Table of contents
Summary
GAF summary
Found 24687 annotations in 24706 lines.
GAF Validation Summary
Errors are reported first.
For rule GO_AR:0000014 (http://www.geneontology.org/GO.annotation_qc.shtml#GO_AR:0000014)
Valid GO term ID, there are 5 violations with type Error.
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 3 violations with type Warning.
GAF Prediction Summary
Found 3 predictions, see prediction file for details.
Used Ontology Summary
go/extensions/go-gaf go/releases/2019-06-28/extensions/go-gaf.owl
Report
SUMMARY
This report generated on 2019-07-01
- Associations: 24687
- Lines in file (incl headers): 30898
- Lines skipped: 6199
!gaf-version: 2.1
!
!The set of protein accessions included in this file is based on UniProt complete proteomes, which may provide more than one protein per gene.
!They include all Swiss-Prot entries for the species plus any TrEMBL entries that have an Ensembl DR line. The TrEMBL entries are likely to overlap with the Swiss-Prot entries or their isoforms.
!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.gaf.gz
!
!Generated: 2019-06-03 16:54
!GO-version: http://purl.obolibrary.org/obo/go/releases/2019-06-02/extensions/go-plus.owl
!
Contents
gorule-0000008
gorule-0000020
gorule-0000033
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 --
UniProtKB A0A1L1RL66 PALM GO:0005622 PMID:9813098 IDA C Paralemmin-1 PALM protein taxon:9031 20170202 AgBase part_of(UBERON:0000955) UniProtKB:A0A1D5PFN2
- WARNING - Violates GO Rule: GORULE:0000008: No annotations should be made to uninformatively high level terms --
UniProtKB Q9YGL6 PALM GO:0005622 PMID:9813098 IDA C Paralemmin-1 PALM protein taxon:9031 20170202 AgBase part_of(UBERON:0000955) UniProtKB:Q9YGL6-2
- WARNING - Violates GO Rule: GORULE:0000008: No annotations should be made to uninformatively high level terms --
UniProtKB Q9YGL6 PALM GO:0005622 PMID:9813098 IDA C Paralemmin-1 PALM protein taxon:9031 20170202 AgBase part_of(UBERON:0000955) UniProtKB:Q9YGL6-3
gorule-0000020
Automatic repair of annotations to merged or obsoleted terms
Messages
- WARNING - Obsolete class: Violates GORULE:0000020, but was repaired (GO:0035068) --
UniProtKB F1P3Z0 AGO3 GO:0035068 GO_REF:0000104 IEA UniRule:UR000107558 C Protein argonaute-3 AGO3|EIF2C3 protein taxon:9031 20190601 UniProt UniProtKB:A0A1D5PIT3
- WARNING - Obsolete class: Violates GORULE:0000020, but was repaired (GO:0035068) --
UniProtKB Q5ZMW0 AGO4 GO:0035068 GO_REF:0000104 IEA UniRule:UR000106187 C Protein argonaute-4 AGO4|EIF2C4 protein taxon:9031 20190601 UniProt UniProtKB:A0A1D5PZS8
- WARNING - Obsolete class with no replacement: Violates GORULE:0000020 (GO:0044130) --
UniProtKB Q90871 IRF8 GO:0044130 GO_REF:0000107 IEA UniProtKB:P23611|ensembl:ENSMUSP00000040245 P Interferon regulatory factor 8 IRF8 protein taxon:9031 20190601 Ensembl UniProtKB:R9PXM4
gorule-0000033
Public Reference IDs (PMID, PMC, doi, or GO_REF) should be preferred over group specific Reference IDs
Messages
- WARNING - Invalid identifier prefix: References should only be from ID prefixes PMID, PMD, doi, or GO_REF (Reactome:R-GGA-2132085) --
UniProtKB A0A1D5PU94 C4A GO:0005576 Reactome:R-GGA-2132085 TAS C Uncharacterized protein C4A protein taxon:9031 20120221 Reactome UniProtKB:F1P587
- WARNING - Invalid identifier prefix: References should only be from ID prefixes PMID, PMD, doi, or GO_REF (Reactome:R-GGA-2132222) --
UniProtKB A0A1D5PU94 C4A GO:0005576 Reactome:R-GGA-2132222 TAS C Uncharacterized protein C4A protein taxon:9031 20120221 Reactome UniProtKB:F1P587
- WARNING - Invalid identifier prefix: References should only be from ID prefixes PMID, PMD, doi, or GO_REF (Reactome:R-GGA-2132233) --
UniProtKB A0A1D5PU94 C4A GO:0005576 Reactome:R-GGA-2132233 TAS C Uncharacterized protein C4A protein taxon:9031 20120221 Reactome UniProtKB:F1P587
- WARNING - Invalid identifier prefix: References should only be from ID prefixes PMID, PMD, doi, or GO_REF (Reactome:R-GGA-2530584) --
UniProtKB A0A1D5PU94 C4A GO:0005576 Reactome:R-GGA-2530584 TAS C Uncharacterized protein C4A protein taxon:9031 20120221 Reactome UniProtKB:F1P587
- WARNING - Invalid identifier prefix: References should only be from ID prefixes PMID, PMD, doi, or GO_REF (Reactome:R-GGA-2132285) --
UniProtKB A0A1D5PU94 C4A GO:0006956 Reactome:R-GGA-2132285 TAS P Uncharacterized protein C4A protein taxon:9031 20180419 Reactome UniProtKB:F1P587
- WARNING - Invalid identifier prefix: References should only be from ID prefixes PMID, PMD, doi, or GO_REF (Reactome:R-GGA-2132281) --
UniProtKB A0A1D5PU94 C4A GO:0030449 Reactome:R-GGA-2132281 TAS P Uncharacterized protein C4A protein taxon:9031 20140218 Reactome UniProtKB:F1P587
- WARNING - Invalid identifier prefix: References should only be from ID prefixes PMID, PMD, doi, or GO_REF (Reactome:R-GGA-9607044) --
UniProtKB A0A3Q3ACS4 PIK3R1 GO:0005829 Reactome:R-GGA-9607044 TAS C Uncharacterized protein PIK3R1 protein taxon:9031 20180430 Reactome UniProtKB:E1C8M4
- WARNING - Invalid identifier prefix: References should only be from ID prefixes PMID, PMD, doi, or GO_REF (Reactome:R-GGA-2132270) --
UniProtKB F1NAP7 MASP2 GO:0001867 Reactome:R-GGA-2132270 TAS P MAp19 MASP2 protein taxon:9031 20140218 Reactome UniProtKB:Q6Q1Q7
- WARNING - Invalid identifier prefix: References should only be from ID prefixes PMID, PMD, doi, or GO_REF (Reactome:R-GGA-2132187) --
UniProtKB F1NAP7 MASP2 GO:0005576 Reactome:R-GGA-2132187 TAS C MAp19 MASP2 protein taxon:9031 20120221 Reactome UniProtKB:Q6Q1Q7
- WARNING - Invalid identifier prefix: References should only be from ID prefixes PMID, PMD, doi, or GO_REF (Reactome:R-GGA-2132206) --
UniProtKB F1NAP7 MASP2 GO:0005576 Reactome:R-GGA-2132206 TAS C MAp19 MASP2 protein taxon:9031 20130205 Reactome UniProtKB:Q6Q1Q7
- WARNING - Invalid identifier prefix: References should only be from ID prefixes PMID, PMD, doi, or GO_REF (Reactome:R-GGA-2132222) --
UniProtKB F1NAP7 MASP2 GO:0005576 Reactome:R-GGA-2132222 TAS C MAp19 MASP2 protein taxon:9031 20130205 Reactome UniProtKB:Q6Q1Q7
- WARNING - Invalid identifier prefix: References should only be from ID prefixes PMID, PMD, doi, or GO_REF (Reactome:R-GGA-2132233) --
UniProtKB F1NAP7 MASP2 GO:0005576 Reactome:R-GGA-2132233 TAS C MAp19 MASP2 protein taxon:9031 20130205 Reactome UniProtKB:Q6Q1Q7
