wiki:QualifiersUsed

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
SOpredicted (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_asscancer_census (34)
Protein Family or Domain
curated_family predicted (33) DEPRECATED Use evidence= instead (with appropriate ECO evidence code)
curated_familyinferred_from_context (89) DEPRECATED Use evidence= instead (with appropriate ECO evidence code)
Warning
warningpredicted (117) DEPRECATED Use evidence= instead (with appropriate ECO evidence code)
Gene Expression
gene_exrepressed_by (18) Will discuss "gene expression" in detail at next curator meeting
gene_exactivates (4) Will discuss "gene expression" in detail at next curator meeting
Genome Organization
genome_orgpredicted (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 5 years ago Last modified on Jul 8, 2015, 2:40:18 PM