obolibrary.org/obo/UBERON_0011369', - 'term_id': 'UBERON_0011369', - 'name': 'omotransversarius muscle', - 'description': 'The omotransversarius is a straplike muscle, which advances and adducts the forelimb, as well as flexes the neck laterally. It covers the transverse processes of the cervical vertebrae, lying to their side. The omotransversarius lies ventral to the trapezius, cranial to the deltoid muscle and is covered cranially by the cleidocervicalis. It extends from the atlas to the spine of the scapula, with its origin on the transverse process of the atlas and its insertion in the distal end of the spine of the scapula. Its name can be split into omo, which is Greek for shoulder, and tranversarius which relates to its attachment to the transverse process of the atlas. This muscle is innervated by the accessory nerve.', - 'source': 'UBERON', - 'subontology': None - }, - 'relationship_type': 'subclass' - } - ] - }], - '/ontology_terms/{term_id_start}/transitive_closure/{term_id_end}': [{ - 'params_url': { - 'term_id_start': 'UBERON_0003663', - 'term_id_end': 'UBERON_0014892' - }, - 'response': { - 'vertices': { - 'UBERON_0003663': { - 'uri': 'http://purl.obolibrary.org/obo/UBERON_0003663', - 'term_id': 'UBERON_0003663', - 'name': 'hindlimb muscle', - 'description': 'Any muscle organ that is part of a hindlimb [Automatically generated definition].', - 'source': 'UBERON', - 'subontology': None - }, - 'UBERON_0014892': { - 'uri': 'http://purl.obolibrary.org/obo/UBERON_0014892', - 'term_id': 'UBERON_0014892', - 'name': 'skeletal muscle organ', - 'description': 'A muscle organ that consists of skeletal muscle tissue ensheathed in epimysium, that develops from myotome and that is innervated by some somatic motor neuron. Skeletal muscles are typically attached (via a tendon) to a bone but there are exceptions (e.g. intrinsic tongue muscles).', - 'source': 'UBERON', - 'subontology': None - } - }, - 'paths': [ - [ - { - 'from': 'UBERON_0003663', - 'to': 'UBERON_0014892', - 'type': 'subclass' - } - ] - ] - } - }] -} diff --git a/tests/acceptance_tests/phenotypes_variants.py b/tests/acceptance_tests/phenotypes_variants.py deleted file mode 100644 index 9861d774..00000000 --- a/tests/acceptance_tests/phenotypes_variants.py +++ /dev/null @@ -1,4734 +0,0 @@ -phenotypes_variants = { - '/phenotypes/variants': [{ - 'params': { - 'term_id': 'EFO_0007937', - 'term_name': 'blood protein measurement', - 'pmid': 'PMID:30072576', - 'p_value': 'lte:0.01' - }, - 'response': [ - { - 'study_id': 'GCST006585_1842', - 'sequence variant': 'variants/d6e116117bfb1ac8cc2bb218a982acd5e28b828b5df51200a33cd734fc5e446f', - 'p_val': 2e-18, - 'p_val_exponent': -18, - 'p_val_mantissa': 2, - 'beta': 0.2115974, - 'beta_ci_lower': 0.1642390405666317, - 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'polyphen2_hvar_score': '0.853', - 'mutation_taster_score': '1', - 'mutation_assessor_score': '2.075', - 'metasvm_pred': None, - 'fathmm_xf': '21.0838', - 'funseq_value': '2', - 'funseq_description': 'coding' - }, - 'source': 'FAVOR', - 'source_url': 'http://favor.genohub.org/' - } - ], - 'p_val': 2e-48, - 'p_val_exponent': -48, - 'p_val_mantissa': 2, - 'beta': -0.754534, - 'beta_ci_lower': -0.8556674074424473, - 'beta_ci_upper': -0.6534005925575528, - 'oddsr_ci_lower': None, - 'oddsr_ci_upper': None, - 'lead_chrom': '2', - 'lead_pos': '216679005', - 'lead_ref': 'G', - 'lead_alt': 'A', - 'direction': '-', - 'source': 'OpenTargets', - 'version': 'October 2022 (22.10)' - }, - { - 'study_id': 'GCST90010170', - 'sequence variant': [ - { - '_id': '5202f89faa20c32b4e8913f42aafa33214885a7ee47f58ccc74efe3c41c0deb8', - 'chr': 'chr14', - 'pos': 94521213, - 'rsid': [ - 'rs61978271' - ], - 'ref': 'T', - 'alt': 'A', - 'spdi': 'NC_000014.9:94521213:T:A', - 'hgvs': 'NC_000014.9:g.94521214T>A', - 'qual': '.', - 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'cadd_rawscore': '0.566277', - 'cadd_phred': '7.91', - 'tg_afr': '0.0424', - 'tg_all': '0.169329', - 'tg_amr': '0.1182', - 'tg_eas': '0.2133', - 'tg_eur': '0.2396', - 'tg_sas': '0.2597' - }, - 'source': 'FAVOR', - 'source_url': 'http://favor.genohub.org/' - } - ], - 'p_val': 4.668955e-24, - 'p_val_exponent': -24, - 'p_val_mantissa': 4.668955, - 'beta': 0.4558209, - 'beta_ci_lower': 0.3728548055999999, - 'beta_ci_upper': 0.5387869944, - 'oddsr_ci_lower': None, - 'oddsr_ci_upper': None, - 'lead_chrom': '14', - 'lead_pos': '94521214', - 'lead_ref': 'T', - 'lead_alt': 'A', - 'direction': '+', - 'source': 'OpenTargets', - 'version': 'October 2022 (22.10)' - } - ] - }] -} diff --git a/tests/acceptance_tests/proteins.py b/tests/acceptance_tests/proteins.py deleted file mode 100644 index 5797b886..00000000 --- a/tests/acceptance_tests/proteins.py +++ /dev/null @@ -1,1608 +0,0 @@ -proteins = { - '/proteins': [{ - 'params': { - 'name': 'CTCF_HUMAN', - 'dbxrefs': 'HGNC:13723' - }, - 'response': [ - { - '_id': 'P49711', - 'name': 'CTCF_HUMAN', - 'full_name': 'Transcriptional repressor CTCF', - 'dbxrefs': [ - { - 'name': 'AGR', - 'id': 'HGNC:13723' - }, - { - 'name': 'AlphaFoldDB', - 'id': 'P49711' - }, - { - 'name': 'Antibodypedia', - 'id': '15816' - }, - { - 'name': 'Bgee', - 'id': 'ENSG00000102974' - }, - { - 'name': 'BioGRID', - 'id': '115906' - }, - { - 'name': 'BioGRID-ORCS', - 'id': '10664' - }, - { - 'name': 'BioMuta', - 'id': 'CTCF' - }, - { - 'name': 'CCDS', - 'id': 'CCDS10841.1' - }, - { - 'name': 'CCDS', - 'id': 'CCDS54029.1' - }, - { - 'name': 'CORUM', - 'id': 'P49711' - }, - { - 'name': 'CTD', - 'id': '10664' - }, - { - 'name': 'ChEMBL', - 'id': 'CHEMBL4523233' - }, - { - 'name': 'ChiTaRS', - 'id': 'CTCF' - }, - { - 'name': 'DIP', - 'id': 'DIP-35252N' - }, - { - 'name': 'DMDM', - 'id': '1706179' - }, - { - 'name': 'DNASU', - 'id': '10664' - }, - { - 'name': 'DisGeNET', - 'id': '10664' - }, - { - 'name': 'EMBL', - 'id': 'U25435' - }, - { - 'name': 'EMBL', - 'id': 'AAB07788.1' - }, - { - 'name': 'EMBL', - 'id': 'AF145477' - }, - { - 'name': 'EMBL', - 'id': 'AAF31318.1' - }, - { - 'name': 'EMBL', - 'id': 'AF145468' - }, - { - 'name': 'EMBL', - 'id': 'AAF31318.1' - }, - { - 'name': 'EMBL', - 'id': 'AF145469' - }, - { - 'name': 'EMBL', - 'id': 'AAF31318.1' - }, - { - 'name': 'EMBL', - 'id': 'AF145470' - }, - { - 'name': 'EMBL', - 'id': 'AAF31318.1' - }, - { - 'name': 'EMBL', - 'id': 'AF145471' - }, - { - 'name': 'EMBL', - 'id': 'AAF31318.1' - }, - { - 'name': 'EMBL', - 'id': 'AF145472' - }, - { - 'name': 'EMBL', - 'id': 'AAF31318.1' - }, - { - 'name': 'EMBL', - 'id': 'AF145473' - }, - { - 'name': 'EMBL', - 'id': 'AAF31318.1' - }, - { - 'name': 'EMBL', - 'id': 'AF145474' - }, - { - 'name': 'EMBL', - 'id': 'AAF31318.1' - }, - { - 'name': 'EMBL', - 'id': 'AF145475' - }, - { - 'name': 'EMBL', - 'id': 'AAF31318.1' - }, - { - 'name': 'EMBL', - 'id': 'AF145476' - }, - { - 'name': 'EMBL', - 'id': 'AAF31318.1' - }, - { - 'name': 'EMBL', - 'id': 'BT009915' - }, - { - 'name': 'EMBL', - 'id': 'AAP88917.1' - }, - { - 'name': 'EMBL', - 'id': 'AB209793' - }, - { - 'name': 'EMBL', - 'id': 'BAD93030.1' - }, - { - 'name': 'EMBL', - 'id': 'AC009095' - }, - { - 'name': 'EMBL', - 'id': 'AC027682' - }, - { - 'name': 'EMBL', - 'id': 'CH471092' - }, - { - 'name': 'EMBL', - 'id': 'EAW83142.1' - }, - { - 'name': 'EMBL', - 'id': 'BC014267' - }, - { - 'name': 'EMBL', - 'id': 'AAH14267.1' - }, - { - 'name': 'EPD', - 'id': 'P49711' - }, - { - 'name': 'Ensembl', - 'id': 'ENST00000264010.10' - }, - { - 'name': 'Ensembl', - 'id': 'ENSP00000264010.4' - }, - { - 'name': 'Ensembl', - 'id': 'ENSG00000102974.16' - }, - { - 'name': 'Ensembl', - 'id': 'ENST00000401394.6' - }, - { - 'name': 'Ensembl', - 'id': 'ENSP00000384707.1' - }, - { - 'name': 'Ensembl', - 'id': 'ENSG00000102974.16' - }, - { - 'name': 'Ensembl', - 'id': 'ENST00000642819.1' - }, - { - 'name': 'Ensembl', - 'id': 'ENSP00000494408.1' - }, - { - 'name': 'Ensembl', - 'id': 'ENSG00000102974.16' - }, - { - 'name': 'Ensembl', - 'id': 'ENST00000644753.1' - }, - { - 'name': 'Ensembl', - 'id': 'ENSP00000493495.1' - }, - { - 'name': 'Ensembl', - 'id': 'ENSG00000102974.16' - }, - { - 'name': 'Ensembl', - 'id': 'ENST00000645699.1' - }, - { - 'name': 'Ensembl', - 'id': 'ENSP00000495348.1' - }, - { - 'name': 'Ensembl', - 'id': 'ENSG00000102974.16' - }, - { - 'name': 'Ensembl', - 'id': 'ENST00000646076.1' - }, - { - 'name': 'Ensembl', - 'id': 'ENSP00000494538.1' - }, - { - 'name': 'Ensembl', - 'id': 'ENSG00000102974.16' - }, - { - 'name': 'EvolutionaryTrace', - 'id': 'P49711' - }, - { - 'name': 'ExpressionAtlas', - 'id': 'P49711' - }, - { - 'name': 'GO', - 'id': 'GO:0000775' - }, - { - 'name': 'GO', - 'id': 'GO:0000793' - }, - { - 'name': 'GO', - 'id': 'GO:0001673' - }, - { - 'name': 'GO', - 'id': 'GO:0005730' - }, - { - 'name': 'GO', - 'id': 'GO:0005654' - }, - { - 'name': 'GO', - 'id': 'GO:0005634' - }, - { - 'name': 'GO', - 'id': 'GO:0043035' - }, - { - 'name': 'GO', - 'id': 'GO:0003700' - }, - { - 'name': 'GO', - 'id': 'GO:0001227' - }, - { - 'name': 'GO', - 'id': 'GO:0000978' - }, - { - 'name': 'GO', - 'id': 'GO:0043565' - }, - { - 'name': 'GO', - 'id': 'GO:0000976' - }, - { - 'name': 'GO', - 'id': 'GO:0001221' - }, - { - 'name': 'GO', - 'id': 'GO:0008270' - }, - { - 'name': 'GO', - 'id': 'GO:0140588' - }, - { - 'name': 'GO', - 'id': 'GO:0007059' - }, - { - 'name': 'GO', - 'id': 'GO:0006306' - }, - { - 'name': 'GO', - 'id': 'GO:0040029' - }, - { - 'name': 'GO', - 'id': 'GO:0071514' - }, - { - 'name': 'GO', - 'id': 'GO:0008285' - }, - { - 'name': 'GO', - 'id': 'GO:0045892' - }, - { - 'name': 'GO', - 'id': 'GO:0000122' - }, - { - 'name': 'GO', - 'id': 'GO:0045893' - }, - { - 'name': 'GO', - 'id': 'GO:0010628' - }, - { - 'name': 'GO', - 'id': 'GO:0071459' - }, - { - 'name': 'GO', - 'id': 'GO:0070602' - }, - { - 'name': 'GO', - 'id': 'GO:0006349' - }, - { - 'name': 'Gene3D', - 'id': '3.30.160.60' - }, - { - 'name': 'GeneCards', - 'id': 'CTCF' - }, - { - 'name': 'GeneID', - 'id': '10664' - }, - { - 'name': 'GeneTree', - 'id': 'ENSGT00940000156672' - }, - { - 'name': 'GeneWiki', - 'id': 'CTCF' - }, - { - 'name': 'Genevisible', - 'id': 'P49711' - }, - { - 'name': 'GenomeRNAi', - 'id': '10664' - }, - { - 'name': 'GlyGen', - 'id': 'P49711' - }, - { - 'name': 'HGNC', - 'id': 'HGNC:13723' - }, - { - 'name': 'HOGENOM', - 'id': 'CLU_002678_77_1_1' - }, - { - 'name': 'HPA', - 'id': 'ENSG00000102974' - }, - { - 'name': 'InParanoid', - 'id': 'P49711' - }, - { - 'name': 'IntAct', - 'id': 'P49711' - }, - { - 'name': 'InterPro', - 'id': 'IPR036236' - }, - { - 'name': 'InterPro', - 'id': 'IPR013087' - }, - { - 'name': 'KEGG', - 'id': 'hsa:10664' - }, - { - 'name': 'MANE-Select', - 'id': 'ENST00000264010.10' - }, - { - 'name': 'MANE-Select', - 'id': 'ENSP00000264010.4' - }, - { - 'name': 'MANE-Select', - 'id': 'NM_006565.4' - }, - { - 'name': 'MANE-Select', - 'id': 'NP_006556.1' - }, - { - 'name': 'MIM', - 'id': '604167' - }, - { - 'name': 'MIM', - 'id': '615502' - }, - { - 'name': 'MINT', - 'id': 'P49711' - }, - { - 'name': 'MalaCards', - 'id': 'CTCF' - }, - { - 'name': 'MassIVE', - 'id': 'P49711' - }, - { - 'name': 'MaxQB', - 'id': 'P49711' - }, - { - 'name': 'OMA', - 'id': 'TESEPMI' - }, - { - 'name': 'OpenTargets', - 'id': 'ENSG00000102974' - }, - { - 'name': 'Orphanet', - 'id': '363611' - }, - { - 'name': 'OrthoDB', - 'id': '5398475at2759' - }, - { - 'name': 'PANTHER', - 'id': 'PTHR24379:SF81' - }, - { - 'name': 'PANTHER', - 'id': 'PTHR24379' - }, - { - 'name': 'PDB', - 'id': '1X6H' - }, - { - 'name': 'PDB', - 'id': '2CT1' - }, - { - 'name': 'PDB', - 'id': '5K5H' - }, - { - 'name': 'PDB', - 'id': '5K5I' - }, - { - 'name': 'PDB', - 'id': '5K5J' - }, - { - 'name': 'PDB', - 'id': '5K5L' - }, - { - 'name': 'PDB', - 'id': '5KKQ' - }, - { - 'name': 'PDB', - 'id': '5T00' - }, - { - 'name': 'PDB', - 'id': '5T0U' - }, - { - 'name': 'PDB', - 'id': '5UND' - }, - { - 'name': 'PDB', - 'id': '5YEF' - }, - { - 'name': 'PDB', - 'id': '5YEG' - }, - { - 'name': 'PDB', - 'id': '5YEH' - }, - { - 'name': 'PDB', - 'id': '5YEL' - }, - { - 'name': 'PDB', - 'id': '6QNX' - }, - { - 'name': 'PDBsum', - 'id': '1X6H' - }, - { - 'name': 'PDBsum', - 'id': '2CT1' - }, - { - 'name': 'PDBsum', - 'id': '5K5H' - }, - { - 'name': 'PDBsum', - 'id': '5K5I' - }, - { - 'name': 'PDBsum', - 'id': '5K5J' - }, - { - 'name': 'PDBsum', - 'id': '5K5L' - }, - { - 'name': 'PDBsum', - 'id': '5KKQ' - }, - { - 'name': 'PDBsum', - 'id': '5T00' - }, - { - 'name': 'PDBsum', - 'id': '5T0U' - }, - { - 'name': 'PDBsum', - 'id': '5UND' - }, - { - 'name': 'PDBsum', - 'id': '5YEF' - }, - { - 'name': 'PDBsum', - 'id': '5YEG' - }, - { - 'name': 'PDBsum', - 'id': '5YEH' - }, - { - 'name': 'PDBsum', - 'id': '5YEL' - }, - { - 'name': 'PDBsum', - 'id': '6QNX' - }, - { - 'name': 'PIR', - 'id': 'G01792' - }, - { - 'name': 'PRO', - 'id': 'PR:P49711' - }, - { - 'name': 'PROSITE', - 'id': 'PS00028' - }, - { - 'name': 'PROSITE', - 'id': 'PS50157' - }, - { - 'name': 'PathwayCommons', - 'id': 'P49711' - }, - { - 'name': 'PaxDb', - 'id': 'P49711' - }, - { - 'name': 'PeptideAtlas', - 'id': 'P49711' - }, - { - 'name': 'Pfam', - 'id': 'PF00096' - }, - { - 'name': 'Pfam', - 'id': 'PF13909' - }, - { - 'name': 'PharmGKB', - 'id': 'PA26998' - }, - { - 'name': 'Pharos', - 'id': 'P49711' - }, - { - 'name': 'PhosphoSitePlus', - 'id': 'P49711' - }, - { - 'name': 'PhylomeDB', - 'id': 'P49711' - }, - { - 'name': 'Proteomes', - 'id': 'UP000005640' - }, - { - 'name': 'ProteomicsDB', - 'id': '56053' - }, - { - 'name': 'ProteomicsDB', - 'id': '5985' - }, - { - 'name': 'RNAct', - 'id': 'P49711' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-5617472' - }, - { - 'name': 'RefSeq', - 'id': 'NP_001177951.1' - }, - { - 'name': 'RefSeq', - 'id': 'NM_001191022.1' - }, - { - 'name': 'RefSeq', - 'id': 'NP_006556.1' - }, - { - 'name': 'RefSeq', - 'id': 'NM_006565.3' - }, - { - 'name': 'RefSeq', - 'id': 'XP_016878357.1' - }, - { - 'name': 'RefSeq', - 'id': 'XM_017022868.1' - }, - { - 'name': 'SIGNOR', - 'id': 'P49711' - }, - { - 'name': 'SMART', - 'id': 'SM00355' - }, - { - 'name': 'SMR', - 'id': 'P49711' - }, - { - 'name': 'STRING', - 'id': '9606.ENSP00000264010' - }, - { - 'name': 'SUPFAM', - 'id': 'SSF57667' - }, - { - 'name': 'SignaLink', - 'id': 'P49711' - }, - { - 'name': 'SwissPalm', - 'id': 'P49711' - }, - { - 'name': 'TreeFam', - 'id': 'TF106430' - }, - { - 'name': 'UCSC', - 'id': 'uc002etl.4' - }, - { - 'name': 'VEuPathDB', - 'id': 'HostDB:ENSG00000102974' - }, - { - 'name': 'eggNOG', - 'id': 'KOG1721' - }, - { - 'name': 'iPTMnet', - 'id': 'P49711' - }, - { - 'name': 'jPOST', - 'id': 'P49711' - }, - { - 'name': 'neXtProt', - 'id': 'NX_P49711' - } - ], - 'source': 'UniProtKB/Swiss-Prot', - 'source_url': 'https://www.uniprot.org/help/downloads' - } - ] - }, { - 'params': { - 'protein_id': 'P49711' - }, - 'response': { - '_id': 'P49711', - 'name': 'CTCF_HUMAN', - 'full_name': 'Transcriptional repressor CTCF', - 'dbxrefs': [ - { - 'name': 'AGR', - 'id': 'HGNC:13723' - }, - { - 'name': 'AlphaFoldDB', - 'id': 'P49711' - }, - { - 'name': 'Antibodypedia', - 'id': '15816' - }, - { - 'name': 'Bgee', - 'id': 'ENSG00000102974' - }, - { - 'name': 'BioGRID', - 'id': '115906' - }, - { - 'name': 'BioGRID-ORCS', - 'id': '10664' - }, - { - 'name': 'BioMuta', - 'id': 'CTCF' - }, - { - 'name': 'CCDS', - 'id': 'CCDS10841.1' - }, - { - 'name': 'CCDS', - 'id': 'CCDS54029.1' - }, - { - 'name': 'CORUM', - 'id': 'P49711' - }, - { - 'name': 'CTD', - 'id': '10664' - }, - { - 'name': 'ChEMBL', - 'id': 'CHEMBL4523233' - }, - { - 'name': 'ChiTaRS', - 'id': 'CTCF' - }, - { - 'name': 'DIP', - 'id': 'DIP-35252N' - }, - { - 'name': 'DMDM', - 'id': '1706179' - }, - { - 'name': 'DNASU', - 'id': '10664' - }, - { - 'name': 'DisGeNET', - 'id': '10664' - }, - { - 'name': 'EMBL', - 'id': 'U25435' - }, - { - 'name': 'EMBL', - 'id': 'AAB07788.1' - }, - { - 'name': 'EMBL', - 'id': 'AF145477' - }, - { - 'name': 'EMBL', - 'id': 'AAF31318.1' - }, - { - 'name': 'EMBL', - 'id': 'AF145468' - }, - { - 'name': 'EMBL', - 'id': 'AAF31318.1' - }, - { - 'name': 'EMBL', - 'id': 'AF145469' - }, - { - 'name': 'EMBL', - 'id': 'AAF31318.1' - }, - { - 'name': 'EMBL', - 'id': 'AF145470' - }, - { - 'name': 'EMBL', - 'id': 'AAF31318.1' - }, - { - 'name': 'EMBL', - 'id': 'AF145471' - }, - { - 