Table of contents
Summary
GAF summary
Found 142027 annotations in 142046 lines.
GAF Validation Summary
Errors are reported first.
For rule GO_AR:0000005 (http://www.geneontology.org/GO.annotation_qc.shtml#GO_AR:0000005)
No ISS or ISS-related annotations to 'protein binding ; GO:0005515', there are 2 violations with type Error.
For rule GO_AR:0000003 (http://www.geneontology.org/GO.annotation_qc.shtml#GO_AR:0000003)
Annotations to 'binding ; GO:0005488' and 'protein binding ; GO:0005515' should be made with IPI and an interactor in the 'with' field, there are 2 violations with type Warning.
GAF Prediction Summary
Found 25 predictions, see prediction file for details.
Used Ontology Summary
go/extensions/go-gaf go/releases/2019-06-08/extensions/go-gaf.owl
Report
Group: goa - Dataset: goa_pig
SUMMARY
This report generated on 2019-06-09
- Associations: 142027
- Lines in file (incl headers): 173681
- Lines skipped: 31642
!gaf-version: 2.1
!
!The set of protein accessions included in this file is based on UniProt reference proteomes, which provide one protein per gene.
!They include the protein sequences annotated in Swiss-Prot or the longest TrEMBL transcript if there is no Swiss-Prot record.
!If a particular protein accession is not annotated with GO, then it will not appear in this file.
!
!Note that the annotation set in this file is filtered in order to reduce redundancy; the full, unfiltered set can be found in
!ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/goa_uniprot_all.gz
!
!Generated: 2019-06-03 16:53
!GO-version: http://purl.obolibrary.org/obo/go/releases/2019-06-02/extensions/go-plus.owl
!
Contents
gorule-0000008
gorule-0000020
other
MESSAGES
gorule-0000008
No annotations should be made to uninformative high level terms
Messages
- WARNING - Violates GO Rule: GORULE:0000008: No annotations should be made to uninformatively high level terms (GO:0005622) --
UniProtKB F1RIT1 TRPV4 GO:0005622 PMID:19790068 IDA C Transient receptor potential cation channel subfamily V member 4 isoform X1 TRPV4 protein taxon:9823 20150803 AgBase part_of(CL:0000138)
- WARNING - Violates GO Rule: GORULE:0000008: No annotations should be made to uninformatively high level terms (GO:0005622) --
UniProtKB Q4PLW0 PLIN2 GO:0005622 PMID:21420243 IDA C Perilipin-2 PLIN2|ADFP|ADRP protein taxon:9823 20150513 AgBase part_of(CL:0000187),part_of(UBERON:0001381)
gorule-0000020
Automatic repair of annotations to merged or obsoleted terms
Messages
- WARNING - Obsolete class: Violates GORULE:0000020, but was repaired (GO:0050880) --
UniProtKB A0A286ZTB8 ITGB1BP1 GO:0050880 GO_REF:0000107 IEA UniProtKB:O14713|ensembl:ENSP00000353850 P Uncharacterized protein ITGB1BP1 protein taxon:9823 20190601 Ensembl
- WARNING - Obsolete class: Violates GORULE:0000020, but was repaired (GO:0050880) --
UniProtKB A0A286ZTP3 FOXC1 GO:0050880 GO_REF:0000107 IEA UniProtKB:Q61572|ensembl:ENSMUSP00000052196 P Uncharacterized protein FOXC1 protein taxon:9823 20190601 Ensembl
- WARNING - Obsolete class: Violates GORULE:0000020, but was repaired (GO:0050880) --
UniProtKB A0A287AA47 GCLM GO:0050880 GO_REF:0000107 IEA UniProtKB:P48507|ensembl:ENSP00000359258 P Glutamate--cysteine ligase regulatory subunit GCLM protein taxon:9823 20190601 Ensembl
