Difference between revisions of "Mapping the GAF to GO OA tables"

From WormBaseWiki
Jump to navigationJump to search
(Created page with "==Mapping the Phenotype2GO GAF to GO OA Tables== {| border=1 cell-padding=5 cell-spacing=10 |- ! OA Table ! GAF Column ! Value for OA Table ! New OA Table |- | gop_paper |...")
 
 
(34 intermediate revisions by the same user not shown)
Line 1: Line 1:
 
==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 7: Line 13:
 
! GAF Column
 
! GAF Column
 
! Value for OA Table
 
! Value for OA Table
−
! New 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
 
| gop_paper
 
| Column 6 DB:Reference
 
| Column 6 DB:Reference
−
| Value after WB_ref: prefix
+
| 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
 
| 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

Retrieved from "https://wiki.wormbase.org/index.php?title=Mapping_the_GAF_to_GO_OA_tables&oldid=26233"