oquat

so

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

`DOI`: Digital Object Identifier

Overall, there were 7 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:10.1126`	7	SO:0001486, SO:0001487, SO:0001488, SO:0001489, SO:0001490, …

`FB`: FlyBase Gene

Overall, there were 42 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:reference_manual`	24	SO:0000062, SO:0000453, SO:0001784, SO:1000044, SO:1000046, …
`FB:km`	6	SO:0000461, SO:0000465, SO:0000512, SO:0000547, SO:0000549, …
`FB:mc`	4	SO:0000796, SO:0000797, SO:0000798, SO:0000799
`FB:gm`	4	SO:0000800, SO:0000801, SO:0000802, SO:0000803
`FB:manual`	2	SO:1000142, SO:1000143
`FB:WG`	1	SO:0000719
`FB:cds`	1	SO:0000934

`GO`: Gene Ontology

Overall, there were 3 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:mah`	3	SO:0001861, SO:0001861, SO:0001871

`HGNC`: HUGO Gene Nomenclature Committee

Overall, there were 1 invalid xrefs to external prefixed with HGNC (standardized to Bioregistry prefix hgnc) that did not match the standard pattern ^\d{1,5}$.

external_xref	usages_count	usages
`HGNC:mw`	1	SO:0001877

`JAX`: Jackson Laboratories Mouse Strain

Overall, there were 2 invalid xrefs to external prefixed with JAX (standardized to Bioregistry prefix jaxmice) that did not match the standard pattern ^\d{6}$.

external_xref	usages_count	usages
`JAX:hdene`	1	SO:0001500
`JAX:hd`	1	SO:0001841

`MGD`: Mouse Genome Informatics

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

external_xref	usages_count	usages
`MGD:tm`	1	SO:0001644

`MGI`: Mouse Genome Informatics

Overall, there were 1 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:hdeen`	1	SO:0001503

`PMC`: PubMed Central

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

external_xref	usages_count	usages
`PMC:126017`	1	SO:0002095

`PMID`: PubMed

Overall, there were 21 invalid xrefs to external prefixed with PMID (standardized to Bioregistry prefix pubmed) that did not match the standard pattern ^\d+$.

external_xref	usages_count	usages
`PMID: 24572720`	5	SO:0002344, SO:0002345, SO:0002346, SO:0002347, SO:0002348
`PMID:12537576:16827941`	4	SO:0001158, SO:0001159, SO:0001160, SO:0001161
`PMID: 118436`	2	SO:0002336, SO:0002337
`PMID: 29474379`	2	SO:0002336, SO:0002337
`PMID: 3136294`	2	SO:0002336, SO:0002337
`PMID:16827941:12537576`	1	SO:0001157
`PMID:12537576:15231738`	1	SO:0001162
`PMID:15388847,PMID:16524884`	1	SO:0002235
`PMID: 19407924`	1	SO:0002293
`PMID: 16236432`	1	SO:0002350
`PMID: 17608616`	1	SO:0002350

`PomBase`: PomBase

Overall, there were 12 invalid xrefs to external prefixed with PomBase (standardized to Bioregistry prefix pombase) that did not match the standard pattern ^S\w+(\.)?\w+(\.)?$.

external_xref	usages_count	usages
`PomBase:mah`	6	SO:0001808, SO:0001811, SO:0001812, SO:0001813, SO:0001905, …
`PomBase:al`	3	SO:0000370, SO:0002022, SO:0002207
`PomBase:vw`	2	SO:0002025, SO:0002215
`PomBase:mh`	1	SO:0002208

`POMBASE`: PomBase

Overall, there were 3 invalid xrefs to external prefixed with POMBASE (standardized to Bioregistry prefix pombase) that did not match the standard pattern ^S\w+(\.)?\w+(\.)?$.

external_xref	usages_count	usages
`POMBASE:mah`	2	SO:0002027, SO:0002028
`POMBASE:vw`	1	SO:0002029

`RFAM`: Rfam database of RNA families

Overall, there were 2 invalid xrefs to external prefixed with RFAM (standardized to Bioregistry prefix rfam) that did not match the standard pattern ^RF\d{5}$.

external_xref	usages_count	usages
`RFAM:jd`	2	SO:0001427, SO:0001459

`SGD`: Saccharomyces Genome Database

Overall, there were 12 invalid xrefs to external prefixed with SGD (standardized to Bioregistry prefix sgd) that did not match the standard pattern ^((S\d+$)|(Y[A-Z]{2}\d{3}[a-zA-Z](\-[A-Z])?))$.

external_xref	usages_count	usages
`SGD:jd`	6	SO:0002001, SO:0002002, SO:0002003, SO:0002004, SO:0002024, …
`SGD:rb`	3	SO:0000236, SO:0000717, SO:0000718
`SGD:se`	3	SO:0002048, SO:0002059, SO:0005853

