| Version 7 (modified by , 6 years ago) (diff) |
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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.
| 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' |
| (continued) | a sequence feature where DNA binding takes place | prz1 GO:0000978 occurs_at(SO:0001865) = has that crazy long-winded '... promoter proximal ... DNA binding' activity at 'CDRE_motif' |
| 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.) 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_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 |
| coincident_with | use for localization to chromatin at a specific sequence or type of sequence region (SO ID); particularly useful for annotating ChIP results | orc1 GO:0000790 coincident_with (SO:0000296) = localizes to 'nuclear chromatin' at 'origin_of_replication' |
| 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
