Annotation Conf. Call, April 10, 2012: Difference between revisions
Jump to navigation
Jump to search
m (→Agenda:) |
m (→Agenda:) |
||
Line 16: | Line 16: | ||
| align="center" style="background:#f0f0f0;"|'''GO ID Function''' | | align="center" style="background:#f0f0f0;"|'''GO ID Function''' | ||
| align="center" style="background:#f0f0f0;"|'''Assigned_by''' | | align="center" style="background:#f0f0f0;"|'''Assigned_by''' | ||
|- | |- | ||
| 4||acts_at(SO id)||P||C||||PomBase | | 4||acts_at(SO id)||P||C||||PomBase | ||
|- | |- | ||
| 3||dependent_on(GO id)||P||C||||BHF-UCL | | 3||dependent_on(GO id)||P||C||||BHF-UCL | ||
|- | |- | ||
| 38||dependent_on(GO id, Pfam id or PomBase id) ||P||C||F||PomBase | | 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 | | 39||dependent_on(GO id, UniProtKB id) ||P||C ||F||UniProt-GOA | ||
|- | |- | ||
| 288||during (GO id)||P||C||F||PomBase | | 288||during (GO id)||P||C||F||PomBase | ||
|- | |- | ||
| 3||exists_during(GO id)||||C||||PomBase | | 3||exists_during(GO id)||||C||||PomBase | ||
|- | |- | ||
| 3||exists_during(GO id)||||||F||UniProt-GOA | | 3||exists_during(GO id)||||||F||UniProt-GOA | ||
|- | |- | ||
| 2||exists_during(GO id) ||||C||||dictyBase | | 2||exists_during(GO id) ||||C||||dictyBase | ||
|- | |- | ||
| 7||happens_during(GO id)||P||||||BHF-UCL | | 7||happens_during(GO id)||P||||||BHF-UCL | ||
|- | |- | ||
| 1||happens_during(GO id)||P||||||PomBase | | 1||happens_during(GO id)||P||||||PomBase | ||
|- | |- | ||
| 39||happens_during(GO id)||P||C||F||UniProt-GOA | | 39||happens_during(GO id)||P||C||F||UniProt-GOA | ||
|- | |- | ||
| 2||has_binding_specificity(SO id)||||C||||PomBase | | 2||has_binding_specificity(SO id)||||C||||PomBase | ||
|- | |- | ||
| 12||has_downstream_target (UniProt id)||P||||||BHF-UCL | | 12||has_downstream_target (UniProt id)||P||||||BHF-UCL | ||
|- | |- | ||
| 18||has_downstream_target(UniProt id)||P||||||UniProt-GOA | | 18||has_downstream_target(UniProt id)||P||||||UniProt-GOA | ||
|- | |- | ||
| 139||has_input(CL, UBERON, UniProt and CHEBI ids) ||P||||F||UniProt-GOA | | 139||has_input(CL, UBERON, UniProt and CHEBI ids) ||P||||F||UniProt-GOA | ||
|- | |- | ||
| 7||has_input(UniProt id) ||P||||||BHF-UCL | | 7||has_input(UniProt id) ||P||||||BHF-UCL | ||
|- | |- | ||
| 1||has_output(UniProt id)||P||||||BHF-UCL | | 1||has_output(UniProt id)||P||||||BHF-UCL | ||
|- | |- | ||
| 1||has_participant(GO id) ||P||||||BHF-UCL | | 1||has_participant(GO id) ||P||||||BHF-UCL | ||
|- | |- | ||
| 49||has_participant(GO, UniProt id) ||P||||F||UniProt-GOA | | 49||has_participant(GO, UniProt id) ||P||||F||UniProt-GOA | ||
|- | |- | ||
| 26||has_regulation_target (ChEBI id, Ensembl, UniProt ids)||P||||||BHF-UCL | | 26||has_regulation_target (ChEBI id, Ensembl, UniProt ids)||P||||||BHF-UCL | ||
|- | |- | ||
| 745||has_regulation_target(UniProt id) ||P||||F||UniProt-GOA | | 745||has_regulation_target(UniProt id) ||P||||F||UniProt-GOA | ||
|- | |- | ||
| 48||has_substrate (Genedb_Spombe, PomBase, PR, GO ids)||P||||F||PomBase | | 48||has_substrate (Genedb_Spombe, PomBase, PR, GO ids)||P||||F||PomBase | ||
|- | |- | ||
| 329||has_substrate(CHEBI and UniProt ids)||P||||F||UniProt-GOA | | 329||has_substrate(CHEBI and UniProt ids)||P||||F||UniProt-GOA | ||
|- | |- | ||
| 1||has_substrate(CL id) ||||||F||BHF-UCL | | 1||has_substrate(CL id) ||||||F||BHF-UCL | ||
|- | |- | ||