- WARNING - Obsolete class: Violates GORULE:0000020, but was repaired (GO:0050880) --
UniProtKB A0A287AFQ6 FOXC2 GO:0050880 GO_REF:0000107 IEA UniProtKB:Q61850|ensembl:ENSMUSP00000055290 P Uncharacterized protein FOXC2 protein taxon:9823 20190601 Ensembl
- WARNING - Obsolete class: Violates GORULE:0000020, but was repaired (GO:1904265) --
UniProtKB A0A287AKB2 YOD1 GO:1904265 GO_REF:0000002 IEA InterPro:IPR039138 F Ubiquitin thioesterase OTU1 isoform 1 YOD1 protein taxon:9823 20190601 InterPro
- WARNING - Obsolete class: Violates GORULE:0000020, but was repaired (GO:0035068) --
UniProtKB A0A287AKR3 DICER1 GO:0035068 GO_REF:0000107 IEA UniProtKB:Q9UPY3|ensembl:ENSP00000437256 C Uncharacterized protein DICER1 protein taxon:9823 20190601 Ensembl
- WARNING - Obsolete class: Violates GORULE:0000020, but was repaired (GO:0050880) --
UniProtKB A0A287AXM6 NOS3 GO:0050880 GO_REF:0000107 IEA UniProtKB:P70313|ensembl:ENSMUSP00000030834 P Nitric oxide synthase NOS3 protein taxon:9823 20190601 Ensembl
- WARNING - Obsolete class: Violates GORULE:0000020, but was repaired (GO:0035068) --
UniProtKB A0A287B559 TARBP2 GO:0035068 GO_REF:0000107 IEA UniProtKB:P97473|ensembl:ENSMUSP00000023813 C RISC-loading complex subunit TARBP2 TARBP2 protein taxon:9823 20190601 Ensembl
- WARNING - Obsolete class: Violates GORULE:0000020, but was repaired (GO:0035068) --
UniProtKB A0A287B559 TARBP2 GO:0035068 GO_REF:0000107 IEA UniProtKB:Q15633|ensembl:ENSP00000266987 C RISC-loading complex subunit TARBP2 TARBP2 protein taxon:9823 20190601 Ensembl
- WARNING - Obsolete class: Violates GORULE:0000020, but was repaired (GO:0035068) --
UniProtKB A0A287B5S7 AGO2 GO:0035068 GO_REF:0000104 IEA UniRule:UR000107560 C Protein argonaute-2 AGO2|EIF2C2 protein taxon:9823 20190601 UniProt
- WARNING - Obsolete class: Violates GORULE:0000020, but was repaired (GO:0050880) --
UniProtKB A0A287BDE2 GCLC GO:0050880 GO_REF:0000107 IEA UniProtKB:P48506|ensembl:ENSP00000497574 P Uncharacterized protein GCLC protein taxon:9823 20190601 Ensembl
- WARNING - Obsolete class: Violates GORULE:0000020, but was repaired (GO:0035068) --
UniProtKB A0A287BE94 TNRC6A GO:0035068 GO_REF:0000107 IEA UniProtKB:Q8NDV7|ensembl:ENSP00000379144 C Uncharacterized protein TNRC6A protein taxon:9823 20190601 Ensembl
- WARNING - Obsolete class: Violates GORULE:0000020, but was repaired (GO:0050880) --
UniProtKB A5A752 EDN3 GO:0050880 GO_REF:0000037 IEA UniProtKB-KW:KW-0838 P Endothelin-3 EDN3 protein taxon:9823 20190601 UniProt
- WARNING - Obsolete class: Violates GORULE:0000020, but was repaired (GO:0050880) --
UniProtKB F1RF79 NPPA GO:0050880 GO_REF:0000038 IEA UniProtKB-KW:KW-0838 P Natriuretic peptides A NPPA protein taxon:9823 20190601 UniProt
- WARNING - Obsolete class: Violates GORULE:0000020, but was repaired (GO:0035068) --
UniProtKB F1RRJ4 XPO5 GO:0035068 GO_REF:0000107 IEA UniProtKB:Q9HAV4|ensembl:ENSP00000265351 C Uncharacterized protein XPO5 protein taxon:9823 20190601 Ensembl
- WARNING - Obsolete class: Violates GORULE:0000020, but was repaired (GO:0035068) --
