Annotation Conf. Call, April 10, 2012: Difference between revisions
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3. What information are groups currently adding into this field? [[File:C16_values_per_group.xls]] | 3. What information are groups currently adding into this field? [[File:C16_values_per_group.xls]] | ||
{| {{table}} | |||
| align="center" style="background:#f0f0f0;"|'''Annotation Count''' | |||
| align="center" style="background:#f0f0f0;"|'''relationship and associated ids types''' | |||
| align="center" style="background:#f0f0f0;"|'''''' | |||
| align="center" style="background:#f0f0f0;"|'''GO ID Process''' | |||
| align="center" style="background:#f0f0f0;"|'''GO ID Component''' | |||
| align="center" style="background:#f0f0f0;"|'''GO ID Function''' | |||
| align="center" style="background:#f0f0f0;"|'''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? |
Revision as of 11:10, 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) | 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? |