oquat

clm

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

AAO: Amphibian gross anatomy

Overall, there were 5 invalid xrefs to external prefixed with AAO (standardized to Bioregistry prefix aao) that did not match the standard pattern ^\d{7}$.

external_xref	usages_count	usages
AAO:EJS	5	UBERON:3000961, UBERON:3000972, UBERON:3000977, UBERON:3000982, UBERON:3010200

AEO: Anatomical Entity Ontology

Overall, there were 23 invalid xrefs to external prefixed with AEO (standardized to Bioregistry prefix aeo) that did not match the standard pattern ^\d{7}$.

external_xref	usages_count	usages
AEO:JB	22	UBERON:0001637, UBERON:0004016, UBERON:0005866, UBERON:0006846, UBERON:0007473, …
AEO:000020	1	UBERON:0001013

BTO: BRENDA Tissue Ontology

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

external_xref	usages_count	usages
BTO:000125	1	CL:1000398

CALOHA: CALIPHO Group Ontology of Human Anatomy

Overall, there were 3 invalid xrefs to external prefixed with CALOHA (standardized to Bioregistry prefix caloha) that did not match the standard pattern ^TS-\d+$.

external_xref	usages_count	usages
CALOHA:paula	3	UBERON:0007808, UBERON:0014454, UBERON:0014455

CARO: Common Anatomy Reference Ontology

Overall, there were 4 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:DOS	3	UBERON:0000026, UBERON:0000475, UBERON:0000478
CARO:mah	1	CL:0000000

CL: Cell Ontology

Overall, there were 4 invalid xrefs to external prefixed with CL (standardized to Bioregistry prefix cl) that did not match the standard pattern ^\d{7}$.

external_xref	usages_count	usages
CL:CVS	2	CL:0005000, CL:0005012
CL:patterns/cellPartOfAnatomicalEntity	1	CL:0011030
CL:tm	1	UBERON:0005158

doi: Digital Object Identifier

Overall, there were 2 invalid xrefs to external prefixed with doi (standardized to Bioregistry prefix doi) that did not match the standard pattern ^10.\d{2,9}/.*$.

external_xref	usages_count	usages
doi:/10.1016/B978-0-12-410424-2.00003-2	1	CL:0000079
doi:/10.1038/s41467-021-27901-5	1	CL:4052006

FB: FlyBase Gene

Overall, there were 16 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	13	CL:0000066, CL:0000134, CL:0000183, CL:0000211, CL:0000219, …
FB:gg	2	UBERON:0000018, UBERON:0001007
FB:DJS	1	UBERON:0001048

Flybase: FlyBase Gene

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

external_xref	usages_count	usages
Flybase:dsj	1	CL:0000362

FMA: Foundational Model of Anatomy

Overall, there were 8 invalid xrefs to external prefixed with FMA (standardized to Bioregistry prefix fma) that did not match the standard pattern ^\d+$.

external_xref	usages_count	usages
FMA:FMA	8	UBERON:0000485, UBERON:0000486, UBERON:0001943, UBERON:0002167, UBERON:0002168, …

GO: Gene Ontology

Overall, there were 9 invalid xrefs to external prefixed with GO (standardized to Bioregistry prefix go) that did not match the standard pattern ^\d{7}$.

external_xref	usages_count	usages
GO:jl	4	GO:0044092, GO:0044093, GO:1902679, GO:1902680
GO:tfm	3	CL:0000506, CL:0000507, CL:0000509
GO:GO	1	UBERON:0000016
GO:curator	1	UBERON:0005863

HPA: Human Protein Atlas tissue profile information

Overall, there were 2 invalid xrefs to external prefixed with HPA (standardized to Bioregistry prefix hpa) that did not match the standard pattern ^ENSG\d{11}$.

external_xref	usages_count	usages
HPA:HPA	2	CL:1001599, CL:1001603

HPO: Human Phenotype Ontology

Overall, there were 1 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:pr	1	UBERON:0035639

MA: Mouse adult gross anatomy

Overall, there were 1 invalid xrefs to external prefixed with MA (standardized to Bioregistry prefix ma) that did not match the standard pattern ^\d+$.

external_xref	usages_count	usages
MA:ma	1	CL:0000362

MESH: Medical Subject Headings

Overall, there were 23 invalid xrefs to external prefixed with MESH (standardized to Bioregistry prefix mesh) that did not match the standard pattern ^(C|D|M)\d{6,9}$.