'name': 'EMBL', - 'id': 'AAF31318.1' - }, - { - 'name': 'EMBL', - 'id': 'AF145472' - }, - { - 'name': 'EMBL', - 'id': 'AAF31318.1' - }, - { - 'name': 'EMBL', - 'id': 'AF145473' - }, - { - 'name': 'EMBL', - 'id': 'AAF31318.1' - }, - { - 'name': 'EMBL', - 'id': 'AF145474' - }, - { - 'name': 'EMBL', - 'id': 'AAF31318.1' - }, - { - 'name': 'EMBL', - 'id': 'AF145475' - }, - { - 'name': 'EMBL', - 'id': 'AAF31318.1' - }, - { - 'name': 'EMBL', - 'id': 'AF145476' - }, - { - 'name': 'EMBL', - 'id': 'AAF31318.1' - }, - { - 'name': 'EMBL', - 'id': 'BT009915' - }, - { - 'name': 'EMBL', - 'id': 'AAP88917.1' - }, - { - 'name': 'EMBL', - 'id': 'AB209793' - }, - { - 'name': 'EMBL', - 'id': 'BAD93030.1' - }, - { - 'name': 'EMBL', - 'id': 'AC009095' - }, - { - 'name': 'EMBL', - 'id': 'AC027682' - }, - { - 'name': 'EMBL', - 'id': 'CH471092' - }, - { - 'name': 'EMBL', - 'id': 'EAW83142.1' - }, - { - 'name': 'EMBL', - 'id': 'BC014267' - }, - { - 'name': 'EMBL', - 'id': 'AAH14267.1' - }, - { - 'name': 'EPD', - 'id': 'P49711' - }, - { - 'name': 'Ensembl', - 'id': 'ENST00000264010.10' - }, - { - 'name': 'Ensembl', - 'id': 'ENSP00000264010.4' - }, - { - 'name': 'Ensembl', - 'id': 'ENSG00000102974.16' - }, - { - 'name': 'Ensembl', - 'id': 'ENST00000401394.6' - }, - { - 'name': 'Ensembl', - 'id': 'ENSP00000384707.1' - }, - { - 'name': 'Ensembl', - 'id': 'ENSG00000102974.16' - }, - { - 'name': 'Ensembl', - 'id': 'ENST00000642819.1' - }, - { - 'name': 'Ensembl', - 'id': 'ENSP00000494408.1' - }, - { - 'name': 'Ensembl', - 'id': 'ENSG00000102974.16' - }, - { - 'name': 'Ensembl', - 'id': 'ENST00000644753.1' - }, - { - 'name': 'Ensembl', - 'id': 'ENSP00000493495.1' - }, - { - 'name': 'Ensembl', - 'id': 'ENSG00000102974.16' - }, - { - 'name': 'Ensembl', - 'id': 'ENST00000645699.1' - }, - { - 'name': 'Ensembl', - 'id': 'ENSP00000495348.1' - }, - { - 'name': 'Ensembl', - 'id': 'ENSG00000102974.16' - }, - { - 'name': 'Ensembl', - 'id': 'ENST00000646076.1' - }, - { - 'name': 'Ensembl', - 'id': 'ENSP00000494538.1' - }, - { - 'name': 'Ensembl', - 'id': 'ENSG00000102974.16' - }, - { - 'name': 'EvolutionaryTrace', - 'id': 'P49711' - }, - { - 'name': 'ExpressionAtlas', - 'id': 'P49711' - }, - { - 'name': 'GO', - 'id': 'GO:0000775' - }, - { - 'name': 'GO', - 'id': 'GO:0000793' - }, - { - 'name': 'GO', - 'id': 'GO:0001673' - }, - { - 'name': 'GO', - 'id': 'GO:0005730' - }, - { - 'name': 'GO', - 'id': 'GO:0005654' - }, - { - 'name': 'GO', - 'id': 'GO:0005634' - }, - { - 'name': 'GO', - 'id': 'GO:0043035' - }, - { - 'name': 'GO', - 'id': 'GO:0003700' - }, - { - 'name': 'GO', - 'id': 'GO:0001227' - }, - { - 'name': 'GO', - 'id': 'GO:0000978' - }, - { - 'name': 'GO', - 'id': 'GO:0043565' - }, - { - 'name': 'GO', - 'id': 'GO:0000976' - }, - { - 'name': 'GO', - 'id': 'GO:0001221' - }, - { - 'name': 'GO', - 'id': 'GO:0008270' - }, - { - 'name': 'GO', - 'id': 'GO:0140588' - }, - { - 'name': 'GO', - 'id': 'GO:0007059' - }, - { - 'name': 'GO', - 'id': 'GO:0006306' - }, - { - 'name': 'GO', - 'id': 'GO:0040029' - }, - { - 'name': 'GO', - 'id': 'GO:0071514' - }, - { - 'name': 'GO', - 'id': 'GO:0008285' - }, - { - 'name': 'GO', - 'id': 'GO:0045892' - }, - { - 'name': 'GO', - 'id': 'GO:0000122' - }, - { - 'name': 'GO', - 'id': 'GO:0045893' - }, - { - 'name': 'GO', - 'id': 'GO:0010628' - }, - { - 'name': 'GO', - 'id': 'GO:0071459' - }, - { - 'name': 'GO', - 'id': 'GO:0070602' - }, - { - 'name': 'GO', - 'id': 'GO:0006349' - }, - { - 'name': 'Gene3D', - 'id': '3.30.160.60' - }, - { - 'name': 'GeneCards', - 'id': 'CTCF' - }, - { - 'name': 'GeneID', - 'id': '10664' - }, - { - 'name': 'GeneTree', - 'id': 'ENSGT00940000156672' - }, - { - 'name': 'GeneWiki', - 'id': 'CTCF' - }, - { - 'name': 'Genevisible', - 'id': 'P49711' - }, - { - 'name': 'GenomeRNAi', - 'id': '10664' - }, - { - 'name': 'GlyGen', - 'id': 'P49711' - }, - { - 'name': 'HGNC', - 'id': 'HGNC:13723' - }, - { - 'name': 'HOGENOM', - 'id': 'CLU_002678_77_1_1' - }, - { - 'name': 'HPA', - 'id': 'ENSG00000102974' - }, - { - 'name': 'InParanoid', - 'id': 'P49711' - }, - { - 'name': 'IntAct', - 'id': 'P49711' - }, - { - 'name': 'InterPro', - 'id': 'IPR036236' - }, - { - 'name': 'InterPro', - 'id': 'IPR013087' - }, - { - 'name': 'KEGG', - 'id': 'hsa:10664' - }, - { - 'name': 'MANE-Select', - 'id': 'ENST00000264010.10' - }, - { - 'name': 'MANE-Select', - 'id': 'ENSP00000264010.4' - }, - { - 'name': 'MANE-Select', - 'id': 'NM_006565.4' - }, - { - 'name': 'MANE-Select', - 'id': 'NP_006556.1' - }, - { - 'name': 'MIM', - 'id': '604167' - }, - { - 'name': 'MIM', - 'id': '615502' - }, - { - 'name': 'MINT', - 'id': 'P49711' - }, - { - 'name': 'MalaCards', - 'id': 'CTCF' - }, - { - 'name': 'MassIVE', - 'id': 'P49711' - }, - { - 'name': 'MaxQB', - 'id': 'P49711' - }, - { - 'name': 'OMA', - 'id': 'TESEPMI' - }, - { - 'name': 'OpenTargets', - 'id': 'ENSG00000102974' - }, - { - 'name': 'Orphanet', - 'id': '363611' - }, - { - 'name': 'OrthoDB', - 'id': '5398475at2759' - }, - { - 'name': 'PANTHER', - 'id': 'PTHR24379:SF81' - }, - { - 'name': 'PANTHER', - 'id': 'PTHR24379' - }, - { - 'name': 'PDB', - 'id': '1X6H' - }, - { - 'name': 'PDB', - 'id': '2CT1' - }, - { - 'name': 'PDB', - 'id': '5K5H' - }, - { - 'name': 'PDB', - 'id': '5K5I' - }, - { - 'name': 'PDB', - 'id': '5K5J' - }, - { - 'name': 'PDB', - 'id': '5K5L' - }, - { - 'name': 'PDB', - 'id': '5KKQ' - }, - { - 'name': 'PDB', - 'id': '5T00' - }, - { - 'name': 'PDB', - 'id': '5T0U' - }, - { - 'name': 'PDB', - 'id': '5UND' - }, - { - 'name': 'PDB', - 'id': '5YEF' - }, - { - 'name': 'PDB', - 'id': '5YEG' - }, - { - 'name': 'PDB', - 'id': '5YEH' - }, - { - 'name': 'PDB', - 'id': '5YEL' - }, - { - 'name': 'PDB', - 'id': '6QNX' - }, - { - 'name': 'PDBsum', - 'id': '1X6H' - }, - { - 'name': 'PDBsum', - 'id': '2CT1' - }, - { - 'name': 'PDBsum', - 'id': '5K5H' - }, - { - 'name': 'PDBsum', - 'id': '5K5I' - }, - { - 'name': 'PDBsum', - 'id': '5K5J' - }, - { - 'name': 'PDBsum', - 'id': '5K5L' - }, - { - 'name': 'PDBsum', - 'id': '5KKQ' - }, - { - 'name': 'PDBsum', - 'id': '5T00' - }, - { - 'name': 'PDBsum', - 'id': '5T0U' - }, - { - 'name': 'PDBsum', - 'id': '5UND' - }, - { - 'name': 'PDBsum', - 'id': '5YEF' - }, - { - 'name': 'PDBsum', - 'id': '5YEG' - }, - { - 'name': 'PDBsum', - 'id': '5YEH' - }, - { - 'name': 'PDBsum', - 'id': '5YEL' - }, - { - 'name': 'PDBsum', - 'id': '6QNX' - }, - { - 'name': 'PIR', - 'id': 'G01792' - }, - { - 'name': 'PRO', - 'id': 'PR:P49711' - }, - { - 'name': 'PROSITE', - 'id': 'PS00028' - }, - { - 'name': 'PROSITE', - 'id': 'PS50157' - }, - { - 'name': 'PathwayCommons', - 'id': 'P49711' - }, - { - 'name': 'PaxDb', - 'id': 'P49711' - }, - { - 'name': 'PeptideAtlas', - 'id': 'P49711' - }, - { - 'name': 'Pfam', - 'id': 'PF00096' - }, - { - 'name': 'Pfam', - 'id': 'PF13909' - }, - { - 'name': 'PharmGKB', - 'id': 'PA26998' - }, - { - 'name': 'Pharos', - 'id': 'P49711' - }, - { - 'name': 'PhosphoSitePlus', - 'id': 'P49711' - }, - { - 'name': 'PhylomeDB', - 'id': 'P49711' - }, - { - 'name': 'Proteomes', - 'id': 'UP000005640' - }, - { - 'name': 'ProteomicsDB', - 'id': '56053' - }, - { - 'name': 'ProteomicsDB', - 'id': '5985' - }, - { - 'name': 'RNAct', - 'id': 'P49711' - }, - { - 'name': 'Reactome', - 'id': 'R-HSA-5617472' - }, - { - 'name': 'RefSeq', - 'id': 'NP_001177951.1' - }, - { - 'name': 'RefSeq', - 'id': 'NM_001191022.1' - }, - { - 'name': 'RefSeq', - 'id': 'NP_006556.1' - }, - { - 'name': 'RefSeq', - 'id': 'NM_006565.3' - }, - { - 'name': 'RefSeq', - 'id': 'XP_016878357.1' - }, - { - 'name': 'RefSeq', - 'id': 'XM_017022868.1' - }, - { - 'name': 'SIGNOR', - 'id': 'P49711' - }, - { - 'name': 'SMART', - 'id': 'SM00355' - }, - { - 'name': 'SMR', - 'id': 'P49711' - }, - { - 'name': 'STRING', - 'id': '9606.ENSP00000264010' - }, - { - 'name': 'SUPFAM', - 'id': 'SSF57667' - }, - { - 'name': 'SignaLink', - 'id': 'P49711' - }, - { - 'name': 'SwissPalm', - 'id': 'P49711' - }, - { - 'name': 'TreeFam', - 'id': 'TF106430' - }, - { - 'name': 'UCSC', - 'id': 'uc002etl.4' - }, - { - 'name': 'VEuPathDB', - 'id': 'HostDB:ENSG00000102974' - }, - { - 'name': 'eggNOG', - 'id': 'KOG1721' - }, - { - 'name': 'iPTMnet', - 'id': 'P49711' - }, - { - 'name': 'jPOST', - 'id': 'P49711' - }, - { - 'name': 'neXtProt', - 'id': 'NX_P49711' - } - ], - 'source': 'UniProtKB/Swiss-Prot', - 'source_url': 'https://www.uniprot.org/help/downloads' - } - }] -} diff --git a/tests/acceptance_tests/proteins_complexes.py b/tests/acceptance_tests/proteins_complexes.py deleted file mode 100644 index 7710d1cc..00000000 --- a/tests/acceptance_tests/proteins_complexes.py +++ /dev/null @@ -1,99 +0,0 @@ -proteins_complexes = { - '/proteins/complexes': [{ - 'params': { - 'protein_id': 'P23511', - 'verbose': 'false' - }, - 'response': [ - { - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/', - 'complex': 'complexes/CPX-1956' - } - ] - }, { - 'params': { - 'protein_id': 'P23511', - 'verbose': 'true' - }, - 'response': [ - { - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/', - 'complex': { - '_id': 'CPX-1956', - 'name': 'CCAAT-binding factor complex', - 'alias': [ - 'Nuclear transcription factor Y complex', - 'NF-Y transcription factor complex', - 'CCAAT box DNA-binding factor complex', - 'CBF complex' - ], - 'molecules': [ - 'P23511(1)', - 'P25208(1)', - 'Q13952(1)' - ], - 'evidence_code': 'ECO:0000353(physical interaction evidence used in manual assertion)', - 'experimental_evidence': 'intact:EBI-6672292', - 'description': 'Transcription factor which binds to the CCAAT box, which occurs in 30% of eukaryotic promoters and appears to be crucial for promoter activity. May also play a role in histone methylation and some acetylation through recruitment of relevant enzymes to active promoters.', - 'complex_assembly': 'Heterotrimer', - 'complex_source': "psi-mi:\"MI:0469\"(IntAct)", - 'reactome_xref': [ - 'R-HSA-381204(identity)' - ], - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/' - } - } - ] - }, { - 'params': { - 'protein_name': 'NFYA_HUMAN', - 'verbose': 'false' - }, - 'response': [ - { - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/', - 'complex': 'complexes/CPX-1956' - } - ] - }, { - 'params': { - 'protein_name': 'NFYA_HUMAN', - 'verbose': 'true' - }, - 'response': [ - { - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/', - 'complex': { - '_id': 'CPX-1956', - 'name': 'CCAAT-binding factor complex', - 'alias': [ - 'Nuclear transcription factor Y complex', - 'NF-Y transcription factor complex', - 'CCAAT box DNA-binding factor complex', - 'CBF complex' - ], - 'molecules': [ - 'P23511(1)', - 'P25208(1)', - 'Q13952(1)' - ], - 'evidence_code': 'ECO:0000353(physical interaction evidence used in manual assertion)', - 'experimental_evidence': 'intact:EBI-6672292', - 'description': 'Transcription factor which binds to the CCAAT box, which occurs in 30% of eukaryotic promoters and appears to be crucial for promoter activity. May also play a role in histone methylation and some acetylation through recruitment of relevant enzymes to active promoters.', - 'complex_assembly': 'Heterotrimer', - 'complex_source': "psi-mi:\"MI:0469\"(IntAct)", - 'reactome_xref': [ - 'R-HSA-381204(identity)' - ], - 'source': 'EBI', - 'source_url': 'https://www.ebi.ac.uk/complexportal/' - } - } - ] - }] -} diff --git a/tests/acceptance_tests/proteins_genes.py b/tests/acceptance_tests/proteins_genes.py deleted file mode 100644 index 1656074c..00000000 --- a/tests/acceptance_tests/proteins_genes.py +++ /dev/null @@ -1,59 +0,0 @@ -proteins_genes = { - '/proteins/genes': [{ - 'params': { - 'protein_name': 'CTCF_HUMAN', - 'dbxrefs': 'HGNC:13723', - }, - 'response': [{ - '_id': 'ENSG00000102974', - 'chr': 'chr16', - 'start': 67562466, - 'end': 67639177, - 'gene_type': 'protein_coding', - 'name': 'CTCF', - 'hgnc': 'HGNC:13723', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'CFAP108', - 'CTCFL paralog', - '11 zinc finger transcriptional repressor', - 'CCCTC-binding factor (zinc finger protein)', - 'FAP108', - 'MRD21', - 'CTCF', - '11-zinc finger protein', - 'transcriptional repressor CTCF', - 'CCCTC-binding factor' - ] - }] - }, { - 'params': { - 'protein_id': 'P49711' - }, - 'response': [{ - '_id': 'ENSG00000102974', - 'chr': 'chr16', - 'start': 67562466, - 'end': 67639177, - 'gene_type': 'protein_coding', - 'name': 'CTCF', - 'hgnc': 'HGNC:13723', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': ['CFAP108', - 'CTCFL paralog', - '11 zinc finger transcriptional repressor', - 'CCCTC-binding factor (zinc finger protein)', - 'FAP108', - 'MRD21', - 'CTCF', - '11-zinc finger protein', - 'transcriptional repressor CTCF', - 'CCCTC-binding factor' - ] - }] - }] -} diff --git a/tests/acceptance_tests/proteins_motifs.py b/tests/acceptance_tests/proteins_motifs.py deleted file mode 100644 index bdd3ed20..00000000 --- a/tests/acceptance_tests/proteins_motifs.py +++ /dev/null @@ -1,104 +0,0 @@ -proteins_motifs = { - '/proteins/motifs': [{ - 'params': { - 'protein_id': 'P18846', - 'name': 'ATF1_HUMAN', - 'full_name': 'Cyclic AMP-dependent transcription factor ATF-1', - 'dbxrefs': 'Ensembl:ENSP00000262053.3', - 'verbose': 'false' - }, - 'response': [ - { - 'source': 'HOCOMOCOv11', - 'motif': 'motifs/ATF1_HUMAN_HOCOMOCOv11' - } - ]}, { - 'params': { - 'protein_id': 'P18846', - 'name': 'ATF1_HUMAN', - 'full_name': 'Cyclic AMP-dependent transcription factor ATF-1', - 'dbxrefs': 'Ensembl:ENSP00000262053.3', - 'verbose': 'true' - }, - 'response': [ - { - 'source': 'HOCOMOCOv11', - 'motif': { - 'name': 'ATF1_HUMAN_HOCOMOCOv11', - 'tf_name': 'ATF1_HUMAN', - 'length': 11, - 'pwm': [ - [ - '0.13987841615191168', - '0.3608848685361665', - '-0.4517428977281205', - '-0.25006525443490907' - ], - [ - '0.3553616298110878', - '-0.7707228823699511', - '0.3663777685862727', - '-0.4032800768485152' - ], - [ - '0.338606483241983', - '-0.8414816866844361', - '0.7066714674964639', - '-1.975404324094267' - ], - [ - '-2.4841943814369576', - '-3.324736791140142', - '-1.9754043240942667', - '1.3195988707291637' - ], - [ - '-2.3936647653320064', - '-2.9606438896517475', - '1.328010168941795', - '-2.4841943814369576' - ], - [ - '1.3217083373824634', - '-2.9606438896517475', - '-2.5837428525823363', - '-2.0963708769895044' - ], - [ - '-1.9754043240942667', - '1.191348924768384', - '-1.4888815002078464', - '-1.0666727869454955' - ], - [ - '-2.2340103118057417', - '-2.5837428525823363', - '1.2450934398879747', - '-1.0666727869454955' - ], - [ - '-1.1380405061628662', - '0.23796182230991783', - '-2.5837428525823363', - '0.8481840389725303' - ], - [ - '0.13987841615191168', - '0.6170180100710398', - '-0.5426512454816383', - '-0.8788317538331962' - ], - [ - '0.7561011054759478', - '-0.7707228823699511', - '-0.2914989252431338', - '-0.4151773801942997' - ] - ], - 'source': 'HOCOMOCOv11', - 'source_url': 'hocomoco11.autosome.org/motif/ATF1_HUMAN.H11MO.0.B' - } - } - ] - }] -} diff --git a/tests/acceptance_tests/proteins_proteins.py b/tests/acceptance_tests/proteins_proteins.py deleted file mode 100644 index dd441939..00000000 --- a/tests/acceptance_tests/proteins_proteins.py +++ /dev/null @@ -1,165 +0,0 @@ -proteins_proteins = { - '/proteins/proteins': [{ - 'params': { - 'protein_id': 'P31946', - 'name': '1433B_HUMAN', - 'detection method': 'affinity chromatography technology', - 'interaction type': 'physical association', - 'pmid': '28514442', - 'source': 'BioGRID', - 'verbose': 'false' - }, - 'response': [ - { - 'protein 1': 'proteins/A2RU30', - 'protein 2': 'proteins/P31946', - 'detection_method': 'affinity chromatography technology', - 'detection_method_code': 'MI:0004', - 'interaction_type': 'physical association', - 'interaction_type_code': 'MI:0915', - 'confidence_values': [ - '0.914379348' - ], - 'source': 'BioGRID', - 'pmids': [ - 'http://pubmed.ncbi.nlm.nih.gov/28514442' - ] - }, - { - 'protein 1': 'proteins/P31946', - 'protein 2': 'proteins/Q15884', - 'detection_method': 'affinity chromatography technology', - 'detection_method_code': 'MI:0004', - 'interaction_type': 'physical association', - 'interaction_type_code': 'MI:0915', - 'confidence_values': [ - '0.900399234' - ], - 'source': 'BioGRID', - 'pmids': [ - 'http://pubmed.ncbi.nlm.nih.gov/28514442' - ] - }, - { - 'protein 1': 'proteins/P31946', - 