Table of contents
Summary
GAF summary
Found 25208 annotations in 25227 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 5 predictions, see prediction file for details.
Used Ontology Summary
go/extensions/go-gaf go/releases/2019-10-03/extensions/go-gaf.owl
Report
SUMMARY
This report generated on 2019-10-07
- Associations: 25208
- Lines in file (incl headers): 31988
- Lines skipped: 6768
!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: 2019-09-16 16:54
!GO-version: http://purl.obolibrary.org/obo/go/releases/2019-09-13/extensions/go-plus.owl
!
Contents
gorule-0000008
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 A0A1D5PFN2 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-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-9607044) --
UniProtKB E1C8M4 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-2132085) --
UniProtKB F1P587 C4A GO:0005576 Reactome:R-GGA-2132085 TAS C Anaphylatoxin-like domain-containing 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 F1P587 C4A GO:0005576 Reactome:R-GGA-2132222 TAS C Anaphylatoxin-like domain-containing 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 F1P587 C4A GO:0005576 Reactome:R-GGA-2132233 TAS C Anaphylatoxin-like domain-containing 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 F1P587 C4A GO:0005576 Reactome:R-GGA-2530584 TAS C Anaphylatoxin-like domain-containing 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 F1P587 C4A GO:0006956 Reactome:R-GGA-2132285 TAS P Anaphylatoxin-like domain-containing 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 F1P587 C4A GO:0030449 Reactome:R-GGA-2132281 TAS P Anaphylatoxin-like domain-containing 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-2132270) --
UniProtKB Q6Q1Q7 MASP2 GO:0001867 Reactome:R-GGA-2132270 TAS P CUB domain-containing protein 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 Q6Q1Q7 MASP2 GO:0005576 Reactome:R-GGA-2132187 TAS C CUB domain-containing protein 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 Q6Q1Q7 MASP2 GO:0005576 Reactome:R-GGA-2132206 TAS C CUB domain-containing protein 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 Q6Q1Q7 MASP2 GO:0005576 Reactome:R-GGA-2132222 TAS C CUB domain-containing protein 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 Q6Q1Q7 MASP2 GO:0005576 Reactome:R-GGA-2132233 TAS C CUB domain-containing protein 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 Q6Q1Q7 MASP2 GO:0006956 Reactome:R-GGA-2132263 TAS P CUB domain-containing protein MASP2 protein taxon:9031 20140218 Reactome UniProtKB:Q6Q1Q7
other
OWLTools check
#Line number RuleID ViolationType Message Line
#------------
#------------
# Validation for #25208 annotations in 25227 lines
#------------
#Line number RuleID ViolationType Message Line
#------------
# GO_AR:0000014 Valid GO term ID Error count: 5
1610 GO_AR:0000014 Error The relation 'has_agent' in the c16 annotation extension is an obsolete relation UniProtKB A0A1D5P1B0 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
1612 GO_AR:0000014 Error The relation 'has_agent' in the c16 annotation extension is an obsolete relation UniProtKB A0A1D5P1B0 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
19488 GO_AR:0000014 Error The relation 'has_agent' in the c16 annotation extension is an obsolete relation UniProtKB E1BVC3 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
19494 GO_AR:0000014 Error The relation 'has_agent' in the c16 annotation extension is an obsolete relation UniProtKB E1BVC3 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
20328 GO_AR:0000014 Error The relation 'has_agent' in the c16 annotation extension is an obsolete relation UniProtKB E1C7W8 PHLDB2 GO:0010717 GO_REF:0000024 ISS UniProtKB:Q86SQ0 P PH domain-containing 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
4137 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 A0A1D5PFN2 PALM GO:0005622 PMID:9813098 IDA C Paralemmin-1 PALM protein taxon:9031 20170202 AgBase part_of(UBERON:0000955) UniProtKB:A0A1D5PFN2
24604 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
24605 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:0006259 DNA metabolic process AnnotationPropagation P GO:0004531 deoxyribonuclease II activity IDA
GO:0090305 nucleic acid phosphodiester bond hydrolysis AnnotationPropagation P GO:0004531 deoxyribonuclease II activity IDA
GO:0005829 cytosol AnnotationPropagation C GO:0042147 retrograde transport, endosome to Golgi ISS
GO:0008144 drug binding FoldBasedPredictor GO:1990239 steroid hormone binding has_direct_input CHEBI:17026 progesterone occurs_in UBERON:0000993 oviduct ISS
GO:0044295 axonal growth cone FoldBasedPredictor GO:2000009 negative regulation of protein localization to cell surface occurs_in GO:0044295 axonal growth cone transports_or_maintains_localization_of UniProtKB:P79795 IMP
Predictions (experimental)