Table of contents

Summary

GAF summary

Found 112212 annotations in 112231 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:0000014 (http://www.geneontology.org/GO.annotation_qc.shtml#GO_AR:0000014) Valid GO term ID, there are 4 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 6 violations with type Warning.

For rule GO_AR:0000014 (http://www.geneontology.org/GO.annotation_qc.shtml#GO_AR:0000014) Valid GO term ID, there are 17 violations with type Warning.

GAF Prediction Summary

Found 25 predictions, see prediction file for details.

Used Ontology Summary

go/extensions/go-gaf    go/releases/2019-10-31/extensions/go-gaf.owl

Report

Group: goa - Dataset: goa_pig

SUMMARY

This report generated on 2019-11-02

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: 2019-10-15 18:51
!GO-version: http://purl.obolibrary.org/obo/go/releases/2019-10-03/extensions/go-plus.owl
!

Contents

gorule-0000002

gorule-0000006

gorule-0000007

gorule-0000008

gorule-0000011

gorule-0000013

gorule-0000015

gorule-0000016

gorule-0000017

gorule-0000018

gorule-0000020

gorule-0000027

gorule-0000028

gorule-0000029

gorule-0000030

gorule-0000033

gorule-0000037

gorule-0000039

gorule-0000042

gorule-0000043

gorule-0000046

gorule-0000050

other

MESSAGES

gorule-0000002

No 'NOT' annotations to 'protein binding ; GO:0005515'

gorule-0000006

IEP and HEP usage is restricted to terms from the Biological Process ontology

gorule-0000007

IPI should not be used with catalytic activity molecular function terms

gorule-0000008

No annotations should be made to uninformative high level terms

Messages

gorule-0000011

ND annotations to root nodes only; and only root nodes can have the evidence code ND.

gorule-0000013

Taxon-appropriate annotation check

gorule-0000015

Dual species taxon check

Messages

gorule-0000016

With/From: IC annotations require a With/From GO ID

gorule-0000017

IDA annotations must not have a With/From entry

gorule-0000018

IPI annotations require a With/From entry

gorule-0000020

Automatic repair of annotations to merged or obsoleted terms

Messages

gorule-0000027

Each identifier in GAF is valid

Messages

gorule-0000028

Aspect can only be one of C, P, F and should be repaired using the GO term

gorule-0000029

All IEAs over a year old are removed

gorule-0000030

Deprecated GO_REFs are not allowed

gorule-0000033

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

Messages

gorule-0000037

IBA annotations should ONLY be assigned_by GO_Central and have PMID:21873635 as a reference

gorule-0000039

Protein complexes can not be annotated to GO:0032991 (protein-containing complex) or its descendants

gorule-0000042

Qualifier: IKR evidence code requires a NOT qualifier

gorule-0000043

Check for valid combination of evidence code and GO_REF

gorule-0000046

The ‘with’ field (GAF column 8) must be the same as the gene product (GAF colummn 2) when annotating to ‘self-binding’ terms.

