This report generated on 2024-07-21
!gaf-version: 2.2
!generated-by: JaponicusDB
!date-generated: 2024-07-21T03:55
!URL: https://www.japonicusdb.org
!contact: helpdesk@pombase.org
No 'NOT' annotations to binding ; GO:0005488 or 'protein binding ; GO:0005515'
IEA, ISS, ISO, ISM, ISA, IBA, RCA annotations ae not allowed for direct annotations to to 'protein binding ; GO:0005515 or GO:0005488 binding''
IEP and HEP usage is restricted to terms from the Biological Process ontology, except when assigned by GOC
IPI should not be used with GO:0003824 catalytic activity or descendents
No annotations should be made to uninformative high level terms
JaponicusDB SJAG_01283 atg4 involved_in GO:0051697 GO_REF:0000107 IEA PomBase:SPAC19B12.08 P Atg8 deconjugator Atg4 protein taxon:4897 20240721 GO_Central
JaponicusDB SJAG_03088 fim1 involved_in GO:1904530 GO_REF:0000107 IEA PomBase:SPBC1778.06c P fimbrin protein taxon:4897 20240721 PomBase
JaponicusDB SJAG_03199 cyt2 involved_in GO:0018063 GO_REF:0000107 IEA PomBase:SPAC24C9.02c P cytochrome c1 heme lyase Cyt2 protein taxon:4897 20240721 GO_Central
JaponicusDB SJAG_04008 cyc3 involved_in GO:0018063 GO_REF:0000107 IEA PomBase:SPBC26H8.12 P cytochrome c heme lyase Cyc3 protein taxon:4897 20240721 GO_Central
JaponicusDB SJAG_04887 cdc8 involved_in GO:1904530 GO_REF:0000107 IEA PomBase:SPAC27F1.02c P tropomyosin protein taxon:4897 20240721 PomBase
JaponicusDB SJAG_04887 cdc8 enables GO:0098772 GO_REF:0000107 IEA PomBase:SPAC27F1.02c F tropomyosin protein taxon:4897 20240721 PomBase
ND evidence code should be to root nodes only, and no terms other than root nodes can have the evidence code ND
Taxon-appropriate annotation check
JaponicusDB SJAG_01820 coq11 involved_in GO:1901006 GO_REF:0000107 IEA PomBase:SPCC1840.09 P ubiquinone biosynthesis protein Coq11 protein taxon:4897 20240721 PomBase
JaponicusDB SJAG_02467 dph5 enables GO:0004164 GO_REF:0000107 IEA PomBase:SPCC576.14 F diphthine synthase Dph5 protein taxon:4897 20240721 InterPro
Dual species taxon check
With/From: IC annotations require a With/From GO ID
IDA annotations must not have a With/From entry
IPI annotations require a With/From entry
Automatic repair of annotations to merged or obsoleted terms
JaponicusDB SJAG_06603 ppt1 enables GO:0002083 GO_REF:0000107 IEA PomBase:SPAC56F8.04c F para-hydroxybenzoate--polyprenyltransferase Ppt1 protein taxon:4897 20240721 UniProt
JaponicusDB SJAG_06603 ppt1 enables GO:0002083 PMID:29191091 EXP F para-hydroxybenzoate--polyprenyltransferase Ppt1 protein taxon:4897 20210711 JaponicusDB part_of(GO:0006744)
JaponicusDB SJAG_00240 SJAG_00240 enables GO:0004024 GO_REF:0000107 IEA PomBase:SPAC5H10.06c F alcohol dehydrogenase Adh4-like protein taxon:4897 20240721 PomBase
JaponicusDB SJAG_01457 fmd1 enables GO:0004024 GO_REF:0000107 IEA PomBase:SPBC1539.07c F glutathione-dependent formaldehyde dehydrogenase protein taxon:4897 20240721 GO_Central
JaponicusDB SJAG_03822 SJAG_03822 enables GO:0004024 GO_REF:0000107 IEA PomBase:SPAC5H10.06c F alcohol dehydrogenase Adh4-like protein taxon:4897 20240721 PomBase
JaponicusDB SJAG_06603 ppt1 enables GO:0047293 GO_REF:0000107 IEA PomBase:SPAC56F8.04c F para-hydroxybenzoate--polyprenyltransferase Ppt1 protein taxon:4897 20240721 UniProt
Check for, and filter, annotations made to retracted publications
GO aspect should match the term's namespace; otherwise it is repaired to the appropriate aspect
IEAs should be less than one year old.
Obsolete GO_REFs are not allowed
IBA annotations should ONLY be assigned_by GO_Central and have GO_REF:0000033 as a reference
Protein complexes can not be annotated to GO:0032991 (protein-containing complex) or its descendants
Qualifier: IKR evidence code requires a NOT qualifier
Check for valid combination of evidence code and GO_REF
The ‘with’ field (GAF column 8) must be the same as the gene product (GAF column 2) when annotating to ‘self-binding’ terms.
Annotations to ISS, ISA and ISO should not be self-referential
References should have only one ID per ID space
Object extensions should conform to the extensions-patterns.yaml file in metadata
Allowed gene product to term relations (gp2term)
Annotations using ISS/ISA/ISO evidence should refer to a gene product (in the 'with' column)
TreeGrafter IEAs should be filtered for GO reference species