Changes between Version 7 and Version 8 of ListOfRelationsForGO


Ignore:
Timestamp:
Jul 31, 2015, 1:49:56 PM (5 years ago)
Author:
vw253
Comment:

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  • ListOfRelationsForGO

    v7 v8  
    44
    55||relation||brief explanation||example annotation||
    6 ||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'||
     6||occurs_at||a 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 annotations||hip3 GO:0030702 occurs_at(SO:0001799) = involved in 'chromatin silencing at centromere' at 'regional_centromere_outer_repeat_region'  rtn1 GO:0006897 occurs_at(GO:0032153) = 'endocytosis' at 'cell division site'||
    77||(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'||
    88||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'||
     
    1616||(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)||
    1717||(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)||
    18 ||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'||
     18||occurs_in||the location where a function or process happens; NOTE: do not use occurs_in with CC annotations||---||
    1919||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'||
    2020||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'||