Messages

gorule-0000050

Annotations to ISS, ISA and ISO should not be self-referential

other

OWLTools check

#Line number RuleID ViolationType Message Line
#------------
#------------
# Validation for #112212 annotations in 112231 lines
#------------
#Line number RuleID ViolationType Message Line
#------------
# GO_AR:0000005 No ISS or ISS-related annotations to 'protein binding ; GO:0005515' Error count: 2
100962 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
105734 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:0000014 Valid GO term ID Error count: 4
59567 GO_AR:0000014 Error The id 'GO:1990967' in the annotation is an obsolete class UniProtKB F1S008 RAB40B GO:1990967 GO_REF:0000107 IEA UniProtKB:Q12829|ensembl:ENSP00000461785 P SOCS box domain-containing protein RAB40B protein taxon:9823 20190925 Ensembl
89466 GO_AR:0000014 Error The id 'GO:1990967' in the annotation is an obsolete class UniProtKB I3LHE8 RAB29 GO:1990967 GO_REF:0000107 IEA UniProtKB:O14966|ensembl:ENSP00000356107 P Ras-related protein Rab-7L1 isoform X1 RAB29 protein taxon:9823 20190925 Ensembl
98048 GO_AR:0000014 Error The id 'GO:0052213' in the annotation is an obsolete class UniProtKB K7GS29 IL33 GO:0052213 GO_REF:0000107 IEA UniProtKB:O95760|ensembl:ENSP00000370842 P Uncharacterized protein IL33 protein taxon:9823 20190925 Ensembl
100944 GO_AR:0000014 Error The id 'GO:0052213' in the annotation is an obsolete class UniProtKB P06867 PLG GO:0052213 PMID:14688145 IDA P Plasminogen PLG protein taxon:9823|taxon:1307 20160531 CAFA occurs_at(GO:0009986)
#------------
# 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
100962 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
105734 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: 6
26590 GO_AR:0000008 Warning Do not annotate to: GO:0072001 'renal system development' The term is considered to high level, as marked via the subset tag: gocheck_do_not_annotate UniProtKB A0A287AZV2 CEP55 GO:0072001 GO_REF:0000107 IEA UniProtKB:Q53EZ4|ensembl:ENSP00000360540 P EABR domain-containing protein CEP55 protein taxon:9823 20190925 Ensembl
46142 GO_AR:0000008 Warning Do not annotate to: GO:0072001 'renal system development' The term is considered to high level, as marked via the subset tag: gocheck_do_not_annotate UniProtKB F1RG13 IFT140 GO:0072001 GO_REF:0000107 IEA UniProtKB:Q96RY7|ensembl:ENSP00000406012 P WD_REPEATS_REGION domain-containing protein IFT140 protein taxon:9823 20190925 Ensembl
47976 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)
60086 GO_AR:0000008 Warning Do not annotate to: GO:0072001 'renal system development' The term is considered to high level, as marked via the subset tag: gocheck_do_not_annotate UniProtKB F1S0I2 TBX18 GO:0072001 GO_REF:0000107 IEA UniProtKB:O95935|ensembl:ENSP00000358677 P T-box transcription factor TBX18 TBX18 protein taxon:9823 20190925 Ensembl
98443 GO_AR:0000008 Warning Do not annotate to: GO:0072001 'renal system development' The term is considered to high level, as marked via the subset tag: gocheck_do_not_annotate UniProtKB K7GT68 ITGA6 GO:0072001 GO_REF:0000107 IEA UniProtKB:P23229|ensembl:ENSP00000386896 P Integrin_alpha2 domain-containing protein ITGA6 protein taxon:9823 20190925 Ensembl
107716 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)
#------------
# GO_AR:0000014 Valid GO term ID Warning count: 17
1179 GO_AR:0000014 Warning The id 'GO:0001158' in the annotation is an alternate id for: GO:0000987 UniProtKB A0A286ZJJ7 LHX1 GO:0001158 GO_REF:0000107 IEA UniProtKB:P63006|ensembl:ENSMUSP00000018842 F Uncharacterized protein LHX1 protein taxon:9823 20190925 Ensembl
12250 GO_AR:0000014 Warning The id 'GO:0001158' in the annotation is an alternate id for: GO:0000987 UniProtKB A0A287A582 TFAP2B GO:0001158 GO_REF:0000107 IEA UniProtKB:Q92481|ensembl:ENSP00000377265 F TF_AP-2 domain-containing protein TFAP2B protein taxon:9823 20190925 Ensembl
35793 GO_AR:0000014 Warning The id 'GO:0001158' in the annotation is an alternate id for: GO:0000987 UniProtKB A0A287BJ14 NANOG GO:0001158 GO_REF:0000107 IEA UniProtKB:Q80Z64|ensembl:ENSMUSP00000012540 F Homeobox domain-containing protein NANOG protein taxon:9823 20190925 Ensembl
37042 GO_AR:0000014 Warning The id 'GO:0001158' in the annotation is an alternate id for: GO:0000987 UniProtKB A0A287BLD4 HMGA1 GO:0001158 GO_REF:0000107 IEA UniProtKB:P17096|ensembl:ENSP00000399888 F Uncharacterized protein HMGA1 protein taxon:9823 20190925 Ensembl
41115 GO_AR:0000014 Warning The id 'GO:0001158' in the annotation is an alternate id for: GO:0000987 UniProtKB A0ZVR0 Irf7 GO:0001158 GO_REF:0000107 IEA UniProtKB:P70434|ensembl:ENSMUSP00000026571 F IRF tryptophan pentad repeat domain-containing protein Irf7|IRF7 protein taxon:9823 20190925 Ensembl
48141 GO_AR:0000014 Warning The id 'GO:0001158' in the annotation is an alternate id for: GO:0000987 UniProtKB F1RJ01 HMGB2 GO:0001158 GO_REF:0000024 ISS UniProtKB:P30681 F High mobility group protein B2 HMGB2 protein taxon:9823 20150512 AgBase
48142 GO_AR:0000014 Warning The id 'GO:0001158' in the annotation is an alternate id for: GO:0000987 UniProtKB F1RJ01 HMGB2 GO:0001158 GO_REF:0000024 ISS UniProtKB:Q3U566 F High mobility group protein B2 HMGB2 protein taxon:9823 20150512 AgBase
52508 GO_AR:0000014 Warning The id 'GO:0001158' in the annotation is an alternate id for: GO:0000987 UniProtKB F1RPV3 TBX19 GO:0001158 GO_REF:0000107 IEA UniProtKB:Q99ME7|ensembl:ENSMUSP00000027859 F T-box transcription factor TBX19 TBX19 protein taxon:9823 20190925 Ensembl
55645 GO_AR:0000014 Warning The id 'GO:0001158' in the annotation is an alternate id for: GO:0000987 UniProtKB F1RUM8 GATA3 GO:0001158 GO_REF:0000107 IEA UniProtKB:P23772|ensembl:ENSMUSP00000100041 F Trans-acting T-cell-specific transcription factor GATA-3 GATA3 protein taxon:9823 20190925 Ensembl
55959 GO_AR:0000014 Warning The id 'GO:0001158' in the annotation is an alternate id for: GO:0000987 UniProtKB F1RV30 SOX9 GO:0001158 GO_REF:0000107 IEA UniProtKB:Q04887|ensembl:ENSMUSP00000000579 F HMG box domain-containing protein SOX9 protein taxon:9823 20190925 Ensembl
59208 GO_AR:0000014 Warning The id 'GO:0001158' in the annotation is an alternate id for: GO:0000987 UniProtKB F1RZG5 HOXD13 GO:0001158 GO_REF:0000107 IEA UniProtKB:P70217|ensembl:ENSMUSP00000001872 F Homeobox domain-containing protein HOXD13 protein taxon:9823 20190925 Ensembl
66544 GO_AR:0000014 Warning The id 'GO:0001158' in the annotation is an alternate id for: GO:0000987 UniProtKB F1S9L1 SOX11 GO:0001158 GO_REF:0000024 ISS UniProtKB:Q7M6Y2 F Transcription factor SOX SOX11 protein taxon:9823 20110621 UniProt
75973 GO_AR:0000014 Warning The id 'GO:0001158' in the annotation is an alternate id for: GO:0000987 UniProtKB F1SMF7 ISL1 GO:0001158 GO_REF:0000107 IEA UniProtKB:P61371|ensembl:ENSP00000230658 F Insulin gene enhancer protein ISL-1 ISL1 protein taxon:9823 20190925 Ensembl
82697 GO_AR:0000014 Warning The id 'GO:0001158' in the annotation is an alternate id for: GO:0000987 UniProtKB F2Z5G6 LDB1 GO:0001158 GO_REF:0000107 IEA UniProtKB:P70662|ensembl:ENSMUSP00000118546 F LID domain-containing protein LDB1 protein taxon:9823 20190925 Ensembl
84913 GO_AR:0000014 Warning The id 'GO:0001158' in the annotation is an alternate id for: GO:0000987 UniProtKB I3L7Q9 ZBTB7B GO:0001158 GO_REF:0000107 IEA UniProtKB:Q64321|ensembl:ENSMUSP00000103058 F Zinc finger and BTB domain-containing protein 7B isoform X1 ZBTB7B protein taxon:9823 20190925 Ensembl
91729 GO_AR:0000014 Warning The id 'GO:0001158' in the annotation is an alternate id for: GO:0000987 UniProtKB I3LMJ2 ZNF704 GO:0001158 GO_REF:0000107 IEA UniProtKB:Q9ERQ3|ensembl:ENSMUSP00000041242 F C2H2-type domain-containing protein ZNF704 protein taxon:9823 20190925 Ensembl
99341 GO_AR:0000014 Warning The id 'GO:0001158' in the annotation is an alternate id for: GO:0000987 UniProtKB O18896 SOX9 GO:0001158 GO_REF:0000024 ISS UniProtKB:Q04887 F Transcription factor SOX-9 SOX9 protein taxon:9823 20110708 UniProt
#------------

