Annotation Conf. Call, April 10, 2012
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
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) | ideally, use child terms, exists_during or happens_during | 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 | |||
7 | WormBase: contains either CheBI or WB identifiers, but not supplied with any relationships. | |||||
491 | SGN: contains genomic identifiers: e.g. AB623205.1; missing a tab? |