Difference between revisions of "Specifications for a DAF for gene-disease data"
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#*In the majority of our annotations Disease_relevant_gene is going to be present, pick this (Gene) as the DB Object for DAF/JSON if Strain, Variation, Transgene are all absent. | #*In the majority of our annotations Disease_relevant_gene is going to be present, pick this (Gene) as the DB Object for DAF/JSON if Strain, Variation, Transgene are all absent. | ||
#*If either Strain, Variation or Transgene is present, pick that as the DB Object for DAF, even though Disease_relevant gene is present. If more than one of these is present, then the order should be Strain>Variation>Transgene. | #*If either Strain, Variation or Transgene is present, pick that as the DB Object for DAF, even though Disease_relevant gene is present. If more than one of these is present, then the order should be Strain>Variation>Transgene. | ||
− | #*Note that Inferred Gene will most likely be present for | + | #*Note that Inferred Gene will most likely be present for a majority of our annotations, it's value which is a gene will be redundant with the Disease relevant gene. This is okay and required for AGR. |
#*Will clean up the data so that only one of Strain, Variation or Transgene is present. | #*Will clean up the data so that only one of Strain, Variation or Transgene is present. | ||
#For WS262: | #For WS262: | ||
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|3||DB||R||1||WB||The database from which the identifiers in 'DB object ID' and 'DB Object Symbol' are drawn|| ||No Acedb tag||WB || | |3||DB||R||1||WB||The database from which the identifiers in 'DB object ID' and 'DB Object Symbol' are drawn|| ||No Acedb tag||WB || | ||
|- | |- | ||
− | |4 ||DB Object ID||R||1| | + | |4 ||DB Object ID||R||1|WBGene00004887||A unique identifier from the database in DB for the entity being annotated; note, no DB prefix||2||Modeled_by||DB:<ID> |
|- | |- | ||
|5 ||DB Object Symbol||R||1||smn-1||A (unique and valid) symbol to which DB object ID is matched||3||Modeled_by||<symbol> | |5 ||DB Object Symbol||R||1||smn-1||A (unique and valid) symbol to which DB object ID is matched||3||Modeled_by||<symbol> | ||
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|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||Does not exist||No acedb tag||Blank, WB not using this for now | |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||Does not exist||No acedb tag||Blank, WB not using this for now | ||
|- | |- | ||
− | |8 || | + | |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||Does not exist||Inducing_chemical, Inducing_agent||WB is using free text for now, will move to using an ontology soon |
|- | |- | ||
− | |9|| | + | |9||Association Type||R||1||is_model_of<br/>is_implicatd_in<br/>is_marker_for||Relationship between the DB object and the disease||does not exist||Association_type||is_model_of' only for DB object type: 'genotype, strain, organism, Fish'<br/>is_implicated in only for alleles, genes, transgenes<br/>model change did not make into WS261, so for now replace: causes_or_contributes _to_condition, causes_condition, contributes_to_condition with 'is_implicated_in' |
|- | |- | ||
− | |10|| | + | |10||Qualifier||O||0 or 1||NOT||Used to indicate that the DB object is not <br/>associated with the DO term/association type||Does not exist||Qualifier||NOT |
|- | |- | ||
− | |11|| | + | |11||DO ID||R||1||DOID:12858||DO identifier for disease||5||Disease_term|| |
|- | |- | ||
− | |12|| | + | |12||With||O||0 or greater||DB:gene_symbol<br/>DB:gene_id<br/>DB:gene_symbol[allele_symbol]<br/>DB:allele_id||EITHER specifies additional genetic components of the model (where DB Object Type is not genotype/strain/fish)OR<br/>specifies the orthologous (usually human) gene in annotations with ‘ISS/ISO’ evidence code||Does not exist ||No acedb tag||Blank, mostly for SGD, mandatory for ISS/ISO evidence codes |
|- | |- | ||
− | |13|| | + | |13||Modifier Association Type||O||0 or 1||condition_ameliorated_by <br/> condition_exacerbated_by||Relationship between the modifier and the disease model||Does not exist||condition_ameliorated_by <br/>condition_exacerbated_by||WB has started using |
|- | |- | ||
− | |14||Modifier | + | |14||Modifier - qualifier||O||0 or 1||NOT||Used to indicate DB object is not <br/>associated with the DO term/association type||Does not exist ||Need to add tag for WS262||WB has started using |
|- | |- | ||
− | |15||Modifier | + | |15||Modifier (genetic)||O||0 or greater||DB:gene_symbol<br/>DB:gene_symbol(allele_symbol)<br/>DB:gene_id<br/>DB:allele_id ||Specifies a genetic object (allele or gene) that modifies the disease model||Does not exist ||Modifier_transgene<br/>Modifier_variation<br/>Modifier_strain<br/>Modifier_gene||WB will start using |
|- | |- | ||
− | |16||Modifier | + | |16||Modifier - experimental conditions||''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)|| Specifies a non-genetic object experimental condition <br/>that modifies the disease model||Does not exist ||Modifier_molecule<br/>Other_modifier||WB will start using |
|- | |- | ||
− | |17|| | + | |17||Evidence Code||R||1 or greater||EXP, IMP, IPM, IGI, IDA, IED, IEP,<br/>IAGP, ISS, ISO, TAS, IC, IEA||From GO: Indicates the kind of evidence in the cited source that supports the disease annotation.<br/>If reference describes multiple methods that each provide evidence, then multiple annotations should be made with same DO term and different evidence codes||7||Evidence_code||'IMP' for now, other evidence codes coming soon |
|- | |- | ||
− | |18|| | + | |18||Genetic sex||O||0 or 1||male/female/hermaphrodite||Genetic sex of the model||Does not exist||Genetic_sex||Use value 'Hermaphrodite' for all rows<br/>May use 'male' or 'female' in the future if authors specify |
|- | |- | ||
− | |19|| | + | |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||Paper_evidence||Use only PMIDs for AGR 0.3,<br/>will get to individual DB identifiers later on |
|- | |- | ||
− | |20|| | + | |20||Date||R||1||20090118||Date on which the annotation was made; format is YYYYMMDD||14||Date_last_updated|| |
|- | |- | ||
− | |21 | + | |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||No acedb tag|| |
− | |||
− | |||
|} | |} | ||
Latest revision as of 18:53, 24 January 2019
Contents
New 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.
