diff --git a/docs/genomics-platform/about-our-data/disease-ontology/hierarchy.png b/docs/genomics-platform/about-our-data/disease-ontology/hierarchy.png new file mode 100644 index 00000000..8c252a86 Binary files /dev/null and b/docs/genomics-platform/about-our-data/disease-ontology/hierarchy.png differ diff --git a/docs/genomics-platform/about-our-data/disease-ontology/index.md b/docs/genomics-platform/about-our-data/disease-ontology/index.md new file mode 100644 index 00000000..11181fd2 --- /dev/null +++ b/docs/genomics-platform/about-our-data/disease-ontology/index.md @@ -0,0 +1,96 @@ +--- +title: St. Jude Cloud's Disease Ontology +--- + +# The St. Jude Cloud Pediatric Cancer Classification Ontology: An Evolving Framework + +Click [here](https://permalinks.stjude.cloud/permalinks/st-jude-cloud-disease-ontology) to download the full St. Jude Cloud custom disease ontology (v0). + +## Introduction: + +Ontologies designed for disease classification have redefined our understanding of diseases by providing a hierarchical structure of complex biomedical data. In cancer research, they are critical for data sharing, integration, and collaboration among researchers. However, existing ontologies on pediatric cancer classification are limited. The World Health Organization (WHO) and OncoTree primarily focus on adult cancers while leaving gaps in many pediatric cancer subtypes driven by molecular etiology presented in recent scientific literature. To enable data sharing and integration of the whole-genome, whole-exome and RNA-seq data generated from 13,956 cases of pediatric cancer and long-term survivors on St. Jude Cloud, we recognized the significance of such gaps and initiated the development of a tailored disease ontology to address this issue. + +## Principles: + +Our goal is to develop a pediatric-centric framework with the capability of integrating new research findings, including those involving rare molecular drivers. Currently, we focus exclusively on pediatric cancer but will consider extension to other childhood catastrophic diseases, such as Bone Marrow Failure and Sickle Cell disease. Our framework is designed to integrate molecular, pathological, and histological features by leveraging existing efforts from OncoTree, WHO, and community knowledge. + +## Methods/Details: + +To achieve these principles, we evaluated existing ontologies, including: + +- OncoTree + +- International Classification of Diseases for Oncology (ICD-O) + +- The World Health Organization (WHO) Hematological and CNS classifications + + +Our primary design is based on OncoTree due to its cancer-focused approach, structure for starting at tissue and breaking out into diseases, and alignment with our guiding principles. However, there have been deviations which initiated the tailored ontology that applies across St. Jude Cloud (*Figure1*). + + +## Key Structural Changes: + +- **Adjustment in Hematological Diseases:** Distinctions between leukemia and lymphoma were introduced, addressing a gap in OncoTree's applicability to the pediatric domain. + +- **Exclusion of Adult-Specific Terms:** We omitted terms exclusive to adult diseases, such as breast cancer and lung cancer (e.g. small cell lung cancer (SCLC)) ensuring our ontology's focus primarily remains tailored to pediatric oncology. + +- **Expansion for Recently Discovered Molecular Drivers:** Recognizing the prominence of new molecular drivers discovered by genome-wide profiling of pediatric diseases, we expanded our ontology to include additional nodes to reflect the current knowledge. For instance: + + - B-Cell Acute Lymphoblastic Leukemia (BALL)1 was subdivided into 28 distinct subtypes, a considerable increase from Oncotree's original nine. + + - Incorporating newly discovered molecular drivers such as DUX42, MEF2D3 NUMT1 or BCL11B4 rearrangements. + + - T-Cell Acute Lymphoblastic Leukemia (TALL)5 was classified into 10 distinct subtypes, up from two in OncoTree. + + - Including commonly activated transcriptional regulators including those oncogenes defining T-ALL subgroups - TAL1, TLX1, TLX3, and NKX2-1.5 + +## Current Status: + +To date, the development was primarily motivated by omics data that was being uploaded to the St. Jude Cloud platform every month for community data sharing. At this cadence, the ontology framework represents an evolving architecture as it is continuously being refined as new data is curated. In addition to the incremental updates, major revision has been planned, with current examples described below. This is to align with recent publications, to work closely with institutional experts who are heavily involved with developing the WHO classifications, thereby updating CNS tumor classification updates from WHO CNS5, to make recent updates from OncoTree. + +## Current Focus: + + **Review of Glioma Tumors6:** + +- There's a notable shift in classifying diffuse intrinsic pontine glioma to midline glioma, reflecting evolving understanding and diagnostic criteria noted by the WHO CNS5 guidelines. + +- Additionally, our disease ontology's inclusion of modifiers such as anaplastic or diffuse diverges from the recent WHO CNS5 classification updates for grading, particularly concerning tumors like astrocytoma and glioblastoma. + +**Review of Embryonal Tumors6:** + +- Recent studies advocate for revisiting the classification of embryonal tumors, for example medulloblastoma groups 3 and 4. Proposals suggest