'protein 2': 'proteins/Q99469', - 'detection_method': 'affinity chromatography technology', - 'detection_method_code': 'MI:0004', - 'interaction_type': 'physical association', - 'interaction_type_code': 'MI:0915', - 'confidence_values': [ - '0.877400464' - ], - 'source': 'BioGRID', - 'pmids': [ - 'http://pubmed.ncbi.nlm.nih.gov/28514442' - ] - } - ] - }, { - 'params': { - 'protein_id': 'P31946', - 'name': '1433B_HUMAN', - 'detection method': 'affinity chromatography technology', - 'interaction type': 'physical association', - 'pmid': '28514442', - 'source': 'BioGRID', - 'verbose': 'true' - }, - 'response': [ - { - 'protein 1': [ - { - '_id': 'A2RU30', - 'name': 'TESP1_HUMAN', - 'full_name': 'Protein TESPA1', - 'source': 'UniProtKB/Swiss-Prot', - 'source_url': 'https://www.uniprot.org/help/downloads' - } - ], - 'protein 2': [ - { - '_id': 'P31946', - 'name': '1433B_HUMAN', - 'full_name': '14-3-3 protein beta/alpha', - 'source': 'UniProtKB/Swiss-Prot', - 'source_url': 'https://www.uniprot.org/help/downloads' - } - ], - 'detection_method': 'affinity chromatography technology', - 'detection_method_code': 'MI:0004', - 'interaction_type': 'physical association', - 'interaction_type_code': 'MI:0915', - 'confidence_values': [ - '0.914379348' - ], - 'source': 'BioGRID', - 'pmids': [ - 'http://pubmed.ncbi.nlm.nih.gov/28514442' - ] - }, - { - 'protein 1': [ - { - '_id': 'P31946', - 'name': '1433B_HUMAN', - 'full_name': '14-3-3 protein beta/alpha', - 'source': 'UniProtKB/Swiss-Prot', - 'source_url': 'https://www.uniprot.org/help/downloads' - } - ], - 'protein 2': [ - { - '_id': 'Q15884', - 'name': 'EREP1_HUMAN', - 'full_name': 'Endosomal transmembrane epsin interactor 1', - 'source': 'UniProtKB/Swiss-Prot', - 'source_url': 'https://www.uniprot.org/help/downloads' - } - ], - 'detection_method': 'affinity chromatography technology', - 'detection_method_code': 'MI:0004', - 'interaction_type': 'physical association', - 'interaction_type_code': 'MI:0915', - 'confidence_values': [ - '0.900399234' - ], - 'source': 'BioGRID', - 'pmids': [ - 'http://pubmed.ncbi.nlm.nih.gov/28514442' - ] - }, - { - 'protein 1': [ - { - '_id': 'P31946', - 'name': '1433B_HUMAN', - 'full_name': '14-3-3 protein beta/alpha', - 'source': 'UniProtKB/Swiss-Prot', - 'source_url': 'https://www.uniprot.org/help/downloads' - } - ], - 'protein 2': [ - { - '_id': 'Q99469', - 'name': 'STAC_HUMAN', - 'full_name': 'SH3 and cysteine-rich domain-containing protein', - 'source': 'UniProtKB/Swiss-Prot', - 'source_url': 'https://www.uniprot.org/help/downloads' - } - ], - 'detection_method': 'affinity chromatography technology', - 'detection_method_code': 'MI:0004', - 'interaction_type': 'physical association', - 'interaction_type_code': 'MI:0915', - 'confidence_values': [ - '0.877400464' - ], - 'source': 'BioGRID', - 'pmids': [ - 'http://pubmed.ncbi.nlm.nih.gov/28514442' - ] - } - ] - }] -} diff --git a/tests/acceptance_tests/proteins_transcripts.py b/tests/acceptance_tests/proteins_transcripts.py deleted file mode 100644 index 7c5b1104..00000000 --- a/tests/acceptance_tests/proteins_transcripts.py +++ /dev/null @@ -1,285 +0,0 @@ -proteins_transcripts = { - '/proteins/transcripts': [{ - 'params': { - 'name': 'CTCF_HUMAN', - 'dbxrefs': 'HGNC:13723', - 'verbose': 'false' - }, - 'response': [ - { - 'source': 'UniprotKB', - 'source_url': 'https://www.uniprot.org/uniprotkb', - 'transcript': 'transcripts/ENST00000264010' - }, - { - 'source': 'UniprotKB', - 'source_url': 'https://www.uniprot.org/uniprotkb', - 'transcript': 'transcripts/ENST00000401394' - }, - { - 'source': 'UniprotKB', - 'source_url': 'https://www.uniprot.org/uniprotkb', - 'transcript': 'transcripts/ENST00000642819' - }, - { - 'source': 'UniprotKB', - 'source_url': 'https://www.uniprot.org/uniprotkb', - 'transcript': 'transcripts/ENST00000644753' - }, - { - 'source': 'UniprotKB', - 'source_url': 'https://www.uniprot.org/uniprotkb', - 'transcript': 'transcripts/ENST00000645699' - }, - { - 'source': 'UniprotKB', - 'source_url': 'https://www.uniprot.org/uniprotkb', - 'transcript': 'transcripts/ENST00000646076' - } - ] - }, { - 'params': { - 'name': 'CTCF_HUMAN', - 'dbxrefs': 'HGNC:13723', - 'verbose': 'true' - }, - 'response': [ - { - 'source': 'UniprotKB', - 'source_url': 'https://www.uniprot.org/uniprotkb', - 'transcript': { - '_id': 'ENST00000264010', - 'transcript_type': 'protein_coding', - 'chr': 'chr16', - 'start': 67562525, - 'end': 67639177, - 'name': 'CTCF-201', - 'gene_name': 'CTCF', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/' - } - }, - { - 'source': 'UniprotKB', - 'source_url': 'https://www.uniprot.org/uniprotkb', - 'transcript': { - '_id': 'ENST00000401394', - 'transcript_type': 'protein_coding', - 'chr': 'chr16', - 'start': 67562572, - 'end': 67639168, - 'name': 'CTCF-202', - 'gene_name': 'CTCF', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/' - } - }, - { - 'source': 'UniprotKB', - 'source_url': 'https://www.uniprot.org/uniprotkb', - 'transcript': { - '_id': 'ENST00000642819', - 'transcript_type': 'protein_coding', - 'chr': 'chr16', - 'start': 67570772, - 'end': 67639162, - 'name': 'CTCF-205', - 'gene_name': 'CTCF', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/' - } - }, - { - 'source': 'UniprotKB', - 'source_url': 'https://www.uniprot.org/uniprotkb', - 'transcript': { - '_id': 'ENST00000644753', - 'transcript_type': 'protein_coding', - 'chr': 'chr16', - 'start': 67570740, - 'end': 67639175, - 'name': 'CTCF-209', - 'gene_name': 'CTCF', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/' - } - }, - { - 'source': 'UniprotKB', - 'source_url': 'https://www.uniprot.org/uniprotkb', - 'transcript': { - '_id': 'ENST00000645699', - 'transcript_type': 'protein_coding', - 'chr': 'chr16', - 'start': 67610589, - 'end': 67638966, - 'name': 'CTCF-214', - 'gene_name': 'CTCF', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/' - } - }, - { - 'source': 'UniprotKB', - 'source_url': 'https://www.uniprot.org/uniprotkb', - 'transcript': { - '_id': 'ENST00000646076', - 'transcript_type': 'protein_coding', - 'chr': 'chr16', - 'start': 67562466, - 'end': 67639176, - 'name': 'CTCF-215', - 'gene_name': 'CTCF', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/' - } - } - ] - }, { - 'params': { - 'protein_id': 'P49711', - 'verbose': 'false' - }, - 'response': [ - { - 'source': 'UniprotKB', - 'source_url': 'https://www.uniprot.org/uniprotkb', - 'transcript': 'transcripts/ENST00000264010' - }, - { - 'source': 'UniprotKB', - 'source_url': 'https://www.uniprot.org/uniprotkb', - 'transcript': 'transcripts/ENST00000401394' - }, - { - 'source': 'UniprotKB', - 'source_url': 'https://www.uniprot.org/uniprotkb', - 'transcript': 'transcripts/ENST00000642819' - }, - { - 'source': 'UniprotKB', - 'source_url': 'https://www.uniprot.org/uniprotkb', - 'transcript': 'transcripts/ENST00000644753' - }, - { - 'source': 'UniprotKB', - 'source_url': 'https://www.uniprot.org/uniprotkb', - 'transcript': 'transcripts/ENST00000645699' - }, - { - 'source': 'UniprotKB', - 'source_url': 'https://www.uniprot.org/uniprotkb', - 'transcript': 'transcripts/ENST00000646076' - } - ] - }, { - 'params': { - 'protein_id': 'P49711', - 'verbose': 'true' - }, - 'response': [ - { - 'source': 'UniprotKB', - 'source_url': 'https://www.uniprot.org/uniprotkb', - 'transcript': { - '_id': 'ENST00000264010', - 'transcript_type': 'protein_coding', - 'chr': 'chr16', - 'start': 67562525, - 'end': 67639177, - 'name': 'CTCF-201', - 'gene_name': 'CTCF', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/' - } - }, - { - 'source': 'UniprotKB', - 'source_url': 'https://www.uniprot.org/uniprotkb', - 'transcript': { - '_id': 'ENST00000401394', - 'transcript_type': 'protein_coding', - 'chr': 'chr16', - 'start': 67562572, - 'end': 67639168, - 'name': 'CTCF-202', - 'gene_name': 'CTCF', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/' - } - }, - { - 'source': 'UniprotKB', - 'source_url': 'https://www.uniprot.org/uniprotkb', - 'transcript': { - '_id': 'ENST00000642819', - 'transcript_type': 'protein_coding', - 'chr': 'chr16', - 'start': 67570772, - 'end': 67639162, - 'name': 'CTCF-205', - 'gene_name': 'CTCF', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/' - } - }, - { - 'source': 'UniprotKB', - 'source_url': 'https://www.uniprot.org/uniprotkb', - 'transcript': { - '_id': 'ENST00000644753', - 'transcript_type': 'protein_coding', - 'chr': 'chr16', - 'start': 67570740, - 'end': 67639175, - 'name': 'CTCF-209', - 'gene_name': 'CTCF', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/' - } - }, - { - 'source': 'UniprotKB', - 'source_url': 'https://www.uniprot.org/uniprotkb', - 'transcript': { - '_id': 'ENST00000645699', - 'transcript_type': 'protein_coding', - 'chr': 'chr16', - 'start': 67610589, - 'end': 67638966, - 'name': 'CTCF-214', - 'gene_name': 'CTCF', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/' - } - }, - { - 'source': 'UniprotKB', - 'source_url': 'https://www.uniprot.org/uniprotkb', - 'transcript': { - '_id': 'ENST00000646076', - 'transcript_type': 'protein_coding', - 'chr': 'chr16', - 'start': 67562466, - 'end': 67639176, - 'name': 'CTCF-215', - 'gene_name': 'CTCF', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/' - } - } - ] - }] -} diff --git a/tests/acceptance_tests/regulatory_regions.py b/tests/acceptance_tests/regulatory_regions.py deleted file mode 100644 index 2300e85f..00000000 --- a/tests/acceptance_tests/regulatory_regions.py +++ /dev/null @@ -1,63 +0,0 @@ -regulatory_regions = { - '/regulatory_regions': [{ - 'params': { - 'type': 'candidate_cis_regulatory_element', - 'region': 'chr1:1157520-1158189', - 'biochemical_activity': 'dELS', - 'source': 'ENCODE_SCREEN (ccREs)' - }, - 'response': [ - { - 'chr': 'chr1', - 'start': 1158135, - 'end': 1158445, - 'name': 'EH38E1310547', - 'biochemical_activity': 'dELS', - 'biochemical_activity_description': 'distal Enhancer-like signal', - 'type': 'candidate_cis_regulatory_element', - 'source': 'ENCODE_SCREEN (ccREs)', - 'source_url': 'https://www.encodeproject.org/files/ENCFF420VPZ/' - }, - { - 'chr': 'chr1', - 'start': 1157436, - 'end': 1157782, - 'name': 'EH38E2777055', - 'biochemical_activity': 'dELS', - 'biochemical_activity_description': 'distal Enhancer-like signal', - 'type': 'candidate_cis_regulatory_element', - 'source': 'ENCODE_SCREEN (ccREs)', - 'source_url': 'https://www.encodeproject.org/files/ENCFF420VPZ/' - }, - { - 'chr': 'chr1', - 'start': 1157885, - 'end': 1158053, - 'name': 'EH38E2777056', - 'biochemical_activity': 'dELS', - 'biochemical_activity_description': 'distal Enhancer-like signal', - 'type': 'candidate_cis_regulatory_element', - 'source': 'ENCODE_SCREEN (ccREs)', - 'source_url': 'https://www.encodeproject.org/files/ENCFF420VPZ/' - } - ] - }, { - 'params': { - 'organism': 'mouse', - 'region': 'chr1:117354694-117354959' - }, - 'response': [ - { - 'chr': 'chr1', - 'start': 117354694, - 'end': 117354959, - 'name': 'EM10E0001169', - 'biochemical_activity': 'CA-CTCF', - 'biochemical_activity_description': 'chromatin accessible + CTCF binding', - 'type': 'candidate_cis_regulatory_element', - 'source': 'ENCODE_SCREEN (ccREs)', - 'source_url': 'https://www.encodeproject.org/files/ENCFF167FJQ' - } - ] - }] -} diff --git a/tests/acceptance_tests/regulatory_regions_biosamples.py b/tests/acceptance_tests/regulatory_regions_biosamples.py deleted file mode 100644 index 614595eb..00000000 --- a/tests/acceptance_tests/regulatory_regions_biosamples.py +++ /dev/null @@ -1,81 +0,0 @@ -regulatory_regions_biosamples = { - '/regulatory_regions/biosamples': [{ - 'params': { - 'type': 'MPRA_expression_tested', - 'region': 'chr10:100038743-100038963', - 'verbose': 'false' - }, - 'response': [ - { - 'activity_score': 0.226, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/', - 'ontology term': 'ontology_terms/EFO_0001187' - }, - { - 'activity_score': -1.242, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF769REH/', - 'ontology term': 'ontology_terms/EFO_0009747' - }, - { - 'activity_score': -0.813, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF802FUV/', - 'ontology term': 'ontology_terms/EFO_0002067' - } - ]}, { - 'params': { - 'type': 'MPRA_expression_tested', - 'region': 'chr10:100038743-100038963', - 'verbose': 'true' - }, - 'response': [ - { - 'activity_score': 0.226, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF475FKV/', - 'ontology term': [ - { - 'uri': 'http://www.ebi.ac.uk/efo/EFO_0001187', - 'term_id': 'EFO_0001187', - 'name': 'hepg2', - 'description': 'human hepatocellular carcinoma (HCC) cells (p53-wt).', - 'source': 'EFO', - 'subontology': None - } - ] - }, - { - 'activity_score': -1.242, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF769REH/', - 'ontology term': [ - { - 'uri': 'http://www.ebi.ac.uk/efo/EFO_0009747', - 'term_id': 'EFO_0009747', - 'name': 'gm25256', - 'description': 'Induced pluripotent stem cell line derived from adult skin (leg) fibroblasts; subject clinically normal; wild-type; FISH test: 46, XY.', - 'source': 'EFO', - 'subontology': None - } - ] - }, - { - 'activity_score': -0.813, - 'source': 'ENCODE_MPRA', - 'source_url': 'https://www.encodeproject.org/files/ENCFF802FUV/', - 'ontology term': [ - { - 'uri': 'http://www.ebi.ac.uk/efo/EFO_0002067', - 'term_id': 'EFO_0002067', - 'name': 'k562', - 'description': 'Human chronic myeloid leukemia in blast crisis established from the pleural effusion of a 53-year-old woman with chronic myeloid leukemia (CML) in blast crisis in 1970; cells can be used as highly sensitive targets in in-vitro natural killer assays; cells produce hemoglobin; cells carry the Philadelphia chromosome with a b3-a2 fusion gene.', - 'source': 'EFO', - 'subontology': None - } - ] - } - ] - }] -} diff --git a/tests/acceptance_tests/regulatory_regions_genes.py b/tests/acceptance_tests/regulatory_regions_genes.py deleted file mode 100644 index c8e92aa8..00000000 --- a/tests/acceptance_tests/regulatory_regions_genes.py +++ /dev/null @@ -1,923 +0,0 @@ -regulatory_regions_genes = { - '/regulatory_regions/genes': [{ - 'params': { - 'type': 'candidate_cis_regulatory_element', - 'region': 'chr1:903900-904900', - 'biochemical_activity': 'ENH', - 'source': 'ENCODE-E2G-DNaseOnly', - 'verbose': 'false' - }, - 'response': [ - { - 'term_name': 'gm13977', - 'score': 0.3723573413012954, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF867ZSX/', - 'gene': 'genes/ENSG00000187583' - }, - { - 'term_name': 'gm13977', - 'score': 0.9034999636026824, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF867ZSX/', - 'gene': 'genes/ENSG00000187634' - }, - { - 'term_name': 'gm13977', - 'score': 0.2779527520706177, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF867ZSX/', - 'gene': 'genes/ENSG00000187642' - }, - { - 'term_name': 'gm13977', - 'score': 0.364082110186384, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF867ZSX/', - 'gene': 'genes/ENSG00000187961' - }, - { - 'term_name': 'gm13977', - 'score': 0.4635109914878867, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF867ZSX/', - 'gene': 'genes/ENSG00000188976' - }, - { - 'term_name': 'gm20000', - 'score': 0.3147376026708981, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF160KXF/', - 'gene': 'genes/ENSG00000187634' - }, - { - 'term_name': 'germinal center', - 'score': 0.4657965200430012, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF803JTD/', - 'gene': 'genes/ENSG00000187583' - }, - { - 'term_name': 'germinal center', - 'score': 0.8897321887480919, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF803JTD/', - 'gene': 'genes/ENSG00000187634' - }, - { - 'term_name': 'germinal center', - 'score': 0.4638311564003655, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF803JTD/', - 'gene': 'genes/ENSG00000187961' - }, - { - 'term_name': 'germinal center', - 'score': 0.5335650795288112, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF803JTD/', - 'gene': 'genes/ENSG00000188976' - }, - { - 'term_name': 'gm10266', - 'score': 0.3406031376248598, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF127QRX/', - 'gene': 'genes/ENSG00000187583' - }, - { - 'term_name': 'gm10266', - 'score': 0.8656274709002525, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF127QRX/', - 