Difference between revisions of "Mapping the GAF to GO OA tables"
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| Column 4: Qualifier | | Column 4: Qualifier | ||
| Value not in the GAF, but will be 'involved_in' | | Value not in the GAF, but will be 'involved_in' | ||
| − | | involved_in | + | | involved_in |
| No, but will need to add three new qualifier values to the OA table ('involved_in', 'enables', 'part_of' and make this multi-value) | | No, but will need to add three new qualifier values to the OA table ('involved_in', 'enables', 'part_of' and make this multi-value) | ||
|- | |- | ||
Revision as of 18:43, 19 February 2015
Mapping the Phenotype2GO GAF to GO OA Tables
GAF2.0 file format:
http://geneontology.org/page/go-annotation-file-gaf-format-20
GAF columns not listed in this table can be ignored.
| OA Table | GAF Column | Value for OA Table | Example Value | New OA Table? |
|---|---|---|---|---|
| gop_wbgene | Column 2: DB Object ID | Exact string in Column 2 | WBGene00000829 | No |
| gop_qualifier | Column 4: Qualifier | Value not in the GAF, but will be 'involved_in' | involved_in | No, but will need to add three new qualifier values to the OA table ('involved_in', 'enables', 'part_of' and make this multi-value) |
| gop_goid | Column 5: GO ID | Exact value in Column 5 | GO:0007072 | No |
| gop_paper | Column 6 DB:Reference | Value after 'WB_ref:' prefix | WBPaper00005654 | No |
| gop_project | No value in the GAF | Will need to add another entry to the drop-down menu | RNAi Phenotype2GO (only if Column 8 contains an RNAi experiment ID) | No |
| gop_curator | No value in the GAF | Will need to have a curator, but the curator will not be dumped as Curator_confirmed | Kevin Howe | No |
| gop_goontology | Column 9: Aspect | Exact string in Column 9 | P | No |
| gop_goinference | Column 7: Evidence Code | Exact value in Column 7 | IEA (all Phenotype2GO-based annotations will use IEA until we have a new ECO ID for these) | No |
| gop_accession | Column 6: GO_REF | na | na | No |
| gop_with_wbgene | Column 8: With/From | na | na | No |
| gop_with_variation | Column 8: With/From | na | Value after 'WB:' prefix that begins WBVar | No |
| gop_with | Column 8: With/From | na | na | No |
| gop_with_rnai | Column 8: With/From | Value after 'WB:' prefix that begins with string WBRNAi | WBRNAi00066077 | YES |
| gop_with_phenotype | Column 8: With/From | Value that corresponds to a Phenotype Ontology ID (these should probably be prefixed with WB:) | WBPhenotype:0000059 | YES |
| gop_xrefto | Column 16: Annotation Extension | na | na | no |
| gop_dbtype | Column 12: DB Object Type | Exact value in Column 12 | gene | no |
| gop_protein | Column 17: Gene Product Form ID | na | na | no |
| gop_comment | na | na | na | no |
| gop_lastupdate | Column 14: Date | Value in GAF will need to be parsed to add dashes conform to OA value | 2014-08-27 | no |
| gop_falsepositive | na | Will be a toggle that when checked indicates the annotation is a false positive. | False Positive | YES |
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