annotating them as Medulloblastoma, non-WNT/non-SHH7,8 emphasizing molecular distinctions over histological classifications. + +- Given the heterogeneity nature of medulloblastoma, there is a new term, histologically defined, that should be evaluated and employed for subtypes such as large cell/anaplastic or desmoplastic/nodular medulloblastoma. + +**Review of Solid Tumors9:** + +- Explore merging subtypes such as osteoblastic osteosarcoma and chondroblastic osteosarcoma under the umbrella of osteosarcoma, aligning with evolving research insights. + +## Conclusion +Our disease ontology is integral to various applications within St. Jude Cloud, driving initiatives like the Genomics Platform and Pediatric Knowledge Base (PeCan). However, its growth and effectiveness rely on community involvement. The current ontology framework has been developed with the input from pathologists and researchers involved in molecular subtyping. We welcome additional input and collaboration from researchers and clinicians to ensure its ongoing improvement and relevance to pediatric oncology, ultimately contributing to better outcomes for children facing cancer and catastrophic diseases. + + +**Contact:** For inquiries, collaborative opportunities, or to provide feedback on improving the St. Jude Cloud disease ontology, please contact support@stjude.cloud. + +![](./hierarchy.png) +**Figure 1: St. Jude Cloud Disease Ontology.** High-level overview of the ontology that supports applications in St. Jude Cloud. + +### References + +1. https://pubmed.ncbi.nlm.nih.gov/36050548/ + +2. https://pubmed.ncbi.nlm.nih.gov/27776115/ + +3. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5105166/ + +4. https://pubmed.ncbi.nlm.nih.gov/36050548/ + +5. https://pubmed.ncbi.nlm.nih.gov/28671688/ + +6. https://academic.oup.com/neuro-oncology/article/23/8/1231/6311214 + +7. https://www.biorxiv.org/content/10.1101/2024.02.09.579680v1.full + +8. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8833659/ + +9. https://ascopubs.org/doi/full/10.1200/CCI.20.00108 \ No newline at end of file diff --git a/docs/genomics-platform/about-our-data/metadata-and-clinical/index.md b/docs/genomics-platform/about-our-data/metadata-and-clinical/index.md index 276df328..5187e7f9 100644 --- a/docs/genomics-platform/about-our-data/metadata-and-clinical/index.md +++ b/docs/genomics-platform/about-our-data/metadata-and-clinical/index.md @@ -9,341 +9,63 @@ redirect_from: Each data request includes a text file called `SAMPLE_INFO.txt` that provides a number of file level properties (sample identifiers, clinical attributes, etc). -### Standard Metadata - - Below are the set of tags which *may* exist for any given file in St. Jude Cloud. All optional metadata will have `sj_` prepended to their tag name. +### Definitions +Below are the set of tags which may exist for any given file in St. Jude Cloud. Tags with ‘sj_’ prepended are required fields. Tags with ‘attr_’ prepended are information queried from the physician or research team’s records at the time of sample submission to St. Jude Cloud and are considered optional, as the level of information gathered for each sample varies. | Property | Description | | -------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| `file_path` | The path to the file in your St. Jude Cloud project. | -| `subject_name` | A unique subject identifier assigned internally at St. Jude. | -| `sample_name` | A unique sample identifier assigned internally at St. Jude. | -| `sample_type` | One of Autopsy, Cell line, Diagnosis, Germline, Metastasis, Relapse, or Xenograft. | -| `sequencing_type` | Whether the file was generated from Whole Genome (WGS), Whole Exome (WES), or RNA-Seq. | -| `file_type` | File type to be rendered in the St. Jude Cloud Genomics Platform data browser. Note that indices will be marked as the file type they accompany, and this is because these files will be vended together in our data browser. If you wish to be able to distinguish these file types, please parse the `file_path`. | -| `description` | Optional field that may contain additional file information. | -| `sj_diseases` | If your data request was process after August 18, 2020, the field should be interpreted as the harmonized St. Jude Cloud diagnosis based on the best available information (data provided by the lab or PI and followup by scientists on the St. Jude Cloud team). If your data request was processed before August 18, 2020, this field should be interpreted as the disease identifier assigned at the time of genomic sequencing (keyly, the diagnosis known at the time of genomic testing may not be the best available information). **If your data request was processed after August 18, 2020 and you'd like to use the most up to date, harmonized diagnosis**, we recommend using `sj_diseases` when including diagnosis in your analysis. If your data request was made before this time *or* if you wish to use the values exactly as provided by the lab or PI, we recommend using the lab-provided value in `attr_diagnosis`. | -| `sj_datasets` | If present, the datasets in the data browser which this file is associated with. | -| `sj_pmid_accessions` | If the file was associated with a paper, the related [Pubmed][pubmed] accession number. | -| `sj_ega_accessions` | If the file was associated with a paper, the related [EGA][ega] accession number. | -| `sj_dataset_accession` | If present, the permanent accession number assigned