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