Difference between revisions of "Mapping the GAF to GO OA tables"
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==Mapping the Phenotype2GO GAF to GO OA Tables== | ==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. | ||
Line 10: | Line 14: | ||
! Value for OA Table | ! Value for OA Table | ||
! Example Value | ! Example Value | ||
− | ! New OA Table | + | ! 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 | | gop_paper | ||
| Column 6 DB:Reference | | Column 6 DB:Reference | ||
| Value after 'WB_ref:' prefix | | Value after 'WB_ref:' prefix | ||
| WBPaper00005654 | | 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 | | no | ||
|- | |- | ||
− | | | + | | gop_lastupdate |
− | | Column | + | | Column 14: Date |
− | | | + | | Value in GAF will need to be parsed to add dashes conform to OA value |
− | | | + | | 2014-10-29 |
| no | | no | ||
|- | |- | ||
|} | |} | ||
+ | |||
+ | |||
+ | {| 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 | ||
+ | |- | ||
+ | |} | ||
+ | |||
+ | |||
+ | Back to [[20141022_-_Phenotype2GO_Pipeline]] | ||
+ | Back to [[Gene Ontology]] |
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
Back to Gene Ontology