Difference between revisions of "Specifications for a DAF for gene-disease data"
Line 27: | Line 27: | ||
|- | |- | ||
|9 ||Association Type||R||1||is_model_of<br/>causes_or_contributes_to_condition<br/> | |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 | + | causes_condition<br/>contributes_to_condition<br/>is_marker_for ||Relationship between the DB object and the disease |
|- | |- | ||
|10||Qualifier||O||0 or 1||NOT||Used to indicate that the DB object is not <br/>associated with the DO term/association type | |10||Qualifier||O||0 or 1||NOT||Used to indicate that the DB object is not <br/>associated with the DO term/association type |
Revision as of 00:30, 28 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 | 1 | 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 | 1 | DOID:12858 | DO identifier for disease | ||||
12 | With | O | 0 or greater | DB:gene_symbol DB:gene_id DB:gene_symbol[allele_symbol] | |||||
13 | Modifier Association Type | O | 0 or 1 | condition_ameliorated_by condition_exacerbated_by |
Relationship between the modifier and the disease model | ||||
14 | Modifier - qualifier | O | 0 or 1 | NOT | Used to indicate DB object is not associated with the DO term/association type | ||||
15 | Modifier (genetic) | O | 0 or greater | DB:gene_symbol DB:gene_symbol(allele_symbol) DB:gene_id DB:allele_id |
Specifies a genetic object (allele or gene) that modifies the disease model | ||||
16 | Modifier - experimental conditions | O | 0 or greater | standard conditions chemical/drug treatments (ChEBI ID, ZECO) dietary manipulations (specifiy entity) surgery/amputation bacterial/virus exposure (taxon ID) |
Specifies a non-genetic object experimental condition that modifies the disease model | ||||
17 | Evidence Code | R | 1 or greater | EXP, IMP, IPM, IGI, IDA, IED, IEP, IAGP ISS, ISO, TAS, IC, IEA ||From GO: Indicates the kind of evidence in the cited source that supports the disease annotation. | |||||
18 | Genetic sex | O | 0 or 1 | male/female/hermaphrodite | genetic sex of the model | ||||
19 | DB:Reference | R | 1 | PMID:14978262 | unique identifier(s) for a single source cited as an authority for the attribution of the DO ID to the DB object ID | ||||
20 | Date | R | 1 | 20090118 | Date on which the annotation was made; format is YYYYMMDD | ||||
21 | Assigned By | R | 1 | WB | The database which made the annotation - one of the values from the set of GO database cross-references |
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