Qualifiers used (Note this refers to qualfier= which cannot be captured by an annotation_extension at present)
see qualifier_counts_by_cv in http://curation.pombase.org/dumps/latest_build/logs/
Ontology/vocabulary | Qualifier | Comment | |
Biological process | |||
GO BP | required (>200) | Used when a gene is essential for a process to occur | |
GO BP | localization_dependency(>200) | DEPRECATED this is being migrated to annotation_extension by Kim | |
GP BP | different_pathway (>50) | DEPRECATED this can be stored by/ obtained from BioGRID, BUT store for later consistency check | |
GO BP | heterologous_system (97) | WILL BE DEPRECATED | |
GO BP | same_pathway (81) | WILL BE DEPRECATED Placeholder, when BioGRID allows A- synthetic interactions these can be migrated | |
GO BP | acts_downstream_of (19) | ||
GO BP | redundant_with (18) | DEPRECATED, remove as confirmed that has IGI and some sort of positive genetic interaction captured | |
GO BP | acts_upstream_of (17) | ||
GO BP | C_term (7) | Used when a gene product is a tandem fusion e.g.http://old.genedb.org/genedb/Search?organism=pombe&name=SPAC19B12.13&isid=true | |
GO BP | N_term (7) | Used when a gene product is a tandem fusion e.g.http://old.genedb.org/genedb/Search?organism=pombe&name=SPAC19B12.13&isid=true | |
GO BP | partially_redundant (7) | ||
GO BP | overexpression (7) | DEPRECATED Overexpression should move to the allele of the phenotype description (VAL removed all, should now be zero) | |
GO BP | activates (13) | Val will find out why this was used instead of +ve regulation? -This probably needs a new GO term, this is annotations for genes which activate a specific checkpoint | |
GO BP | synthetic_rescue (11) | DEPRECATED this can be stored by/ obtained from BioGRID, BUT keep these for later consistency check | |
GO BP | phenotypic_enhancement (7) | DEPRECATED this can be stored by/ obtained from BioGRID, BUT keep these for later consistency check | |
GO BP | phenotypic_suppression (7) | DEPRECATED this can be stored by/ obtained from BioGRID, BUT keep these for later consistency check | |
GO BP | synthetic_lethality (18) | DEPRECATED this can be stored by/ obtained from BioGRID, BUT keep these for later consistency check | |
GO BP | dosage_rescue (43) | DEPRECATED this can be stored by/ obtained from BioGRID, BUT keep these for later consistency check | |
GO BP | synthetic_growth_defect (4) | DEPRECATED this can be stored by/ obtained from BioGRID, BUT keep these for later consistency check | |
GO BP | transcriptionally_regulates (26) | DEPRECATED, migrate to pre-compose process | |
GO BP | antagonistic_interaction(4) | ||
Molecular function | |||
GO MF | contributes_to (286) | Official GO qulaifier <add link to description> | |
GO MF | heterologous_system (69) | WILL BE DEPRECATED | |
GO MF | C_term (17) | Used when a gene product is a tandem fusion e.g.http://old.genedb.org/genedb/Search? | |
GO MF | N_term (9) | Used when a gene product is a tandem fusion e.g.http://old.genedb.org/genedb/Search? | |
GO MF | major (4) | Used when there is a major and minor version of an enzyme activity | |
GO MF | minor (4) | Used when there is a major and minor version of an enzyme activity | |
GO MF | inhibits (3) | This can probably be captured with the GO annotation, is there a difference between inhibits and negatively regulates? inhibits seems narrower? | |
GO MF | constitutive (2) | used with protein binding to indicate that protein A is ALWAYS bound to protein B...move to complex? | |
GO MF | partially_redundant (3) | ||
GO MF | redundant_with (3) | ||
GO MF | in_vitro (5) | Probably not necessary | |
Cellular Component | |||
GO CC | heterologous_system (49) | WILL BE DEPRECATED | |
GO CC | colocalizes_with (47) | Official GO qualifier <add link to description> | |
GO CC | predominantly (22) | ||
GO CC | constitutive (11) | ||
GO CC | N_term (8) | Used when a gene product is a tandem fusion e.g.http://old.genedb.org/genedb/Search? | |
GO CC | C_term (4) | Used when a gene product is a tandem fusion e.g.http://old.genedb.org/genedb/Search? | |
Phenotype | |||
FYPO | deletion (5715) | DEPRECATED use allele= Kim will migrate this to allele | |
FYPO | overexpression (80) | DEPRECATED use allele= Kim will migrate this to allele | |
FYPO | fitness_profiling (479) | DEPRECATED use evidence (ECO:0000336) | |
FYPO | at_high_temperature (66) | DEPRECATED use condition | |
FYPO | at_normal_temperature (66) | DEPRECATED use condition | |
FYPO | high_penetrance (4) | DEPRECATED use extension | |
FYPO | low_penetrance (25) | DEPRECATED use extension | |
FYPO | weak (3) | DEPRECATED use extension | |
FYPO | in_minimal_media (4) | DEPRECATED use condition=(condition_vocab:condition_id) IN PROGRESS | |
FYPO | in_rich_media (1) | DEPRECATED use condition=(condition_vocab:condition_id) IN PROGRESS | |
FYPO | in_presence_of_TBC (2) | DEPRECATED use condition=(condition_vocab:condition_id) IN PROGRESS | |
FYPO | caffeine_mediated_override (1) | DEPRECATED use condition=(condition_vocab:condition_id) IN PROGRESS | |
FYPO | at_low_temperature (2) | DEPRECATED use condition=(condition_vocab:condition_id) IN PROGRESS | |
FYPO | during_nutrient_limitation (3) | DEPRECATED use condition=(condition_vocab:condition_id) IN PROGRESS | |
Protein Modifications | |||
PSI_MOD | predicted (150) | DEPRECATED Use evidence= instead (with appropriate ECO evidence code) | |
PSI_MOD | in vitro (4) | - | |
PSI_MOD | inhibits (2) | - | |
Protein Sequence feature | |||
SO | predicted (352) | DEPRECATED Use evidence= instead (with appropriate ECO evidence code) | |
SO | inferred_from_context (2) | DEPRECATED Use evidence= instead (with appropriate ECO evidence code) | |
SO | region (53) | ||
Disease Association | |||
dis_ass | cancer_census (34) | ||
Protein Family or Domain | |||
curated_family | predicted (33) | DEPRECATED Use evidence= instead (with appropriate ECO evidence code) | |
curated_family | inferred_from_context (89) | DEPRECATED Use evidence= instead (with appropriate ECO evidence code) | |
Warning | |||
warning | predicted (117) | DEPRECATED Use evidence= instead (with appropriate ECO evidence code) | |
Gene Expression | |||
gene_ex | repressed_by (18) | Will discuss "gene expression" in detail at next curator meeting | |
gene_ex | activates (4) | Will discuss "gene expression" in detail at next curator meeting | |
Genome Organization | |||
genome_org | predicted (11) | DEPRECATED Use evidence= instead (with appropriate ECO evidence code) | |
Misc Functional group | |||
M_f_g | predicted (59) | DEPRECATED Use evidence= instead (with appropriate ECO evidence code) | |
Complementation | |||
complementation | full | Use with complementation to describe if it's a full complementation. Not a great way of doing it and will be changed at some point | |
complementation | partial | Use with complementation to describe if it's a partial complementation. Not a great way of doing it and will be changed at some point |
Last modified 6 years ago
Last modified on Jul 8, 2015, 2:40:18 PM