UniProtKB I3L5V9 AGO3 GO:0035068 GO_REF:0000104 IEA UniRule:UR000107558 C Protein argonaute-3 AGO3|EIF2C3 protein taxon:9823 20190601 UniProt
- WARNING - Obsolete class: Violates GORULE:0000020, but was repaired (GO:0035068) --
UniProtKB K7GND3 DHX9 GO:0035068 GO_REF:0000107 IEA UniProtKB:Q08211|ensembl:ENSP00000356520 C ATP-dependent RNA helicase A DHX9 protein taxon:9823 20190601 Ensembl
- WARNING - Obsolete class: Violates GORULE:0000020, but was repaired (GO:0050880) --
UniProtKB P01183 AVP GO:0050880 GO_REF:0000037 IEA UniProtKB-KW:KW-0838 P Vasopressin-neurophysin 2-copeptin AVP protein taxon:9823 20190601 UniProt
- WARNING - Obsolete class: Violates GORULE:0000020, but was repaired (GO:0050880) --
UniProtKB P07634 NPPB GO:0050880 GO_REF:0000037 IEA UniProtKB-KW:KW-0838 P Natriuretic peptides B NPPB protein taxon:9823 20190601 UniProt
- WARNING - Obsolete class: Violates GORULE:0000020, but was repaired (GO:0050880) --
UniProtKB P09558 EDN1 GO:0050880 GO_REF:0000037 IEA UniProtKB-KW:KW-0838 P Endothelin-1 EDN1 protein taxon:9823 20190601 UniProt
- WARNING - Obsolete class: Violates GORULE:0000020, but was repaired (GO:0050880) --
UniProtKB P18104 NPPC GO:0050880 GO_REF:0000037 IEA UniProtKB-KW:KW-0838 P C-type natriuretic peptide NPPC|CNP protein taxon:9823 20190601 UniProt
- WARNING - Obsolete class: Violates GORULE:0000020, but was repaired (GO:0050880) --
UniProtKB P24259 NPPA GO:0050880 GO_REF:0000037 IEA UniProtKB-KW:KW-0838 P Natriuretic peptides A NPPA protein taxon:9823 20190601 UniProt
other
OWLTools check
#Line number RuleID ViolationType Message Line
#------------
#------------
# Validation for #142027 annotations in 142046 lines
#------------
#Line number RuleID ViolationType Message Line
#------------
# GO_AR:0000005 No ISS or ISS-related annotations to 'protein binding ; GO:0005515' Error count: 2
130219 GO_AR:0000005 Error No ISS or ISS-related annotations to 'protein binding ; GO:0005515' UniProtKB P07200 TGFB1 GO:0005515 GO_REF:0000024 ISS UniProtKB:P01137 F Transforming growth factor beta-1 proprotein TGFB1 protein taxon:9823 20141202 AgBase
135301 GO_AR:0000005 Error No ISS or ISS-related annotations to 'protein binding ; GO:0005515' UniProtKB Q28833 VWF GO:0005515 GO_REF:0000024 ISS UniProtKB:P04275 F von Willebrand factor VWF|F8VWF protein taxon:9823 20070328 UniProt
#------------
# GO_AR:0000003 Annotations to 'binding ; GO:0005488' and 'protein binding ; GO:0005515' should be made with IPI and an interactor in the 'with' field Warning count: 2
130219 GO_AR:0000003 Warning Annotations to 'binding' (GO:0005488) and 'protein binding' (GO:0005515) should be made with an IPI evidence code and the interactor in the 'with' field UniProtKB P07200 TGFB1 GO:0005515 GO_REF:0000024 ISS UniProtKB:P01137 F Transforming growth factor beta-1 proprotein TGFB1 protein taxon:9823 20141202 AgBase
135301 GO_AR:0000003 Warning Annotations to 'binding' (GO:0005488) and 'protein binding' (GO:0005515) should be made with an IPI evidence code and the interactor in the 'with' field UniProtKB Q28833 VWF GO:0005515 GO_REF:0000024 ISS UniProtKB:P04275 F von Willebrand factor VWF|F8VWF protein taxon:9823 20070328 UniProt
#------------
Predictions
GO:0005739 mitochondrion AnnotationPropagation C GO:1901029 negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway ISS
GO:0055114 oxidation-reduction process AnnotationPropagation P GO:0097257 leukotriene B4 12-hydroxy dehydrogenase activity TAS
GO:0006468 protein phosphorylation AnnotationPropagation P GO:0070123 transforming growth factor beta receptor activity, type III ISS
GO:0007178 transmembrane receptor protein serine/threonine kinase signaling pathway AnnotationPropagation P GO:0070123 transforming growth factor beta receptor activity, type III ISS
GO:0005623 cell AnnotationPropagation C GO:0042147 retrograde transport, endosome to Golgi ISS
GO:0005829 cytosol AnnotationPropagation C GO:0042147 retrograde transport, endosome to Golgi ISS
GO:0010452 histone H3-K36 methylation AnnotationPropagation P GO:0046975 histone methyltransferase activity (H3-K36 specific) ISS
GO:0016310 phosphorylation AnnotationPropagation P GO:0050145 nucleoside monophosphate kinase activity EXP
GO:0046940 nucleoside monophosphate phosphorylation AnnotationPropagation P GO:0050145 nucleoside monophosphate kinase activity EXP
GO:0005739 mitochondrion AnnotationPropagation C GO:0090615 mitochondrial mRNA processing ISS
GO:0006468 protein phosphorylation AnnotationPropagation P GO:0050254 rhodopsin kinase activity ISS
GO:0071108 protein K48-linked deubiquitination AnnotationPropagation P GO:1990380 Lys48-specific deubiquitinase activity ISS
GO:0005623 cell AnnotationPropagation C GO:0051480 regulation of cytosolic calcium ion concentration ISS
GO:0005739 mitochondrion AnnotationPropagation C GO:0097345 mitochondrial outer membrane permeabilization ISS
GO:0005623 cell AnnotationPropagation C GO:0051480 regulation of cytosolic calcium ion concentration ISS
GO:0005623 cell AnnotationPropagation C GO:0035356 cellular triglyceride homeostasis ISS
GO:0006508 proteolysis AnnotationPropagation P GO:0070006 metalloaminopeptidase activity ISS
GO:0030974 thiamine pyrophosphate transmembrane transport AnnotationPropagation P GO:0090422 thiamine pyrophosphate transmembrane transporter activity ISS
GO:0035461 vitamin transmembrane transport AnnotationPropagation P GO:0090422 thiamine pyrophosphate transmembrane transporter activity ISS
GO:0005739 mitochondrion AnnotationPropagation C GO:0033615 mitochondrial proton-transporting ATP synthase complex assembly ISS
GO:0016311 dephosphorylation AnnotationPropagation P GO:0052834 inositol monophosphate phosphatase activity ISS
GO:0005783 endoplasmic reticulum FoldBasedPredictor GO:0005515 protein binding occurs_in GO:0005783 endoplasmic reticulum IPI
GO:0006858 extracellular transport FoldBasedPredictor GO:0045056 transcytosis occurs_in GO:0034364 high-density lipoprotein particle occurs_in UBERON:0000201 endothelial blood brain barrier IMP
GO:0034364 high-density lipoprotein particle FoldBasedPredictor GO:0045056 transcytosis occurs_in GO:0034364 high-density lipoprotein particle occurs_in UBERON:0000201 endothelial blood brain barrier IMP
GO:0097223 sperm part FoldBasedPredictor GO:0045177 apical part of cell exists_during GO:0048240 sperm capacitation part_of CL:0000019 sperm IDA
Predictions (experimental)