- 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
Changes to DAF
Changes official as of the DWG-DQM call, July 5th, 2017
- Column 3: DB: which was the database from which the identifiers in 'DB object ID' and 'DB Object Symbol' are drawn, is now deleted (Column 3 is now DB Object ID)
- Column 4: DB Object Symbol: Doesn't need the database prefix 'WB:" as it's tied to the ObjectID field which does
- Column 7: is new, for additional genetic components, note that DQM's script will fill in the symbol for the required format: <DB_object_id>;<DB_object_symbol>
- Column 9: Association Type has only 3 allowed values, these values are no longer valid: causes_or_contributes _to_condition, causes_condition, contributes_to_condition
- Column 12: With Ortholog, mostly for SGD
Rules for DAF/JSON
- Selecting DB Object:
- In the majority of our annotations Disease_relevant_gene is going to be present, pick this (Gene) as the DB Object for DAF/JSON if Strain, Variation, Transgene are all absent.
- If either Strain, Variation or Transgene is present, pick that as the DB Object for DAF, even though Disease_relevant gene is present. If more than one of these is present, then the order should be Strain>Variation>Transgene.
- Note that Inferred Gene will most likely be present for a majority of our annotations, it's value which is a gene will be redundant with the Disease relevant gene. This is okay and required for AGR.
- Will clean up the data so that only one of Strain, Variation or Transgene is present.
- For WS262:
- will have to hack this for DAF/JSON: Change Association type: causes_condition, causes_or_contributes_to_condition, and contributes_to_condition to is_implicated_in (all three have been deprecated by AGR DWG), this will be changed in the data for WS262.
DAF columns: definitions and content
Column | Content | Required(R) Optional(O) |
Cardinality | Example | Definition | Old DAF column | Acedb tag | Required format/Restriction | |
---|---|---|---|---|---|---|---|---|---|
1 | Taxon | R | 1 | taxon:6239 | NCBI taxonomic identifier for the organism | 13 | No acedb tag | taxon:#### | |
2 | DB Object Type | R | 1 | gene, allele, transgene, genotype, fish | The type of object being annotated | 2 | Modeled_by | WB uses gene, alllele, strain or transgene | |
3 | DB | R | 1 | WB | The database from which the identifiers in 'DB object ID' and 'DB Object Symbol' are drawn | No Acedb tag | WB | ||
4 | DB Object ID | R | WBGene00004887 | A unique identifier from the database in DB for the entity being annotated; note, no DB prefix | 2 | Modeled_by | DB:<ID> | ||
5 | DB Object Symbol | R | 1 | smn-1 | A (unique and valid) symbol to which DB object ID is matched | 3 | Modeled_by | <symbol> | |
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 | Inferred_gene | WBGene ID; repeat WBGene ID here even if 'DB Object Type' is 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 |
Does not exist | No acedb tag | Blank, WB not using this for now | |
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 | Inducing_chemical, Inducing_agent | WB is using free text for now, will move to using an ontology soon | |
9 | Association Type | R | 1 | is_model_of is_implicatd_in is_marker_for |
Relationship between the DB object and the disease | does not exist | Association_type | is_model_of' only for DB object type: 'genotype, strain, organism, Fish' is_implicated in only for alleles, genes, transgenes model change did not make into WS261, so for now replace: causes_or_contributes _to_condition, causes_condition, contributes_to_condition with 'is_implicated_in' | |
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 | Qualifier | NOT | |
11 | DO ID | R | 1 | DOID:12858 | DO identifier for disease | 5 | Disease_term | ||
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 | No acedb tag | Blank, mostly for SGD, 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 | condition_ameliorated_by condition_exacerbated_by |
WB has started using | |
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 | Need to add tag for WS262 | WB has started using | |
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 | Modifier_transgene Modifier_variation Modifier_strain Modifier_gene |
WB will start using | |
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 | Modifier_molecule Other_modifier |
WB will start using | |
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 | Evidence_code | '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 | Genetic_sex | 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 | Paper_evidence | 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 | Date_last_updated | ||
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 | No acedb tag |
Old pre-AGR WormBase DAF
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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