'gene': 'genes/ENSG00000187634' - }, - { - 'term_name': 'gm10266', - 'score': 0.3147830446567518, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF127QRX/', - 'gene': 'genes/ENSG00000187642' - }, - { - 'term_name': 'gm10266', - 'score': 0.3630857524296153, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF127QRX/', - 'gene': 'genes/ENSG00000187961' - }, - { - 'term_name': 'gm10266', - 'score': 0.46200060499669504, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF127QRX/', - 'gene': 'genes/ENSG00000188976' - }, - { - 'term_name': 'lower leg skin', - 'score': 0.33477313588501445, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF557BXA/', - 'gene': 'genes/ENSG00000187634' - }, - { - 'term_name': 'type b pancreatic cell', - 'score': 0.2949658163495387, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF766CCV/', - 'gene': 'genes/ENSG00000187583' - }, - { - 'term_name': 'type b pancreatic cell', - 'score': 0.7018896710881366, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF766CCV/', - 'gene': 'genes/ENSG00000187634' - }, - { - 'term_name': 'type b pancreatic cell', - 'score': 0.21162151723038655, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF766CCV/', - 'gene': 'genes/ENSG00000187642' - }, - { - 'term_name': 'type b pancreatic cell', - 'score': 0.3338513170681796, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF766CCV/', - 'gene': 'genes/ENSG00000187961' - }, - { - 'term_name': 'type b pancreatic cell', - 'score': 0.3686060170577029, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF766CCV/', - 'gene': 'genes/ENSG00000188976' - }, - { - 'term_name': 'type b pancreatic cell', - 'score': 0.42470187448508967, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF766CCV/', - 'gene': 'genes/ENSG00000225880' - }, - { - 'term_name': 'type b pancreatic cell', - 'score': 0.4255071709653973, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF766CCV/', - 'gene': 'genes/ENSG00000228794' - }, - { - 'term_name': 'left lobe of liver', - 'score': 0.2277319768193479, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF059DHV/', - 'gene': 'genes/ENSG00000187583' - }, - { - 'term_name': 'left lobe of liver', - 'score': 0.6572571797148196, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF059DHV/', - 'gene': 'genes/ENSG00000187634' - } - ] - }, { - 'params': { - 'type': 'candidate_cis_regulatory_element', - 'region': 'chr1:903900-904900', - 'biochemical_activity': 'ENH', - 'source': 'ENCODE-E2G-DNaseOnly', - 'verbose': 'true' - }, - 'response': [ - { - 'term_name': 'gm13977', - 'score': 0.3723573413012954, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF867ZSX/', - 'gene': [ - { - '_id': 'ENSG00000187583', - 'chr': 'chr1', - 'start': 966481, - 'end': 975865, - 'gene_type': 'protein_coding', - 'name': 'PLEKHN1', - 'hgnc': 'HGNC:25284', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'PLEKHN1', - 'cardiolipin and phosphatidic acid-binding protein', - 'CLPABP', - 'PH domain-containing family N member 1', - 'pleckstrin homology domain-containing family N member 1', - 'pleckstrin homology domain containing N1' - ] - } - ] - }, - { - 'term_name': 'gm13977', - 'score': 0.9034999636026824, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF867ZSX/', - 'gene': [ - { - '_id': 'ENSG00000187634', - 'chr': 'chr1', - 'start': 923922, - 'end': 944575, - 'gene_type': 'protein_coding', - 'name': 'SAMD11', - 'hgnc': 'HGNC:28706', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'SAMD11', - 'sterile alpha motif domain-containing protein 11', - 'sterile alpha motif domain containing 11', - 'MRS', - 'SAM domain-containing protein 11' - ] - } - ] - }, - { - 'term_name': 'gm13977', - 'score': 0.2779527520706177, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF867ZSX/', - 'gene': [ - { - '_id': 'ENSG00000187642', - 'chr': 'chr1', - 'start': 975197, - 'end': 982117, - 'gene_type': 'protein_coding', - 'name': 'PERM1', - 'hgnc': 'HGNC:28208', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'PGC-1 and ERR-induced regulator in muscle 1', - 'PGC-1 and ERR-induced regulator in muscle protein 1', - 'PPARGC1 and ESRR induced regulator, muscle 1', - 'C1orf170', - 'PPARGC1 and ESRR-induced regulator in muscle 1', - 'PERM1', - 'peroxisome proliferator-activated receptor gamma coactivator 1 and estrogen-related receptor-induced regulator in muscle 1', - 'pGC-1 and ERR-induced regulator in muscle protein 1' - ] - } - ] - }, - { - 'term_name': 'gm13977', - 'score': 0.364082110186384, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF867ZSX/', - 'gene': [ - { - '_id': 'ENSG00000187961', - 'chr': 'chr1', - 'start': 960583, - 'end': 965719, - 'gene_type': 'protein_coding', - 'name': 'KLHL17', - 'hgnc': 'HGNC:24023', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'kelch-like protein 17', - 'actinfilin', - 'kelch like family member 17', - 'kelch-like 17', - 'KLHL17', - 'AF' - ] - } - ] - }, - { - 'term_name': 'gm13977', - 'score': 0.4635109914878867, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF867ZSX/', - 'gene': [ - { - '_id': 'ENSG00000188976', - 'chr': 'chr1', - 'start': 944202, - 'end': 959309, - 'gene_type': 'protein_coding', - 'name': 'NOC2L', - 'hgnc': 'HGNC:24517', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'protein NOC2 homolog', - 'NET15', - 'novel INHAT (inhibitor of histone acetyltransferase) repressor', - 'nucleolar complex associated 2 homolog', - 'NOC2L', - 'NET7', - 'NOC2-like protein', - 'NOC2 like nucleolar associated transcriptional repressor', - 'protein phosphatase 1, regulatory subunit 12', - 'novel INHAT repressor', - 'NOC2L nucleolar associated transcriptional repressor', - 'NIR', - 'nucleolar complex protein 2 homolog', - 'PPP1R112' - ] - } - ] - }, - { - 'term_name': 'gm20000', - 'score': 0.3147376026708981, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF160KXF/', - 'gene': [ - { - '_id': 'ENSG00000187634', - 'chr': 'chr1', - 'start': 923922, - 'end': 944575, - 'gene_type': 'protein_coding', - 'name': 'SAMD11', - 'hgnc': 'HGNC:28706', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'SAMD11', - 'sterile alpha motif domain-containing protein 11', - 'sterile alpha motif domain containing 11', - 'MRS', - 'SAM domain-containing protein 11' - ] - } - ] - }, - { - 'term_name': 'germinal center', - 'score': 0.4657965200430012, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF803JTD/', - 'gene': [ - { - '_id': 'ENSG00000187583', - 'chr': 'chr1', - 'start': 966481, - 'end': 975865, - 'gene_type': 'protein_coding', - 'name': 'PLEKHN1', - 'hgnc': 'HGNC:25284', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'PLEKHN1', - 'cardiolipin and phosphatidic acid-binding protein', - 'CLPABP', - 'PH domain-containing family N member 1', - 'pleckstrin homology domain-containing family N member 1', - 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] - } - ] - }, - { - 'term_name': 'gm10266', - 'score': 0.46200060499669504, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF127QRX/', - 'gene': [ - { - '_id': 'ENSG00000188976', - 'chr': 'chr1', - 'start': 944202, - 'end': 959309, - 'gene_type': 'protein_coding', - 'name': 'NOC2L', - 'hgnc': 'HGNC:24517', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'protein NOC2 homolog', - 'NET15', - 'novel INHAT (inhibitor of histone acetyltransferase) repressor', - 'nucleolar complex associated 2 homolog', - 'NOC2L', - 'NET7', - 'NOC2-like protein', - 'NOC2 like nucleolar associated transcriptional repressor', - 'protein phosphatase 1, regulatory subunit 12', - 'novel INHAT repressor', - 'NOC2L nucleolar associated transcriptional repressor', - 'NIR', - 'nucleolar complex protein 2 homolog', - 'PPP1R112' - ] - } - ] - }, - { - 'term_name': 'lower leg skin', - 'score': 0.33477313588501445, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF557BXA/', - 'gene': [ - { - '_id': 'ENSG00000187634', - 'chr': 'chr1', - 'start': 923922, - 'end': 944575, - 'gene_type': 'protein_coding', - 'name': 'SAMD11', - 'hgnc': 'HGNC:28706', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'SAMD11', - 'sterile alpha motif domain-containing protein 11', - 'sterile alpha motif domain containing 11', - 'MRS', - 'SAM domain-containing protein 11' - ] - } - ] - }, - { - 'term_name': 'type b pancreatic cell', - 'score': 0.2949658163495387, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF766CCV/', - 'gene': [ - { - '_id': 'ENSG00000187583', - 'chr': 'chr1', - 'start': 966481, - 'end': 975865, - 'gene_type': 'protein_coding', - 'name': 'PLEKHN1', - 'hgnc': 'HGNC:25284', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 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'https://www.encodeproject.org/files/ENCFF766CCV/', - 'gene': [ - { - '_id': 'ENSG00000187961', - 'chr': 'chr1', - 'start': 960583, - 'end': 965719, - 'gene_type': 'protein_coding', - 'name': 'KLHL17', - 'hgnc': 'HGNC:24023', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'kelch-like protein 17', - 'actinfilin', - 'kelch like family member 17', - 'kelch-like 17', - 'KLHL17', - 'AF' - ] - } - ] - }, - { - 'term_name': 'type b pancreatic cell', - 'score': 0.3686060170577029, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF766CCV/', - 'gene': [ - { - '_id': 'ENSG00000188976', - 'chr': 'chr1', - 'start': 944202, - 'end': 959309, - 'gene_type': 'protein_coding', - 'name': 'NOC2L', - 'hgnc': 'HGNC:24517', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'protein NOC2 homolog', - 'NET15', - 'novel INHAT (inhibitor of 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'cardiolipin and phosphatidic acid-binding protein', - 'CLPABP', - 'PH domain-containing family N member 1', - 'pleckstrin homology domain-containing family N member 1', - 'pleckstrin homology domain containing N1' - ] - } - ] - }, - { - 'term_name': 'left lobe of liver', - 'score': 0.6572571797148196, - 'source': 'ENCODE-E2G-DNaseOnly', - 'source_url': 'https://www.encodeproject.org/files/ENCFF059DHV/', - 'gene': [ - { - '_id': 'ENSG00000187634', - 'chr': 'chr1', - 'start': 923922, - 'end': 944575, - 'gene_type': 'protein_coding', - 'name': 'SAMD11', - 'hgnc': 'HGNC:28706', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'SAMD11', - 'sterile alpha motif domain-containing protein 11', - 'sterile alpha motif domain containing 11', - 'MRS', - 'SAM domain-containing protein 11' - ] - } - ] - } - ] - }] -} diff --git a/tests/acceptance_tests/sqtls.py b/tests/acceptance_tests/sqtls.py deleted file mode 100644 index 85f5ebf1..00000000 --- a/tests/acceptance_tests/sqtls.py +++ /dev/null @@ -1,5198 +0,0 @@ -sqtls = { - '/variants/genes': [{ - 'params': { - 'p_value': 'lte:0.01', - 'label': 'splice_QTL', - 'verbose': 'false' - }, - 'response': [ - { - 'sequence variant': 'variants/beefe645ce50d0cb68a4af0cd4f3894d662b1a2d3253bff82b9a4ad33f46ebee', - 'gene': 'genes/ENSG00000196126', - 'beta': 1.00545e-185, - 'label': 'splice_QTL', - 'log10pvalue': 47.31058191489651, - 'slope': -1.30689, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'suprapubic skin', - 'chr': 'chr6', - 'intron_chr': 'chr6', - 'intron_start': 32517752, - 'intron_end': 32518054 - }, - { - 'sequence variant': 'variants/1a8989e965641c5692b20f48bcb37b2098a0e24105a80fbb7f4c0328c3e27e6f', - 'gene': 'genes/ENSG00000173295', - 'beta': 1.02933e-30, - 'label': 'splice_QTL', - 'log10pvalue': 9.526952656200873, - 'slope': 0.379832, - 'source': 'GTEx', - 'source_url': 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- 'source': 'FAVOR', - 'source_url': 'http://favor.genohub.org/', - 'annotations': { - 'freq': { - '1000genomes': { - 'ref:long': 0.8325, - 'alt:long': 0.1675 - }, - 'alspac': { - 'ref:long': 0.7174, - 'alt:long': 0.2826 - }, - 'daghestan': { - 'ref:long': 0.7929, - 'alt:long': 0.2071 - }, - 'estonian': { - 'ref:long': 0.6848, - 'alt:long': 0.3152 - }, - 'exac': { - 'ref:long': 0.7113, - 'alt:long': 0.2887 - }, - 'finrisk': { - 'ref:long': 0.7107, - 'alt:long': 0.2893 - }, - 'genome_dk': { - 'ref:long': 0.525, - 'alt:long': 0.475 - }, - 'gnomad': { - 'ref:long': 0.7728, - 'alt:long': 0.2272 - }, - 'gnomad_exomes': { - 'ref:long': 0.7651, - 'alt:long': 0.2349 - }, - 'goesp': { - 'ref:long': 0.7676, - 'alt:long': 0.2324 - }, - 'gonl': { - 'ref:long': 0.7124, - 'alt:long': 0.2876 - }, - 'korean': { - 'ref:long': 0.86, - 'alt:long': 0.14 - }, - 'korea1k': { - 'ref:long': 0.8706, - 'alt:long': 0.1294 - }, - 'mgp': { - 'ref:long': 0.7622, - 'alt:long': 0.2378 - }, - 'northernsweden': { - 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'3.20576e+07', - 'ref_annovar': 'CT', - 'alt_annovar': '-', - 'ref_vcf': 'ACT', - 'alt_vcf': 'A', - 'bravo_an': '264690', - 'bravo_af': '0.113979', - 'filter_status': 'PASS', - 'af_total': 0.112065, - 'af_asj_female': 0.0862656, - 'af_eas_female': 0.0372928, - 'af_afr_male': 0.184437, - 'af_female': 0.11444, - 'af_fin_male': 0.0533736, - 'af_oth_female': 0.10929, - 'af_ami': 0.175615, - 'af_oth': 0.104554, - 'af_male': 0.109538, - 'af_ami_female': 0.17094, - 'af_afr': 0.185814, - 'af_eas_male': 0.0421615, - 'af_sas': 0.15448, - 'af_nfe_female': 0.087415, - 'af_asj_male': 0.103846, - 'af_raw': 0.112217, - 'af_oth_male': 0.0996205, - 'af_nfe_male': 0.0877587, - 'af_asj': 0.0945214, - 'af_amr_male': 0.0546088, - 'af_amr_female': 0.0536379, - 'af_fin': 0.0538756, - 'af_afr_female': 0.186987, - 'af_sas_male': 0.157916, - 'af_amr': 0.0541886, - 'af_nfe': 0.0875597, - 'af_eas': 0.0399106, - 'af_ami_male': 0.180751, - 'af_fin_female': 0.0554669, - 'cadd_rawscore': '-0.283074', - 'cadd_phred': 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'vietnamese': { - 'ref:long': 0.3785, - 'alt:long': 0.6215 - }, - 'dbgap_popfreq': { - 'ref:long': 0.532, - 'alt:long': 0.468 - } - }, - 'varinfo': '8-144462092-G-A', - 'vid': '7.90177e+09', - 'variant_vcf': '8-144462092-G-A', - 'variant_annovar': '8-144462092-144462092-G-A', - 'start_position': '1.44462e+08', - 'end_position': '1.44462e+08', - 'ref_annovar': 'G', - 'alt_annovar': 'A', - 'ref_vcf': 'G', - 'alt_vcf': 'A', - 'apc_conservation': 1.90138, - 'apc_conservation_v2': 4.30169, - 'apc_epigenetics_active': 25.5662, - 'apc_epigenetics': 22.5931, - 'apc_epigenetics_repressed': 2.50671, - 'apc_epigenetics_transcription': 15.4886, - 'apc_local_nucleotide_diversity': 1.15872, - 'apc_local_nucleotide_diversity_v2': 0.0172545, - 'apc_local_nucleotide_diversity_v3': 0.0328091, - 'apc_mappability': 2.26089, - 'apc_micro_rna': 99.4512, - 'apc_mutation_density': 0.0173821, - 'apc_protein_function': 20.2494, - 'apc_protein_function_v2': 4.92793e-10, - 'apc_protein_function_v3': 2.96949, - 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-0.355645, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'tibial nerve', - 'chr': 'chr8', - 'intron_chr': 'chr8', - 'intron_start': 144450770, - 'intron_end': 144452359 - }, - { - 'sequence variant': { - '_id': 'ce034d93a37aedd0ecde7adb3044e03be26b444f3314a6b13bce9aa9dc8d9b15', - 'chr': 'chr16', - 'pos': 78270007, - 'rsid': [ - 'rs12444769' - ], - 'ref': 'A', - 'alt': 'G', - 'spdi': 'NC_000016.10:78270007:A:G', - 'hgvs': 'NC_000016.10:g.78270008A>G', - 'qual': '.', - 'filter': None, - 'format': '.', - 'source': 'FAVOR', - 'source_url': 'http://favor.genohub.org/', - 'annotations': { - 'freq': { - '1000genomes': { - 'ref:long': 0.2774, - 'alt:long': 0.7226 - }, - 'alspac': { - 'ref:long': 0.4458, - 'alt:long': 0.5542 - }, - 'estonian': { - 'ref:long': 0.5748, - 'alt:long': 0.4252 - }, - 'genome_dk': { - 'ref:long': 0.375, - 'alt:long': 0.625 - }, - 'gnomad': { - 'ref:long': 0.3766, - 'alt:long': 0.6234 - }, - 'gonl': { - 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'G', - 'ref_vcf': 'A', - 'alt_vcf': 'G', - 'apc_conservation': 15.064, - 'apc_conservation_v2': 14.7884, - 'apc_epigenetics_active': 0.627318, - 'apc_epigenetics': 1.01436, - 'apc_epigenetics_repressed': 4.88515, - 'apc_epigenetics_transcription': 5.5662, - 'apc_local_nucleotide_diversity': 0.567576, - 'apc_local_nucleotide_diversity_v2': 0.0817039, - 'apc_local_nucleotide_diversity_v3': 0.0833533, - 'apc_mappability': 5.18561, - 'apc_micro_rna': 99.4512, - 'apc_mutation_density': 0.0846675, - 'apc_protein_function': 20.2494, - 'apc_protein_function_v2': 4.92793e-10, - 'apc_protein_function_v3': 2.96949, - 