Difference between revisions of "Mapping the GAF to GO OA tables"
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| − | + | | Value after 'WB:' prefix that begins WBVar | |
| − | + | | WBVar00000004 | |
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| gop_dbtype | | gop_dbtype | ||
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| Exact value in Column 12 | | Exact value in Column 12 | ||
| gene | | gene | ||
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| Column 14: Date | | Column 14: Date | ||
| Value in GAF will need to be parsed to add dashes conform to OA value | | Value in GAF will need to be parsed to add dashes conform to OA value | ||
| − | | 2014- | + | | 2014-10-29 |
| no | | no | ||
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| − | | | + | |} |
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| − | | Will | + | |
| − | | | + | {| border=1 cell-padding=5 cell-spacing=10 |
| − | | | + | |- |
| + | | 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) OR Variation phenotype2GO (only if Column 8 contains a WBVar) | ||
| + | | 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 | ||
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|} | |} | ||
Latest revision as of 20:02, 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_goinference | Column 7: Evidence Code | IEA (all Phenotype2GO-based annotations will use IEA until we have a new ECO ID for these) | IEA | No |
| gop_with_rnai | Column 8: With/From | Value after 'WB:' prefix that begins with string WBRNAi | WBRNAi00066077 | No |
| gop_with_phenotype | Column 8: With/From | Value that corresponds to a Phenotype Ontology ID | WBPhenotype:0000059 | No |
| gop_with_variation | Column 8: With/From | Value after 'WB:' prefix that begins WBVar | WBVar00000004 | No |
| gop_goontology | Column 9: Aspect | Exact string in Column 9 | P | No |
| gop_dbtype | Column 12: DB Object Type | Exact value in Column 12 | gene | no |
| gop_lastupdate | Column 14: Date | Value in GAF will need to be parsed to add dashes conform to OA value | 2014-10-29 | 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) OR Variation phenotype2GO (only if Column 8 contains a WBVar) | 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 |
Back to 20141022_-_Phenotype2GO_Pipeline
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