in St. Jude Cloud. | -| `sj_embargo_date` | The [embargo date](../../requesting-data/glossary/#embargo-date), which specifies the first date which the files can be used in a publication. | - -### Clinical and Phenotypic Information - -Also included is a set of phenotypic information queried from the physician or research team's records at the time of sample submission to St. Jude Cloud. These are all considered to be *optional*, as the level of information gathered for each sample varies. If empty, the physician or research team did not indicate a value for the field. All basic clinical or phenotypic information will have `attr_` prepended to their tag name. - -| Property | Description | -| -------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------ | +| `file_path` | The path to the file in your St. Jude Cloud project. | +| `file_id` | A unique identifier for the file on DNAnexus, you can see this value listed as “ID” in the DNAnexus user interface. | +| `subject_name` | A unique subject identifier assigned internally at St. Jude.| +| `sample_name` | A unique sample identifier assigned internally at St. Jude. | +| `sample_type` | One of Autopsy, Cell line, Diagnosis, Germline, Metastasis, Relapse, or Xenograft.| +| `sequencing_type` | Whether the file was generated from Whole Genome (WGS), Whole Exome (WES), or RNA-Seq. | +| `file_type` | Specifies the type of file. Note that index files will be labeled as the file type they accompany and will automatically be selected together in our data browser. If you wish to distinguish between the two in your project, please parse the `file_path` where index files are appended with an additional string, such as `.bai`. | +| `description` | Optional field that may contain additional file information. | +| `file_size` | The size of the file in bytes, not exceeding 12 integers. | +| `sj_dataset_accession` | The permanent accession number assigned to a dataset in St. Jude Cloud. | +| `sj_embargo_date` | The [embargo date](../../requesting-data/glossary/#embargo-date), which specifies the first date which the files can be used in a publication. | +| `sj_long_disease_name` | The complete written name of the disease associated with the disease code store in the `sj_disease` attribute. For more information about our ontology go [here](https://university.stjude.cloud/docs/genomics-platform/about-our-data/disease-ontology).| | `attr_age_at_diagnosis` | Age at first diagnosis. This field is normalized as a decimal value. If empty, the physician or research team did not indicate a value for this field. | -| `attr_diagnosis` | Unharmonized primary diagnosis as reported by the lab or PI upon submission of data to St. Jude Cloud. | -| `attr_ethnicity` | Self-reported ethnicity. Values are normalized according to the [US Census Bureau classifications][censusburea]. | -| `attr_race` | Self-reported race. Values are normalized according to the [US Census Bureau classifications][censusburea]. | -| `attr_sex` | Self-reported sex. | -| `attr_oncotree_disease_code` | The disease code (assigned at the time of genomic sequencing) as specified by [Oncotree Version 2019-03-01][oncotree_2019_03_01]. | - -### Diagnosis Codes +| `attr_diagnosis` | Unharmonized primary diagnosis as reported by the lab or PI upon submission of data to St. Jude Cloud. | +| `attr_sex` | Self-reported sex. | +| `attr_ethnicity` | Self-reported ethnicity. Values are normalized according to the [US Census Bureau classifications][censusburea]. | +| `attr_race` | Self-reported race. Values are normalized according to the [US Census Bureau classifications][censusburea]. | +| `attr_oncotree_disease_code` | The disease code (assigned at the time of genomic sequencing) as specified by [Oncotree Version 2019-03-01][oncotree_2019_03_01]. | +| `attr_library_selection_protocol` | The laboratory method used to prepare and select the DNA or RNA for sequencing from a sample. The possible values are PCR, PolyA, Total, Random, Not Available, or Not Applicable. | +| `attr_read_length` | The read length used, when available. | +| `attr_sequencing_platform` | This defines which sequencing platform was used to generate the data, when available. | +| `attr_read_type` | The sequencing read type, if available. | +| `attr_inferred_strandedness` | Computationally determined strandedness of RNA-seq data, if applicable. | +| `sj_publication_titles` | The title of associated publications(s), if the file was associated with a paper(s). | +| `sj_pub_accessions` | The related St. Jude Cloud accession number(s), if the file was associated with a paper(s). These group the files into publications as displayed on the Genomics Platform data browser. | +| `sj_pmid_accessions` | The related [Pubmed][pubmed] accession number, if the file was associated with a paper. | +| `attr_subtype_biomarkers` | A molecular mutation, SV or fusion event associated with a particular disease subtype that is used to define membership in that subtype. | +| `sj_associated_diagnoses` | List of all available associated diagnoses for the subject (from the tumor samples or from a patient's clinical history.| +| `attr_germline_sample` | The paired germline sample that was used when creating the Somatic VCF file, if applicable. | +| `attr_diagnosis_group` | Each file is categorized into one of five diagnosis groups based on the type of tumor - hematologic malignancy, solid tumor, brain tumor, germ cell tumor, or not applicable (for germline samples). | +| `sj_ega_accessions` | The related [EGA][ega] accession number, if the file was associated with a paper. | +| `sj_access_unit` | Lists which Data Access Unit (DAU) the file belongs to. For more on Data Access Units, see here. (https://university.stjude.cloud/docs/genomics-platform/about-our-data/dau-and-datasets/#data-access-unit) | +| `sj_diseases` | If your data request was process after August 18, 2020, the field should be interpreted as the harmonized St. Jude Cloud diagnosis based on the best available information (data provided by the lab or PI and followup by scientists on the St. Jude Cloud team). If your data request was processed before August 18, 2020, this field should be interpreted as the disease identifier assigned at the time of genomic sequencing (keyly, the diagnosis known at the time of genomic testing may not be the best available information). **If your data request was processed after August 18, 2020 and you'd like to use the most up to date, harmonized diagnosis**, we recommend using `sj_diseases` when including diagnosis in your analysis. If your data request was made before this time *or* if you wish to use the values exactly as provided by the lab or PI, we recommend using the lab-provided value in `attr_diagnosis`. For more information about our disease ontology go [here](https://university.stjude.cloud/docs/genomics-platform/about-our-data/disease-ontology). | +| `sj_datasets` | The dataset(s) in the data browser which this file is associated with. | +| `sj_pipeline_name` | Specifies which specific version of the pipeline was used when generating the file. | +| `attr_tissue_preservative` | The preservation method used for the tissue sample, with two options: FFPE (formalin-fixed, paraffin-embedded) or Fresh/Frozen. | +| `attr_lab_strandedness` | Lab reported strandedness of RNA-seq data. | + + +### Disease Codes !!!note During the release of the St. Jude Cloud paper, we undertook a massive effort to curate and harmonize diagnosis values within St. Jude Cloud. We provide two values for diagnosis, and you should select carefully which value you use based on your use case: -1. `sj_diseases`, which, since August 18, 2020, represents the harmonized diagnosis value curated by scientists on the St. Jude Cloud team (before that time it represented the diagnosis known at time of sequencing). +1. `sj_diseases`, which, since August 18, 2020, represents the harmonized diagnosis value curated by scientists on the St. Jude Cloud team (before that time it represented the diagnosis known at time of sequencing). For more information about our disease ontology go [here](https://university.stjude.cloud/docs/genomics-platform/about-our-data/disease- +ontology). 2. `attr_diagnosis`, which contains the unharmonized diagnosis value directly as it was submitted to us from the lab or PI. -**If your data request was processed after August 18, 2020 and you'd like to use the most up to date, harmonized diagnosis**, we recommend using `sj_diseases` field. If your data request was made before this time *or* if you wish to use the values exactly as provided by the lab or PI, we recommend using the value in `attr_diagnosis`. +**If your data request was processed after August 18, 2020 and you'd like to use the most up to date, harmonized diagnosis**, we recommend using `sj_diseases` field. If your data request was made before this time *or* if you wish to use the values exactly as provided by the lab or PI, we recommend using the value in `attr_diagnosis`. For more information about our disease ontology go [here](https://university.stjude.cloud/docs/genomics-platform/about-our-data/disease-ontology). !!! -The `SAMPLE_INFO.txt` file that comes with your data request will contain the list of associated harmonized diagnosis codes (`sj_diseases`) for each sample. These codes represent the harmonized diagnosis values curated by the St. Jude Cloud team and reflect the most up to date information about the sample. Below, we include the full set of diagnosis values in St. Jude Cloud Genomics Platform, the category of the tumor, and the closest available OncoTree term. We regularly work with the OncoTree committee to update new subtypes, so any discrepancies between our diagnosis code and the OncoTree term can be interpreted as more granular classifications that OncoTree does not yet account for. - - -| Tumor Category | Diagnosis | Diagnosis Code | Corresponding Oncotree Code | -|------------------------|------------------------------------------------------------------------------|-----------------|-----------------------------| -| Brain Tumor | Acoustic Neuroma | ANM | | -| Brain Tumor | Anaplastic Ganglioglioma | AGNG | AGNG | -| Brain Tumor | Astrocytoma, NOS | ASTR | ASTR | -| Brain Tumor | Atypical Meningioma | ATM | ATM | -| Brain Tumor | Atypical Teratoid/Rhabdoid Tumor | ATRT | ATRT | -| Brain Tumor | Brain Tumor | BT | | -| Brain Tumor | Central Neurocytoma | CNC | CNC | -| Brain Tumor | Choroid Plexus Carcinoma | CPC | CPC | -| Brain Tumor | Choroid Plexus Papilloma | CPP | CPP | -| Brain Tumor | Colloid Cyst | CCY | MBT | -| Brain Tumor | Craniopharyngioma, Adamantinomatous Type | ACPG | ACPG | -| Brain Tumor | Craniopharyngioma, NOS | CPG | SELT | -| Brain Tumor | Desmoplastic Infantile Astrocytoma | DIA | DIA | -| Brain Tumor | Desmoplastic/Nodular Medulloblastoma | DMBL | DMBL | -| Brain Tumor | Desmoplastic/Nodular