Mapping the GAF to GO OA tables

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Mapping the Phenotype2GO GAF to GO OA Tables

GAF2.0 file format:

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

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