'apc_proximity_to_coding': 4.22027, - 'apc_proximity_to_coding_v2': 15.1786, - 'apc_proximity_to_tsstes': 5.77062, - 'apc_transcription_factor': 6.67311, - 'bravo_an': '264690', - 'bravo_af': '0.644743', - 'filter_status': 'PASS', - 'fathmm_xf': '3.66101', - 'funseq_description': 'noncoding', - 'af_total': 0.624623, - 'af_asj_female': 0.646992, - 'af_eas_female': 0.885417, - 'af_afr_male': 0.790184, - 'af_female': 0.627867, - 'af_fin_male': 0.439603, - 'af_oth_female': 0.63945, - 'af_ami': 0.521158, - 'af_oth': 0.636664, - 'af_male': 0.62116, - 'af_ami_female': 0.553419, - 'af_afr': 0.785393, - 'af_eas_male': 0.894174, - 'af_sas': 0.682577, - 'af_nfe_female': 0.544038, - 'af_asj_male': 0.65621, - 'af_raw': 0.625588, - 'af_oth_male': 0.633721, - 'af_nfe_male': 0.543112, - 'af_asj': 0.651324, - 'af_amr_male': 0.575698, - 'af_amr_female': 0.581765, - 'af_fin': 0.442642, - 'af_afr_female': 0.781309, - 'af_sas_male': 0.689245, - 'af_amr': 0.578324, - 'af_nfe': 0.543648, - 'af_eas': 0.890135, - 'af_ami_male': 0.486047, - 'af_fin_female': 0.452167, - 'cadd_rawscore': '1.0916', - 'cadd_phred': '13.05', - 'tg_afr': '0.8313', - 'tg_all': '0.722644', - 'tg_amr': '0.5173', - 'tg_eas': '0.8631', - 'tg_eur': '0.5606', - 'tg_sas': '0.7434' - } - }, - 'gene': { - '_id': 'ENSG00000186153', - 'chr': 'chr16', - 'start': 78099399, - 'end': 79212667, - 'gene_id': 'ENSG00000186153.18', - 'hgnc': 'HGNC:12799', - 'name': 'WWOX', - 'gene_type': 'protein_coding', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'SDR41C1', - 'WWOX', - 'short chain dehydrogenase/reductase family 41C member 1', - 'WOX1', - 'DEE28', - 'EIEE28', - 'SCAR12', - 'PRO0128', - 'fragile site FRA16D oxidoreductase', - 'WW domain-containing oxidoreductase', - 'WW domain-containing protein WWOX', - 'FRA16D', - 'WW domain containing oxidoreductase', - 'HHCMA56', - 'FOR', - 'D16S432E' - ] - }, - 'beta': 2.18892e-12, - 'label': 'splice_QTL', - 'log10pvalue': 12.78602561066493, - 'slope': 0.492844, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'suprapubic skin', - 'chr': 'chr16', - 'intron_chr': 'chr16', - 'intron_start': 78164289, - 'intron_end': 78386860 - }, - { - 'sequence variant': { - '_id': '224657e8313bed9c6d05c4ddc1bd402b50fa937e0727ad8d1898607b0e84e4c9', - 'chr': 'chr11', - 'pos': 125751324, - 'rsid': [ - 'rs497125' - ], - 'ref': 'T', - 'alt': 'C', - 'spdi': 'NC_000011.10:125751324:T:C', - 'hgvs': 'NC_000011.10:g.125751325T>C', - 'qual': '.', - 'filter': None, - 'format': '.', - 'source': 'FAVOR', - 'source_url': 'http://favor.genohub.org/', - 'annotations': { - 'freq': { - '1000genomes': { - 'ref:long': 0.1759, - 'alt:long': 0.8241 - }, - 'alspac': { - 'ref:long': 0.1876, - 'alt:long': 0.8124 - }, - 'daghestan': { - 'ref:long': 0.1989, - 'alt:long': 0.8011 - }, - 'estonian': { - 'ref:long': 0.1578, - 'alt:long': 0.8422 - }, - 'genome_dk': { - 'ref:long': 0.075, - 'alt:long': 0.925 - }, - 'gnomad': { - 'ref:long': 0.1621, - 'alt:long': 0.8379 - }, - 'gonl': { - 'ref:long': 0.1623, - 'alt:long': 0.8377 - }, - 'hapmap': { - 'ref:long': 0.13, - 'alt:long': 0.87 - }, - 'korean': { - 'ref:long': 0.1829, - 'alt:long': 0.8171 - }, - 'korea1k': { - 'ref:long': 0.1785, - 'alt:long': 0.8215 - }, - 'northernsweden': { - 'ref:long': 0.2317, - 'alt:long': 0.7683 - }, - 'qatari': { - 'ref:long': 0.09722, - 'alt:long': 0.9028 - }, - 'sgdp_prj': { - 'ref:long': 0.1586, - 'alt:long': 0.8414 - }, - 'siberian': { - 'ref:long': 0.1607, - 'alt:long': 0.8393 - }, - 'tommo': { - 'ref:long': 0.2133, - 'alt:long': 0.7867 - }, - 'topmed': { - 'ref:long': 0.1662, - 'alt:long': 0.8338 - }, - 'twinsuk': { - 'ref:long': 0.1901, - 'alt:long': 0.8099 - }, - 'vietnamese': { - 'ref:long': 0.1604, - 'alt:long': 0.8396 - }, - 'dbgap_popfreq': { - 'ref:long': 0.1755, - 'alt:long': 0.8245 - } - }, - 'varinfo': '11-125751325-T-C', - 'vid': '1.46686e+09', - 'variant_vcf': '11-125751325-T-C', - 'variant_annovar': '11-125751325-125751325-T-C', - 'start_position': '1.25751e+08', - 'end_position': '1.25751e+08', - 'ref_annovar': 'T', - 'alt_annovar': 'C', - 'ref_vcf': 'T', - 'alt_vcf': 'C', - 'apc_conservation': 6.73876, - 'apc_conservation_v2': 6.51449, - 'apc_epigenetics_active': 1.6063, - 'apc_epigenetics': 1.94822, - 'apc_epigenetics_repressed': 4.59744, - 'apc_epigenetics_transcription': 1.21181, - 'apc_local_nucleotide_diversity': 9.22229, - 'apc_local_nucleotide_diversity_v2': 4.4116, - 'apc_local_nucleotide_diversity_v3': 3.24951, - 'apc_mappability': 8.10064, - 'apc_micro_rna': 99.4512, - 'apc_mutation_density': 3.96969, - 'apc_protein_function': 20.2494, - 'apc_protein_function_v2': 4.92793e-10, - 'apc_protein_function_v3': 2.96949, - 'apc_proximity_to_coding': 0.287503, - 'apc_proximity_to_coding_v2': 15.1786, - 'apc_proximity_to_tsstes': 9.37327, - 'apc_transcription_factor': 3.14279, - 'bravo_an': '264690', - 'bravo_af': '0.833753', - 'filter_status': 'PASS', - 'fathmm_xf': '5.28609', - 'funseq_description': 'noncoding', - 'af_total': 0.838145, - 'af_asj_female': 0.876705, - 'af_eas_female': 0.820885, - 'af_afr_male': 0.905292, - 'af_female': 0.841103, - 'af_fin_male': 0.795936, - 'af_oth_female': 0.807273, - 'af_ami': 0.715556, - 'af_oth': 0.81797, - 'af_male': 0.834997, - 'af_ami_female': 0.723404, - 'af_afr': 0.904968, - 'af_eas_male': 0.839074, - 'af_sas': 0.850099, - 'af_nfe_female': 0.824263, - 'af_asj_male': 0.878205, - 'af_raw': 0.837892, - 'af_oth_male': 0.829198, - 'af_nfe_male': 0.822867, - 'af_asj': 0.87741, - 'af_amr_male': 0.734351, - 'af_amr_female': 0.730613, - 'af_fin': 0.797466, - 'af_afr_female': 0.904693, - 'af_sas_male': 0.853796, - 'af_amr': 0.732732, - 'af_nfe': 0.823675, - 'af_eas': 0.830671, - 'af_ami_male': 0.706977, - 'af_fin_female': 0.802326, - 'cadd_rawscore': '0.720345', - 'cadd_phred': '9.197', - 'tg_afr': '0.9107', - 'tg_all': '0.824081', - 'tg_amr': '0.6873', - 'tg_eas': '0.8393', - 'tg_eur': '0.8221', - 'tg_sas': '0.7904' - } - }, - 'gene': { - '_id': 'ENSG00000110060', - 'chr': 'chr11', - 'start': 125893484, - 'end': 125903221, - 'gene_id': 'ENSG00000110060.9', - 'hgnc': 'HGNC:25461', - 'name': 'PUS3', - 'gene_type': 'protein_coding', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'pseudouridine synthase 3', - 'DEG1', - 'NEDMIGS', - '2610020J05Rik', - 'tRNA pseudouridine synthase 3', - 'tRNA-uridine isomerase 3', - 'MRT55', - 'PUS3', - 'FKSG32', - 'pseudouridylate synthase 3', - 'tRNA pseudouridine(38/39) synthase', - 'tRNA pseudouridylate synthase 3' - ] - }, - 'beta': 3.00634e-8, - 'label': 'splice_QTL', - 'log10pvalue': 5.267862871429704, - 'slope': -0.35073, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'tibial artery', - 'chr': 'chr11', - 'intron_chr': 'chr11', - 'intron_start': 125895789, - 'intron_end': 125903170 - } - ] - }] -} diff --git a/tests/acceptance_tests/studies.py b/tests/acceptance_tests/studies.py deleted file mode 100644 index dd4bde1e..00000000 --- a/tests/acceptance_tests/studies.py +++ /dev/null @@ -1,32 +0,0 @@ -studies = { - '/studies': [{ - 'params': { - 'study_id': 'GCST007798', - 'pmid': '30929738' - }, - 'response': [ - { - '_id': 'GCST007798', - 'name': 'GCST007798', - 'ancestry_initial': "['European=341215']", - 'ancestry_replication': '[]', - 'n_cases': '40544.0', - 'n_initial': '341215', - 'n_replication': '', - 'pmid': 'PMID:30929738', - 'pub_author': 'Ferreira MAR', - 'pub_date': '2019-03-28', - 'pub_journal': 'Am J Hum Genet', - 'pub_title': 'Genetic Architectures of Childhood- and Adult-Onset Asthma Are Partly Distinct.', - 'has_sumstats': 'False', - 'num_assoc_loci': '75', - 'study_source': 'GCST', - 'trait_reported': 'Asthma', - 'trait_efos': "['MONDO_0004979']", - 'trait_category': 'respiratory or thoracic disease', - 'source': 'OpenTargets', - 'version': 'October 2022 (22.10)' - } - ] - }] -} diff --git a/tests/acceptance_tests/transcripts.py b/tests/acceptance_tests/transcripts.py deleted file mode 100644 index af798914..00000000 --- a/tests/acceptance_tests/transcripts.py +++ /dev/null @@ -1,122 +0,0 @@ -transcripts = { - '/transcripts': [{ - 'params': { - 'region': 'chr1:711800-740000', - 'transcript_type': 'processed_transcript' - }, - 'response': [ - { - '_id': 'ENST00000419394', - 'transcript_type': 'processed_transcript', - 'chr': 'chr1', - 'start': 586944, - 'end': 720194, - 'name': 'ENST00000419394', - 'gene_name': 'ENSG00000230021', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/' - }, - { - '_id': 'ENST00000635509', - 'transcript_type': 'processed_transcript', - 'chr': 'chr1', - 'start': 594307, - 'end': 827769, - 'name': 'ENST00000635509', - 'gene_name': 'ENSG00000230021', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/' - }, - { - '_id': 'ENST00000634337', - 'transcript_type': 'processed_transcript', - 'chr': 'chr1', - 'start': 594307, - 'end': 827796, - 'name': 'ENST00000634337', - 'gene_name': 'ENSG00000230021', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/' - }, - { - '_id': 'ENST00000648019', - 'transcript_type': 'processed_transcript', - 'chr': 'chr1', - 'start': 594457, - 'end': 733064, - 'name': 'ENST00000648019', - 'gene_name': 'ENSG00000230021', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/' - }, - { - '_id': 'ENST00000440200', - 'transcript_type': 'processed_transcript', - 'chr': 'chr1', - 'start': 601435, - 'end': 720200, - 'name': 'ENST00000440200', - 'gene_name': 'ENSG00000230021', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/' - }, - { - '_id': 'ENST00000441245', - 'transcript_type': 'processed_transcript', - 'chr': 'chr1', - 'start': 701935, - 'end': 720150, - 'name': 'ENST00000441245', - 'gene_name': 'ENSG00000230021', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/' - }, - { - '_id': 'ENST00000414688', - 'transcript_type': 'processed_transcript', - 'chr': 'chr1', - 'start': 711866, - 'end': 732212, - 'name': 'ENST00000414688', - 'gene_name': 'ENSG00000230021', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/' - }, - { - '_id': 'ENST00000447954', - 'transcript_type': 'processed_transcript', - 'chr': 'chr1', - 'start': 720052, - 'end': 724564, - 'name': 'ENST00000447954', - 'gene_name': 'ENSG00000230021', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/' - } - ] - }, { - 'params': { - 'transcript_id': 'ENST00000447954' - }, - 'response': { - '_id': 'ENST00000447954', - 'transcript_type': 'processed_transcript', - 'chr': 'chr1', - 'start': 720052, - 'end': 724564, - 'name': 'ENST00000447954', - 'gene_name': 'ENSG00000230021', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/' - } - }] -} diff --git a/tests/acceptance_tests/transcripts_genes.py b/tests/acceptance_tests/transcripts_genes.py deleted file mode 100644 index 590400f7..00000000 --- a/tests/acceptance_tests/transcripts_genes.py +++ /dev/null @@ -1,99 +0,0 @@ -transcripts_genes = { - '/transcripts/genes': [{ - 'params': { - 'transcript_type': 'processed_pseudogene', - 'region': 'chr1:711800-740000', - 'verbose': 'false' - }, - 'response': [ - { - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'version': 'v43', - 'gene': 'genes/ENSG00000229376' - } - ] - }, { - 'params': { - 'transcript_type': 'processed_pseudogene', - 'region': 'chr1:711800-740000', - 'verbose': 'true' - }, - 'response': [ - { - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'version': 'v43', - 'gene': { - '_id': 'ENSG00000229376', - 'chr': 'chr1', - 'start': 722091, - 'end': 724903, - 'gene_type': 'processed_pseudogene', - 'hgnc': 'HGNC:37742', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'capicua homolog pseudogene 3', - 'capicua transcriptional repressor pseudogene 3', - 'CICP3' - ] - } - } - ] - }, { - 'params': { - 'transcript_id': 'ENST00000443707', - 'verbose': 'false' - }, - 'response': [ - { - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'version': 'v43', - 'gene': 'genes/ENSG00000230108' - } - ] - }, { - 'params': { - 'transcript_id': 'ENST00000443707', - 'verbose': 'true' - }, - 'response': [ - { - 'source': 'GENCODE', - 'source_url': 'https://www.gencodegenes.org/human/', - 'version': 'v43', - 'gene': { - '_id': 'ENSG00000230108', - 'chr': 'GL000256.2', - 'start': 2874846, - 'end': 2877616, - 'gene_type': 'protein_coding', - 'hgnc': 'HGNC:11892', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'tumor necrotic factor alpha', - 'TNF-alpha', - 'TNLG1F', - 'TNF', - 'DIF', - 'tumor necrosis factor ligand superfamily member 2', - 'APC1 protein', - 'TNF, macrophage-derived', - 'TNFA', - 'tumor necrosis factor-alpha', - 'tumor necrosis factor ligand 1F', - 'TNF-a', - 'TNF, monocyte-derived', - 'tumor necrosis factor', - 'TNFSF2' - ] - } - } - ] - }] -} diff --git a/tests/acceptance_tests/transcripts_proteins.py b/tests/acceptance_tests/transcripts_proteins.py deleted file mode 100644 index 49d6c5c9..00000000 --- a/tests/acceptance_tests/transcripts_proteins.py +++ /dev/null @@ -1,327 +0,0 @@ -transcripts_proteins = { - '/transcripts/proteins': [{ - 'params': { - 'region': 'chr16:67562500-67640000', - 'transcript_type': 'protein_coding', - 'verbose': 'false' - }, - 'response': [ - { - 'source': 'UniprotKB', - 'source_url': 'https://www.uniprot.org/uniprotkb', - 'protein': 'proteins/P49711' - }, - { - 'source': 'UniprotKB', - 'source_url': 'https://www.uniprot.org/uniprotkb', - 'protein': 'proteins/P49711' - }, - { - 'source': 'UniprotKB', - 'source_url': 'https://www.uniprot.org/uniprotkb', - 'protein': 'proteins/P49711' - }, - { - 'source': 'UniprotKB', - 'source_url': 'https://www.uniprot.org/uniprotkb', - 'protein': 'proteins/P49711' - }, - { - 'source': 'UniprotKB', - 'source_url': 'https://www.uniprot.org/uniprotkb', - 'protein': 'proteins/P49711' - }, - { - 'source': 'UniprotKB', - 'source_url': 'https://www.uniprot.org/uniprotkb', - 'protein': 'proteins/P49711' - } - ] - }, { - 'params': { - 'transcript_id': 'ENST00000401394', - 'verbose': 'false' - }, - 'response': [ - { - 'source': 'UniprotKB', - 'source_url': 'https://www.uniprot.org/uniprotkb', - 'protein': 'proteins/P49711' - } - ] - }, { - 'params': { - 'transcript_id': 'ENST00000401394', - 'verbose': 'true' - }, - 'response': [{'source': 'UniprotKB', - 'source_url': 'https://www.uniprot.org/uniprotkb', - 'protein': [{'_id': 'P49711', - 'name': 'CTCF_HUMAN', - 'full_name': 'Transcriptional repressor CTCF', - 'dbxrefs': [{'name': 'AGR', 'id': 'HGNC:13723'}, - {'name': 'AlphaFoldDB', - 'id': 'P49711'}, - {'name': 'Antibodypedia', - 'id': '15816'}, - {'name': 'Bgee', - 'id': 'ENSG00000102974'}, - {'name': 'BioGRID', 'id': '115906'}, - {'name': 'BioGRID-ORCS', - 'id': '10664'}, - {'name': 'BioMuta', 'id': 'CTCF'}, - {'name': 'CCDS', 'id': 'CCDS10841.1'}, - {'name': 'CCDS', 'id': 'CCDS54029.1'}, - {'name': 'CORUM', 'id': 'P49711'}, - {'name': 'CTD', 'id': '10664'}, - {'name': 'ChEMBL', - 'id': 'CHEMBL4523233'}, - {'name': 'ChiTaRS', 'id': 'CTCF'}, - {'name': 'DIP', 'id': 'DIP-35252N'}, - {'name': 'DMDM', 'id': '1706179'}, - {'name': 'DNASU', 'id': '10664'}, - {'name': 'DisGeNET', 'id': '10664'}, - {'name': 'EMBL', 'id': 'U25435'}, - {'name': 'EMBL', 'id': 'AAB07788.1'}, - {'name': 'EMBL', 'id': 'AF145477'}, - {'name': 'EMBL', 'id': 'AAF31318.1'}, - {'name': 'EMBL', 'id': 'AF145468'}, - {'name': 'EMBL', 'id': 'AAF31318.1'}, - {'name': 'EMBL', 'id': 'AF145469'}, - {'name': 'EMBL', 'id': 'AAF31318.1'}, - {'name': 'EMBL', 'id': 'AF145470'}, - {'name': 'EMBL', 'id': 'AAF31318.1'}, - {'name': 'EMBL', 'id': 'AF145471'}, - {'name': 'EMBL', 'id': 'AAF31318.1'}, - {'name': 'EMBL', 'id': 'AF145472'}, - {'name': 'EMBL', 'id': 'AAF31318.1'}, - {'name': 'EMBL', 'id': 'AF145473'}, - {'name': 'EMBL', 'id': 'AAF31318.1'}, - {'name': 'EMBL', 'id': 'AF145474'}, - {'name': 'EMBL', 'id': 'AAF31318.1'}, - {'name': 'EMBL', 'id': 'AF145475'}, - {'name': 'EMBL', 'id': 'AAF31318.1'}, - {'name': 'EMBL', 'id': 'AF145476'}, - {'name': 'EMBL', 'id': 'AAF31318.1'}, - {'name': 'EMBL', 'id': 'BT009915'}, - {'name': 'EMBL', 'id': 'AAP88917.1'}, - {'name': 'EMBL', 'id': 'AB209793'}, - {'name': 'EMBL', 'id': 'BAD93030.1'}, - {'name': 'EMBL', 'id': 'AC009095'}, - {'name': 'EMBL', 'id': 'AC027682'}, - {'name': 'EMBL', 'id': 'CH471092'}, - {'name': 'EMBL', 'id': 'EAW83142.1'}, - {'name': 'EMBL', 'id': 'BC014267'}, - {'name': 'EMBL', 'id': 'AAH14267.1'}, - {'name': 'EPD', 