Medulloblastoma, SHH subtype | DMBLSHH | DMBL | -| Brain Tumor | Dysembryoplastic Neuroepithelial Tumor | DNT | DNT | -| Brain Tumor | Embryonal Tumor, Brain | EMBT | EMBT | -| Brain Tumor | Embryonal Tumor with Multilayered Rosettes, Brain | ETMR | EMBT | -| Brain Tumor | Ependymomal Tumor | EPMT | EPMT | -| Brain Tumor | Ependymomal Tumor, Anaplastic | APE | APE | -| Brain Tumor | Ependymomal Tumor, Posterior Fossa | EPMTPF | EPMT | -| Brain Tumor | Ependymomal Tumor, Spinal Tumor | EPMTST | EPMT | -| Brain Tumor | Ependymomal Tumor, Supratentorial | EPMTSU | EPMT | -| Brain Tumor | Fibrillary Astrocytoma | FASTR | DASTR | -| Brain Tumor | Gangliocytoma | GNC | GNC | -| Brain Tumor | Ganglioglioma | GNG | GNG | -| Brain Tumor | Glioblastoma | GB | GB | -| Brain Tumor | Glioma, NOS | GNOS | GNOS | -| Brain Tumor | High-Grade Calvarium Sarcoma | HGCS | | -| Brain Tumor | High-Grade Glioma, NOS | HGGNOS | HGGNOS | -| Brain Tumor | High-Grade Neuroepithelial Tumor | HGNET | HGNET | -| Brain Tumor | Large Cell/Anaplastic Medulloblastoma | AMBL | AMBL | -| Brain Tumor | Large Cell/Anaplastic Medulloblastoma, SHH subtype | AMBLSHH | AMBL | -| Brain Tumor | Low-Grade Glioma, NOS | LGGNOS | LGGNOS | -| Brain Tumor | Low-Grade Glioneuronal Tumor | LGGNT | MBT | -| Brain Tumor | Low-Grade Neuroepithelial Tumor | LGNET | LGNET | -| Brain Tumor | Medulloblastoma | MBL | MBL | -| Brain Tumor | Medulloblastoma, Group 3 | MBLG3 | MBL | -| Brain Tumor | Medulloblastoma, Group 4 | MBLG4 | MBL | -| Brain Tumor | Medulloblastoma, SHH subtype | MBLSHH | MBL | -| Brain Tumor | Medulloblastoma with Extensive Nodularity, SHH subtype | MBENSHH | MBEN | -| Brain Tumor | Medulloblastoma, WNT subtype | MBLWNT | MBL | -| Brain Tumor | Medulloepithelioma | MDEP | MDEP | -| Brain Tumor | Meningioma | MNG | MNG | -| Brain Tumor | Miscellaneous Brain Tumor | MBT | MBT | -| Brain Tumor | Mixed Myxopapillary Anaplastic Ependymoma, Spinal Tumor | MEPMST | EPMT | -| Brain Tumor | Myxopapillary Ependymoma | MPE | MPE | -| Brain Tumor | Myxopapillary Ependymoma, Fourth Ventricle | MPEFV | MPE | -| Brain Tumor | Myxopapillary Ependymoma, Posterior Fossa | MPEPF | MPE | -| Brain Tumor | Neuroepithelioma | NEP | | -| Brain Tumor | Oligodendroglioma | ODG | ODG | -| Brain Tumor | Papillary Ependymoma, NOS | PEPNOS | EPMT | -| Brain Tumor | Pilocytic Astrocytoma | PAST | PAST | -| Brain Tumor | Pilomyxoid Astrocytoma | PMA | PMA | -| Brain Tumor | Pineal Anlage Tumor | PAT | PINT | -| Brain Tumor | Pineal Parenchymal Tumor of Intermediate Differentiation | PPTID | PPTID | -| Brain Tumor | Pineoblastoma | PBL | PBL | -| Brain Tumor | Pineocytoma | PINC | PINC | -| Brain Tumor | Pleomorphic Xanthoastrocytoma | PXA | PXA | -| Brain Tumor | Primitive Neuroectodermal Tumor | PNET | PNET | -| Brain Tumor | Subependymal Giant Cell Astrocytoma | SEGA | | -| Germ Cell Tumor | Choriocarcinoma | CCA | | -| Germ Cell Tumor | Dysgerminoma | DYS | | -| Germ Cell Tumor | Dysgerminoma, Ovarian | ODYS | ODYS | -| Germ Cell Tumor | Dysgerminoma, Pelvis | PDYS | | -| Germ Cell Tumor | Embryonal Carcinoma, NOS | ECNOS | | -| Germ Cell Tumor | Germ Cell Tumor, Brain | BGCT | BGCT | -| Germ Cell Tumor | Germ Cell Tumor, NOS | GCT | | -| Germ Cell Tumor | Germinoma | GMN | GMN | -| Germ Cell Tumor | Mixed Germ Cell Tumor, Brain | BMGCT | BMGCT | -| Germ Cell Tumor | Mixed Germ Cell Tumor, NOS | MGCTNOS | | -| Germ Cell Tumor | Mixed Germ Cell Tumor, Ovary | OMGCT | OMGCT | -| Germ Cell Tumor | Mixed Germ Cell Tumor, Testis | MGCT | MGCT | -| Germ Cell Tumor | Teratocarcinoma | TTC | | -| Germ Cell Tumor | Teratoma, NOS | TTNOS | | -| Germ Cell Tumor | Yolk Sac Tumor, Brain | BYST | BYST | -| Germ Cell Tumor | Yolk Sac Tumor, NOS | YSTNOS | | -| Germ Cell Tumor | Yolk Sac Tumor, Ovary | OYST | OYST | -| Germ Cell Tumor | Yolk Sac Tumor, Sacrococcygeal or Presacral | SPYST | | -| Hematologic Malignancy | Acute Leukemias of Ambiguous Lineage | ALAL | ALAL | -| Hematologic Malignancy | Acute Lymphoblastic Leukemia, NOS | ALLNOS | LNM | -| Hematologic Malignancy | Acute Megakaryoblastic Leukemia | AMKL | AMKL | -| Hematologic Malignancy | Acute Megakaryoblastic Leukemia, KMT2A rearrangement | AMKLKMT2A | AMKL | -| Hematologic Malignancy | Acute Monoblastic Leukemia | AMOL | AMOL | -| Hematologic Malignancy | Acute Myeloid Leukemia | AML | AML | -| Hematologic Malignancy | Acute Myeloid Leukemia, Core Binding Factor | CBF | AMLRGA | -| Hematologic Malignancy | Acute Myeloid Leukemia, KMT2A rearrangement | AMLKMT2A | AMLRGA | -| Hematologic Malignancy | Acute Myeloid Leukemia, RUNX1-RUNX1T1 | AMLRUNX1RUNX1T1 | AMLRUNX1RUNX1T1 | -| Hematologic Malignancy | Acute Myelomonocytic Leukemia | AMML | AMML | -| Hematologic Malignancy | Acute Myelomonocytic Leukemia, KMT2A rearrangement | AMMLKMT2A | AMML | -| Hematologic Malignancy | Acute Myelomonocytic Leukemia, NPM1 alteration | AMMLNPM1 | AMML | -| Hematologic Malignancy | Acute Promyelocytic Leukemia | APML | AML | -| Hematologic Malignancy | Acute Promyelocytic Leukemia, PML-RARA | APLPMLRARA | APLPMLRARA | -| Hematologic Malignancy | Acute Undifferentiated Leukemia | AUL | AUL | -| Hematologic Malignancy | Acute Undifferentiated Leukemia, KMT2A rearrangement | AULKMT2A | AUL | -| Hematologic Malignancy | Anaplastic Large Cell Lymphoma | ALCL | ALCL | -| Hematologic Malignancy | Atypical Dendritic Cell Tumor | ADCT | | -| Hematologic Malignancy | B-cell Acute Lymphoblastic