`SO`: Sequence types and features ontology

Overall, there were 1,224 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`	885	SO:0000001, SO:0000002, SO:0000006, SO:0000013, SO:0000020, …
`SO:xp`	109	SO:0000078, SO:0000087, SO:0000088, SO:0000089, SO:0000090, …
`SO:ma`	76	SO:0000036, SO:0000037, SO:0000040, SO:0000042, SO:0000051, …
`SO:cb`	41	SO:0000059, SO:0000061, SO:0000419, SO:0000694, SO:0000836, …
`SO:nlw`	21	SO:0000708, SO:0000709, SO:0001464, SO:0001465, SO:0001466, …
`SO:as`	14	SO:0000140, SO:0000365, SO:0000367, SO:0000942, SO:0000943, …
`SO:cjm`	11	SO:0000162, SO:0000163, SO:0000164, SO:0000196, SO:0000197, …
`SO:immuno_workshop`	8	SO:0000704, SO:0001023, SO:0001024, SO:0001025, SO:0001026, …
`SO:rd`	7	SO:0000150, SO:0000307, SO:0000337, SO:0000339, SO:0000468, …
`SO:vw`	7	SO:0001794, SO:0001795, SO:0001796, SO:0001798, SO:0001799, …
`SO:bm`	6	SO:0001218, SO:0001483, SO:0001745, SO:0001746, SO:0001902, …
`SO:ls`	4	SO:0000007, SO:0000148, SO:0000149, SO:0000688
`SO:regcreative`	4	SO:0000167, SO:0000627, SO:0001055, SO:0001058
`SO:ml`	4	SO:0001668, SO:0001980, SO:0001981, SO:0001982
`SO:ds`	4	SO:0002329, SO:0002330, SO:0002331, SO:0002332
`SO:andrewgibson`	3	SO:0001915, SO:0001916, SO:0001917
`SO:rtapella`	3	SO:0001918, SO:0001919, SO:0001920
`SO:jk`	2	SO:0000931, SO:0000978
`SO:chado`	2	SO:0001416, SO:0001417
`SO:jh`	1	SO:0000552
`SO:SG`	1	SO:0000727
`SO:GAR`	1	SO:0000839
`SO:jestill`	1	SO:0001642
`SO:db`	1	SO:0001645
`SO:AF`	1	SO:0001658
`SO:KE`	1	SO:0001731
`SO:mc`	1	SO:0001740
`SO:hd`	1	SO:0001741
`SO:BM`	1	SO:0001744
`SO:myl`	1	SO:0001959
`SO:rs`	1	SO:0002049
`SO:nrs`	1	SO:0002095

`UniProt`: UniProt Protein

Overall, there were 21 invalid xrefs to external prefixed with UniProt (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
`UniProt:curation_manual`	19	SO:0001064, SO:0001066, SO:0001067, SO:0001080, SO:0001083, …
`UniProt:curator_manual`	1	SO:0001077
`UniProt:Curation_manual`	1	SO:0001093

`uniprot`: UniProt Protein

Overall, there were 31 invalid xrefs to external prefixed with uniprot (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
`uniprot:feature_type`	28	SO:0000417, SO:0000418, SO:0000419, SO:0000691, SO:0000725, …
`uniprot:feature`	2	SO:0001655, SO:0100020
`uniprot:curation`	1	SO:0001091

`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:ems`	1	SO:0000274

`xenbase`: Xenbase

Overall, there were 5 invalid xrefs to external prefixed with xenbase (standardized to Bioregistry prefix xenbase) that did not match the standard pattern ^XB\-\w+\-\d+$.

external_xref	usages_count	usages
`xenbase:jb`	5	SO:0001203, SO:0001204, SO:0001205, SO:0001206, SO:0001207

`ZFIN`: Zebrafish Information Network Gene

Overall, there were 6 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:dh`	3	SO:0001477, SO:0001478, SO:0001479
`ZFIN:mh`	2	SO:0001480, SO:0001481
`ZFIN:st`	1	SO:0002217

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oquat

so

DOI: Digital Object Identifier

FB: FlyBase Gene

GO: Gene Ontology

HGNC: HUGO Gene Nomenclature Committee

JAX: Jackson Laboratories Mouse Strain

MGD: Mouse Genome Informatics

MGI: Mouse Genome Informatics

PMC: PubMed Central

PMID: PubMed

PomBase: PomBase

POMBASE: PomBase

RFAM: Rfam database of RNA families

SGD: Saccharomyces Genome Database

SO: Sequence types and features ontology

UniProt: UniProt Protein

uniprot: UniProt Protein

WB: WormBase

xenbase: Xenbase

ZFIN: Zebrafish Information Network Gene