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covoc

This document details the invalid local unique identifiers used in CURIEs for node, synonym, and definition cross-references in covoc. See the GitHub repository.

ATC: Anatomical Therapeutic Chemical Classification System

Overall, there were 3 invalid xrefs to external prefixed with ATC (standardized to Bioregistry prefix atc) that did not match the standard pattern ^[A-Z](\d+([A-Z]{1,2}(\d+)?)?)?$.

external_xref	usages_count	usages
ATC: D11AX22	1	CHEBI:6078
ATC: N02BB02	1	CHEBI:62088
ATC: C09BA13	1	CHEBI:6960

CARO: Common Anatomy Reference Ontology

Overall, there were 1 invalid xrefs to external prefixed with CARO (standardized to Bioregistry prefix caro) that did not match the standard pattern ^\d{7}$.

external_xref	usages_count	usages
CARO:mah	1	CL:0000000

ChEMBL: ChEMBL

Overall, there were 4 invalid xrefs to external prefixed with ChEMBL (standardized to Bioregistry prefix chembl) that did not match the standard pattern ^CHEMBL\d+$.

external_xref	usages_count	usages
ChEMBL:477164	1	COVOC:0030001
ChEMBL:1201580	1	COVOC:0030002
ChEMBL:2106041	1	COVOC:0030004
ChEMBL:519846	1	COVOC:0030005

FB: FlyBase Gene

Overall, there were 1 invalid xrefs to external prefixed with FB (standardized to Bioregistry prefix flybase) that did not match the standard pattern ^FB\w{2}\d{7}$.

external_xref	usages_count	usages
FB:ma	1	CL:0000134

GenPept: GenPept

Overall, there were 24 invalid xrefs to external prefixed with GenPept (standardized to Bioregistry prefix genpept) that did not match the standard pattern ^\w{3}\d{5}(\.\d+)?$.

external_xref	usages_count	usages
GenPept:YP_009724390	3	PR:P0DTC2, PR:P0DTC2, PR:P0DTC2
GenPept:YP_009724391	3	PR:P0DTC3, PR:P0DTC3, PR:P0DTC3
GenPept:YP_009724392	3	PR:P0DTC4, PR:P0DTC4, PR:P0DTC4
GenPept:YP_009724393	3	PR:P0DTC5, PR:P0DTC5, PR:P0DTC5
GenPept:YP_009724395	3	PR:P0DTC7, PR:P0DTC7, PR:P0DTC7
GenPept:YP_009725299	2	PR:000050272, PR:000050272
GenPept:YP_009725295	2	PR:P0DTC1-1, PR:P0DTC1-1
GenPept:YP_009724397	2	PR:P0DTC9, PR:P0DTC9
GenPept:YP_009724389	2	PR:P0DTD1-1, PR:P0DTD1-1
GenPept:YP_009742610	1	PR:000050272

GEO: NCBI Gene Expression Omnibus

Overall, there were 1 invalid xrefs to external prefixed with GEO (standardized to Bioregistry prefix geo) that did not match the standard pattern ^G(PL|SM|SE|DS)\d+$.

external_xref	usages_count	usages
GEO:000000374	1	COVOC:0070006

Gmelin: Gmelins Handbuch der anorganischen Chemie

Overall, there were 2 invalid xrefs to external prefixed with Gmelin (standardized to Bioregistry prefix gmelin) that did not match the standard pattern ^[1-9][0-9]{3,6}$.

external_xref	usages_count	usages
Gmelin:485	1	CHEBI:15379
Gmelin:509	1	CHEBI:16240

HPO: Human Phenotype Ontology

Overall, there were 20 invalid xrefs to external prefixed with HPO (standardized to Bioregistry prefix hp) that did not match the standard pattern ^\d{7}$.

external_xref	usages_count	usages
HPO:probinson	18	HP:0000822, HP:0000969, HP:0000988, HP:0000989, HP:0001025, …
HPO:sdoelken	1	HP:0001945
HPO:skoehler	1	HP:0003326

ICD11: International Classification of Diseases, 11th Revision

Overall, there were 2 invalid xrefs to external prefixed with ICD11 (standardized to Bioregistry prefix icd11) that did not match the standard pattern ^[1-9]\d*$.

external_xref	usages_count	usages
ICD11:RA01.0	1	MONDO:0100096
ICD11:RA01.2	1	MONDO:0100096

ICD9: International Classification of Diseases, 9th Revision

Overall, there were 7 invalid xrefs to external prefixed with ICD9 (standardized to Bioregistry prefix icd9) that did not match the standard pattern ^(\d\d\d|V\d\d|E[8-9]\d\d)(\.\d{1,2})?$.

external_xref	usages_count	usages
ICD9:390-459.99	1	MONDO:0004995
ICD9:420-429.99	1	MONDO:0004995
ICD9:490-496.99	1	MONDO:0005002
ICD9:060-066.99	1	MONDO:0005108
ICD9:460-519.99	1	EFO:0000684
ICD9:500-508.99	1	EFO:0000684
ICD9:510-519.99	1	EFO:0000684

IEDB: Immune Epitope Database

Overall, there were 1 invalid xrefs to external prefixed with IEDB (standardized to Bioregistry prefix iedb) that did not match the standard pattern ^[0-9]+$.

