wiki:ListOfRelationsForGO

Version 6 (modified by mah79, 6 years ago) (diff)

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Relations used in GO annotation extensions

Also see OBO file on GO web site

relationbrief explanationexample annotation
occurs_ata sequence feature 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'
(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 annotationsrtn1 GO:0006897 occurs_in(GO:0032153) = 'endocytosis' at 'cell division site'
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: https://github.com/pombase/pombase-legacy/blob/master/load-pombase-chado.yaml