'id': 'P49711'}, - {'name': 'Ensembl', - 'id': 'ENST00000264010.10'}, - {'name': 'Ensembl', - 'id': 'ENSP00000264010.4'}, - {'name': 'Ensembl', - 'id': 'ENSG00000102974.16'}, - {'name': 'Ensembl', - 'id': 'ENST00000401394.6'}, - {'name': 'Ensembl', - 'id': 'ENSP00000384707.1'}, - {'name': 'Ensembl', - 'id': 'ENSG00000102974.16'}, - {'name': 'Ensembl', - 'id': 'ENST00000642819.1'}, - {'name': 'Ensembl', - 'id': 'ENSP00000494408.1'}, - {'name': 'Ensembl', - 'id': 'ENSG00000102974.16'}, - {'name': 'Ensembl', - 'id': 'ENST00000644753.1'}, - {'name': 'Ensembl', - 'id': 'ENSP00000493495.1'}, - {'name': 'Ensembl', - 'id': 'ENSG00000102974.16'}, - {'name': 'Ensembl', - 'id': 'ENST00000645699.1'}, - {'name': 'Ensembl', - 'id': 'ENSP00000495348.1'}, - {'name': 'Ensembl', - 'id': 'ENSG00000102974.16'}, - {'name': 'Ensembl', - 'id': 'ENST00000646076.1'}, - {'name': 'Ensembl', - 'id': 'ENSP00000494538.1'}, - {'name': 'Ensembl', - 'id': 'ENSG00000102974.16'}, - {'name': 'EvolutionaryTrace', - 'id': 'P49711'}, - {'name': 'ExpressionAtlas', - 'id': 'P49711'}, - {'name': 'GO', 'id': 'GO:0000775'}, - {'name': 'GO', 'id': 'GO:0000793'}, - {'name': 'GO', 'id': 'GO:0001673'}, - {'name': 'GO', 'id': 'GO:0005730'}, - {'name': 'GO', 'id': 'GO:0005654'}, - {'name': 'GO', 'id': 'GO:0005634'}, - {'name': 'GO', 'id': 'GO:0043035'}, - {'name': 'GO', 'id': 'GO:0003700'}, - {'name': 'GO', 'id': 'GO:0001227'}, - {'name': 'GO', 'id': 'GO:0000978'}, - {'name': 'GO', 'id': 'GO:0043565'}, - {'name': 'GO', 'id': 'GO:0000976'}, - {'name': 'GO', 'id': 'GO:0001221'}, - {'name': 'GO', 'id': 'GO:0008270'}, - {'name': 'GO', 'id': 'GO:0140588'}, - {'name': 'GO', 'id': 'GO:0007059'}, - {'name': 'GO', 'id': 'GO:0006306'}, - {'name': 'GO', 'id': 'GO:0040029'}, - {'name': 'GO', 'id': 'GO:0071514'}, - {'name': 'GO', 'id': 'GO:0008285'}, - {'name': 'GO', 'id': 'GO:0045892'}, - {'name': 'GO', 'id': 'GO:0000122'}, - {'name': 'GO', 'id': 'GO:0045893'}, - {'name': 'GO', 'id': 'GO:0010628'}, - {'name': 'GO', 'id': 'GO:0071459'}, - {'name': 'GO', 'id': 'GO:0070602'}, - {'name': 'GO', 'id': 'GO:0006349'}, - {'name': 'Gene3D', - 'id': '3.30.160.60'}, - {'name': 'GeneCards', 'id': 'CTCF'}, - {'name': 'GeneID', 'id': '10664'}, - {'name': 'GeneTree', - 'id': 'ENSGT00940000156672'}, - {'name': 'GeneWiki', 'id': 'CTCF'}, - {'name': 'Genevisible', - 'id': 'P49711'}, - {'name': 'GenomeRNAi', - 'id': '10664'}, - {'name': 'GlyGen', 'id': 'P49711'}, - {'name': 'HGNC', 'id': 'HGNC:13723'}, - {'name': 'HOGENOM', - 'id': 'CLU_002678_77_1_1'}, - {'name': 'HPA', - 'id': 'ENSG00000102974'}, - {'name': 'InParanoid', - 'id': 'P49711'}, - {'name': 'IntAct', 'id': 'P49711'}, - {'name': 'InterPro', - 'id': 'IPR036236'}, - {'name': 'InterPro', - 'id': 'IPR013087'}, - {'name': 'KEGG', 'id': 'hsa:10664'}, - {'name': 'MANE-Select', - 'id': 'ENST00000264010.10'}, - {'name': 'MANE-Select', - 'id': 'ENSP00000264010.4'}, - {'name': 'MANE-Select', - 'id': 'NM_006565.4'}, - {'name': 'MANE-Select', - 'id': 'NP_006556.1'}, - {'name': 'MIM', 'id': '604167'}, - {'name': 'MIM', 'id': '615502'}, - {'name': 'MINT', 'id': 'P49711'}, - {'name': 'MalaCards', 'id': 'CTCF'}, - {'name': 'MassIVE', 'id': 'P49711'}, - {'name': 'MaxQB', 'id': 'P49711'}, - {'name': 'OMA', 'id': 'TESEPMI'}, - {'name': 'OpenTargets', - 'id': 'ENSG00000102974'}, - {'name': 'Orphanet', - 'id': '363611'}, - {'name': 'OrthoDB', - 'id': '5398475at2759'}, - {'name': 'PANTHER', - 'id': 'PTHR24379:SF81'}, - {'name': 'PANTHER', - 'id': 'PTHR24379'}, - {'name': 'PDB', 'id': '1X6H'}, - {'name': 'PDB', 'id': '2CT1'}, - {'name': 'PDB', 'id': '5K5H'}, - {'name': 'PDB', 'id': '5K5I'}, - {'name': 'PDB', 'id': '5K5J'}, - {'name': 'PDB', 'id': '5K5L'}, - {'name': 'PDB', 'id': '5KKQ'}, - {'name': 'PDB', 'id': '5T00'}, - {'name': 'PDB', 'id': '5T0U'}, - {'name': 'PDB', 'id': '5UND'}, - {'name': 'PDB', 'id': '5YEF'}, - {'name': 'PDB', 'id': '5YEG'}, - {'name': 'PDB', 'id': '5YEH'}, - {'name': 'PDB', 'id': '5YEL'}, - {'name': 'PDB', 'id': '6QNX'}, - {'name': 'PDBsum', 'id': '1X6H'}, - {'name': 'PDBsum', 'id': '2CT1'}, - {'name': 'PDBsum', 'id': '5K5H'}, - {'name': 'PDBsum', 'id': '5K5I'}, - {'name': 'PDBsum', 'id': '5K5J'}, - {'name': 'PDBsum', 'id': '5K5L'}, - {'name': 'PDBsum', 'id': '5KKQ'}, - {'name': 'PDBsum', 'id': '5T00'}, - {'name': 'PDBsum', 'id': '5T0U'}, - {'name': 'PDBsum', 'id': '5UND'}, - {'name': 'PDBsum', 'id': '5YEF'}, - {'name': 'PDBsum', 'id': '5YEG'}, - {'name': 'PDBsum', 'id': '5YEH'}, - {'name': 'PDBsum', 'id': '5YEL'}, - {'name': 'PDBsum', 'id': '6QNX'}, - {'name': 'PIR', 'id': 'G01792'}, - {'name': 'PRO', 'id': 'PR:P49711'}, - {'name': 'PROSITE', - 'id': 'PS00028'}, - {'name': 'PROSITE', - 'id': 'PS50157'}, - {'name': 'PathwayCommons', - 'id': 'P49711'}, - {'name': 'PaxDb', 'id': 'P49711'}, - {'name': 'PeptideAtlas', - 'id': 'P49711'}, - {'name': 'Pfam', 'id': 'PF00096'}, - {'name': 'Pfam', 'id': 'PF13909'}, - {'name': 'PharmGKB', - 'id': 'PA26998'}, - {'name': 'Pharos', 'id': 'P49711'}, - {'name': 'PhosphoSitePlus', - 'id': 'P49711'}, - {'name': 'PhylomeDB', - 'id': 'P49711'}, - {'name': 'Proteomes', - 'id': 'UP000005640'}, - {'name': 'ProteomicsDB', - 'id': '56053'}, - {'name': 'ProteomicsDB', - 'id': '5985'}, - {'name': 'RNAct', 'id': 'P49711'}, - {'name': 'Reactome', - 'id': 'R-HSA-5617472'}, - {'name': 'RefSeq', - 'id': 'NP_001177951.1'}, - {'name': 'RefSeq', - 'id': 'NM_001191022.1'}, - {'name': 'RefSeq', - 'id': 'NP_006556.1'}, - {'name': 'RefSeq', - 'id': 'NM_006565.3'}, - {'name': 'RefSeq', - 'id': 'XP_016878357.1'}, - {'name': 'RefSeq', - 'id': 'XM_017022868.1'}, - {'name': 'SIGNOR', 'id': 'P49711'}, - {'name': 'SMART', 'id': 'SM00355'}, - {'name': 'SMR', 'id': 'P49711'}, - {'name': 'STRING', - 'id': '9606.ENSP00000264010'}, - {'name': 'SUPFAM', 'id': 'SSF57667'}, - {'name': 'SignaLink', - 'id': 'P49711'}, - {'name': 'SwissPalm', - 'id': 'P49711'}, - {'name': 'TreeFam', - 'id': 'TF106430'}, - {'name': 'UCSC', 'id': 'uc002etl.4'}, - {'name': 'VEuPathDB', - 'id': 'HostDB:ENSG00000102974'}, - {'name': 'eggNOG', 'id': 'KOG1721'}, - {'name': 'iPTMnet', 'id': 'P49711'}, - {'name': 'jPOST', 'id': 'P49711'}, - {'name': 'neXtProt', 'id': 'NX_P49711'}], - 'source': 'UniProtKB/Swiss-Prot', - 'source_url': 'https://www.uniprot.org/help/downloads'}]}] - }] -} diff --git a/tests/acceptance_tests/variants.py b/tests/acceptance_tests/variants.py deleted file mode 100644 index ea9dc5d5..00000000 --- a/tests/acceptance_tests/variants.py +++ /dev/null @@ -1,3871 +0,0 @@ -variants = { - '/variants/freq': [{ - 'params': { - 'source': '1000genomes', - 'region': 'chr3:186741137-186742238', - 'funseq_description': 'noncoding', - 'min_alt_freq': '0.1', - 'max_alt_freq': '0.8' - }, - 'response': [ - { - '_id': '0c4f244c856ee3250337b7207966457a7889505c1356e6b9d9c30f1134e25627', - 'chr': 'chr3', - 'pos': 186741418, - 'rsid': [ - 'rs530299758' - ], - 'ref': 'C', - 'alt': 'G', - 'spdi': 'NC_000003.12:186741418:C:G', - 'hgvs': 'NC_000003.12:g.186741419C>G', - 'qual': '.', - 'filter': None, - 'annotations': { - 'freq': { - '1000genomes': { - 'ref:long': 0.9998, - 'alt:long': 0.0001997 - }, - 'gnomad': { - 'ref:long': 1, - 'alt:long': 0 - }, - 'dbgap_popfreq': { - 'ref:long': 0.9999, - 'alt:long': 0 - } - }, - 'varinfo': '3-186741419-C-G', - 'vid': '5.33463e+09', - 'variant_vcf': '3-186741419-C-G', - 'variant_annovar': '3-186741419-186741419-C-G', - 'start_position': '1.86741e+08', - 'end_position': '1.86741e+08', - 'ref_annovar': 'C', - 'alt_annovar': 'G', - 'ref_vcf': 'C', - 'alt_vcf': 'G', - 'apc_conservation': 1.52841, - 'apc_conservation_v2': 3.09873, - 'apc_epigenetics_active': 2.44739, - 'apc_epigenetics': 2.44821, - 'apc_epigenetics_repressed': 1.57901, - 'apc_epigenetics_transcription': 2.87007, - 'apc_local_nucleotide_diversity': 1.30443, - 'apc_local_nucleotide_diversity_v2': 2.8, - 'apc_local_nucleotide_diversity_v3': 1.93422, - 'apc_mappability': 5.18561, - 'apc_micro_rna': 99.4512, - 'apc_mutation_density': 3.00481, - 'apc_protein_function': 20.2494, - 'apc_protein_function_v2': 4.92793e-10, - 'apc_protein_function_v3': 2.96949, - 'apc_proximity_to_coding': 1.85991, - 'apc_proximity_to_coding_v2': 15.1786, - 'apc_proximity_to_tsstes': 9.85383, - 'apc_transcription_factor': 3.14279, - 'fathmm_xf': '4.26452', - 'funseq_description': 'noncoding', - 'cadd_rawscore': '-0.133021', - 'cadd_phred': '0.824', - 'tg_all': '0.000199681', - 'tg_amr': '0.0014' - }, - 'source': 'FAVOR', - 'source_url': 'http://favor.genohub.org/' - }, - { - '_id': '1f6ebc041b19bf309d6ad93e59b3f187768860ba22db4feaf0c0ffbf18e048b5', - 'chr': 'chr3', - 'pos': 186741393, - 'rsid': [ - 'rs5030083' - ], - 'ref': 'C', - 'alt': 'T', - 'spdi': 'NC_000003.12:186741393:C:T', - 'hgvs': 'NC_000003.12:g.186741394C>T', - 'qual': '.', - 'filter': None, - 'annotations': { - 'freq': { - '1000genomes': { - 'ref:long': 0.9669, - 'alt:long': 0.03315 - }, - 'alspac': { - 'ref:long': 0.9707, - 'alt:long': 0.02932 - }, - 'estonian': { - 'ref:long': 0.9694, - 'alt:long': 0.03058 - }, - 'genome_dk': { - 'ref:long': 0.95, - 'alt:long': 0.05 - }, - 'gnomad': { - 'ref:long': 0.9596, - 'alt:long': 0.04039 - }, - 'gonl': { - 'ref:long': 0.9669, - 'alt:long': 0.03307 - }, - 'hapmap': { - 'ref:long': 1, - 'alt:long': 0 - }, - 'korean': { - 'ref:long': 0.9925, - 'alt:long': 0.007529 - }, - 'korea1k': { - 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0.42957, - 'af_amr_female': 0.450424, - 'af_fin': 0.367375, - 'af_afr_female': 0.48946, - 'af_sas_male': 0.348055, - 'af_amr': 0.438593, - 'af_nfe': 0.407944, - 'af_eas': 0.296855, - 'af_ami_male': 0.199531, - 'af_fin_female': 0.376806, - 'cadd_rawscore': '0.791846', - 'cadd_phred': '9.849', - 'tg_afr': '0.5038', - 'tg_all': '0.408746', - 'tg_amr': '0.4611', - 'tg_eas': '0.2946', - 'tg_eur': '0.4165', - 'tg_sas': '0.3528' - }, - 'source': 'FAVOR', - 'source_url': 'http://favor.genohub.org/' - } - ] - }] -} diff --git a/tests/acceptance_tests/variants_drugs.py b/tests/acceptance_tests/variants_drugs.py deleted file mode 100644 index 84d9f5dd..00000000 --- a/tests/acceptance_tests/variants_drugs.py +++ /dev/null @@ -1,82 +0,0 @@ -variants_drugs = { - '/variants/drugs': [{ - 'params': { - 'variant_id': 'b8d8a33facd5b62cb7f1004ae38419b8d914082ea9b217bef008a6a7f0218687', - 'region': 'chr1:230714130-230714230', - 'rsid': 'rs5050', - 'funseq_description': 'noncoding', - 'pmid': '20824505', - 'phenotype_categories': 'Toxicity', - 'verbose': 'false' - }, - 'response': [ - { - 'sequence variant': 'variants/b8d8a33facd5b62cb7f1004ae38419b8d914082ea9b217bef008a6a7f0218687', - 'drug': 'drugs/PA448497', - 'gene_symbol': [ - 'AGT' - ], - 'pmid': '20824505', - 'study_parameters': [ - { - 'study_parameter_id': '1009568432', - 'study_type': 'cohort', - 'study_cases': '68', - 'study_controls': '357', - 'p-value': '< 0.05', - 'biogeographical_groups': 'East Asian' - } - ], - 'phenotype_categories': [ - 'Toxicity' - ], - 'source': 'pharmGKB', - 'source_url': 'https://www.pharmgkb.org/variantAnnotation/1009360953' - } - ] - }, { - 'params': { - 'variant_id': 'b8d8a33facd5b62cb7f1004ae38419b8d914082ea9b217bef008a6a7f0218687', - 'region': 'chr1:230714130-230714230', - 'rsid': 'rs5050', - 'funseq_description': 'noncoding', - 'pmid': '20824505', - 'phenotype_categories': 'Toxicity', - 'verbose': 'true' - }, - 'response': [ - { - 'sequence variant': 'variants/b8d8a33facd5b62cb7f1004ae38419b8d914082ea9b217bef008a6a7f0218687', - 'drug': [ - { - '_id': 'PA448497', - 'name': 'aspirin', - 'drug_ontology_terms': [], - 'source': 'pharmGKB', - 'source_url': 'https://www.pharmgkb.org/chemical/PA448497' - } - ], - 'gene_symbol': [ - 'AGT' - ], - 'pmid': '20824505', - 'study_parameters': [ - { - 'study_parameter_id': '1009568432', - 'study_type': 'cohort', - 'study_cases': '68', - 'study_controls': '357', - 'p-value': '< 0.05', - 'biogeographical_groups': 'East Asian' - } - ], - 'phenotype_categories': [ - 'Toxicity' - ], - 'source': 'pharmGKB', - 'source_url': 'https://www.pharmgkb.org/variantAnnotation/1009360953' - } - ] - } - ] -} diff --git a/tests/acceptance_tests/variants_genes.py b/tests/acceptance_tests/variants_genes.py deleted file mode 100644 index d2d87bad..00000000 --- a/tests/acceptance_tests/variants_genes.py +++ /dev/null @@ -1,5444 +0,0 @@ -variants_genes = { - '/variants/genes': [{ - 'params': { - 'variant_id': '22f170e54c30a59e737beba20444f192201126f0b1415a7c9a106d1d01fe98d0', - 'p_value': 'lte:0.01' - }, - 'response': [ - { - 'sequence variant': 'variants/22f170e54c30a59e737beba20444f192201126f0b1415a7c9a106d1d01fe98d0', - 'gene': 'genes/ENSG00000272512', - 'beta': 2.64602e-18, - 'label': 'eQTL', - 'log10pvalue': 5.707188121622835, - 'slope': 0.418051, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'coronary artery', - 'chr': 'chr1', - 'intron_chr': None, - 'intron_start': None, - 'intron_end': None - }, - { - 'sequence variant': 'variants/22f170e54c30a59e737beba20444f192201126f0b1415a7c9a106d1d01fe98d0', - 'gene': 'genes/ENSG00000272512', - 'beta': 1.92016e-24, - 'label': 'eQTL', - 'log10pvalue': 5.18550801587269, - 'slope': 0.320967, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'breast epithelium', - 'chr': 'chr1', - 'intron_chr': None, - 'intron_start': None, - 'intron_end': None - }, - { - 'sequence variant': 'variants/22f170e54c30a59e737beba20444f192201126f0b1415a7c9a106d1d01fe98d0', - 'gene': 'genes/ENSG00000224969', - 'beta': 0.0000316253, - 'label': 'eQTL', - 'log10pvalue': 4.528354834938668, - 'slope': -0.256088, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'thyroid gland', - 'chr': 'chr1', - 'intron_chr': None, - 'intron_start': None, - 'intron_end': None - }, - { - 'sequence variant': 'variants/22f170e54c30a59e737beba20444f192201126f0b1415a7c9a106d1d01fe98d0', - 'gene': 'genes/ENSG00000188157', - 'beta': 2.39494e-9, - 'label': 'splice_QTL', - 'log10pvalue': 6.352940915207888, - 'slope': -0.370198, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'omental fat pad', - 'chr': 'chr1', - 'intron_chr': 'chr1', - 'intron_start': 1054551, - 'intron_end': 1054824 - }, - { - 'sequence variant': 'variants/22f170e54c30a59e737beba20444f192201126f0b1415a7c9a106d1d01fe98d0', - 'gene': 'genes/ENSG00000188290', - 'beta': 1.03948e-16, - 'label': 'splice_QTL', - 'log10pvalue': 7.362780537768552, - 'slope': -0.351271, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'omental fat pad', - 'chr': 'chr1', - 'intron_chr': 'chr1', - 'intron_start': 999787, - 'intron_end': 999866 - }, - { - 'sequence variant': 'variants/22f170e54c30a59e737beba20444f192201126f0b1415a7c9a106d1d01fe98d0', - 'gene': 'genes/ENSG00000272512', - 'beta': 8.46305e-20, - 'label': 'eQTL', - 'log10pvalue': 9.881037919877619, - 'slope': 0.347608, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'right atrium auricular region', - 'chr': 'chr1', - 'intron_chr': None, - 'intron_start': None, - 'intron_end': None - }, - { - 'sequence variant': 'variants/22f170e54c30a59e737beba20444f192201126f0b1415a7c9a106d1d01fe98d0', - 'gene': 'genes/ENSG00000188290', - 'beta': 2.09509e-26, - 'label': 'splice_QTL', - 'log10pvalue': 9.479933275489538, - 'slope': -0.359479, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'upper lobe of left lung', - 'chr': 'chr1', - 'intron_chr': 'chr1', - 'intron_start': 999787, - 'intron_end': 999866 - }, - { - 'sequence variant': 'variants/22f170e54c30a59e737beba20444f192201126f0b1415a7c9a106d1d01fe98d0', - 'gene': 'genes/ENSG00000272512', - 'beta': 2.55246e-12, - 'label': 'eQTL', - 'log10pvalue': 4.539736780805899, - 'slope': 0.376631, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'cerebellum', - 'chr': 'chr1', - 'intron_chr': None, - 'intron_start': None, - 'intron_end': None - }, - { - 'sequence variant': 'variants/22f170e54c30a59e737beba20444f192201126f0b1415a7c9a106d1d01fe98d0', - 'gene': 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- 'label': 'eQTL', - 'log10pvalue': 4.55561321469842, - 'slope': 0.0961202, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'breast epithelium', - 'chr': 'chr1', - 'intron_chr': None, - 'intron_start': None, - 'intron_end': None - }, - { - 'sequence variant': 'variants/22f170e54c30a59e737beba20444f192201126f0b1415a7c9a106d1d01fe98d0', - 'gene': 