- WARNING - Invalid identifier prefix: References should only be from ID prefixes PMID, PMD, doi, or GO_REF (Reactome:R-GGA-2132263) --
UniProtKB F1NAP7 MASP2 GO:0006956 Reactome:R-GGA-2132263 TAS P MAp19 MASP2 protein taxon:9031 20140218 Reactome UniProtKB:Q6Q1Q7
other
OWLTools check
#Line number RuleID ViolationType Message Line
#------------
#------------
# Validation for #24687 annotations in 24706 lines
#------------
#Line number RuleID ViolationType Message Line
#------------
# GO_AR:0000014 Valid GO term ID Error count: 5
2016 GO_AR:0000014 Error The relation 'has_agent' in the c16 annotation extension is an obsolete relation UniProtKB A0A1D5P7I0 CLASP1 GO:0010717 PMID:23940118 IMP P Uncharacterized protein CLASP1 protein taxon:9031 20150521 UniProt happens_during(GO:0007369),has_agent(GO:0043256),occurs_in(CL:0000352) UniProtKB:E1BVC3
2028 GO_AR:0000014 Error The relation 'has_agent' in the c16 annotation extension is an obsolete relation UniProtKB A0A1D5P7I0 CLASP1 GO:1904261 PMID:23940118 IMP P Uncharacterized protein CLASP1 protein taxon:9031 20150521 UniProt happens_during(GO:0001837),happens_during(GO:0007369),has_agent(GO:0043256),occurs_in(CL:0000352) UniProtKB:E1BVC3
9699 GO_AR:0000014 Error The relation 'has_agent' in the c16 annotation extension is an obsolete relation UniProtKB A0A3Q2U2T5 CLASP2 GO:0010717 PMID:23940118 IMP P Uncharacterized protein CLASP2 protein taxon:9031 20170214 UniProt happens_during(GO:0007369),has_agent(GO:0043256),occurs_in(CL:0000352) UniProtKB:A0A1D5P1B0
9701 GO_AR:0000014 Error The relation 'has_agent' in the c16 annotation extension is an obsolete relation UniProtKB A0A3Q2U2T5 CLASP2 GO:1904261 PMID:23940118 IMP P Uncharacterized protein CLASP2 protein taxon:9031 20170214 UniProt happens_during(GO:0001837),happens_during(GO:0007369),has_agent(GO:0043256),occurs_in(CL:0000352) UniProtKB:A0A1D5P1B0
10545 GO_AR:0000014 Error The relation 'has_agent' in the c16 annotation extension is an obsolete relation UniProtKB A0A3Q2U6L4 PHLDB2 GO:0010717 GO_REF:0000024 ISS UniProtKB:Q86SQ0 P Uncharacterized protein PHLDB2 protein taxon:9031 20150521 UniProt happens_during(GO:0007369),has_agent(GO:0043256),occurs_in(CL:0000352) UniProtKB:E1C7W8
#------------
# GO_AR:0000008 No annotations should be made to uninformative high level terms Warning count: 3
6542 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 A0A1L1RL66 PALM GO:0005622 PMID:9813098 IDA C Paralemmin-1 PALM protein taxon:9031 20170202 AgBase part_of(UBERON:0000955) UniProtKB:A0A1D5PFN2
24388 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 Q9YGL6 PALM GO:0005622 PMID:9813098 IDA C Paralemmin-1 PALM protein taxon:9031 20170202 AgBase part_of(UBERON:0000955) UniProtKB:Q9YGL6-2
24389 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 Q9YGL6 PALM GO:0005622 PMID:9813098 IDA C Paralemmin-1 PALM protein taxon:9031 20170202 AgBase part_of(UBERON:0000955) UniProtKB:Q9YGL6-3
#------------
Predictions
GO:0032259 methylation AnnotationPropagation P GO:0046539 histamine N-methyltransferase activity IDA
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
Predictions (experimental)