Difference between revisions of "Specifications for a DAF for gene-disease data"
From WormBaseWiki
Jump to navigationJump to searchLine 8: | Line 8: | ||
|+DAF columns and mapping of gene-disease data to columns | |+DAF columns and mapping of gene-disease data to columns | ||
|- | |- | ||
− | !Column !! | + | !Column !!Content!!Required(R)<br/>Optional(O)!!Cardinality!!Example!!Definition!!Model tag!!New/Exists!!Comment!! |
|- | |- | ||
− | |1 ||Taxon|| | + | |1 ||Taxon||R||1||taxon:6239||NCBI taxonomic identifier for the organism |
|- | |- | ||
− | |2 ||DB Object Type|| | + | |2 ||DB Object Type||R||1||gene, allele, transgene, genotype, fish||The type of object being annotated |
|- | |- | ||
− | |3 ||DB|| | + | |3 ||DB||R||1||WB||The database from which the identifiers in 'DB object ID' and 'DB Object Symbol' are drawn. |
|- | |- | ||
− | |4 ||DB Object ID|| | + | |4 ||DB Object ID||R||1|WB:WBGene00004887||A unique identifier from the database in DB for the entity being annotated |
|- | |- | ||
− | |5 ||DB Object Symbol|| | + | |5 ||DB Object Symbol||R||1||smn-1||A (unique and valid) symbol to which DB object ID is matched |
|- | |- | ||
− | |6 ||Inferred Gene Association|| | + | |6 ||Inferred Gene Association||O||0 or greater||WB:WBGene00004887||Database ID for inferred gene/marker association that can be made based on the DB object ID |
|- | |- | ||
− | |7 ||Gene Product Form ID|| | + | |7 ||Gene Product Form ID||O||0 or 1||UniProtKB id or PRO ID||this field allows the annotation <br/>of specific variants of that gene or gene product. |
|- | |- | ||
− | |8 ||Experimental Conditions <br/> (to create the model)|| | + | |8 ||Experimental Conditions <br/> (to create the model)||O||0 or greater||standard conditions<br/>chemical/drug treatments (ChEBI ID, ZECO)<br/>dietary manipulations (specifiy entity)<br/>surgery/amputation<br/>bacterial/virus exposure (taxon ID)||Experimental/environmental (i.e. non-genetic) conditions <br/>required for the model, used particularly for induced models |
|- | |- | ||
− | |9 || Association Type|| | + | |9 ||Association Type||R||1||is_model_of<br/>causes_or_contributes_to_condition<br/> |
+ | causes_condition<br/>contributes_to_condition<br/>is_marker_for||Relationship between the DB object and the disease | ||
|- | |- | ||
− | |10||Qualifier||''O''||0 or 1|| | + | |10||Qualifier||''O''||0 or 1||NOT||Used to indicate that the DB object is not <br/>associated with the DO term/association type |
|- | |- | ||
|11||DO ID||''R''||0 or greater||(no value, leave empty) | |11||DO ID||''R''||0 or greater||(no value, leave empty) |
Revision as of 23:59, 27 January 2017
New AGR Disease Working Group specified DAF
- These specifications have been discussed and specified by the Disease Working Group of the AGR
- Annotations from the computational pipeline that WB currently has for assigning 'Potential models' will not be included in the MOD-specific DAFs. The plan is to have a separate AGR orthology pipeline to link human genes, orthologs from model organisms and disease.
- Note that all models are not in place yet in WB, though some of the data is already being curated in the Caltech Ontology Annotator curation tool for disease.