'genes/ENSG00000188157', - 'beta': 2.35671e-41, - 'label': 'splice_QTL', - 'log10pvalue': 11.688899130584923, - 'slope': -0.417545, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'thyroid gland', - 'chr': 'chr1', - 'intron_chr': 'chr1', - 'intron_start': 1054551, - 'intron_end': 1054824 - }, - { - 'sequence variant': 'variants/22f170e54c30a59e737beba20444f192201126f0b1415a7c9a106d1d01fe98d0', - 'gene': 'genes/ENSG00000272512', - 'beta': 1.59762e-55, - 'label': 'eQTL', - 'log10pvalue': 7.840441829598651, - 'slope': 0.335871, - 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'thyroid gland', - 'chr': 'chr1', - 'intron_chr': None, - 'intron_start': None, - 'intron_end': None - }, - { - 'sequence variant': 'variants/22f170e54c30a59e737beba20444f192201126f0b1415a7c9a106d1d01fe98d0', - 'gene': 'genes/ENSG00000272512', - 'beta': 3.38843e-38, - 'label': 'eQTL', - 'log10pvalue': 5.083541313717933, - 'slope': 0.390829, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'body of pancreas', - 'chr': 'chr1', - 'intron_chr': None, - 'intron_start': None, - 'intron_end': None - }, - { - 'sequence variant': 'variants/22f170e54c30a59e737beba20444f192201126f0b1415a7c9a106d1d01fe98d0', - 'gene': 'genes/ENSG00000188290', - 'beta': 4.27226e-27, - 'label': 'splice_QTL', - 'log10pvalue': 13.750285689294042, - 'slope': -0.475304, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'esophagus muscularis mucosa', - 'chr': 'chr1', - 'intron_chr': 'chr1', - 'intron_start': 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'ref:long': 0.2265, - 'alt:long': 0 - }, - 'gonl': { - 'ref:long': 0.2355, - 'alt:long': 0 - }, - 'korean': { - 'ref:long': 0.1307, - 'alt:long': 0 - }, - 'korea1k': { - 'ref:long': 0.1119, - 'alt:long': 0 - }, - 'mgp': { - 'ref:long': 0.2341, - 'alt:long': 0 - }, - 'northernsweden': { - 'ref:long': 0.28, - 'alt:long': 0 - }, - 'qatari': { - 'ref:long': 0.2778, - 'alt:long': 0 - }, - 'sgdp_prj': { - 'ref:long': 0.15, - 'alt:long': 0 - }, - 'siberian': { - 'ref:long': 0.1538, - 'alt:long': 0 - }, - 'tommo': { - 'ref:long': 0.09564, - 'alt:long': 0 - }, - 'topmed': { - 'ref:long': 0.28, - 'alt:long': 0 - }, - 'twinsuk': { - 'ref:long': 0.2543, - 'alt:long': 0 - }, - 'dbgap_popfreq': { - 'ref:long': 0.2683, - 'alt:long': 0 - } - }, - 'varinfo': '1-981169-A-G', - 'vid': '2.46351e+06', - 'variant_vcf': '1-981169-A-G', - 'variant_annovar': '1-981169-981169-A-G', - 'start_position': '981169', - 'end_position': '981169', - 'ref_annovar': 'A', - 'alt_annovar': 'G', - 'ref_vcf': 'A', - 'alt_vcf': 'G', - 'apc_conservation': 0.54059, - 'apc_conservation_v2': 0.987718, - 'apc_epigenetics_active': 9.29603, - 'apc_epigenetics': 10.9147, - 'apc_epigenetics_repressed': 5.50979, - 'apc_epigenetics_transcription': 3.20664, - 'apc_local_nucleotide_diversity': 3.00724, - 'apc_local_nucleotide_diversity_v2': 0.0719121, - 'apc_local_nucleotide_diversity_v3': 0.0845642, - 'apc_mappability': 6.72026, - 'apc_micro_rna': 99.4512, - 'apc_mutation_density': 0.0713297, - 'apc_protein_function': 20.2494, - 'apc_protein_function_v2': 4.92793e-10, - 'apc_protein_function_v3': 2.96949, - 'apc_proximity_to_coding': 14.076, - 'apc_proximity_to_coding_v2': 15.1786, - 'apc_proximity_to_tsstes': 13.3714, - 'apc_transcription_factor': 9.69058, - 'bravo_an': '264690', - 'bravo_af': '0.720035', - 'filter_status': 'PASS', - 'fathmm_xf': '2.18201', - 'funseq_value': '1', - 'funseq_description': 'coding', - 'af_total': 0.716829, - 'af_asj_female': 0.733825, - 'af_eas_female': 0.881579, - 'af_afr_male': 0.621451, - 'af_female': 0.714635, - 'af_fin_male': 0.730779, - 'af_oth_female': 0.739927, - 'af_ami': 0.707589, - 'af_oth': 0.734608, - 'af_male': 0.719163, - 'af_ami_female': 0.693617, - 'af_afr': 0.623712, - 'af_eas_male': 0.871429, - 'af_sas': 0.825972, - 'af_nfe_female': 0.744993, - 'af_asj_male': 0.726633, - 'af_raw': 0.716789, - 'af_oth_male': 0.729087, - 'af_nfe_male': 0.743827, - 'af_asj': 0.730445, - 'af_amr_male': 0.794057, - 'af_amr_female': 0.790437, - 'af_fin': 0.734477, - 'af_afr_female': 0.625641, - 'af_sas_male': 0.826456, - 'af_amr': 0.792492, - 'af_nfe': 0.744502, - 'af_eas': 0.87612, - 'af_ami_male': 0.723005, - 'af_fin_female': 0.746203, - 'cadd_rawscore': '-0.016826', - 'cadd_phred': '1.604', - 'refseq_category': 'UTR5', - 'tg_afr': '0.5998', - 'tg_all': '0.758586', - 'tg_amr': '0.781', - 'tg_eas': '0.88', - 'tg_eur': '0.7584', - 'tg_sas': '0.8323' - } - }, - 'gene': { - '_id': 'ENSG00000188157', - 'chr': 'chr1', - 'start': 1020119, - 'end': 1056118, - 'gene_id': 'ENSG00000188157.15', - 'hgnc': 'HGNC:329', - 'name': 'AGRN', - 'gene_type': 'protein_coding', - 'source': 'GENCODE', - 'version': 'v43', - 'source_url': 'https://www.gencodegenes.org/human/', - 'alias': [ - 'agrin proteoglycan', - 'AGRIN', - 'CMS8', - 'agrin', - 'CMSPPD', - 'AGRN' - ] - }, - 'beta': 2.64254e-8, - 'label': 'splice_QTL', - 'log10pvalue': 6.212810955776666, - 'slope': -0.4544, - 'source': 'GTEx', - 'source_url': 'https://www.gtexportal.org/home/datasets', - 'biological_context': 'stomach', - 'chr': 'chr1', - 'intron_chr': 'chr1', - 'intron_start': 1054551, - 'intron_end': 1054824 - } - ] - }] -} diff --git a/tests/acceptance_tests/variants_ld.py b/tests/acceptance_tests/variants_ld.py deleted file mode 100644 index 216db5bd..00000000 --- a/tests/acceptance_tests/variants_ld.py +++ /dev/null @@ -1,1506 +0,0 @@ -variants_ld = { - '/variants/variant_ld': [{ - 'params': { - 'variant_id': 'ec046cdcc26b8ee9e79f9db305b1e9d5a6bdaba2d2064176f9a4ea50007b1e9a', - 'r2': 'gte:0.8', - 'd_prime': 'gt:0.9', - 'ancestry': 'EUR', - 'verbose': 'false' - }, - 'response': [ - { - 'chr': 'chr11', - 'ancestry': 'EUR', - 'd_prime': 0.965, - 'r2': 0.859, - 'label': 'linkage disequilibrum', - 'variant_1_base_pair': 'C:T', - 'variant_1_rsid': 'rs7929797', - 'variant_2_base_pair': 'A:G', - 'variant_2_rsid': 'rs963167', - 'source': 'TopLD', - 'source_url': 'http://topld.genetics.unc.edu/', - 'sequence variant': 'b77f0423e569b3d16d80b8091f1bd28439d9ba90afa9843e1ad6d98ae1aa62a8' - }, - { - 'chr': 'chr11', - 'ancestry': 'EUR', - 'd_prime': 0.956, - 'r2': 0.851, - 'label': 'linkage disequilibrum', - 'variant_1_base_pair': 'C:T', - 'variant_1_rsid': 'rs7395330', - 'variant_2_base_pair': 'A:G', - 'variant_2_rsid': 'rs963167', - 'source': 'TopLD', - 'source_url': 'http://topld.genetics.unc.edu/', - 'sequence variant': 'd95f8850ae016e91e0c334fcfc39e45038667c7f277f6f54f89046f3801e1756' - }, - { - 'chr': 'chr11', - 'ancestry': 'EUR', - 'd_prime': 0.958, - 'r2': 0.854, - 'label': 'linkage disequilibrum', - 'variant_1_base_pair': 'C:T', - 'variant_1_rsid': 'rs4061964', - 'variant_2_base_pair': 'A:G', - 'variant_2_rsid': 'rs963167', - 'source': 'TopLD', - 'source_url': 'http://topld.genetics.unc.edu/', - 'sequence variant': 'e7c8f6a72221d4eb0a904754c2becef1d9bf673f62073bd087f67a0acefd5d91' - }, - { - 'chr': 'chr11', - 'ancestry': 'EUR', - 'd_prime': 0.931, - 'r2': 0.812, - 'label': 'linkage disequilibrum', - 'variant_1_base_pair': 'GA:G', - 'variant_1_rsid': 'chr11:9079066:GA:G', - 'variant_2_base_pair': 'A:G', - 'variant_2_rsid': 'rs963167', - 'source': 'TopLD', - 'source_url': 'http://topld.genetics.unc.edu/', - 'sequence variant': '78d49701ce233730dd5ae31ff4a480ef167787438aaf284e9e4fbc458658e0e5' - }, - { - 'chr': 'chr11', - 'ancestry': 'EUR', - 'd_prime': 0.976, - 'r2': 0.848, - 'label': 'linkage disequilibrum', - 'variant_1_base_pair': 'T:A', - 'variant_1_rsid': 'rs10732200', - 'variant_2_base_pair': 'A:G', - 'variant_2_rsid': 'rs963167', - 'source': 'TopLD', - 'source_url': 'http://topld.genetics.unc.edu/', - 'sequence variant': '78d8b25b5b2facb7065d73277ad77d3c7920627604a1fde43c51a126942f7218' - }, - { - 'chr': 'chr11', - 'ancestry': 'EUR', - 'd_prime': 0.907, - 'r2': 0.821, - 'label': 'linkage disequilibrum', - 'variant_1_base_pair': 'C:A', - 'variant_1_rsid': 'rs11042174', - 'variant_2_base_pair': 'A:G', - 'variant_2_rsid': 'rs963167', - 'source': 'TopLD', - 'source_url': 'http://topld.genetics.unc.edu/', - 'sequence variant': 'b47173f88d978432b1f12916bddde4570c3a02c454db082564da5bb37a67b89f' - }, - { - 'chr': 'chr11', - 'ancestry': 'EUR', - 'd_prime': 0.949, - 'r2': 0.872, - 'label': 'linkage disequilibrum', - 'variant_1_base_pair': 'A:C', - 'variant_1_rsid': 'rs10840169', - 'variant_2_base_pair': 'A:G', - 'variant_2_rsid': 'rs963167', - 'source': 'TopLD', - 'source_url': 'http://topld.genetics.unc.edu/', - 'sequence variant': '602498c777481b11c4b835dbc5637fa5b9855223a05df2dc6dcddc4df4c7f935' - }, - { - 'chr': 'chr11', - 'ancestry': 'EUR', - 'd_prime': 0.923, - 'r2': 0.814, - 'label': 'linkage disequilibrum', - 'variant_1_base_pair': 'A:G', - 'variant_1_rsid': 'rs2647530', - 'variant_2_base_pair': 'A:G', - 'variant_2_rsid': 'rs963167', - 'source': 'TopLD', - 'source_url': 'http://topld.genetics.unc.edu/', - 'sequence variant': '07210d5c9b7aedba471f029ab0e6159ce68ca6a8388e346d1c4876c3f5f1debf' - } - ] - }, { - 'params': { - 'variant_id': 'ec046cdcc26b8ee9e79f9db305b1e9d5a6bdaba2d2064176f9a4ea50007b1e9a', - 'r2': 'gte:0.8', - 'd_prime': 'gt:0.9', - 'ancestry': 'EUR', - 'verbose': 'true' - }, - 'response': [ - { - 'chr': 'chr11', - 'ancestry': 'EUR', - 'd_prime': 0.965, - 'r2': 0.859, - 'label': 'linkage disequilibrum', - 'variant_1_base_pair': 'C:T', - 'variant_1_rsid': 'rs7929797', - 'variant_2_base_pair': 'A:G', - 'variant_2_rsid': 'rs963167', - 'source': 'TopLD', - 'source_url': 'http://topld.genetics.unc.edu/', - 'sequence variant': [ - { - '_id': 'b77f0423e569b3d16d80b8091f1bd28439d9ba90afa9843e1ad6d98ae1aa62a8', - 'chr': 'chr11', - 'pos': 9071938, - 'rsid': [ - 'rs7929797' - ], - 'ref': 'C', - 'alt': 'T', - 'spdi': 'NC_000011.10:9071938:C:T', - 'hgvs': 'NC_000011.10:g.9071939C>T', - 'qual': '.', - 'filter': None, - 'annotations': { - 'freq': { - '1000genomes': { - 'ref:long': 0.1713, - 'alt:long': 0.8287 - }, - 'alspac': { - 'ref:long': 0.1033, - 'alt:long': 0.8967 - }, - 'estonian': { - 'ref:long': 0.1384, - 'alt:long': 0.8616 - }, - 'genome_dk': { - 'ref:long': 0.15, - 'alt:long': 0.85 - }, - 'gnomad': { - 'ref:long': 0.1196, - 'alt:long': 0.8804 - }, - 'gonl': { - 'ref:long': 0.1232, - 'alt:long': 0.8768 - }, - 'hgdp_stanford': { - 'ref:long': 0.1747, - 'alt:long': 0.8253 - }, - 'hapmap': { - 'ref:long': 0.1453, - 'alt:long': 0.8547 - }, - 'korean': { - 'ref:long': 0.1481, - 'alt:long': 0.8519 - }, - 'korea1k': { - 'ref:long': 0.1578, - 'alt:long': 0.8422 - }, - 'northernsweden': { - 'ref:long': 0.1317, - 'alt:long': 0.8683 - }, - 'page_study': { - 'ref:long': 0.1246, - 'alt:long': 0.8754 - }, - 'prjeb36033': { - 'ref:long': 0.1556, - 'alt:long': 0.8444 - }, - 'qatari': { - 'ref:long': 0.1019, - 'alt:long': 0.8981 - }, - 'sgdp_prj': { - 'ref:long': 0.1225, - 'alt:long': 0.8775 - }, - 'siberian': { - 'ref:long': 0.03571, - 'alt:long': 0.9643 - }, - 'tommo': { - 'ref:long': 0.1122, - 'alt:long': 0.8878 - }, - 'topmed': { - 'ref:long': 0.119, - 'alt:long': 0.881 - }, - 'twinsuk': { - 'ref:long': 0.1076, - 'alt:long': 0.8924 - }, - 'dbgap_popfreq': { - 'ref:long': 0.1199, - 'alt:long': 0.8801 - } - }, - 'varinfo': '11-9071939-C-T', - 'vid': '1.11827e+09', - 'variant_vcf': '11-9071939-C-T', - 'variant_annovar': '11-9071939-9071939-C-T', - 'start_position': '9.07194e+06', - 'end_position': '9.07194e+06', - 'ref_annovar': 'C', - 'alt_annovar': 'T', - 'ref_vcf': 'C', - 'alt_vcf': 'T', - 'apc_conservation': 5.42321, - 'apc_conservation_v2': 5.79002, - 'apc_epigenetics_active': 4.87814, - 'apc_epigenetics': 3.44504, - 'apc_epigenetics_repressed': 1.44574, - 'apc_epigenetics_transcription': 0.892325, - 'apc_local_nucleotide_diversity': 6.18963, - 'apc_local_nucleotide_diversity_v2': 2.63609, - 'apc_local_nucleotide_diversity_v3': 3.05273, - 'apc_mappability': 5.64182, - 'apc_micro_rna': 99.4512, - 'apc_mutation_density': 2.50257, - 'apc_protein_function': 20.2494, - 'apc_protein_function_v2': 4.92793e-10, - 'apc_protein_function_v3': 2.96949, - 'apc_proximity_to_coding': 4.22027, - 'apc_proximity_to_coding_v2': 15.1786, - 'apc_proximity_to_tsstes': 2.60187, - 'apc_transcription_factor': 9.21084, - 'bravo_an': '264690', - 'bravo_af': '0.881012', - 'filter_status': 'PASS', - 'fathmm_xf': '0.60771', - 'funseq_description': 'noncoding', - 'af_total': 0.87813, - 'af_asj_female': 0.805114, - 'af_eas_female': 0.82296, - 'af_afr_male': 0.897356, - 'af_female': 0.882695, - 'af_fin_male': 0.847705, - 'af_oth_female': 0.866364, - 'af_ami': 0.92, - 'af_oth': 0.867688, - 'af_male': 0.873272, - 'af_ami_female': 0.923404, - 'af_afr': 0.898407, - 'af_eas_male': 0.79521, - 'af_sas': 0.771068, - 'af_nfe_female': 0.885846, - 'af_asj_male': 0.813222, - 'af_raw': 0.877997, - 'af_oth_male': 0.86907, - 'af_nfe_male': 0.885488, - 'af_asj': 0.808921, - 'af_amr_male': 0.856755, - 'af_amr_female': 0.859566, - 'af_fin': 0.84861, - 'af_afr_female': 0.899302, - 'af_sas_male': 0.769137, - 'af_amr': 0.85797, - 'af_nfe': 0.885695, - 'af_eas': 0.808087, - 'af_ami_male': 0.916279, - 'af_fin_female': 0.851481, - 'cadd_rawscore': '0.335993', - 'cadd_phred': '5.706', - 'tg_afr': '0.8949', - 'tg_all': '0.828674', - 'tg_amr': '0.8184', - 'tg_eas': '0.7768', - 'tg_eur': '0.8678', - 'tg_sas': '0.7597' - }, - 'source': 'FAVOR', - 'source_url': 'http://favor.genohub.org/' - } - ] - }, - { - 'chr': 'chr11', - 'ancestry': 'EUR', - 'd_prime': 0.956, - 'r2': 0.851, - 'label': 'linkage disequilibrum', - 'variant_1_base_pair': 'C:T', - 'variant_1_rsid': 'rs7395330', - 'variant_2_base_pair': 'A:G', - 'variant_2_rsid': 'rs963167', - 'source': 'TopLD', - 'source_url': 'http://topld.genetics.unc.edu/', - 'sequence variant': [ - { - '_id': 'd95f8850ae016e91e0c334fcfc39e45038667c7f277f6f54f89046f3801e1756', - 'chr': 'chr11', - 'pos': 9073018, - 'rsid': [ - 'rs7395330' - ], - 'ref': 'C', - 'alt': 'T', - 'spdi': 'NC_000011.10:9073018:C:T', - 'hgvs': 'NC_000011.10:g.9073019C>T', - 'qual': '.', - 'filter': None, - 'annotations': { - 'freq': { - '1000genomes': { - 'ref:long': 0.1713, - 'alt:long': 0 - }, - 'alspac': { - 'ref:long': 0.103, - 'alt:long': 0 - }, - 'daghestan': { - 'ref:long': 0.1831, - 'alt:long': 0 - }, - 'estonian': { - 'ref:long': 0.1386, - 'alt:long': 0 - }, - 'genome_dk': { - 'ref:long': 0.15, - 'alt:long': 0 - }, - 'gnomad': { - 'ref:long': 0.1199, - 'alt:long': 0 - }, - 'gonl': { - 'ref:long': 0.1242, - 'alt:long': 0 - }, - 'hapmap': { - 'ref:long': 0.09416, - 'alt:long': 0 - 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'0.198337', - 'cadd_phred': '4.041', - 'tg_afr': '0.2746', - 'tg_all': '0.659944', - 'tg_amr': '0.7637', - 'tg_eas': '0.7798', - 'tg_eur': '0.8608', - 'tg_sas': '0.7771' - }, - 'source': 'FAVOR', - 'source_url': 'http://favor.genohub.org/' - } - ] - }, - { - 'chr': 'chr11', - 'ancestry': 'EUR', - 'd_prime': 0.949, - 'r2': 0.872, - 'label': 'linkage disequilibrum', - 'variant_1_base_pair': 'A:C', - 'variant_1_rsid': 'rs10840169', - 'variant_2_base_pair': 'A:G', - 'variant_2_rsid': 'rs963167', - 'source': 'TopLD', - 'source_url': 'http://topld.genetics.unc.edu/', - 'sequence variant': [ - { - '_id': '602498c777481b11c4b835dbc5637fa5b9855223a05df2dc6dcddc4df4c7f935', - 'chr': 'chr11', - 'pos': 9081683, - 'rsid': [ - 'rs10840169' - ], - 'ref': 'A', - 'alt': 'C', - 'spdi': 'NC_000011.10:9081683:A:C', - 'hgvs': 'NC_000011.10:g.9081684A>C', - 'qual': '.', - 'filter': None, - 'annotations': { - 'freq': { - '1000genomes': { - 'ref:long': 0.3524, - 'alt:long': 0.6476 - }, - 'alspac': { - 'ref:long': 0.08044, - 'alt:long': 0.9196 - }, - 'genome_dk': { - 'ref:long': 0.15, - 'alt:long': 0.85 - }, - 'gnomad': { - 'ref:long': 0.2718, - 'alt:long': 0.7282 - }, - 'korean': { - 'ref:long': 0.2667, - 'alt:long': 0.7333 - }, - 'korea1k': { - 'ref:long': 0.1501, - 'alt:long': 0.8499 - }, - 'page_study': { - 'ref:long': 0.3529, - 'alt:long': 0.6471 - }, - 'qatari': { - 'ref:long': 0.2778, - 'alt:long': 0.7222 - }, - 'sgdp_prj': { - 'ref:long': 0.1978, - 'alt:long': 0.8022 - }, - 'siberian': { - 'ref:long': 0.03704, - 'alt:long': 0.963 - }, - 'tommo': { - 'ref:long': 0.1088, - 'alt:long': 0.8912 - }, - 'topmed': { - 'ref:long': 0.2848, - 'alt:long': 0.7152 - }, - 'twinsuk': { - 'ref:long': 0.08495, - 'alt:long': 0.915 - }, - 'dbgap_popfreq': { - 'ref:long': 0.2235, - 