Specifications for a DAF for gene-disease data

New AGR Disease Working Group specified DAF

• 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'

• 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, but please confirm with other DQMs
• Note that all models are not in place yet in WB to curate the data, this data is denoted by 'Coming soon'

DAF columns and mapping of gene-disease data to columns

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	No value	Do NOT fill in 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	No value	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	No value	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	causes_condition	'causes_condition' for all 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	No value	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	No value	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	NO value	Coming soon
14	Modifier - qualifier	O	0 or 1	NOT	Used to indicate DB object is not associated with the DO term/association type	No value	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	NO value	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	No value	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	hermaphrodite	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
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.

Mapping of GAF column to gene-disease data

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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