| 1||has_target_anatomical_entity(GO id)||||||F||BHF-UCL | | 1||has_target_anatomical_entity(GO id)||||||F||BHF-UCL | ||
|- | |- | ||
| 37||has_target_cell(CL id)||P||||||UniProt-GOA | | 37||has_target_cell(CL id)||P||||||UniProt-GOA | ||
|- | |- | ||
| 1||has_upstream_or_downstream_target(UniProt 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 | | 76||in_presence_of(GO, ChEBI, UniProt id)||P||||||UniProt-GOA | ||
|- | |- | ||
| 1||in_presence_of(UniProt id) ||||||F||BHF-UCL | | 1||in_presence_of(UniProt id) ||||||F||BHF-UCL | ||
|- | |- | ||
| 3||independent_of(GO id)||||C||||PomBase | | 3||independent_of(GO id)||||C||||PomBase | ||
|- | |- | ||
| 1||independent_of(GO ID)||P||||||UniProt-GOA | | 1||independent_of(GO ID)||P||||||UniProt-GOA | ||
|- | |- | ||
| 4||localization_dependency (PomBase ids)||P||||||PomBase | | 4||localization_dependency (PomBase ids)||P||||||PomBase | ||
|- | |- | ||
| 93||localization_dependent_on(CHEBI and GO id)||||C||F||UniProt-GOA | | 93||localization_dependent_on(CHEBI and GO id)||||C||F||UniProt-GOA | ||
|- | |- | ||
| 1||localization_target (PomBase ids)||P||||||PomBase | | 1||localization_target (PomBase ids)||P||||||PomBase | ||
|- | |- | ||
| 60||localizes(GO, PomBase ids)||P||C||||PomBase | | 60||localizes(GO, PomBase ids)||P||C||||PomBase | ||
|- | |- | ||
| 10||localizes(UBERON id) ||P||C||F||BHF-UCL | | 10||localizes(UBERON id) ||P||C||F||BHF-UCL | ||
|- | |- | ||
| 1||localizes(UniProtKB id)||P||||||dictyBase | | 1||localizes(UniProtKB id)||P||||||dictyBase | ||
|- | |- | ||
| 27131||occurs_in(CL id)||P||||F||MGI | | 27131||occurs_in(CL id)||P||||F||MGI | ||
|- | |- | ||
| 15||occurs_in(CL id) P||P||||||BHF-UCL | | 15||occurs_in(CL id) P||P||||||BHF-UCL | ||
|- | |- | ||
| 30,477||occurs_in(GO id)||||||F||IntAct | | 30,477||occurs_in(GO id)||||||F||IntAct | ||
|- | |- | ||
| 9||occurs_in(Pfam or GO id) ||P||||F||PomBase | | 9||occurs_in(Pfam or GO id) ||P||||F||PomBase | ||
|- | |- | ||
| 11,095||occurs_in(Reactome protein complex identifier)||P||C||F||Reactome | | 11,095||occurs_in(Reactome protein complex identifier)||P||C||F||Reactome | ||
|- | |- | ||
| 1113||occurs_in(UBERON,CL id) ||P||C||F||UniProt-GOA | | 1113||occurs_in(UBERON,CL id) ||P||C||F||UniProt-GOA | ||
|- | |- | ||
| 265||part_of (CL, UBERON id, GO id) ||P||C||||UniProt-GOA | | 265||part_of (CL, UBERON id, GO id) ||P||C||||UniProt-GOA | ||
|- | |- | ||
| 10880||part_of(CL id)||||C||||MGI | | 10880||part_of(CL id)||||C||||MGI | ||
|- | |- | ||
| 1||protease_activator(PomBase)||P||||||PomBase | | 1||protease_activator(PomBase)||P||||||PomBase | ||
|- | |- | ||
| 1||protease_inhibitor_of(PomBase||F||||||PomBase | | 1||protease_inhibitor_of(PomBase||F||||||PomBase | ||
|- | |- | ||
| 2||required_for(GO id)||||C||F||PomBase | | 2||required_for(GO id)||||C||F||PomBase | ||
|- | |- | ||
| 2||requires_substance(ChEBI ID)||F||||||UniProt-GOA | | 2||requires_substance(ChEBI ID)||F||||||UniProt-GOA | ||
|- | |- | ||
| 2||stabilizes(UniProt id)||P||||||UniProt-GOA | | 2||stabilizes(UniProt id)||P||||||UniProt-GOA | ||
|- | |- | ||
| 2||stablizes(PomBase ids)||P||||||PomBase | | 2||stablizes(PomBase ids)||P||||||PomBase | ||
|- | |- | ||
| 1||transcriptionally_regulates(PomBase id)||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? |
Revision as of 11:13, 5 April 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) | 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?