Predictions

GO:0005739 mitochondrion AnnotationPropagation C GO:0033615 mitochondrial proton-transporting ATP synthase complex assembly ISS
GO:0005739 mitochondrion AnnotationPropagation C GO:1901029 negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway 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:0071108 protein K48-linked deubiquitination AnnotationPropagation P GO:1990380 Lys48-specific deubiquitinase activity ISS
GO:0006468 protein phosphorylation AnnotationPropagation P GO:0050254 rhodopsin kinase activity 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: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:0006508 proteolysis AnnotationPropagation P GO:0070006 metalloaminopeptidase activity 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:0005739 mitochondrion AnnotationPropagation C GO:0090615 mitochondrial mRNA processing ISS
GO:0005829 cytosol AnnotationPropagation C GO:0042147 retrograde transport, endosome to Golgi ISS
GO:0005623 cell AnnotationPropagation C GO:0051480 regulation of cytosolic calcium ion concentration ISS
GO:0005623 cell AnnotationPropagation C GO:0051311 meiotic metaphase plate congression IMP
GO:0010452 histone H3-K36 methylation AnnotationPropagation P GO:0046975 histone methyltransferase activity (H3-K36 specific) ISS
GO:0005739 mitochondrion AnnotationPropagation C GO:0097345 mitochondrial outer membrane permeabilization ISS
GO:0016311 dephosphorylation AnnotationPropagation P GO:0097657 3',5'-nucleotide bisphosphate phosphatase activity ISS
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:0005783 endoplasmic reticulum FoldBasedPredictor GO:0005515 protein binding occurs_in GO:0005783 endoplasmic reticulum IPI
GO:0071560 cellular response to transforming growth factor beta stimulus FoldBasedPredictor GO:1900182 positive regulation of protein localization to nucleus occurs_in UBERON:0002137 aortic valve part_of GO:0071560 cellular response to transforming growth factor beta stimulus transports_or_maintains_localization_of ENSEMBL:ENSSSCG00000017251 IGI

Predictions (experimental)