external_xref	usages_count	usages
MESH:A03.734.414	1	UBERON:0000006
MESH:A07.231.114.056	1	UBERON:0000947
MESH:A09.371.060.217	1	UBERON:0000964
MESH:A10.165.114	1	UBERON:0001013
MESH:A09.371.060.067	1	UBERON:0001766
MESH:A09.371.060.217.325	1	UBERON:0001772
MESH:A09.371.060.217.228	1	UBERON:0001777
MESH:A08.800.800.720	1	UBERON:0001780
MESH:A09.371.060	1	UBERON:0001801
MESH:A07.231.432.952	1	UBERON:0001979
MESH:A10.272.491	1	UBERON:0001986
MESH:A08.186.211.132.810.428.200	1	UBERON:0002037
MESH:A07.541.459	1	UBERON:0002099
MESH:A04.411.125	1	UBERON:0002185
MESH:A03.159.183.079	1	UBERON:0003703
MESH:A03.159.183.158	1	UBERON:0003704
MESH:A08.800.800.720.800	1	UBERON:0003726
MESH:A04.760	1	UBERON:0004785
MESH:A07.231.114.565	1	UBERON:0005616
MESH:A07.231.908.670.385	1	UBERON:0005617
MESH:A12.207	1	UBERON:0006314
MESH:A07.231.432	1	UBERON:0010523
MESH:A08.663.542.122	1	UBERON:0011925

MGI: Mouse Genome Informatics

Overall, there were 49 invalid xrefs to external prefixed with MGI (standardized to Bioregistry prefix mgi) that did not match the standard pattern ^\d+$.

external_xref	usages_count	usages
MGI:csmith	19	UBERON:0001166, UBERON:0001167, UBERON:0001174, UBERON:0001200, UBERON:0001201, …
MGI:anna	12	UBERON:0000076, UBERON:0000114, UBERON:0000325, UBERON:0001070, UBERON:0001532, …
MGI:cwg	9	UBERON:0001013, UBERON:0001901, UBERON:0002173, UBERON:0002185, UBERON:0002186, …
MGI:smb	4	UBERON:0001772, UBERON:0001804, UBERON:0003604, UBERON:0014389
MGI:pvb	1	UBERON:0000087
MGI:rbabiuk	1	UBERON:0001213
MGI:monikat	1	UBERON:0002511
MGI:Anna	1	UBERON:0005203
MGI:cs	1	UBERON:0034932

MP: Mammalian Phenotype Ontology

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

external_xref	usages_count	usages
MP:MP	1	UBERON:0008835

NCI_Thesaurus: NCI Thesaurus

Overall, there were 1 invalid xrefs to external prefixed with NCI_Thesaurus (standardized to Bioregistry prefix ncit) that did not match the standard pattern ^[CRPA]\d+$.

external_xref	usages_count	usages
NCI_Thesaurus:Small_Intestinal_Glandular_Cell	1	CL:1001598

NCIT: NCI Thesaurus

Overall, there were 1 invalid xrefs to external prefixed with NCIT (standardized to Bioregistry prefix ncit) that did not match the standard pattern ^[CRPA]\d+$.

external_xref	usages_count	usages
NCIT:NCIT	1	UBERON:0010499

ncithesaurus: NCI Thesaurus

Overall, there were 32 invalid xrefs to external prefixed with ncithesaurus (standardized to Bioregistry prefix ncit) that did not match the standard pattern ^[CRPA]\d+$.

external_xref	usages_count	usages
ncithesaurus:Abdominal_Wall	1	UBERON:0003697
ncithesaurus:Splenic_Vein	1	UBERON:0003713
ncithesaurus:Cortical_Cell_Layer_of_the_Cerebellum	1	UBERON:0004130
ncithesaurus:Bowman_s_Membrane	1	UBERON:0004370
ncithesaurus:Aortic_Segment	1	UBERON:0005800
ncithesaurus:Myelinated_Nerve_Fiber	1	UBERON:0006135
ncithesaurus:Communicating_Artery	1	UBERON:0006347
ncithesaurus:Lobe	1	UBERON:0009912
ncithesaurus:Pulmonary_Lobule	1	UBERON:0010368
ncithesaurus:Phrenic_Vein	1	UBERON:0012193
ncithesaurus:Systemic_Vein	1	UBERON:0013140
ncithesaurus:Choroidal_Artery	1	UBERON:0013151
ncithesaurus:Interlobular_Duct	1	UBERON:0014716
ncithesaurus:Perivascular_Space	1	UBERON:0014930
ncithesaurus:Right_Ear	1	UBERON:0035174
ncithesaurus:Left_Ear	1	UBERON:0035295
ncithesaurus:Esophageal_Artery	1	UBERON:0035539
ncithesaurus:Superficial_Vein	1	UBERON:0035550
ncithesaurus:Deep_Vein	1	UBERON:0035552
ncithesaurus:Egg	1	CL:0000021
ncithesaurus:Beta_Cell	1	CL:0000169
ncithesaurus:Life	1	UBERON:0000104
ncithesaurus:Developmental_Stage	1	UBERON:0000105
ncithesaurus:Atlanto-occipital_Joint-Atlanto	1	UBERON:0000220
ncithesaurus:Whole_Organism	1	UBERON:0000468
ncithesaurus:Digestive_System	1	UBERON:0001007
ncithesaurus:Pleural_Fluid	1	UBERON:0001087
ncithesaurus:Heart_Muscle	1	UBERON:0001133
ncithesaurus:Peritoneal_Fluid	1	UBERON:0001268
ncithesaurus:Upper_Jaw	1	UBERON:0001709
ncithesaurus:Lower_Jaw	1	UBERON:0001710
ncithesaurus:Transudate	1	UBERON:0007779

NIF_Subcellular: NIF Standard Ontology: Subcellular Entities

Overall, there were 52 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:nlx_subcell_20090513	2	GO:0031012, GO:0031012
NIF_Subcellular:sao772007592	2	GO:0031045, GO:0031045
NIF_Subcellular:sao593830697	2	GO:0043209, GO:0043209
NIF_Subcellular:sao1872343973	2	GO:0097427, GO:0097427
NIF_Subcellular:sao1890444066	2	GO:0097454, GO:0097454
NIF_Subcellular:sao707332678	2	GO:1901589, GO:1901589
NIF_Subcellular:sao1615953555	1	GO:0000785
NIF_Subcellular:sao445485807	1	GO:0000791
NIF_Subcellular:sao581845896	1	GO:0000792
NIF_Subcellular:sao1337158144	1	GO:0005575
NIF_Subcellular:sao1425028079	1	GO:0005615
NIF_Subcellular:sao1702920020	1	GO:0005634
NIF_Subcellular:sao1617136075	1	GO:0005640
NIF_Subcellular:sao1820400233	1	GO:0005730
NIF_Subcellular:sao585356902	1	GO:0005764
NIF_Subcellular:sao1140587416	1	GO:0005766
NIF_Subcellular:sao451912436	1	GO:0005794
NIF_Subcellular:sao819927218	1	GO:0005798
NIF_Subcellular:sao95019936	1	GO:0005814
NIF_Subcellular:sao101633890	1	GO:0005829
NIF_Subcellular:sao1429207766	1	GO:0005840
NIF_Subcellular:sao1846835077	1	GO:0005874
NIF_Subcellular:sao952483289	1	GO:0005882
NIF_Subcellular:sao1588493326	1	GO:0005884
NIF_Subcellular:sao1663586795	1	GO:0005886
NIF_Subcellular:sao671419673	1	GO:0005902
NIF_Subcellular:sao1922892319	1	GO:0005911
NIF_Subcellular:sao787716553	1	GO:0005929
NIF_Subcellular:sao1153182838	1	GO:0012506
NIF_Subcellular:sao885490876	1	GO:0030133
NIF_Subcellular:sao1770195789	1	GO:0030424
NIF_Subcellular:sao830981606	1	GO:0031090
NIF_Subcellular:sao180601769	1	GO:0031410
NIF_Subcellular:sao1124888485	1	GO:0031594
NIF_Subcellular:sao1687101204	1	GO:0031965
NIF_Subcellular:sao221389602	1	GO:0031982
NIF_Subcellular:sao11978067	1	GO:0036064
NIF_Subcellular:sao867568886	1	GO:0043005
NIF_Subcellular:sao1044911821	1	GO:0043025
NIF_Subcellular:sao1539965131	1	GO:0043226
NIF_Subcellular:sao414196390	1	GO:0043227
NIF_Subcellular:sao1456184038	1	GO:0043228
NIF_Subcellular:sao914572699	1	GO:0045202
NIF_Subcellular:sao1397492660	1	UBERON:0000482
NIF_Subcellular:sao1145756102	1	UBERON:0001130
NIF_Subcellular:sao7547390221	1	UBERON:0011860