Leukemia, BCR-ABL1 | BALLBCRABL1 | BLLBCRABL1 | -| Hematologic Malignancy | B-cell Acute Lymphoblastic Leukemia, BCR-ABL1 like | BALLBCRABL1L | BLLBCRABL1L | -| Hematologic Malignancy | B-cell Acute Lymphoblastic Leukemia, CRLF2 rearrangement | BALLCRLF2 | BLLRGA | -| Hematologic Malignancy | B-cell Acute Lymphoblastic Leukemia, Dicentric | BALLDICENTRIC | BLLRGA | -| Hematologic Malignancy | B-cell Acute Lymphoblastic Leukemia, Down Syndrome | BALLDOWN | BLLRGA | -| Hematologic Malignancy | B-cell Acute Lymphoblastic Leukemia, DUX4-IGH | BALLDUX4IGH | BLLRGA | -| Hematologic Malignancy | B-cell Acute Lymphoblastic Leukemia, DUX4-IGH like | BALLDUX4IGHL | BLLRGA | -| Hematologic Malignancy | B-cell Acute Lymphoblastic Leukemia, ETV6-RUNX1 | BALLETV6RUNX1 | BLLETV6RUNX1 | -| Hematologic Malignancy | B-cell Acute Lymphoblastic Leukemia, ETV6-RUNX1 like | BALLETV6RUNX1L | BLLRGA | -| Hematologic Malignancy | B-cell Acute Lymphoblastic Leukemia, HLF rearrangement | BALLHLF | BLLRGA | -| Hematologic Malignancy | B-cell Acute Lymphoblastic Leukemia, Hyperdiploidy | BALLHYPER | BLLHYPER | -| Hematologic Malignancy | B-cell Acute Lymphoblastic Leukemia, Hypodiploidy | BALLHYPO | BLLHYPO | -| Hematologic Malignancy | B-cell Acute Lymphoblastic Leukemia, iAMP21 | BALLIAMP21 | BLLIAMP21 | -| Hematologic Malignancy | B-cell Acute Lymphoblastic Leukemia, IGH-CEBPD | BALLIGHCEBPD | BLLRGA | -| Hematologic Malignancy | B-cell Acute Lymphoblastic Leukemia, IKZF1 N159Y | BALLIKZF1 | BLLRGA | -| Hematologic Malignancy | B-cell Acute Lymphoblastic Leukemia, KMT2A rearrangement | BALLKMT2A | BLLKMT2A | -| Hematologic Malignancy | B-cell Acute Lymphoblastic Leukemia, KMT2A rearrangement like | BALLKMT2AL | BLLRGA | -| Hematologic Malignancy | B-cell Acute Lymphoblastic Leukemia, MEF2D rearrangement | BALLMEF2D | BLLRGA | -| Hematologic Malignancy | B-cell Acute Lymphoblastic Leukemia, MYC rearrangement | BALLMYC | BLLRGA | -| Hematologic Malignancy | B-cell Acute Lymphoblastic Leukemia, NOS | BALLNOS | BLLNOS | -| Hematologic Malignancy | B-cell Acute Lymphoblastic Leukemia, NUTM1 rearrangement | BALLNUTM1 | BLLRGA | -| Hematologic Malignancy | B-cell Acute Lymphoblastic Leukemia, PAX5 alteration | BALLPAX5 | BLLRGA | -| Hematologic Malignancy | B-cell Acute Lymphoblastic Leukemia, PAX5 P80R | BALLPAX5P80R | BLLRGA | -| Hematologic Malignancy | B-cell Acute Lymphoblastic Leukemia, TCF3-PBX1 | BALLTCF3PBX1 | BLLTCF3PBX1 | -| Hematologic Malignancy | B-cell Acute Lymphoblastic Leukemia, ZEB2 alteration and CEBPE rearrangement | BALLZEB2CEBPE | BLLRGA | -| Hematologic Malignancy | B-cell Acute Lymphoblastic Leukemia, ZNF384 rearrangement | BALLZNF384 | BLLRGA | -| Hematologic Malignancy | B-cell Acute Lymphoblastic Leukemia, ZNF384 rearrangement like | BALLZNF384L | BLLRGA | -| Hematologic Malignancy | B-cell Lymphoblastic Lymphoma, BCR-ABL1 like | BLLBCRABL1L | BLLBCRABL1L | -| Hematologic Malignancy | B-cell Lymphoblastic Lymphoma, TCF3-PBX1 | BLLTCF3PBX1 | BLLTCF3PBX1 | -| Hematologic Malignancy | Blood Cancer of Unknown Primary | BCUP | CUP | -| Hematologic Malignancy | Burkitt Lymphoma | BL | BL | -| Hematologic Malignancy | Chronic Myeloid Leukemia | CML | CML | -| Hematologic Malignancy | Diffuse Large B-cell Lymphoma, NOS | DLBCLNOS | DLBCLNOS | -| Hematologic Malignancy | Extranodal Marginal Zone Lymphoma | EMZL | MZL | -| Hematologic Malignancy | Follicular Lymphoma | FL | FL | -| Hematologic Malignancy | General Leukemia | GENLK | | -| Hematologic Malignancy | High-Grade B-Cell Lymphoma, NOS | HGBCL | HGBCL | -| Hematologic Malignancy | Hodgkin Lymphoma | HL | HL | -| Hematologic Malignancy | Langerhans Cell Histiocytosis | LCH | LCH | -| Hematologic Malignancy | Lymphocyte-Depleted Classical Hodgkin Lymphoma | LDCHL | LDCHL | -| Hematologic Malignancy | Lymphocyte-Rich Classical Hodgkin Lymphoma | LRCHL | LRCHL | -| Hematologic Malignancy | Mixed Cellularity Classical Hodgkin Lymphoma | MCCHL | MCCHL | -| Hematologic Malignancy | Mycosis Fungoides | MYCF | MYCF | -| Hematologic Malignancy | Myelodysplastic Syndromes | MDS | MDS | -| Hematologic Malignancy | Myeloid Sarcoma | MS | MS | -| Hematologic Malignancy | Nodular Lymphocyte-Predominant Hodgkin Lymphoma | NLPHL | NLPHL | -| Hematologic Malignancy | Nodular Sclerosis Classical Hodgkin Lymphoma | NSCHL | NSCHL | -| Hematologic Malignancy | Non-Hodgkin Lymphoma | NHL | NHL | -| Hematologic Malignancy | Rosai-Dorfman Disease | RDD | RDD | -| Hematologic Malignancy | T-cell Acute Lymphoblastic Leukemia, BCL11B rearrangement | TALLBCL11B | TLL | -| Hematologic Malignancy | T-cell Acute Lymphoblastic Leukemia, HOXA rearrangement | TALLHOXA | TLL | -| Hematologic Malignancy | T-cell Acute Lymphoblastic Leukemia, KMT2A rearrangement | TALLKMT2A | TLL | -| Hematologic Malignancy | T-cell Acute Lymphoblastic Leukemia, LMO2 rearrangement | TALLLMO2 | TLL | -| Hematologic Malignancy | T-cell Acute Lymphoblastic Leukemia, NKX2 rearrangement | TALLNKX2 | TLL | -| Hematologic Malignancy | T-cell Acute Lymphoblastic Leukemia, NOS | TALLNOS | TLL | -| Hematologic Malignancy | T-cell Acute Lymphoblastic Leukemia, SET-NUP214 | TALLSETNUP214 | TLL | -| Hematologic Malignancy | T-cell Acute Lymphoblastic Leukemia, TAL1 rearrangement | TALLTAL1 | TLL | -| Hematologic Malignancy | T-cell Acute Lymphoblastic Leukemia, TLX1 rearrangement | TALLTLX1 | TLL | -| Hematologic Malignancy | T-cell Acute Lymphoblastic Leukemia, TLX3 rearrangement | TALLTLX3 | TLL | -| Hematologic Malignancy | T-cell Lymphoblastic Lymphoma, LMO1 rearrangement | TLLLMO1 | TLL | -| Hematologic Malignancy | T-cell Lymphoblastic Lymphoma, NKX2 rearrangement | TLLNKX2 | TLL | -| Hematologic Malignancy | T-cell Lymphoblastic Lymphoma, NOS | TLLNOS | TLL | -| Hematologic Malignancy | T-cell Lymphoblastic Lymphoma, TAL1 rearrangement | TLLTAL1 | TLL | -| Hematologic Malignancy | Therapy-Related Acute Myeloid Leukemia | TAML | TAML | -| Hematologic Malignancy | Therapy-Related Myelodysplastic Syndrome | TMDS | TMDS | -| Hematologic Malignancy | Therapy-Related Myeloid Sarcoma | TMS | TMN | -| Non-Malignancy | Non-Malignancy | NM | | -| Normal | CNS Ewing Sarcoma Family Tumor, CIC alteration | CEFTCIC | ESST | -| Normal | Control Sample | NORM | | -| Sickle Cell Disease | Sickle Cell Disease | SCD | | -| Solid Tumor | Acinar Cell Carcinoma | ACN | ACN | -| Solid Tumor | Adenocarcinoma, NOS | ADNOS | ADNOS | -| Solid Tumor | Adenoid Cystic Carcinoma of the Lacrimal Gland | ACLG | ACLG | -| Solid Tumor | Adenoid Cystic Carcinoma of the Salivary Gland | ACYC | ACYC | -| Solid Tumor | Adenomatoid Odontogenic Tumor | AOT | ODGC | -| Solid Tumor | Adrenocortical Carcinoma | ACC | ACC | -| Solid Tumor | Alveolar Rhabdomyosarcoma | ARMS | ARMS | -| Solid Tumor | Alveolar Soft Part Sarcoma | ASPS | ASPS | -| Solid Tumor | Aneurysmal Bone Cyst | ABC | ABC | -| Solid Tumor | Angiomatoid Fibrous Histiocytoma | AFH | AFH | -| Solid Tumor | Basal Cell Carcinoma | BCC | BCC | -| Solid Tumor | BCOR-CCNB3 sarcoma | BCS | SARCNOS | -| Solid Tumor | Botryoid Type Embryonal Rhabdomyosarcoma | BERMS | ERMS | -| Solid Tumor | Carcinoma, NOS | CNOS | CUP | -| Solid Tumor | Chondroblastic Osteosarcoma | CHOS | CHOS | -| Solid Tumor | Chondroblastoma | CHBL | CHBL | -| Solid Tumor | Chondrosarcoma | CHS | CHS | -| Solid Tumor | Chordoma | CHDM | CHDM | -| Solid Tumor | Clear Cell Sarcoma | CCS | CCS | -| Solid Tumor | Clear Cell Sarcoma of Kidney | CCSK | CCSK | -| Solid Tumor | Congenital Melanocytic Nevus | CMLN | SKCN | -| Solid Tumor | Congenital Mesoblastic Nephroma | CMN | RCC | -| Solid Tumor | Dermatofibrosarcoma Protuberans | DFSP | DFSP | -| Solid Tumor | Desmoid/Aggressive Fibromatosis | DES | DES | -| Solid Tumor | Desmoplastic Small Round Cell Tumor | DSRCT | DSRCT | -| Solid Tumor | Embryonal Rhabdomyosarcoma | ERMS | ERMS | -| Solid Tumor | Endometrioid Adenocarcinoma, NOS | EACNOS | ADNOS | -| Solid Tumor | Epithelioid Hemangioendothelioma | EHAE | EHAE | -| Solid Tumor | Epithelioid Sarcoma | EPIS | EPIS | -| Solid Tumor | Ewing Sarcoma | EWS | ES | -| Solid Tumor | Fibroblastic Osteosarcoma | FIOS | FIOS | -| Solid Tumor | Fibromyxoid Sarcoma | FMS | | -| Solid Tumor | Fibrosarcoma, Abdominal | AFIBS | FIBS | -| Solid Tumor | Fibrosarcoma, NOS | FIBS | FIBS | -| Solid Tumor | Follicular Thyroid Cancer | THFO | THFO | -| Solid Tumor | Ganglioneuroblastoma | GNBL | GNBL | -| Solid Tumor | Ganglioneuroma | GN | GN | -| Solid Tumor | Gastrointestinal Neuroendocrine Tumor | GINET | GINET | -| Solid Tumor | Gastrointestinal Stromal Tumor | GIST | GIST | -| Solid Tumor | General Bone Tumor | GENBN | | -| Solid Tumor | Giant Cell Tumor, NOS | GICT | GCTB | -| Solid Tumor | Granulosa Cell Tumor | GRCT | GRCT | -| Solid Tumor | Hepatoblastoma | HB | LIHB | -| Solid Tumor | Hepatocellular Carcinoma | HCC | HCC | -| Solid Tumor | High Grade Sarcoma | HGS | | -| Solid Tumor | Hurthle Cell Thyroid Cancer | THHC | THHC | -| Solid Tumor | Infantile Fibrosarcoma | IFS | IFS | -| Solid Tumor | Inflammatory Myofibroblastic Lung Tumor | IMTL | IMTL | -| Solid Tumor | Inflammatory Myofibroblastic Stomach Tumor | IMTS | IMT | -| Solid Tumor | Juvenile Xanthogranuloma | JXG | JXG | -| Solid Tumor | Leiomyosarcoma, NOS | LMS | LMS | -| Solid Tumor | Lipoblastoma | LBL | | -| Solid Tumor | Lipofibromatosis | LFBR | | -| Solid Tumor | Liposarcoma | LIPO | LIPO | -| Solid Tumor | Liver Malignancy, NOS | LMNOS | | -| Solid Tumor | Malignant Fibrous Histiocytoma | MFH | MFH | -| Solid Tumor | Malignant Mesenchymoma | MME | | -| Solid Tumor | Malignant Mesenchymoma of the Liver | MMEL | | -| Solid Tumor | Malignant Peripheral Nerve Sheath Tumor | MPNST | MPNST | -| Solid Tumor | Malignant Rhabdoid Tumor of the Bladder | MRTB | | -| Solid Tumor | Malignant Rhabdoid Tumor of the Liver | MRTL | MRTL | -| Solid Tumor | Malignant Thymoma | MTHYM | THYM | -| Solid Tumor | Melanocytic Nevus | MLN | MEL | -| Solid Tumor | Melanoma | MEL | MEL | -| Solid Tumor | Mesenchymal Chondrosarcoma | MCHS | MCHS | -| Solid Tumor | Mixed Spindle Cell and Embryonal Rhabdomyosarcoma | MSCERMS | RMS | -| Solid Tumor | Mucinous Adenocarcinoma, NOS | MACNOS | | -| Solid Tumor | Mucinous Adenocarcinoma of the Colon and Rectum | MACR | MACR | -| Solid Tumor | Mucoepidermoid Carcinoma | MUCC | MUCC | -| Solid Tumor | Myeloproliferative Neoplasms | MPN | MPN | -| Solid Tumor | Myopericytoma | MPC | MPC | -| Solid Tumor | Myositis Ossificans | MO | | -| Solid Tumor | Nasopharyngeal Carcinoma | NPC | NPC | -| Solid Tumor | Neuroblastoma | NBL | NBL | -| Solid Tumor | Neurofibroma | NFIB | NFIB | -| Solid Tumor | Neurothekeoma | NTK | | -| Solid Tumor | Osteoblastoma | OB | | -| Solid Tumor | Osteoid Osteoma | OO | | -| Solid Tumor | Osteosarcoma | OS | OS | -| Solid Tumor | Pancreatic Neuroendocrine Tumor | PANET | PANET | -| Solid Tumor | Papillary Renal Cell Carcinoma | PRCC | PRCC | -| Solid