GORULE Violations Assigned by LncRNAWiki

Generated by GOA at EMBL-EBI logo - 2026-07-25 08:02:45.454239

Total Lines

339896

LncRNAWiki

53

Valid Lines

45 (84.91%)

Total Problems Detected

8

File Header

!gpa-version: 1.2
!collation date: 2026-07-22
RuleDescriptionCount
⛔️GORULE:0000001 GAF lines are parsed according to GAF 2.2 specifications 4
✅GORULE:0000002 No 'NOT' annotations to binding ; GO:0005488 or 'protein binding ; GO:0005515' 0
✅GORULE:0000005 IEA, ISS, ISO, ISM, ISA, IBA, RCA annotations are not allowed for direct annotations to protein binding ; GO:0005515 or GO:0005488 binding 0
✅GORULE:0000006 IEP and HEP usage is restricted to terms from the Biological Process ontology, except when assigned by GOC 0
✅GORULE:0000007 IPI should not be used with GO:0003824 catalytic activity or descendants 0
✅GORULE:0000008 No annotations should be made to uninformative high level terms 0
✅GORULE:0000011 ND evidence code should be to root nodes only, and no terms other than root nodes can have the evidence code ND 0
✅GORULE:0000013 Taxon-appropriate annotation check 0
✅GORULE:0000015 Dual species taxon check 0
✅GORULE:0000016 With/From: IC annotations require a With/From GO ID 0
✅GORULE:0000017 IDA annotations must not have a With/From entry 0
✅GORULE:0000018 IPI annotations require a With/From entry 0
✅GORULE:0000020 Automatic repair of annotations to merged or obsoleted terms 0
✅GORULE:0000022 Check for, and filter, annotations made to retracted publications 0
⛔️GORULE:0000027 Each identifier in GAF is valid 4
✅GORULE:0000030 Obsolete GO_REFs are not allowed 0
✅GORULE:0000033 Group-specific Reference IDs are not allowed, only public reference IDs (PMID, doi, or GO_REF) 0
✅GORULE:0000039 Protein complexes can not be annotated to GO:0032991 (protein-containing complex) or its descendants 0
✅GORULE:0000042 Qualifier: IKR evidence code requires a NOT qualifier 0
✅GORULE:0000043 Check for valid combination of evidence code and GO_REF 0
✅GORULE:0000046 The 'with' field (GAF column 8) must be the same as the gene product (GAF column 2) when annotating to 'self-binding' terms. 0
✅GORULE:0000050 Annotations to ISS, ISA and ISO should not be self-referential 0
✅GORULE:0000053 'NOT' annotation should not have extension 0
✅GORULE:0000055 References should have only one ID per ID space 0
✅GORULE:0000063 Annotations using ISS/ISA/ISO evidence should refer to a gene product (in the 'with' column) 0
✅GORULE:0000065 Term candidate for obsoletion 0

Messages

⛔️ GORULE:0000001-GAF lines are parsed according to GAF 2.2 specifications

  • Total Violations: 4
  • Line 54663 – RNAcentral URS00026A27F2_9606 is_active_in GO:0005634 PMID:40505346 ECO:0000314 upstream,positiveeffect 20250928 LncRNAWiki contributor=https://orcid.org/0000-0003-4331-2023|noctua-model-id=gomodel:68b0f0d000000332|model-state=production
    GORULE:0000001-GPAD lines are parsed according to GPAD 1.2 specifications-'with' missing namespace
  • Line 54666 – UniProtKB Q9Y4X4 involved_in GO:0048255 PMID:35526050 ECO:0000316 URS00007E42F7_9606 20250928 LncRNAWiki noctua-model-id=gomodel:68b0f0d000000357|contributor=https://orcid.org/0000-0003-4331-2023|model-state=production
    GORULE:0000001-GPAD lines are parsed according to GPAD 1.2 specifications-'with' missing namespace
  • Line 54668 – RNAcentral URS00007E42F7_9606 involved_in GO:0060965 PMID:35526050 ECO:0000315 URS00002B7450_9606 20250831 LncRNAWiki part_of(GO:0048255) noctua-model-id=gomodel:68b0f0d000000357|contributor=https://orcid.org/0000-0003-4331-2023|model-state=production
    GORULE:0000001-GPAD lines are parsed according to GPAD 1.2 specifications-'with' missing namespace
  • Line 54680 – RNAcentral URS0000A765A8_9606 enables GO:0043021 PMID:29245011 ECO:0000353 URS0002A35FEB_9606 20250928 LncRNAWiki part_of(GO:0008284),part_of(GO:0043568),part_of(GO:0048255) noctua-model-id=gomodel:68b0f0d000000388|contributor=https://orcid.org/0000-0003-4331-2023|contributor=https://orcid.org/0009-0004-4855-0893|model-state=production
    GORULE:0000001-GPAD lines are parsed according to GPAD 1.2 specifications-'with' missing namespace

✅ GORULE:0000002-No 'NOT' annotations to binding ; GO:0005488 or 'protein binding ; GO:0005515'

  • All checks passed - 0 violations

✅ GORULE:0000005-IEA, ISS, ISO, ISM, ISA, IBA, RCA annotations are not allowed for direct annotations to protein binding ; GO:0005515 or GO:0005488 binding