NIFSTD: NIF Standard Ontology

Overall, there were 3 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:sao1415726815	1	CL:0000119
NIFSTD:FMAID_7191	1	UBERON:0002104
NIFSTD:sao862606388	1	CL:0000598

NLM: National Library of Medicine Catalog

Overall, there were 3 invalid xrefs to external prefixed with NLM (standardized to Bioregistry prefix nlm) that did not match the standard pattern ^\d+$.

external_xref	usages_count	usages
NLM:endocrine+system	1	UBERON:0000949
NLM:alimentary+system	1	UBERON:0001007
NLM:nervous+system	1	UBERON:0001016

SO: Sequence types and features ontology

Overall, there were 6 invalid xrefs to external prefixed with SO (standardized to Bioregistry prefix so) that did not match the standard pattern ^\d{7}$.

external_xref	usages_count	usages
SO:ke	3	SO:0000001, SO:0000110, SO:0001260
SO:immuno_workshop	1	SO:0000704
SO:cb	1	SO:0001411
SO:ma	1	SO:0005855

TAO: Teleost Anatomy Ontology

Overall, there were 3 invalid xrefs to external prefixed with TAO (standardized to Bioregistry prefix tao) that did not match the standard pattern ^\d{7}$.

external_xref	usages_count	usages
TAO:curator	2	UBERON:0005744, UBERON:0013685
TAO:MAH	1	UBERON:0001703

UBERON: Uber Anatomy Ontology

Overall, there were 45 invalid xrefs to external prefixed with UBERON (standardized to Bioregistry prefix uberon) that did not match the standard pattern ^\d+$.

external_xref	usages_count	usages
UBERON:cjm	38	UBERON:0000004, UBERON:0000977, UBERON:0001027, UBERON:0001242, UBERON:0001277, …
UBERON:xp	2	UBERON:0003133, UBERON:0003134
UBERON:md	2	UBERON:0013739, UBERON:0013740
UBERON:automatic	1	UBERON:0004766
UBERON:drseb	1	UBERON:0019207
UBERON:EJS	1	UBERON:1000021

VSAO: Vertebrate Skeletal Anatomy Ontology

Overall, there were 3 invalid xrefs to external prefixed with VSAO (standardized to Bioregistry prefix vsao) that did not match the standard pattern ^\d{7}$.

external_xref	usages_count	usages
VSAO:curator	1	UBERON:0002204
VSAO:0000150-modified	1	UBERON:0004710
VSAO:NI	1	UBERON:0007272

WB: WormBase

Overall, there were 1 invalid xrefs to external prefixed with WB (standardized to Bioregistry prefix wormbase) that did not match the standard pattern ^(CE[0-9]{5}|WB[A-Z][a-z]+\d+)$.

external_xref	usages_count	usages
WB:rynl	1	UBERON:0001016

XAO: Xenopus Anatomy Ontology

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

external_xref	usages_count	usages
XAO:curators	1	UBERON:0009500
XAO:EJS	1	UBERON:0015179

ZFA: Zebrafish anatomy and development ontology

Overall, there were 5 invalid xrefs to external prefixed with ZFA (standardized to Bioregistry prefix zfa) that did not match the standard pattern ^\d{7}$.

external_xref	usages_count	usages
ZFA:curator	3	UBERON:0008229, UBERON:0014371, UBERON:0014903
ZFA:yb	1	UBERON:0002539
ZFA:CVS	1	UBERON:0018674

ZFIN: Zebrafish Information Network Gene

Overall, there were 37 invalid xrefs to external prefixed with ZFIN (standardized to Bioregistry prefix zfin) that did not match the standard pattern ^ZDB\-\w+\-\d+\-\d+$.

external_xref	usages_count	usages
ZFIN:curator	35	UBERON:0000966, UBERON:0000991, UBERON:0001016, UBERON:0001081, UBERON:0001083, …
ZFIN:dsf	1	GO:0044458
ZFIN:yb	1	UBERON:0003066

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