GAF Taxonomy Reasoning: Difference between revisions
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[[GO Moose]] | == Algorithm == | ||
== Report Format == | |||
Each line is in two parts. The part before the :: separator is the error report. The part after is the GAF line, copied verbatim. | |||
The report part before the delimiter is | |||
<GO ID> "<Term name>" only_in <TAX ID> "<Taxon name>" | |||
This is not ideal, as GO ID is redundant with col 5 of the GAF, which is repeated after the :: | |||
ideally the report part would show the ID that is directly linked to the taxon - but it doesn't do this yet. | |||
Example line: | |||
GO:0007595 "lactation" only_in NCBITaxon:40674 "Mammalia" :: Ensembl ENSGALP00000029396 ENSGALP00000029396 GO:0007595 GO_REF:0000002 IEA InterPro:IPR003626 P protein NCBITaxon:9 | |||
031 20091214 UniProtKB | |||
== Implementation == | |||
The script [http://geneontology.svn.sourceforge.net/viewvc/geneontology/go-moose/bin/go-gaf-inference.pl go-gaf-inference.pl] is distributed as part pf [[GO Moose]]. | |||
[[Category:Taxon]] | [[Category:Taxon]] | ||
[[Category:GAF]] | [[Category:GAF]] | ||
[[Category:Reasoning]] | [[Category:Reasoning]] |
Revision as of 20:28, 6 January 2010
Algorithm
Report Format
Each line is in two parts. The part before the :: separator is the error report. The part after is the GAF line, copied verbatim.
The report part before the delimiter is
<GO ID> "<Term name>" only_in <TAX ID> "<Taxon name>"
This is not ideal, as GO ID is redundant with col 5 of the GAF, which is repeated after the ::
ideally the report part would show the ID that is directly linked to the taxon - but it doesn't do this yet.
Example line:
GO:0007595 "lactation" only_in NCBITaxon:40674 "Mammalia" :: Ensembl ENSGALP00000029396 ENSGALP00000029396 GO:0007595 GO_REF:0000002 IEA InterPro:IPR003626 P protein NCBITaxon:9
031 20091214 UniProtKB
Implementation
The script go-gaf-inference.pl is distributed as part pf GO Moose.