external_xref	usages_count	usages
IEDB:BP	1	PR:000000001

KEGG: Kyoto Encyclopedia of Genes and Genomes

Overall, there were 1 invalid xrefs to external prefixed with KEGG (standardized to Bioregistry prefix kegg) that did not match the standard pattern ^([CHDEGTMKR]\d+)|(\w+:[\w\d\.-]*)|([a-z]{3,5})|(\w{2,4}\d{5})$.

external_xref	usages_count	usages
KEGG:05310	1	MONDO:0004979

MeSH: Medical Subject Headings

Overall, there were 1 invalid xrefs to external prefixed with MeSH (standardized to Bioregistry prefix mesh) that did not match the standard pattern ^(C|D)\d{6,9}$.

external_xref	usages_count	usages
MeSH:Q000401	1	EFO:0004352

MONDO: Mondo Disease Ontology

Overall, there were 18 invalid xrefs to external prefixed with MONDO (standardized to Bioregistry prefix mondo) that did not match the standard pattern ^\d{7}$.

external_xref	usages_count	usages
MONDO:patterns/infectious_disease_by_agent	3	MONDO:0005108, MONDO:0100096, MONDO:0100096
MONDO:patterns/specific_infectious_disease_by_agent	3	MONDO:0005091, MONDO:0005108, MONDO:0005812
MONDO:ambiguous	2	MONDO:0002280, MONDO:0005015
MONDO:design_pattern	2	MONDO:0004995, EFO:0000684
MONDO:patterns/location	2	MONDO:0004995, EFO:0000684
MONDO:patterns/location_top	2	MONDO:0004995, EFO:0000684
MONDO:patterns/inflammatory_disease_by_site	1	MONDO:0002258
MONDO:cjm	1	MONDO:0004995
MONDO:patterns/chronic	1	MONDO:0005002
MONDO:Lexical	1	MONDO:0007186

NCIT: NCI Thesaurus

Overall, there were 6 invalid xrefs to external prefixed with NCIT (standardized to Bioregistry prefix ncit) that did not match the standard pattern ^C\d+$.

external_xref	usages_count	usages
NCIT:P378	6	MONDO:0005002, MONDO:0005015, MONDO:0005091, MONDO:0005108, MONDO:0005249, …

NIF_Subcellular: NIF Standard Ontology: Subcellular Entities

Overall, there were 4 invalid xrefs to external prefixed with NIF_Subcellular (standardized to Bioregistry prefix nlx.sub) that did not match the standard pattern ^\d+$.

external_xref	usages_count	usages
NIF_Subcellular:sao1337158144	2	GO:0005575, GO:0005575
NIF_Subcellular:nlx_subcell_100315	1	GO:0005575
NIF_Subcellular:sao1820400233	1	GO:0005730

NIFSTD: NIF Standard Ontology

Overall, there were 2 invalid xrefs to external prefixed with NIFSTD (standardized to Bioregistry prefix nif.std) that did not match the standard pattern ^BAMSC\d+$.

external_xref	usages_count	usages
NIFSTD:birnlex_2110	1	EFO:0000264
NIFSTD:birnlex_2087	1	EFO:0000651

PRO: Protein Ontology

Overall, there were 42 invalid xrefs to external prefixed with PRO (standardized to Bioregistry prefix pr) that did not match the standard pattern ^(?:\d{9}|[OPQ][0-9][A-Z0-9]{3}[0-9](?:-\d+)?|[A-NR-Z][0-9](?:[A-Z][A-Z0-9]{2}[0-9]){1,2}(?:-\d+)?)$.

external_xref	usages_count	usages
PRO:DAN	22	PR:000000001, PR:000000001, PR:000050252, PR:000050252, PR:000050272, …
PRO:DNx	12	PR:000001341, PR:000001471, PR:000003137, PR:000018931, PR:000018931, …
PRO:WCB	4	PR:000000001, PR:000001341, PR:P12821, PR:Q9H2X3
PRO:JAN	2	PR:000001471, PR:P22301
PRO:CNA	1	PR:000003137
PRO:YC	1	PR:P0DTC9

ReO: Reagent Ontology

Overall, there were 1 invalid xrefs to external prefixed with ReO (standardized to Bioregistry prefix reo) that did not match the standard pattern ^\d{7}$.

external_xref	usages_count	usages
ReO:mhb	1	CL:0000010

UMLS: Unified Medical Language System Concept Unique Identifier

Overall, there were 2 invalid xrefs to external prefixed with UMLS (standardized to Bioregistry prefix umls) that did not match the standard pattern ^C\d+$.

external_xref	usages_count	usages
UMLS:CN236658	1	MONDO:0002050
UMLS:C0026565 | UMLS:C0026566	1	EFO:0004352

UniProtKB: UniProt Protein

Overall, there were 2 invalid xrefs to external prefixed with UniProtKB (standardized to Bioregistry prefix uniprot) that did not match the standard pattern ^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\.\d+)?$.

external_xref	usages_count	usages
UniProtKB:P0DTC1-1	1	PR:P0DTC1-1
UniProtKB:P0DTD1-1	1	PR:P0DTD1-1

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