Tumor | Papillary Thyroid Cancer | THPA | THPA | -| Solid Tumor | Papillary Tumor of the Pineal Region | PTPR | PTPR | -| Solid Tumor | Paraganglioma | PGNG | PGNG | -| Solid Tumor | Parosteal Osteosarcoma | PAOS | PAOS | -| Solid Tumor | Periosteal Osteosarcoma | PEOS | PEOS | -| Solid Tumor | Peripheral Primitive Neuroectodermal Tumor | PPNET | PNET | -| Solid Tumor | Pheochromocytoma | PHC | PHC | -| Solid Tumor | Pineal Tumor | PINT | PINT | -| Solid Tumor | Pleuropulmonary Blastoma | PPB | PPB | -| Solid Tumor | Renal Cell Carcinoma | RCC | RCC | -| Solid Tumor | Renal Epitheloid Angiomyolipoma | EAML | RAML | -| Solid Tumor | Retinoblastoma | RBL | RBL | -| Solid Tumor | Rhabdoid Cancer, Kidney | MRT | MRT | -| Solid Tumor | Rhabdoid Tumor, NOS | RTNOS | CUP | -| Solid Tumor | Rhabdomyosarcoma | RMS | RMS | -| Solid Tumor | Round Cell Sarcoma, NOS | RCSNOS | RCSNOS | -| Solid Tumor | Serous Surface Papillary Carcinoma | SSPC | | -| Solid Tumor | Signet Ring Cell Carcinoma of the Stomach | SSRCC | SSRCC | -| Solid Tumor | Small Cell Osteosarcoma | SCOS | SCOS | -| Solid Tumor | Soft Tissue Perineuroma | STP | | -| Solid Tumor | Soft Tissue Sarcoma, NOS | STSNOS | SARCNOS | -| Solid Tumor | Solid Cancer of Unknown Primary | SCUP | CUP | -| Solid Tumor | Solid Tumor | ST | | -| Solid Tumor | Solitary Fibrous Tumor/Hemangiopericytoma | SFT | SFT | -| Solid Tumor | Spindle Cell Rhabdomyosarcoma | SCRMS | SCRMS | -| Solid Tumor | Spindle Cell Sarcoma, NOS | SCSNOS | | -| Solid Tumor | Spindle Cell/Sclerosing Rhabdomyosarcoma | SCSRMS | SCSRMS | -| Solid Tumor | Spindle Epithelial Tumor with Thymus-Like Differentiation | SETTLE | | -| Solid Tumor | Spitzoid Melanoma | SPZM | SPZM | -| Solid Tumor | Squamous Cell Carcinoma, NOS | SCCNOS | SCCNOS | -| Solid Tumor | Synovial Sarcoma | SYNS | SYNS | -| Solid Tumor | Telangiectatic Osteosarcoma | TEOS | TEOS | -| Solid Tumor | Thyroid Gland Follicular Adenoma with Papillary Hyperplasia | TFAPH | CUP | -| Solid Tumor | Undifferentiated Embryonal Sarcoma of the Liver | UESL | UESL | -| Solid Tumor | Wilms | WT | WT | -| Solid Tumor | Wilms, Bilateral | WTB | WT | - - +The `SAMPLE_INFO.txt` file that comes with your data request will contain the list of associated harmonized diagnosis codes (`sj_diseases`) for each sample. These codes represent the harmonized diagnosis values curated by the St. Jude Cloud team and reflect the most up to date information about the sample. For more information about our full disease ontology, please navigate to our [St. Jude Cloud Disease Ontology section](https://university.stjude.cloud/docs/genomics-platform/about-our-data/ontology) to read our white paper and access our downloadable disease ontology. [pubmed]: https://www.ncbi.nlm.nih.gov/pubmed/ @@ -355,5 +77,7 @@ The `SAMPLE_INFO.txt` file that comes with your data request will contain the li ## Similar Topics [About our Decision Process & Terminology](../../requesting-data/glossary) + [Making a Data Request](../../requesting-data/making-a-data-request) + [Managing Data Overview](../../managing-data/working-with-our-data) diff --git a/package-lock.json b/package-lock.json index 8ebbf456..0d3aa3a9 100644 --- a/package-lock.json +++ b/package-lock.json @@ -13878,7 +13878,7 @@ "lodash.topath": { "version": "4.5.2", "resolved": "https://registry.npmjs.org/lodash.topath/-/lodash.topath-4.5.2.tgz", - "integrity": "sha512-1/W4dM+35DwvE/iEd1M9ekewOSTlpFekhw9mhAtrwjVqUr83/ilQiyAvmg4tVX7Unkcfl1KC+i9WdaT4B6aQcg==" + "integrity": "sha1-NhY1Hzu6YZlKCTGYlmC9AyVP0Ak=" }, "lodash.uniq": { "version": "4.5.0", @@ -19221,7 +19221,7 @@ "postcss-functions": { "version": "3.0.0", "resolved": "https://registry.npmjs.org/postcss-functions/-/postcss-functions-3.0.0.tgz", - "integrity": "sha512-N5yWXWKA+uhpLQ9ZhBRl2bIAdM6oVJYpDojuI1nF2SzXBimJcdjFwiAouBVbO5VuOF3qA6BSFWFc3wXbbj72XQ==", + "integrity": "sha1-DpTQFERwCkgd4g3k1V+yZAVkJQ4=", "requires": { "glob": "^7.1.2", "object-assign": "^4.1.1", @@ -19258,12 +19258,12 @@ "color-name": { "version": "1.1.3", "resolved": "https://registry.npmjs.org/color-name/-/color-name-1.1.3.tgz", - "integrity": "sha512-72fSenhMw2HZMTVHeCA9KCmpEIbzWiQsjN+BHcBbS9vr1mtt+vJjPdksIBNUmKAW8TFUDPJK5SUU3QhE9NEXDw==" + "integrity": "sha1-p9BVi9icQveV3UIyj3QIMcpTvCU=" }, "has-flag": { "version": "3.0.0", "resolved": "https://registry.npmjs.org/has-flag/-/has-flag-3.0.0.tgz", - "integrity": "sha512-sKJf1+ceQBr4SMkvQnBDNDtf4TXpVhVGateu0t918bl30FnbE2m4vNLX+VWe/dpjlb+HugGYzW7uQXH98HPEYw==" + "integrity": "sha1-tdRU3CGZriJWmfNGfloH87lVuv0=" }, "postcss": { "version": "6.0.23", @@ -20119,7 +20119,7 @@ "pretty-hrtime": { "version": "1.0.3", "resolved": "https://registry.npmjs.org/pretty-hrtime/-/pretty-hrtime-1.0.3.tgz", - "integrity": "sha512-66hKPCr+72mlfiSjlEB1+45IjXSqvVAIy6mocupoww4tBFE9R9IhwwUGoI4G++Tc9Aq+2rxOt0RFU6gPcrte0A==" + "integrity": "sha1-t+PqQkNaTJsnWdmeDyAesZWALuE=" }, "probe-image-size": { "version": "6.0.0", diff --git a/src/config/docs.yaml b/src/config/docs.yaml index 64022048..e4a860b8 100644 --- a/src/config/docs.yaml +++ b/src/config/docs.yaml @@ -43,6 +43,8 @@ domains: path: /docs/genomics-platform/about-our-data/file-formats-and-sequencing/ - title: "Metadata and Clinical Information" path: /docs/genomics-platform/about-our-data/metadata-and-clinical/ + - title: "St. Jude Cloud's Disease Ontology" + path: /docs/genomics-platform/about-our-data/disease-ontology/ - title: "Managing Data" collapsable: true pages: