= Relations used in GO annotation extensions =

Also see [http://viewvc.geneontology.org/viewvc/GO-SVN/trunk/ontology/extensions/go_annotation_extension_relations.obo OBO file on GO web site]

||relation||brief explanation||example annotation||
||occurs_at||a 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 annotations||hip3 GO:0030702 occurs_at(SO:0001799) = involved in 'chromatin silencing at centromere' at 'regional_centromere_outer_repeat_region'||
||exists_during||use 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_during||use for function or process that takes place during a specific cell cycle phase or when another process is taking place||srw1 GO:0008054 happens_during(GO:0000080) = involved in 'cyclin catabolic process' during 'G1 phase of mitotic cell cycle'||
||has_regulation_target||a 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.)||none yet, but a few to change to this||
||has_direct_input||formerly has_substrate; a gene product or other molecule that a function or process acts on||set11 GO:0016279 has_substrate(PomBase:SPCC31H12.04c| PomBase:SPCC16C4.13c) = 'protein-lysine N-methyltransferase activity' with substrates Rpl1201 & Rpl1202||
||independent_of||only 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 not||pxl1 GO:0005826 independent_of(GO:0031028) = located at 'actomyosin contractile ring' whether 'septation initiation signaling cascade' happens or not
||has_indirect_input||was 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_input||gene 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_on||various sorts of requirement for localization; deprecated (as of early 2014) except where the information can't be captured by a phenotype annotation||examples 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_in||the location where a function or process happens; NOTE: do not use occurs_in with CC annotations||rtn1 GO:0006897 occurs_in(GO:0032153) = 'endocytosis' at 'cell division site'||
||part_of||same meaning as in ontology files; typical use is for CC in a particular cell type||pom2 GO:0005739 part_of(CL:0000415) = 'mitochondrion' of 'diploid cell'||
||requires_sequence_feature||was 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 BP||btb3 GO:0005515 with PomBase:SPAC24H6.03 requires_feature(Pfam:00651) = 'protein binding' to Cul3 requires btb3's 'BTB/POZ domain'||
||requires_direct_regulator||was requires_regulator; the annotated gene product is a catalytic subunit of a complex, and requires a regulatory subunit for activity||sid2 GO:0004674 requires_regulator(PomBase:SPBC428.13c) = 'protein serine/threonine kinase activity' requires regulatory subunit Mob1||
||requires_substance||the annotated gene product participates in a BP (or MF?) only if a specific substance is present||tnr3 thiamin pyrophosphokinase activity requires_substance mg2+ or no activity||
||requires_localization||gene product involved in BP only if it's located at CC||bqt4 GO:0045141 requires_localization(GO:0005637) = Bqt4 localization to 'nuclear inner membrane' required for Bqt4 participation in 'meiotic telomere clustering'||
||required_for||bit 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 case2||case1: 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 GO||case2: 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 by||binding of a substance increases enzyme activity||binding of magnesium to mal1 increases its maltase alpha-glucosidase activity activity||
||inhibited by||binding of a substance decreases enzyme activity||binding of mercury to mal1 reduces its maltase alpha-glucosidase activity activity||



Relations not used in S. pombe annotation extensions

||has_input||parent of has_substrate; participates in the start of a function or process and is changed by it||
||has_output||participates in the end of a function or process and is changed by it; produced by a f or p||
||has_part||same meaning as in ontology files||
||has_participant||parent of has_input and has_output||
||has_target_anatomical_entity||now obsolete in GO set||
||has_target_cell||now obsolete in GO set||
||localizes_to||the 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