Annotation Conf. Call, April 10, 2012: Difference between revisions
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http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/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)? | 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)? | ||
Emily OR: SVN /trunk/ontology/extensions/gorel.owl ? | |||
Emily: how can we reason over range identifiers? e.g. range: TEMP:0000001 ! gene product or complex | |||
Revision as of 09:37, 10 April 2012
Agenda:
Update Contact Info in GAF config file
The email address mentioned in the GAF conf (config) file is used to contact your group to report errors in your GAF file (for example, SGD's config is named as gene_association.sgd.conf). So, please take a moment to check the config file and make sure the email address is correct. The config file can be found in the Submission directory-
http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/gene-associations/submission/
It is not enough if you have the right email address in the top part of your GAF file.
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
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)?
Emily OR: SVN /trunk/ontology/extensions/gorel.owl ?
Emily: how can we reason over range identifiers? e.g. range: TEMP:0000001 ! gene product or complex
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?