  • All checks passed - 0 violations

✅ GORULE:0000006-IEP and HEP usage is restricted to terms from the Biological Process ontology, except when assigned by GOC

  • All checks passed - 0 violations

✅ GORULE:0000007-IPI should not be used with GO:0003824 catalytic activity or descendants

  • All checks passed - 0 violations

✅ GORULE:0000008-No annotations should be made to uninformative high level terms

  • All checks passed - 0 violations

✅ GORULE:0000011-ND evidence code should be to root nodes only, and no terms other than root nodes can have the evidence code ND

  • All checks passed - 0 violations

✅ GORULE:0000013-Taxon-appropriate annotation check

  • All checks passed - 0 violations

✅ GORULE:0000015-Dual species taxon check

  • All checks passed - 0 violations

✅ GORULE:0000016-With/From: IC annotations require a With/From GO ID

  • All checks passed - 0 violations

✅ GORULE:0000017-IDA annotations must not have a With/From entry

  • All checks passed - 0 violations

✅ GORULE:0000018-IPI annotations require a With/From entry

  • All checks passed - 0 violations

✅ GORULE:0000020-Automatic repair of annotations to merged or obsoleted terms

  • All checks passed - 0 violations

✅ GORULE:0000022-Check for, and filter, annotations made to retracted publications

  • All checks passed - 0 violations

⛔️ GORULE:0000027-Each identifier in GAF is valid

  • Total Violations: 4
  • Line 54664 – RNAcentral URS00026A27F2_9606 enables GO:0003713 PMID:40505346 ECO:0000353 UniProtKB:Q15637andUniProtKB:P10109 20250928 LncRNAWiki part_of(GO:0045944),occurs_in(GO:0005634) contributor=https://orcid.org/0000-0003-4331-2023|noctua-model-id=gomodel:68b0f0d000000332|model-state=production
    GORULE:0000027-Each identifier in GAF is valid-Bad id syntax for UniProtKB:Q15637andUniProtKB:P10109
  • Line 54670 – RNAcentral URS00007E42F7_9606 involved_in GO:0048255 PMID:35526050 ECO:0000315 UniProtKB:Q9Y4X4andUniProtKB:P01106 20250928 LncRNAWiki noctua-model-id=gomodel:68b0f0d000000357|contributor=https://orcid.org/0000-0003-4331-2023|model-state=production
    GORULE:0000027-Each identifier in GAF is valid-Bad id syntax for UniProtKB:Q9Y4X4andUniProtKB:P01106
  • Line 54671 – RNAcentral URS0002345A90_9606 enables GO:0003714 PMID:36736696 ECO:0000353 UniProtKB:Q7RTP0andUniProtKB:Q96AE4 20250928 LncRNAWiki part_of(GO:0007162),part_of(GO:0030513) noctua-model-id=gomodel:68b0f0d000000368|contributor=https://orcid.org/0000-0003-4331-2023|model-state=production
    GORULE:0000027-Each identifier in GAF is valid-Bad id syntax for UniProtKB:Q7RTP0andUniProtKB:Q96AE4
  • Line 54689 – MGI MGI:1918577 enables GO:0140463 PMID:36200826 ECO:0000353 Smarca5Mmus(MGI:MGI:1935129) 20250928 LncRNAWiki part_of(GO:0031452),part_of(GO:0042692) contributor=https://orcid.org/0000-0003-4331-2023|contributor=https://orcid.org/0009-0004-4855-0893|model-state=production|noctua-model-id=gomodel:68b0f0d000000427
    GORULE:0000027-Each identifier in GAF is valid-Prefix not found in db-xrefs: Smarca5Mmus(MGI

✅ GORULE:0000030-Obsolete GO_REFs are not allowed

  • All checks passed - 0 violations

✅ GORULE:0000033-Group-specific Reference IDs are not allowed, only public reference IDs (PMID, doi, or GO_REF)

  • All checks passed - 0 violations

✅ GORULE:0000039-Protein complexes can not be annotated to GO:0032991 (protein-containing complex) or its descendants

  • All checks passed - 0 violations

✅ GORULE:0000042-Qualifier: IKR evidence code requires a NOT qualifier

  • All checks passed - 0 violations

✅ GORULE:0000043-Check for valid combination of evidence code and GO_REF

  • All checks passed - 0 violations

✅ GORULE:0000046-The 'with' field (GAF column 8) must be the same as the gene product (GAF column 2) when annotating to 'self-binding' terms.

  • All checks passed - 0 violations

✅ GORULE:0000050-Annotations to ISS, ISA and ISO should not be self-referential

  • All checks passed - 0 violations

✅ GORULE:0000053-'NOT' annotation should not have extension

  • All checks passed - 0 violations

✅ GORULE:0000055-References should have only one ID per ID space

  • All checks passed - 0 violations

✅ GORULE:0000063-Annotations using ISS/ISA/ISO evidence should refer to a gene product (in the 'with' column)

  • All checks passed - 0 violations

✅ GORULE:0000065-Term candidate for obsoletion

  • All checks passed - 0 violations