Annotation Conf. Call, April 10, 2012

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Agenda:

Discussion of the annotation_extension field

1. Introduction to the basic format of this field

2. Data inappropriate for the Annotation Extension field

3. What information are groups currently adding into this field? File:C16 values per group.xls

4. How can we improve the quality of this data?

Kimberly: I'd just like clarification on the exact relations file to use. I'm assuming that these two links point to the same relations file, so it doesn't matter which one we grab for our curation form?

http://www.geneontology.org/scratch/xps/go_annotation_extension_relations.obo

http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/scratch/xps/go_annotation_extension_relations.obo

Will the relations file eventually be submitted to OBO or be made available for download from the GO web site (like the ontologies, GO references and evidence codes files)?


Total number of annotations from all groups with a filled c.16 field = 83,588 Kimberly: Would it be possible to link out from each of the examples in the table below to an instance of that curation described on the wiki?

Annotation Count relationship and associated ids types GO ID Process GO ID Component GO ID Function Assigned_by
4 acts_at(SO id) P C PomBase
3 dependent_on(GO id) P C BHF-UCL
38 dependent_on(GO id, Pfam id or PomBase id) P C F PomBase
39 dependent_on(GO id, UniProtKB id) P C F UniProt-GOA
288 during (GO id) P C F PomBase
3 exists_during(GO id) C PomBase
3 exists_during(GO id) F UniProt-GOA
2 exists_during(GO id) C dictyBase
7 happens_during(GO id) P BHF-UCL
1 happens_during(GO id) P PomBase
39 happens_during(GO id) P C F UniProt-GOA
2 has_binding_specificity(SO id) C PomBase
12 has_downstream_target (UniProt id) P BHF-UCL
18 has_downstream_target(UniProt id) P UniProt-GOA
139 has_input(CL, UBERON, UniProt and CHEBI ids) P F UniProt-GOA
7 has_input(UniProt id) P BHF-UCL
1 has_output(UniProt id) P BHF-UCL
1 has_participant(GO id) P BHF-UCL
49 has_participant(GO, UniProt id) P F UniProt-GOA
26 has_regulation_target (ChEBI id, Ensembl, UniProt ids) P BHF-UCL
745 has_regulation_target(UniProt id) P F UniProt-GOA
48 has_substrate (Genedb_Spombe, PomBase, PR, GO ids) P F PomBase
329 has_substrate(CHEBI and UniProt ids) P F UniProt-GOA
1 has_substrate(CL id) F BHF-UCL
1 has_target_anatomical_entity(GO id) F BHF-UCL
37 has_target_cell(CL id) P UniProt-GOA
1 has_upstream_or_downstream_target(UniProt id) P UniProt-GOA
76 in_presence_of(GO, ChEBI, UniProt id) P UniProt-GOA
1 in_presence_of(UniProt id) F BHF-UCL
3 independent_of(GO id) C PomBase
1 independent_of(GO ID) P UniProt-GOA
4 localization_dependency (PomBase ids) P PomBase
93 localization_dependent_on(CHEBI and GO id) C F UniProt-GOA
1 localization_target (PomBase ids) P PomBase
60 localizes(GO, PomBase ids) P C PomBase
10 localizes(UBERON id) P C F BHF-UCL
1 localizes(UniProtKB id) P dictyBase
27131 occurs_in(CL id) P F MGI
15 occurs_in(CL id) P P BHF-UCL
30,477 occurs_in(GO id) F IntAct
9 occurs_in(Pfam or GO id) P F PomBase
11,095 occurs_in(Reactome protein complex identifier) P C F Reactome
1113 occurs_in(UBERON,CL id) P C F UniProt-GOA
265 part_of (CL, UBERON id, GO id) P C UniProt-GOA
10880 part_of(CL id) C MGI
1 protease_activator(PomBase) P PomBase
1 protease_inhibitor_of(PomBase F PomBase
2 required_for(GO id) C F PomBase
2 requires_substance(ChEBI ID) F UniProt-GOA
2 stabilizes(UniProt id) P UniProt-GOA
2 stablizes(PomBase ids) P PomBase
1 transcriptionally_regulates(PomBase id) P PomBase

WormBase: contains either CheBI or WB identifiers, but not supplied with any relationships.

SGN: contains genomic identifiers, but not supplied with any relationships: e.g. AB623205.1; missing a tab?