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 16:
 
! New OA Table?
 
! New OA Table?
 
|-  
 
|-  
−
| gop_paper
 
−
| Column 6 DB:Reference
 
−
| Value after 'WB_ref:' prefix
 
−
| WBPaper00005654
 
−
| No
 
−
|-
 
 
| gop_wbgene
 
| gop_wbgene
 
| Column 2: DB Object ID
 
| Column 2: DB Object ID
Line 22: Line 22:
 
| No
 
| No
 
|-
 
|-
−
| gop_project
+
|gop_qualifier
−
| No value in the GAF
+
| Column 4: Qualifier
−
| Will need to add another entry to the drop-down menu
+
| Value not in the GAF, but will be 'involved_in'
−
| RNAi Phenotype2GO (only if Column 8 contains an RNAi experiment ID)
+
| involved_in
−
| No
+
| 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_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_goid
 
| gop_goid
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| Exact value in Column 5
 
| Exact value in Column 5
 
| GO:0007072
 
| GO:0007072
 +
| No
 +
|-
 +
| gop_paper
 +
| Column 6 DB:Reference
 +
| Value after 'WB_ref:' prefix
 +
| WBPaper00005654
 
| No
 
| No
 
|-
 
|-
 
| gop_goinference
 
| gop_goinference
 
| Column 7: Evidence Code
 
| 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)
 
| IEA (all Phenotype2GO-based annotations will use IEA until we have a new ECO ID for these)
 +
| IEA
 
| No
 
| No
 
|-
 
|-
−
| gop_accession
+
| gop_with_rnai
−
| Column 6: GO_REF
+
| Column 8: With/From
−
| na
+
| Value after 'WB:' prefix that begins with string WBRNAi
−
| na
+
| WBRNAi00066077
−
| No
+
| No  
 
|-
 
|-
−
| gop_with_wbgene
+
| gop_with_phenotype
 
| Column 8: With/From
 
| Column 8: With/From
−
| na
+
| Value that corresponds to a Phenotype Ontology ID
−
| na
+
| WBPhenotype:0000059
 
| No
 
| No
 
|-
 
|-
 
| gop_with_variation
 
| gop_with_variation
 
| Column 8: With/From
 
| Column 8: With/From
−
| na
 
 
| Value after 'WB:' prefix that begins WBVar
 
| Value after 'WB:' prefix that begins WBVar
 +
| WBVar00000004
 
| No
 
| No
 
|-
 
|-
−
| gop_with
+
| gop_goontology
−
| Column 8: With/From
+
| Column 9: Aspect
−
| na
+
| Exact string in Column 9
−
| na
+
| P
 
| No
 
| 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_qualifier
 
−
| Column 4: Qualifier
 
−
| Value not in the GAF
 
−
| involved_in (this is the default qualifier for all GO Biological Process annotations; will need to add three new qualifiers ('involved_in', 'enables', 'part_of' to the drop-down menu)
 
−
| no
 
−
|-
 
−
| gop_xrefto
 
−
| Column 16: Annotation Extension
 
−
| na
 
−
| na
 
−
| no
 
 
|-
 
|-
 
| gop_dbtype
 
| gop_dbtype
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| Exact value in Column 12
 
| Exact value in Column 12
 
| gene
 
| gene
−
| no
 
−
|-
 
−
| gop_protein
 
−
| Column 17: Gene Product Form ID
 
−
| na
 
−
| na
 
−
| no
 
−
|-
 
−
| gop_comment
 
−
| na
 
−
| na
 
−
| na
 
 
| no
 
| no
 
|-
 
|-
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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
−
| 2014-08-27
+
| 2014-10-29
 
| no
 
| no
 
|-
 
|-
−
| gop_falsepositive
+
|}
−
| na
+
 
−
| Will be a toggle that when checked indicates the annotation is a false positive.
+
 
−
| False Positive
+
{| border=1 cell-padding=5 cell-spacing=10
−
| YES
+
|-
 +
| 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
 
|-
 
|-
 
|}
 
|}

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


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