Merge pull request #726 from bigbio/mondo-changes

Major PR to update some inconsistencies in the specification.
bigbio · Oct 11, 2024 · 93d7199 · 93d7199
2 parents ad76680 + 5b5f5e2
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diff --git a/.gitignore b/.gitignore
@@ -57,3 +57,4 @@ release.properties
 
 new_path/
 /new_path/
+.vscode/
diff --git a/sdrf-proteomics/README.adoc b/sdrf-proteomics/README.adoc
@@ -115,6 +115,7 @@ The list of ontologies/controlled vocabularies (CV) supported are:
 -	NCBI organismal classification
 -	PATO - the Phenotype and Trait Ontology
 -	PRIDE Controlled Vocabulary (CV)
+- Mondo Disease Ontology (MONDO): A unified disease ontology integrating multiple disease resources.
 
 [[sdrf-file-format]]
 == SDRF-Proteomics file format
@@ -190,7 +191,7 @@ NOTE: Additional characteristics can be added depending on the type of the exper
 
 Some important notes:
 
-- Each characteristic name in the column header SHOULD be a CV term from the EFO ontology. For example, the header _characteristics[organism]_ corresponds to the ontology term Organism.
+- Each characteristic name in the column header SHOULD be a CV term from the EFO ontology. For example, the header _characteristics[organism]_ corresponds to the ontology term Organism. However the values could be from EFO or other ontologies. For example, we RECOMMEND to use MONDO for diseases because it has better coverage than EFO.
 
 - Multiple values (columns) for the same characteristics term are allowed in SDRF-Proteomics. However, it is RECOMMENDED not to use the same column in the same file. If you have multiple phenotypes, you can specify what it refers to or use another more specific term, e.g., "immunophenotype".
 
@@ -242,6 +243,24 @@ The model of the mass spectrometer SHOULD be specified as _comment[instrument]_.
 
 Additionally, it is strongly RECOMMENDED to include comment[MS2 analyzer type]. This is important, e.g., for Orbitrap models where MS2 scans can be acquired either in the Orbitrap or in the ion trap. Setting this value allows differentiating high-resolution MS/MS data. Possible values of _comment[MS2 analyzer type]_ are mass analyzer types.
 
+[[technology-type]]
+=== Technology type
+
+Technology type is used in SDRF and MAGE-TAB formats to specify the technology applied in the study to capture the data. For transcriptomics, common values include technologies such as microarray, RNA-seq, and ChIP-seq (as seen in https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-13567[ArrayExpress Example]). In SDRF-Proteomics, the technology type field is REQUIRED to describe the experimental approach used to generate the data. We RECOMMEND including the technology type column immediately after the `assay name`` column in the SDRF file, clearly indicating which technology was used to produce the data files.
+
+|===
+|        |  assay name      | technology type     
+|sample 1|  run 1           | proteomic profiling by mass spectrometry                   
+|===
+
+NOTE: While we RECOMMEND positioning the technology type column after the assay name, in some original templates, this column was placed before the assay name. We will allow the technology type column to appear either directly before or after the assay name column but RECOMMEND placing it after the assay name for consistency. 
+
+For proteomics experiments the possible values for technology types can be obtained from PRIDE Ontology term https://www.ebi.ac.uk/ols4/ontologies/pride/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPRIDE_0000663[technology type].
+
+Here, the list of valid values: 
+
+- proteomic profiling by mass spectrometry
+
 [[additional-data-files]]
 === Additional Data files technical properties
 

diff --git a/templates/README.adoc b/templates/README.adoc
@@ -17,7 +17,7 @@ NOTE: Each of the templates is a tsv file with the minimum columns to describe t
 *Sample attributes*: Minimum sample attributes for primary cells from different species and cell lines
 
 |===
-|                                       | Default            |Human              | Vertebrates       | Invertebrates   | Plants            | Cell lines
+|                                       | Default            |Human              | Vertebrates       | Invertebrates     | Plants            | Cell lines
 |source name                            | :white_check_mark: |:white_check_mark: |:white_check_mark: |:white_check_mark: |:white_check_mark: |:white_check_mark:
 |characteristics[organism]              | :white_check_mark: |:white_check_mark: |:white_check_mark: |:white_check_mark: |:white_check_mark: |:white_check_mark:
 |characteristics[strain/breed]          |                    |                   |                   |:zero:             |                   |:zero:
@@ -35,6 +35,7 @@ NOTE: Each of the templates is a tsv file with the minimum columns to describe t
 |characteristics[biological replicate]  |:white_check_mark:  |:white_check_mark: |:white_check_mark: |:white_check_mark: |:white_check_mark: |:white_check_mark:
 |                                       |                    |                   |                   |                   |                   |
 |assay name                             | :white_check_mark: |:white_check_mark: |:white_check_mark: |:white_check_mark: |:white_check_mark: |:white_check_mark:
+|technology type                        | :white_check_mark: |:white_check_mark: |:white_check_mark: |:white_check_mark: |:white_check_mark: |:white_check_mark:
 |comment[data file]                     | :white_check_mark: |:white_check_mark: |:white_check_mark: |:white_check_mark: |:white_check_mark: |:white_check_mark:
 |comment[technical replicate]           | :white_check_mark: |:white_check_mark: |:white_check_mark: |:white_check_mark: |:white_check_mark: |:white_check_mark:
 |comment[fraction identifier]           | :white_check_mark: |:white_check_mark: |:white_check_mark: |:white_check_mark: |:white_check_mark: |:white_check_mark:

diff --git a/templates/sdrf-cell-line.sdrf.tsv b/templates/sdrf-cell-line.sdrf.tsv
@@ -1 +1 @@
-source name	characteristics[organism]	characteristics[organism part]	characteristics[cell type]	characteristics[disease]	characteristics[cell line]	characteristics[biological replicate]	technology type	assay name	comment[technical replicate]	comment[data file]	comment[fraction identifier]	comment[label]	comment[cleavage agent details]	comment[instrument]
+source name	characteristics[organism]	characteristics[organism part]	characteristics[cell type]	characteristics[disease]	characteristics[cell line]	characteristics[biological replicate]	assay name	 technology type	comment[technical replicate]	comment[data file]	comment[fraction identifier]	comment[label]	comment[cleavage agent details]	comment[instrument]
diff --git a/templates/sdrf-default.sdrf.tsv b/templates/sdrf-default.sdrf.tsv
@@ -1,2 +1,2 @@
-source name	characteristics[organism]	characteristics[organism part]	characteristics[disease]	characteristics[biological replicate]	technology type	assay name	comment[technical replicate]	comment[data file]	comment[fraction identifier]	comment[label]	comment[cleavage agent details]	comment[instrument]
+source name	characteristics[organism]	characteristics[organism part]	characteristics[disease]	characteristics[biological replicate]	assay name	technology type	comment[technical replicate]	comment[data file]	comment[fraction identifier]	comment[label]	comment[cleavage agent details]	comment[instrument]
 
diff --git a/templates/sdrf-human.sdrf.tsv b/templates/sdrf-human.sdrf.tsv
@@ -1 +1 @@
-source name	characteristics[organism]	characteristics[organism part]	characteristics[cell type]	characteristics[ancestry category]	characteristics[age]	characteristics[sex]	characteristics[disease]	characteristics[individual]	characteristics[biological replicate]	technology type	assay name	comment[technical replicate]	comment[data file]	comment[fraction identifier]	comment[label]	comment[instrument]	comment[cleavage agent details]
+source name	characteristics[organism]	characteristics[organism part]	characteristics[cell type]	characteristics[ancestry category]	characteristics[age]	characteristics[sex]	characteristics[disease]	characteristics[individual]	characteristics[biological replicate]	assay name	technology type	comment[technical replicate]	comment[data file]	comment[fraction identifier]	comment[label]	comment[instrument]	comment[cleavage agent details]
diff --git a/templates/sdrf-invertebrates.sdrf.tsv b/templates/sdrf-invertebrates.sdrf.tsv
@@ -1 +1 @@
-source name	characteristics[organism]	characteristics[organism part]	characteristics[disease]	characteristics[cell type]	characteristics[biological replicate]	technology type	assay name	comment[technical replicate]	comment[data file]	comment[fraction identifier]	comment[label]	comment[instrument]	comment[cleavage agent details]
+source name	characteristics[organism]	characteristics[organism part]	characteristics[disease]	characteristics[cell type]	characteristics[biological replicate]	assay name	technology type	comment[technical replicate]	comment[data file]	comment[fraction identifier]	comment[label]	comment[instrument]	comment[cleavage agent details]
diff --git a/templates/sdrf-nonvertebrates.sdrf.tsv b/templates/sdrf-nonvertebrates.sdrf.tsv
diff --git a/templates/sdrf-plants.sdrf.tsv b/templates/sdrf-plants.sdrf.tsv
@@ -1 +1 @@
-source name	characteristics[organism]	characteristics[organism part]	characteristics[cell type]	characteristics[disease]	characteristics[biological replicate]	technology type	assay name	comment[technical replicate]	comment[data file]	comment[fraction identifier]	comment[label]	comment[instrument]	comment[cleavage agent details]
+source name	characteristics[organism]	characteristics[organism part]	characteristics[cell type]	characteristics[disease]	characteristics[biological replicate]	assay name	technology type	comment[technical replicate]	comment[data file]	comment[fraction identifier]	comment[label]	comment[instrument]	comment[cleavage agent details]
diff --git a/templates/sdrf-vertebrates.sdrf.tsv b/templates/sdrf-vertebrates.sdrf.tsv
@@ -1 +1 @@
-source name	characteristics[organism]	characteristics[organism part]	characteristics[cell type]	characteristics[developmental stage]	characteristics[disease]	characteristics[biological replicate]	technology type	assay name	comment[technical replicate]	comment[data file]	comment[fraction identifier]	comment[label]	comment[cleavage agent details]	comment[instrument]
+source name	characteristics[organism]	characteristics[organism part]	characteristics[cell type]	characteristics[developmental stage]	characteristics[disease]	characteristics[biological replicate]	assay name	technology type	comment[technical replicate]	comment[data file]	comment[fraction identifier]	comment[label]	comment[cleavage agent details]	comment[instrument]
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		new_path/
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		.vscode/
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		@@ -1 +1 @@
		source name characteristics[organism] characteristics[organism part] characteristics[cell type] characteristics[disease] characteristics[cell line] characteristics[biological replicate] technology type assay name comment[technical replicate] comment[data file] comment[fraction identifier] comment[label] comment[cleavage agent details] comment[instrument]
		source name characteristics[organism] characteristics[organism part] characteristics[cell type] characteristics[disease] characteristics[cell line] characteristics[biological replicate] assay name technology type comment[technical replicate] comment[data file] comment[fraction identifier] comment[label] comment[cleavage agent details] comment[instrument]
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		@@ -1,2 +1,2 @@
		source name characteristics[organism] characteristics[organism part] characteristics[disease] characteristics[biological replicate] technology type assay name comment[technical replicate] comment[data file] comment[fraction identifier] comment[label] comment[cleavage agent details] comment[instrument]
		source name characteristics[organism] characteristics[organism part] characteristics[disease] characteristics[biological replicate] assay name technology type comment[technical replicate] comment[data file] comment[fraction identifier] comment[label] comment[cleavage agent details] comment[instrument]