Version 9 (modified by vw253, 6 years ago) (diff)


Relations used in GO annotation extensions

Also see examples (and links) on the GO wiki, and our GO annotation guidelines, especially the specific notes on various terms and extensions.

relationbrief explanationexample annotation
occurs_ata sequence feature where a BP happens, or a location where a BP happens (note: used to be acts_at, then changed to occurs_at for BP and has_substrate for MF); NOTE: do not use occurs_at with CC annotationship3 GO:0030702 occurs_at(SO:0001799) = involved in 'chromatin silencing at centromere' at 'regional_centromere_outer_repeat_region' 'endocytosis' occurs_at(cell division site)
(continued)a sequence feature where DNA binding takes placeprz1 GO:0000978 occurs_at(SO:0001865) = has that crazy long-winded '... promoter proximal ... DNA binding' activity at 'CDRE_motif'
exists_duringuse for localization to CC at particular time (e.g. cell cycle phase or when another process is occurring)cdr2 GO:0071341 exists_during(GO:0000085) = localizes to 'medial cortical node' during 'G2 phase of mitotic cell cycle'
happens_duringuse for function or process that takes place during a specific cell cycle phase or when another process is taking placesrw1 GO:0008054 happens_during(GO:0000080) = involved in 'cyclin catabolic process' during 'G1 phase of mitotic cell cycle'
has_regulation_targeta gene product whose activity (MF) is regulated by a 'regulator' MF; a gene product whose participation in a process is regulated by a 'regulation of' BP; or a gene whose expression is regulated by a 'regulation of gene expression' BP (regulation of transcription, regulation of translation, etc.) NOTE: GO has more specific "chained" relations under discussion, which are intended to distinguish among these and other cases.ubc4 GO:0042787 has_regulation_target(PomBase:SPAC1783.07c) = involved in 'protein ubiquitination involved in ubiquitin-dependent protein catabolic process' and acts on Pap1
ace2 GO:0001077 has_regulation_target(PomBase:SPAC6F12.12) = has that crazily-named "RNA pol II transcription factor yada yada" activity, and regulates transcription of par2
could probably add more ...
has_direct_inputformerly has_substrate; a gene product or other molecule that a function or process acts onset11 GO:0016279 has_substrate(PomBase:SPCC31H12.04c| PomBase:SPCC16C4.13c) = 'protein-lysine N-methyltransferase activity' with substrates Rpl1201 & Rpl1202
coincident_withuse for localization to chromatin at a specific sequence or type of sequence region (SO ID); particularly useful for annotating ChIP resultsorc1 GO:0000790 coincident_with (SO:0000296) = localizes to 'nuclear chromatin' at 'origin_of_replication'
independent_ofonly used for localization to date, where it can mean localization to a CC happens whether a particular BP occurs or not, OR localization to a CC happens whether another gene product is present or notpxl1 GO:0005826 independent_of(GO:0031028) = located at 'actomyosin contractile ring' whether 'septation initiation signaling cascade' happens or not
has_indirect_inputwas indirectly_localizes (now a narrow synonym); describes the downstream substrate of a localization process; NOTE this is not for use with transporters which use has_substrate it is possible these terms will merge into their parents; NOTE: GO may obsolete this relation and use has_inputgene A methylates gene B and the methylation of geneB is responsible for its subsequent localization of Gene B (i.e. an output of the gene is doing the localizing, not the gene product itself), or if there are numerous steps between a modification and the localization event
localization_dependent_onvarious sorts of requirement for localization; deprecated (as of early 2014) except where the information can't be captured by a phenotype annotationexamples on next few lines
(continued)localization to CC requires a BP to occur (if no phenotype can be annotated for any BP participant, as in example)localization_dependent_on(GO:0016192) = end4 localization to 'cell division site' requires 'vesicle-mediated transport' (expt. in PMID:15827087 used brefeldin A)
(continued)localization to CC requires another CC to be present (if no phenotype can be annotated for any CC member, as in example)fim1 GO:0005826 localization_dependent_on(GO:0031941) = localization to 'actomyosin contractile ring' requires 'filamentous actin' (expt. in PMID:11694585 used Latrunculin A to depolymerize F-actin)
occurs_inthe location where a function or process happens; NOTE: do not use occurs_in with CC annotations---
part_ofsame meaning as in ontology files; typical use is for CC in a particular cell typepom2 GO:0005739 part_of(CL:0000415) = 'mitochondrion' of 'diploid cell'
requires_sequence_featurewas requires_feature (now a broad synonym); a protein domain or other feature must be present in a gene product for it to participate in a MF or BPbtb3 GO:0005515 with PomBase:SPAC24H6.03 requires_feature(Pfam:00651) = 'protein binding' to Cul3 requires btb3's 'BTB/POZ domain'
requires_direct_regulatorwas requires_regulator; the annotated gene product is a catalytic subunit of a complex, and requires a regulatory subunit for activitysid2 GO:0004674 requires_regulator(PomBase:SPBC428.13c) = 'protein serine/threonine kinase activity' requires regulatory subunit Mob1
requires_substancethe annotated gene product participates in a BP (or MF?) only if a specific substance is presenttnr3 thiamin pyrophosphokinase activity requires_substance mg2+ or no activity
requires_localizationgene product involved in BP only if it's located at CCbqt4 GO:0045141 requires_localization(GO:0005637) = Bqt4 localization to 'nuclear inner membrane' required for Bqt4 participation in 'meiotic telomere clustering'
required_forbit of a grab bag; tried to discuss with GO; would like to deprecate. replaced case1 with requires_localization (see above). However; A has used this for MOD see case2case1: bqt4 GO:0005637 required_for(GO:0045141) = Bqt4 localization to 'nuclear inner membrane' required for Bqt4 participation in 'meiotic telomere clustering'. Case2: fkh2 MOD:00047 required_for GO:0000978 = O-phospho-L-threonine modification required_for RNA polymerase II core promoter proximal region sequence-specific DNA binding
(continued)2nd of 2 annotations; replaced with nested extension that gets stripped out before sending to GOcase2: old ext: bqt4 GO:0005515 with PomBase:SPCC594.07c required_for(GO:0045141) = Bqt4 'protein binding' to Bqt3 required for Bqt4 participation in 'meiotic telomere clustering'; new ext: GO:0045141 annotation_extension=dependent_on(GO:0005515^has_substrate(PomBase:SPCC594.07c))
activated bybinding of a substance increases enzyme activitybinding of magnesium to mal1 increases its maltase alpha-glucosidase activity activity
inhibited bybinding of a substance decreases enzyme activitybinding of mercury to mal1 reduces its maltase alpha-glucosidase activity activity

Relations not used in S. pombe annotation extensions

has_inputparent of has_substrate; participates in the start of a function or process and is changed by it
has_outputparticipates in the end of a function or process and is changed by it; produced by a f or p
has_partsame meaning as in ontology files
has_participantparent of has_input and has_output
has_target_anatomical_entitynow obsolete in GO set
has_target_cellnow obsolete in GO set
localizes_tothe destination of a localization process (not used because precomposed terms preferred)

Chado restrictions are here: