GAF summary

Found 128499 annotations in 128518 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.

For rule GO_AR:0000008 (http://www.geneontology.org/GO.annotation_qc.shtml#GO_AR:0000008) No annotations should be made to uninformative high level terms, there are 2 violations with type Warning.

GAF Prediction Summary

Found 23 predictions, see prediction file for details.

Used Ontology Summary

go/extensions/go-gaf    go/releases/2019-09-12/extensions/go-gaf.owl

Report

Group: goa - Dataset: goa_pig

SUMMARY

This report generated on 2019-09-13

Associations: 128499
Lines in file (incl headers): 189650
Lines skipped: 61139

Header From Original Association File

!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: 2019-07-29 13:51
!GO-version: http://purl.obolibrary.org/obo/go/releases/2019-07-17/extensions/go-plus.owl
!

MESSAGES

gorule-0000008

No annotations should be made to uninformative high level terms

total: 2

Messages

WARNING - Violates GO Rule: GORULE:0000008: No annotations should be made to uninformatively high level terms -- UniProtKB F1RIT1 TRPV4 GO:0005622 PMID:19790068 IDA C ANK_REP_REGION domain-containing protein 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 -- 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

total: 1

Messages

WARNING - Obsolete class with no replacement: Violates GORULE:0000020 (GO:1900402) -- UniProtKB F1RNT5 MLXIP GO:1900402 GO_REF:0000107 IEA UniProtKB:Q9HAP2|ensembl:ENSP00000312834 P BHLH domain-containing protein MLXIP protein taxon:9823 20190727 Ensembl

gorule-0000033

Public Reference IDs (PMID, PMC, doi, or GO_REF) should be preferred over group specific Reference IDs

total: 13

Messages

WARNING - Invalid identifier prefix: References should only be from ID prefixes PMID, PMD, doi, or GO_REF (Reactome:R-NUL-9619396) -- UniProtKB F1RGR1 CAMKK1 GO:0005829 Reactome:R-NUL-9619396 TAS C Protein kinase domain-containing protein CAMKK1 protein taxon:9823 20180914 Reactome
WARNING - Invalid identifier prefix: References should only be from ID prefixes PMID, PMD, doi, or GO_REF (Reactome:R-NUL-9034605) -- UniProtKB P24786 NTRK3 GO:0005886 Reactome:R-NUL-9034605 TAS C NT-3 growth factor receptor NTRK3|TRKC protein taxon:9823 20180108 Reactome
WARNING - Invalid identifier prefix: References should only be from ID prefixes PMID, PMD, doi, or GO_REF (Reactome:R-SSC-2162073) -- UniProtKB P31006 GUK1 GO:0005829 Reactome:R-SSC-2162073 TAS C Guanylate kinase GUK1|GUK protein taxon:9823 20120314 Reactome
WARNING - Invalid identifier prefix: References should only be from ID prefixes PMID, PMD, doi, or GO_REF (Reactome:R-NUL-443942) -- UniProtKB P42706 THPO GO:0005576 Reactome:R-NUL-443942 TAS C Thrombopoietin THPO protein taxon:9823 20091019 Reactome
WARNING - Invalid identifier prefix: References should only be from ID prefixes PMID, PMD, doi, or GO_REF (Reactome:R-NUL-437938) -- UniProtKB Q00655 SYK GO:0004715 Reactome:R-NUL-437938 TAS F Tyrosine-protein kinase SYK SYK protein taxon:9823 20150728 Reactome
WARNING - Invalid identifier prefix: References should only be from ID prefixes PMID, PMD, doi, or GO_REF (Reactome:R-NUL-437938) -- UniProtKB Q00655 SYK GO:0005829 Reactome:R-NUL-437938 TAS C Tyrosine-protein kinase SYK SYK protein taxon:9823 20090918 Reactome
WARNING - Invalid identifier prefix: References should only be from ID prefixes PMID, PMD, doi, or GO_REF (Reactome:R-NUL-437945) -- UniProtKB Q00655 SYK GO:0005829 Reactome:R-NUL-437945 TAS C Tyrosine-protein kinase SYK SYK protein taxon:9823 20090918 Reactome
WARNING - Invalid identifier prefix: References should only be from ID prefixes PMID, PMD, doi, or GO_REF (Reactome:R-NUL-3814821) -- UniProtKB Q29011 ACAN GO:0005576 Reactome:R-NUL-3814821 TAS C Aggrecan core protein ACAN|AGC1 protein taxon:9823 20130828 Reactome
WARNING - Invalid identifier prefix: References should only be from ID prefixes PMID, PMD, doi, or GO_REF (Reactome:R-SSC-2161617) -- UniProtKB Q29073 PTGR1 GO:0005829 Reactome:R-SSC-2161617 TAS C Prostaglandin reductase 1 PTGR1|LTB4DH protein taxon:9823 20120224 Reactome
WARNING - Invalid identifier prefix: References should only be from ID prefixes PMID, PMD, doi, or GO_REF (Reactome:R-SSC-2161847) -- UniProtKB Q29073 PTGR1 GO:0005829 Reactome:R-SSC-2161847 TAS C Prostaglandin reductase 1 PTGR1|LTB4DH protein taxon:9823 20120224 Reactome
WARNING - Invalid identifier prefix: References should only be from ID prefixes PMID, PMD, doi, or GO_REF (Reactome:R-SSC-2161847) -- UniProtKB Q29073 PTGR1 GO:0036185 Reactome:R-SSC-2161847 TAS F Prostaglandin reductase 1 PTGR1|LTB4DH protein taxon:9823 20120417 Reactome
WARNING - Invalid identifier prefix: References should only be from ID prefixes PMID, PMD, doi, or GO_REF (Reactome:R-SSC-2161617) -- UniProtKB Q29073 PTGR1 GO:0097257 Reactome:R-SSC-2161617 TAS F Prostaglandin reductase 1 PTGR1|LTB4DH protein taxon:9823 20150207 Reactome
WARNING - Invalid identifier prefix: References should only be from ID prefixes PMID, PMD, doi, or GO_REF (DOI:10.1016/j.procbio.2011.10.027) -- UniProtKB Q66T47 ACVR2B GO:1901389 DOI:10.1016/j.procbio.2011.10.027 IMP P Activin receptor type-2B ACVR2B protein taxon:9823 20160111 AgBase

other

total: 0

OWLTools check

#Line number RuleID ViolationType Message Line
#------------
#------------
# Validation for #128499 annotations in 128518 lines
#------------
#Line number RuleID ViolationType Message Line
#------------
# GO_AR:0000005 No ISS or ISS-related annotations to 'protein binding ; GO:0005515' Error count: 2
116824 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
121894 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
116824 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
121894 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
#------------
# GO_AR:0000008 No annotations should be made to uninformative high level terms Warning count: 2
56568 GO_AR:0000008 Warning Do not annotate to: GO:0005622 'intracellular' The term is considered to high level, as marked via the subset tag: gocheck_do_not_annotate UniProtKB F1RIT1 TRPV4 GO:0005622 PMID:19790068 IDA C ANK_REP_REGION domain-containing protein TRPV4 protein taxon:9823 20150803 AgBase part_of(CL:0000138)
123922 GO_AR:0000008 Warning Do not annotate to: GO:0005622 'intracellular' The term is considered to high level, as marked via the subset tag: gocheck_do_not_annotate 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)
#------------

Predictions

GO:0005829 cytosol AnnotationPropagation C GO:0042147 retrograde transport, endosome to Golgi ISS
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:0006468 protein phosphorylation AnnotationPropagation P GO:0050254 rhodopsin kinase activity ISS
GO:0005623 cell AnnotationPropagation C GO:0035356 cellular triglyceride homeostasis ISS
GO:0005623 cell AnnotationPropagation C GO:0051480 regulation of cytosolic calcium ion concentration 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:0005623 cell AnnotationPropagation C GO:0051480 regulation of cytosolic calcium ion concentration ISS
GO:0071108 protein K48-linked deubiquitination AnnotationPropagation P GO:1990380 Lys48-specific deubiquitinase activity ISS
GO:0005739 mitochondrion AnnotationPropagation C GO:0097345 mitochondrial outer membrane permeabilization ISS
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:0010452 histone H3-K36 methylation AnnotationPropagation P GO:0046975 histone methyltransferase activity (H3-K36 specific) 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: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:0090615 mitochondrial mRNA processing ISS
GO:0006508 proteolysis AnnotationPropagation P GO:0070006 metalloaminopeptidase 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

Table of contents

Summary

Report

Group: goa - Dataset: goa_pig

SUMMARY

Header From Original Association File

Contents

MESSAGES

gorule-0000008

Messages

gorule-0000020

Messages

gorule-0000033

Messages

other

OWLTools check

Predictions

Predictions (experimental)