Specifications for a DAF for gene-disease data
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Jump to navigationJump to searchNew DAF specs as specified by the AGR Disease Working Group
- These specifications have been discussed and specified by the Disease Working Group of the AGR
https://docs.google.com/spreadsheets/d/1PrUI8CwV7AejBloWG2e6SNXEz_FSpCeMEwHhcKE9KmU/edit?usp=sharing and scroll to the tab 'DAF spec-v2 (for developers)'
- 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 and their orthologs from model organisms.
- Note that all models are not in place yet in WB to curate the data, this data is denoted by 'Coming soon', mos of this data is Optional, anyway.
- Header for file:
!daf-version: 0.1 !Date: 02/08/2017 !Project_name: WormBase (WB) Version WS258 !URL: http://www.wormbase.org/ !Contact Email: wormbase-help@wormbase.org !Funding: NHGRI at US NIH, grant number U41 HG002223
- Use column headers, from 'Content' column on tab 'DAF spec-v2 (for developers)' here:
https://docs.google.com/spreadsheets/d/1PrUI8CwV7AejBloWG2e6SNXEz_FSpCeMEwHhcKE9KmU/edit?usp=sharing
- Name of file: disease_association.WB.WS258.txt
- Source of DO ID translation to name should be from the DO file:
raw.githubusercontent.com/DiseaseOntology/HumanDiseaseOntology/master/src/ontology/doid-merged.obo
DAF columns and content
Column | Content | Required(R) Optional(O) |
Cardinality | Example | Definition | Old DAF column | Comment/Restriction | |
---|---|---|---|---|---|---|---|---|
1 | Taxon | R | 1 | taxon:6239 | NCBI taxonomic identifier for the organism | 13 | ||
2 | DB Object Type | R | 1 | gene, allele, transgene, genotype, fish | The type of object being annotated | 2 | Will be 'Gene' for now | |
3 | DB | R | 1 | WB | The database from which the identifiers in 'DB object ID' and 'DB Object Symbol' are drawn | 1 | ||
4 | DB Object ID | R | 1 | WB:WBGene00004887 | A unique identifier from the database in DB for the entity being annotated | 2 | ||
5 | DB Object Symbol | R | 1 | smn-1 | A (unique and valid) symbol to which DB object ID is matched | 3 | ||
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 | Does not exist | Fill in WBGene ID even if 'DB Object Type' = gene | |
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 |
Blank, May use in the future | ||
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 |
Does not exist | Blank, Coming soon | |
9 | Association Type | R | 1 | is_model_of causes_or_contributes_to_condition causes_condition contributes_to_condition is_marker_for |
Relationship between the DB object and the disease | does not exist | Use 'causes_condition' for all rows of manual annotations for now, is_model_of' only for DB object type of 'genotype, strain, organism, Fish' | |
10 | Qualifier | O | 0 or 1 | NOT | Used to indicate that the DB object is not associated with the DO term/association type |
Does not exist | Blank, Coming soon | |
11 | DO ID | R | 1 | DOID:12858 | DO identifier for disease | 5 | ||
12 | With | O | 0 or greater | DB:gene_symbol DB:gene_id DB:gene_symbol[allele_symbol] DB:allele_id |
EITHER specifies additional genetic components of the model (where DB Object Type is not genotype/strain/fish)OR specifies the orthologous (usually human) gene in annotations with ‘ISS/ISO’ evidence code |
Does not exist | Blank, Coming soon, mandatory for ISS/ISO evidence codes | |
13 | Modifier Association Type | O | 0 or 1 | condition_ameliorated_by condition_exacerbated_by |
Relationship between the modifier and the disease model | Does not exist | Blank, Coming soon | |
14 | Modifier - qualifier | O | 0 or 1 | NOT | Used to indicate DB object is not associated with the DO term/association type |
Does not exist | Blank, Coming soon | |
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 | Does not exist | Blank, Coming soon | |
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 |
Does not exist | Blank, Coming soon | |
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. If reference describes multiple methods that each provide evidence, then multiple annotations should be made with same DO term and different evidence codes |
7 | 'IMP' for now, other evidence codes coming soon | |
18 | Genetic sex | O | 0 or 1 | male/female/hermaphrodite | Genetic sex of the model | Does not exist | Use value 'Hermaphrodite' for all rows, May use 'male' or 'female' in the future if authors specify | |
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 | 6 | Use only PMIDs for AGR 0.3, will get to individual DB identifiers later on | |
20 | Date | R | 1 | 20090118 | Date on which the annotation was made; format is YYYYMMDD | 14 | ||
21 | Assigned By | R | 1 | WB | The database which made the annotation - one of the values from the set of GO database cross-references | 15 |
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) |
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