Column | Content | Required(R) Optional(O) |
Cardinality | Example | Definition | Model tag | New/Exists | Comment | |
---|---|---|---|---|---|---|---|---|---|
1 | Taxon | R | 1 | taxon:6239 | NCBI taxonomic identifier for the organism | ||||
2 | DB Object Type | R | 1 | gene, allele, transgene, genotype, fish | The type of object being annotated | ||||
3 | DB | R | 1 | WB | The database from which the identifiers in 'DB object ID' and 'DB Object Symbol' are drawn. | ||||
4 | DB Object ID | R | WB:WBGene00004887 | A unique identifier from the database in DB for the entity being annotated | |||||
5 | DB Object Symbol | R | 1 | smn-1 | A (unique and valid) symbol to which DB object ID is matched | ||||
6 | Inferred Gene Association | O | 0 or greater | WB:WBGene00004887 | Database ID for inferred gene/marker association that can be made based on the DB object ID | ||||
7 | Gene Product Form ID | O | 0 or 1 | UniProtKB id or PRO ID | this field allows the annotation of specific variants of that gene or gene product. | ||||
8 | Experimental Conditions (to create the model) |
O | 0 or greater | standard conditions chemical/drug treatments (ChEBI ID, ZECO) dietary manipulations (specifiy entity) surgery/amputation bacterial/virus exposure (taxon ID) |
Experimental/environmental (i.e. non-genetic) conditions required for the model, used particularly for induced models | ||||
9 | Association Type | R | 1 | is_model_of causes_or_contributes_to_condition causes_condition | |||||
10 | Qualifier | O | 0 or 1 | NOT | Used to indicate that the DB object is not associated with the DO term/association type | ||||
11 | DO ID | R | 0 or greater | (no value, leave empty) | |||||
12 | With | O | 1 | gene (all annotations have this value) | |||||
13 | Modifier Association Type | O | 1 or 2 | taxon:6239 | |||||
14 | Modifier - qualifier | O | 1 | 20130422 (this is the date of annotation dumped under Date_last_updated; for potential_model genes, use the date on which the OMIM homology script is run) | |||||
15 | Modifier (genetic) | O | 1 | WB | |||||
16 | Modifier - experimental conditions | O | 0 or greater | (no value, leave empty) | |||||
17 | Evidence Code | R | 0 or greater | (no value, leave empty) | |||||
18 | Genetic sex | O | |||||||
19 | DB:Reference | R | |||||||
20 | Date | R | |||||||
21 | Assigned By | R |
Current WormBase DAF (pre-AGR)
DAF 2.0 for gene-disease data includes all genes with the Experimental_model and/or Potential_model tags.
Format: The gene-disease association file is a 17 column tab-delimited file, where 11 columns have to have data and 6 are optional.
Column | Column Name | Required? | Cardinality | Example |
---|---|---|---|---|
1 | DB | required | 1 | WB |
2 | DB Object ID | required | 1 | WBGene00007799 |
3 | DB Object Symbol | required | 1 | nrx-1 |
4 | Qualifier | optional | 0 or greater | (no value, leave empty) |
5 | GO ID | required | 1 | DOID:0060041 |
6 | DB:Reference (|DB:Reference) | required | 1 or greater (separate values with pipes) |
WBPaper00041363|WBPaperXXXXXXXX |
7 | Evidence code | required | 1 | IMP or ISS (use 'IMP' for Experimental_model genes and ISS for Potential_model genes) |
8 | With (or) From | optional | 0 or greater (separate values with pipes) |
OMIM:600565|OMIM:600566 |
9 | Aspect | required | 1 | D (D for disease ontology, all annotations have this value) |
10 | DB Object Name | optional | 0 or 1 | (no value, leave empty) |
11 | DB Object Synonym (|Synonym) | optional | 0 or greater | (no value, leave empty) |
12 | DB Object Type | required | 1 | gene (all annotations have this value) |
13 | Taxon | required | 1 or 2 | taxon:6239 |
14 | Date | required | 1 | 20130422 (this is the date of annotation dumped under Date_last_updated; for potential_model genes, use the date on which the OMIM homology script is run) |
15 | Assigned By | required | 1 | WB |
16 | Annotation Extension | optional | 0 or greater | (no value, leave empty) |
17 | Gene Product Form ID | optional | 0 or greater | (no value, leave empty) |
Back To Disease and Drugs