'alt:long': 0.7765 - } - }, - 'varinfo': '11-9081684-A-C', - 'vid': '1.1183e+09', - 'variant_vcf': '11-9081684-A-C', - 'variant_annovar': '11-9081684-9081684-A-C', - 'start_position': '9.08168e+06', - 'end_position': '9.08168e+06', - 'ref_annovar': 'A', - 'alt_annovar': 'C', - 'ref_vcf': 'A', - 'alt_vcf': 'C', - 'apc_conservation': 2.73877, - 'apc_conservation_v2': 2.35529, - 'apc_epigenetics_active': 2.37346, - 'apc_epigenetics': 2.84018, - 'apc_epigenetics_repressed': 3.65998, - 'apc_epigenetics_transcription': 3.19032, - 'apc_local_nucleotide_diversity': 5.19088, - 'apc_local_nucleotide_diversity_v2': 2.69951, - 'apc_local_nucleotide_diversity_v3': 2.71823, - 'apc_mappability': 1.48618, - 'apc_micro_rna': 99.4512, - 'apc_mutation_density': 2.63245, - 'apc_protein_function': 20.2494, - 'apc_protein_function_v2': 4.92793e-10, - 'apc_protein_function_v3': 2.96949, - 'apc_proximity_to_coding': 12.2324, - 'apc_proximity_to_coding_v2': 15.1786, - 'apc_proximity_to_tsstes': 7.61549, - 'apc_transcription_factor': 4.69789, - 'bravo_an': '264690', - 'bravo_af': '0.715188', - 'filter_status': 'PASS', - 'fathmm_xf': '1.0519', - 'funseq_description': 'noncoding', - 'af_total': 0.729336, - 'af_asj_female': 0.778661, - 'af_eas_female': 0.82128, - 'af_afr_male': 0.427265, - 'af_female': 0.728691, - 'af_fin_male': 0.844264, - 'af_oth_female': 0.729508, - 'af_ami': 0.935412, - 'af_oth': 0.733023, - 'af_male': 0.730022, - 'af_ami_female': 0.944681, - 'af_afr': 0.432282, - 'af_eas_male': 0.802021, - 'af_sas': 0.779499, - 'af_nfe_female': 0.876561, - 'af_asj_male': 0.783974, - 'af_raw': 0.72919, - 'af_oth_male': 0.736692, - 'af_nfe_male': 0.875507, - 'af_asj': 0.781156, - 'af_amr_male': 0.803372, - 'af_amr_female': 0.80102, - 'af_fin': 0.845805, - 'af_afr_female': 0.436554, - 'af_sas_male': 0.777508, - 'af_amr': 0.802355, - 'af_nfe': 0.876117, - 'af_eas': 0.810897, - 'af_ami_male': 0.925234, - 'af_fin_female': 0.850728, - 'cadd_rawscore': '-0.023616', - 'cadd_phred': '1.547', - 'tg_afr': '0.329', - 'tg_all': '0.647564', - 'tg_amr': '0.7161', - 'tg_eas': '0.6974', - 'tg_eur': '0.8598', - 'tg_sas': '0.7597' - }, - 'source': 'FAVOR', - 'source_url': 'http://favor.genohub.org/' - } - ] - }, - { - 'chr': 'chr11', - 'ancestry': 'EUR', - 'd_prime': 0.923, - 'r2': 0.814, - 'label': 'linkage disequilibrum', - 'variant_1_base_pair': 'A:G', - 'variant_1_rsid': 'rs2647530', - 'variant_2_base_pair': 'A:G', - 'variant_2_rsid': 'rs963167', - 'source': 'TopLD', - 'source_url': 'http://topld.genetics.unc.edu/', - 'sequence variant': [ - { - '_id': '07210d5c9b7aedba471f029ab0e6159ce68ca6a8388e346d1c4876c3f5f1debf', - 'chr': 'chr11', - 'pos': 9084088, - 'rsid': [ - 'rs2647530' - ], - 'ref': 'A', - 'alt': 'G', - 'spdi': 'NC_000011.10:9084088:A:G', - 'hgvs': 'NC_000011.10:g.9084089A>G', - 'qual': '.', - 'filter': None, - 'annotations': { - 'freq': { - '1000genomes': { - 'ref:long': 0.8115, - 'alt:long': 0.1885 - }, - 'alspac': { - 'ref:long': 0.891, - 'alt:long': 0.109 - }, - 'chileans': { - 'ref:long': 0.8147, - 'alt:long': 0.1853 - }, - 'estonian': { - 'ref:long': 0.8641, - 'alt:long': 0.1359 - }, - 'genome_dk': { - 'ref:long': 0.85, - 'alt:long': 0.15 - }, - 'gnomad': { - 'ref:long': 0.8592, - 'alt:long': 0.1408 - }, - 'gonl': { - 'ref:long': 0.8707, - 'alt:long': 0.1293 - }, - 'hgdp_stanford': { - 'ref:long': 0.809, - 'alt:long': 0.191 - }, - 'hapmap': { - 'ref:long': 0.8316, - 'alt:long': 0.1684 - }, - 'korean': { - 'ref:long': 0.8368, - 'alt:long': 0.1632 - }, - 'korea1k': { - 'ref:long': 0.8297, - 'alt:long': 0.1703 - }, - 'northernsweden': { - 'ref:long': 0.87, - 'alt:long': 0.13 - }, - 'prjeb36033': { - 'ref:long': 0.8409, - 'alt:long': 0.1591 - }, - 'qatari': { - 'ref:long': 0.8565, - 'alt:long': 0.1435 - }, - 'sgdp_prj': { - 'ref:long': 0.3544, - 'alt:long': 0.6456 - }, - 'siberian': { - 'ref:long': 0.5, - 'alt:long': 0.5 - }, - 'tommo': { - 'ref:long': 0.882, - 'alt:long': 0.118 - }, - 'topmed': { - 'ref:long': 0.8567, - 'alt:long': 0.1433 - }, - 'twinsuk': { - 'ref:long': 0.8851, - 'alt:long': 0.1149 - }, - 'vietnamese': { - 'ref:long': 0.7454, - 'alt:long': 0.2546 - }, - 'dbgap_popfreq': { - 'ref:long': 0.8679, - 'alt:long': 0.1321 - } - }, - 'varinfo': '11-9084089-A-G', - 'vid': '1.1183e+09', - 'variant_vcf': '11-9084089-A-G', - 'variant_annovar': '11-9084089-9084089-A-G', - 'start_position': '9.08409e+06', - 'end_position': '9.08409e+06', - 'ref_annovar': 'A', - 'alt_annovar': 'G', - 'ref_vcf': 'A', - 'alt_vcf': 'G', - 'apc_conservation': 0.63715, - 'apc_conservation_v2': 0.602357, - 'apc_epigenetics_active': 8.25438, - 'apc_epigenetics': 7.50488, - 'apc_epigenetics_repressed': 5.54396, - 'apc_epigenetics_transcription': 1.89144, - 'apc_local_nucleotide_diversity': 4.58096, - 'apc_local_nucleotide_diversity_v2': 1.58316, - 'apc_local_nucleotide_diversity_v3': 1.60306, - 'apc_mappability': 8.10064, - 'apc_micro_rna': 99.4512, - 'apc_mutation_density': 1.55657, - 'apc_protein_function': 20.2494, - 'apc_protein_function_v2': 4.92793e-10, - 'apc_protein_function_v3': 2.96949, - 'apc_proximity_to_coding': 2.59407, - 'apc_proximity_to_coding_v2': 15.1786, - 'apc_proximity_to_tsstes': 6.94444, - 'apc_transcription_factor': 11.4619, - 'bravo_an': '264690', - 'bravo_af': '0.143334', - 'filter_status': 'PASS', - 'fathmm_xf': '0.431069', - 'funseq_description': 'noncoding', - 'af_total': 0.142387, - 'af_asj_female': 0.194318, - 'af_eas_female': 0.196949, - 'af_afr_male': 0.167548, - 'af_female': 0.139629, - 'af_fin_male': 0.125726, - 'af_oth_female': 0.147273, - 'af_ami': 0.0644444, - 'af_oth': 0.148234, - 'af_male': 0.145321, - 'af_ami_female': 0.0553191, - 'af_afr': 0.164775, - 'af_eas_male': 0.223952, - 'af_sas': 0.215557, - 'af_nfe_female': 0.119809, - 'af_asj_male': 0.184379, - 'af_raw': 0.142486, - 'af_oth_male': 0.14924, - 'af_nfe_male': 0.12058, - 'af_asj': 0.189645, - 'af_amr_male': 0.152135, - 'af_amr_female': 0.150729, - 'af_fin': 0.126516, - 'af_afr_female': 0.162414, - 'af_sas_male': 0.218042, - 'af_amr': 0.151526, - 'af_nfe': 0.120134, - 'af_eas': 0.21144, - 'af_ami_male': 0.0744186, - 'af_fin_female': 0.129058, - 'cadd_rawscore': '-0.143592', - 'cadd_phred': '0.772', - 'tg_afr': '0.1762', - 'tg_all': '0.188498', - 'tg_amr': '0.1816', - 'tg_eas': '0.2282', - 'tg_eur': '0.1352', - 'tg_sas': '0.2239' - }, - 'source': 'FAVOR', - 'source_url': 'http://favor.genohub.org/' - } - ] - } - ] - }] -} diff --git a/tests/acceptance_tests/variants_phenotypes.py b/tests/acceptance_tests/variants_phenotypes.py deleted file mode 100644 index 71e510a7..00000000 --- a/tests/acceptance_tests/variants_phenotypes.py +++ /dev/null @@ -1,224 +0,0 @@ -variants_phenotypes = { - '/variants/phenotypes': [{ - 'params': { - 'region': 'chr1:1022580-1023580', - 'rsid': 'rs2710889', - 'p_value': 'lte:0.01' - }, - 'response': [ - { - 'study_id': 'GCST007841', - 'ontology term': 'ontology_terms/EFO_0004339', - 'p_val': 2e-12, - 'p_val_exponent': -12, - 'p_val_mantissa': 2, - 'beta': 0, - 'beta_ci_lower': 0, - 'beta_ci_upper': 0, - 'oddsr_ci_lower': None, - 'oddsr_ci_upper': None, - 'lead_chrom': '1', - 'lead_pos': '1023573', - 'lead_ref': 'A', - 'lead_alt': 'G', - 'direction': '', - 'source': 'OpenTargets', - 'version': 'October 2022 (22.10)' - }, - { - 'study_id': 'NEALE2_20015_raw', - 'ontology term': 'ontology_terms/EFO_0011011', - 'p_val': 6.25672e-9, - 'p_val_exponent': -9, - 'p_val_mantissa': 6.25672, - 'beta': 0.0518207, - 'beta_ci_lower': 0.034338676, - 'beta_ci_upper': 0.069302724, - 'oddsr_ci_lower': None, - 'oddsr_ci_upper': None, - 'lead_chrom': '1', - 'lead_pos': '1023573', - 'lead_ref': 'A', - 'lead_alt': 'G', - 'direction': '+', - 'source': 'OpenTargets', - 'version': 'October 2022 (22.10)' - } - ] - }, { - 'params': { - 'region': 'chr1:1022580-1023580', - 'rsid': 'rs2710889', - 'p_value': 'lte:0.01', - 'verbose': 'true' - }, - 'response': [ - { - 'study_id': 'GCST007841', - 'ontology term': [ - { - 'uri': 'http://www.ebi.ac.uk/efo/EFO_0004339', - 'term_id': 'EFO_0004339', - 'name': 'body height', - 'description': 'The distance from the sole to the crown of the head with body standing on a flat surface and fully extended.', - 'source': 'EFO', - 'subontology': None - } - ], - 'p_val': 2e-12, - 'p_val_exponent': -12, - 'p_val_mantissa': 2, - 'beta': 0, - 'beta_ci_lower': 0, - 'beta_ci_upper': 0, - 'oddsr_ci_lower': None, - 'oddsr_ci_upper': None, - 'lead_chrom': '1', - 'lead_pos': '1023573', - 'lead_ref': 'A', - 'lead_alt': 'G', - 'direction': '', - 'source': 'OpenTargets', - 'version': 'October 2022 (22.10)' - }, - { - 'study_id': 'NEALE2_20015_raw', - 'ontology term': [ - { - 'uri': 'http://www.ebi.ac.uk/efo/EFO_0011011', - 'term_id': 'EFO_0011011', - 'name': 'sitting height measurement', - 'description': 'Quantification of some aspect of height, when assuming a sitting position.', - 'source': 'EFO', - 'subontology': None - } - ], - 'p_val': 6.25672e-9, - 'p_val_exponent': -9, - 'p_val_mantissa': 6.25672, - 'beta': 0.0518207, - 'beta_ci_lower': 0.034338676, - 'beta_ci_upper': 0.069302724, - 'oddsr_ci_lower': None, - 'oddsr_ci_upper': None, - 'lead_chrom': '1', - 'lead_pos': '1023573', - 'lead_ref': 'A', - 'lead_alt': 'G', - 'direction': '+', - 'source': 'OpenTargets', - 'version': 'October 2022 (22.10)' - } - ] - }, { - 'params': { - 'variant_id': '1f3e4afc831fff5a67f2401fb5dc7ef55b0e177f633b7fd88036962bacb925d9', - 'p_value': 'lte:0.01', - 'verbose': 'false' - }, - 'response': [ - { - 'study_id': 'GCST007841', - 'ontology term': 'ontology_terms/EFO_0004339', - 'p_val': 2e-12, - 'p_val_exponent': -12, - 'p_val_mantissa': 2, - 'beta': 0, - 'beta_ci_lower': 0, - 'beta_ci_upper': 0, - 'oddsr_ci_lower': None, - 'oddsr_ci_upper': None, - 'lead_chrom': '1', - 'lead_pos': '1023573', - 'lead_ref': 'A', - 'lead_alt': 'G', - 'direction': '', - 'source': 'OpenTargets', - 'version': 'October 2022 (22.10)' - }, - { - 'study_id': 'NEALE2_20015_raw', - 'ontology term': 'ontology_terms/EFO_0011011', - 'p_val': 6.25672e-9, - 'p_val_exponent': -9, - 'p_val_mantissa': 6.25672, - 'beta': 0.0518207, - 'beta_ci_lower': 0.034338676, - 'beta_ci_upper': 0.069302724, - 'oddsr_ci_lower': None, - 'oddsr_ci_upper': None, - 'lead_chrom': '1', - 'lead_pos': '1023573', - 'lead_ref': 'A', - 'lead_alt': 'G', - 'direction': '+', - 'source': 'OpenTargets', - 'version': 'October 2022 (22.10)' - } - ] - }, { - 'params': { - 'variant_id': '1f3e4afc831fff5a67f2401fb5dc7ef55b0e177f633b7fd88036962bacb925d9', - 'p_value': 'lte:0.01', - 'verbose': 'true' - }, - 'response': [ - { - 'study_id': 'GCST007841', - 'ontology term': [ - { - 'uri': 'http://www.ebi.ac.uk/efo/EFO_0004339', - 'term_id': 'EFO_0004339', - 'name': 'body height', - 'description': 'The distance from the sole to the crown of the head with body standing on a flat surface and fully extended.', - 'source': 'EFO', - 'subontology': None - } - ], - 'p_val': 2e-12, - 'p_val_exponent': -12, - 'p_val_mantissa': 2, - 'beta': 0, - 'beta_ci_lower': 0, - 'beta_ci_upper': 0, - 'oddsr_ci_lower': None, - 'oddsr_ci_upper': None, - 'lead_chrom': '1', - 'lead_pos': '1023573', - 'lead_ref': 'A', - 'lead_alt': 'G', - 'direction': '', - 'source': 'OpenTargets', - 'version': 'October 2022 (22.10)' - }, - { - 'study_id': 'NEALE2_20015_raw', - 'ontology term': [ - { - 'uri': 'http://www.ebi.ac.uk/efo/EFO_0011011', - 'term_id': 'EFO_0011011', - 'name': 'sitting height measurement', - 'description': 'Quantification of some aspect of height, when assuming a sitting position.', - 'source': 'EFO', - 'subontology': None - } - ], - 'p_val': 6.25672e-9, - 'p_val_exponent': -9, - 'p_val_mantissa': 6.25672, - 'beta': 0.0518207, - 'beta_ci_lower': 0.034338676, - 'beta_ci_upper': 0.069302724, - 'oddsr_ci_lower': None, - 'oddsr_ci_upper': None, - 'lead_chrom': '1', - 'lead_pos': '1023573', - 'lead_ref': 'A', - 'lead_alt': 'G', - 'direction': '+', - 'source': 'OpenTargets', - 'version': 'October 2022 (22.10)' - } - ] - }] -} diff --git a/tests/response_times/response_times.py b/tests/response_times/response_times.py new file mode 100644 index 00000000..09a7274a --- /dev/null +++ b/tests/response_times/response_times.py @@ -0,0 +1,111 @@ +import requests +import time +import os +import hashlib +import csv + +INPUT_FILE = 'urls.txt' +OUTPUT_DIR = 'responses' +TIME_LOG_FILE = 'average_response_time.csv' +DIFF_LOG_FILE = 'differences.txt' +TEST_DEV = False + + +def read_urls(file_path): + with open(file_path, 'r') as file: + return [line.strip() for line in file if line.strip()] + + +def fetch_url(url): + start_time = time.time() + try: + response = requests.get(url, timeout=10) + response.raise_for_status() + return response.text, time.time() - start_time + except requests.RequestException as e: + print(f'{str(e)}') + return str(e), time.time() - start_time + + +def get_response_filename(url): + # using md5 of endpoint to avoid very large filenames + sanitized_name = hashlib.md5(url.encode()).hexdigest() + '.txt' + return os.path.join(OUTPUT_DIR, sanitized_name) + + +def save_response(url, response_text): + os.makedirs(OUTPUT_DIR, exist_ok=True) + filename = get_response_filename(url) + with open(filename, 'w', encoding='utf-8') as file: + file.write(response_text) + + +def compare_responses(url, new_response): + filename = get_response_filename(url) + if os.path.exists(filename): + with open(filename, 'r', encoding='utf-8') as file: + old_response = file.read() + if old_response != new_response: + with open(DIFF_LOG_FILE, 'a', encoding='utf-8') as diff_file: + diff_file.write(f'Difference found for {url}:\n\n') + diff_file.write(f'--- Previous Response ---\n{old_response}\n') + diff_file.write(f'--- New Response ---\n{new_response}\n') + diff_file.write('=' * 80 + '\n') + + +def load_previous_times(): + response_times = {} + if os.path.exists(TIME_LOG_FILE): + with open(TIME_LOG_FILE, 'r', encoding='utf-8') as file: + reader = csv.reader(file) + next(reader, None) + for row in reader: + if len(row) == 3: + url, avg_time, count = row + response_times[url] = [float(avg_time), int(count)] + return response_times + + +def save_average_times(times): + with open(TIME_LOG_FILE, 'w', encoding='utf-8', newline='') as file: + writer = csv.writer(file) + writer.writerow( + ['URL', 'Average Response Time (s)', 'Number of Calls']) + for url, (avg_time, count) in times.items(): + writer.writerow([url, avg_time, count]) + + +def main(): + urls = read_urls(INPUT_FILE) + response_times = load_previous_times() + + os.makedirs(OUTPUT_DIR, exist_ok=True) + if os.path.exists(DIFF_LOG_FILE): + os.remove(DIFF_LOG_FILE) # Clear previous diff logs + + for url in urls: + if TEST_DEV: + url = url.replace('api', 'api-dev') + + print(f'Fetching: {url}') + + response_text, response_time = fetch_url(url) + + compare_responses(url, response_text) + save_response(url, response_text) + + if url in response_times: + previous_avg, count = response_times[url] + new_avg = ((previous_avg * count) + response_time) / (count + 1) + response_times[url] = [new_avg, count + 1] + else: + response_times[url] = [response_time, 1] + + save_average_times(response_times) + + print( + f"Saved responses in '{OUTPUT_DIR}/', average times in '{TIME_LOG_FILE}', and differences in '{DIFF_LOG_FILE}' if any.") + + +if __name__ == '__main__': + main() diff --git a/tests/response_times/urls.txt b/tests/response_times/urls.txt new file mode 100644 index 00000000..99b0eaff --- /dev/null +++ b/tests/response_times/urls.txt @@ -0,0 +1,95 @@ +https://api.catalog.igvf.org/api/variants?spdi=NC_000020.11%3A3658947%3AA%3AG&organism=Homo%20sapiens&page=0 +https://api.catalog.igvf.org/api/variants?hgvs=NC_000020.11%3Ag.3658948A%3EG&organism=Homo%20sapiens&page=0 +https://api.catalog.igvf.org/api/variants?region=chr1%3A1157520-1158189&organism=Homo%20sapiens&page=0 +https://api.catalog.igvf.org/api/variants?mouse_strain=A_J&organism=Mus%20musculus&page=0 +https://api.catalog.igvf.org/api/variants/freq?source=bravo_af&minimum_af=0&maximum_af=1&organism=Homo%20sapiens&page=0 +https://api.catalog.igvf.org/api/variants/freq?source=bravo_af®ion=chr3%3A186741137-186742238&minimum_af=0&maximum_af=1&organism=Homo%20sapiens&page=0 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