Warnings
This lists any sorts of things that should be fixed upstream, but are instead manually curated in the Bioregistry.
License Conflicts
The following chart shows which manual annotations in the OBO Foundry are inconsistent with those extracted by the OLS.
| Prefix | OBO License | OLS License |
|---|
MIRIAM
The following issues are with the integrity of the data in the MIRIAM registry ( identifiers.org).
Incorrect Pattern
The following entries have an incorrect value in the pattern field.
| Prefix | Name | MIRIAM | Correct |
|---|---|---|---|
ark |
Archival Resource Key | ^(ark\:)/*[0-9A-Za-z]+(?:/[\w/.=*+@\$-]*)?(?:\?.*)?$ |
^/*[0-9A-Za-z]+(?:/[\w/.=*+@\$-]*)?(?:\?.*)?$ |
atcc |
American Type Culture Collection | ^\d+$ |
^([a-zA-Z]+-)?\d+(\.\d)?$ |
bigg.compartment |
BiGG Compartment | ^[a-z_A-Z]+$ |
^c|cm|cx|e|f|g|h|i|im|l|m|mm|n|p|r|s|u|um|v|w|x|y$ |
bigg.metabolite |
BiGG Metabolite | ^[a-z_A-Z0-9]+$ |
^[a-z_A-Z0-9]+(\[[c|cm|cx|e|f|g|h|i|im|l|m|mm|n|p|r|s|u|um|v|w|x|y]\])?$ |
biodeep |
BioDeep Database | ^BioDeep_\d{11}$ |
^\d{11}$ |
biofactoid |
Biofactoid | ^[0-9a-f]{8}-[0-9a-f]{4}-[1-5][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}$ |
^[0-9a-fA-F]{8}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{4}\-[0-9a-fA-F]{12}$ |
biomodels.kisao |
Kinetic Simulation Algorithm Ontology | ^KISAO_\d+$ |
^\d+$ |
biomodels.teddy |
Terminology for Description of Dynamics | ^TEDDY_\d{7}$ |
^\d+$ |
bioportal |
BioPortal | ^\d+$ |
^(\d+)|(\w+)$ |
bto |
BRENDA Tissue Ontology | ^BTO:\d{7}$ |
^\d{7}$ |
ccds |
Consensus CDS | ^CCDS\d+\.\d+$ |
^CCDS\d+(\.\d+)?$ |
cco |
Cell Cycle Ontology | ^CCO:\w+$ |
^\w+$ |
cellosaurus |
Cellosaurus | ^CVCL_[A-Z0-9]{4}(\.txt)?$ |
^[A-Z0-9]{4}$ |
chebi |
Chemical Entities of Biological Interest | ^CHEBI:\d+$ |
^\d+$ |
cheminf |
Chemical Information Ontology | ^CHEMINF:\d+$ |
^\d{6}$ |
cl |
Cell Ontology | ^CL:\d{7}$ |
^\d{7}$ |
classyfire |
ClassyFire | ^C[0-9]{7}$ |
^\d{7}$ |
cog |
Cluster of orthologous genes | ^COG[0-9]+$ |
^COG\d+$ |
cosmic |
COSMIC Gene | ^[A-Z0-9]+$ |
^[A-Z0-9][A-Z0-9-]*$ |
did |
Decentralized Identifier | ^did:[a-z0-9]+:[A-Za-z0-9.\-:]+$ |
^[a-z0-9]+:[A-Za-z0-9.\-:]+$ |
doi |
Digital Object Identifier | ^(doi\:)?10\.\d+/.*$ |
^10.\d{2,9}/.*$ |
doid |
Human Disease Ontology | ^DOID:\d+$ |
^\d+$ |
drugcentral |
Drug Central | ^[0-9]+$ |
^\d+$ |
eccode |
Enzyme Commission Code | ^\d+\.-\.-\.-|\d+\.\d+\.-\.-|\d+\.\d+\.\d+\.-|\d+\.\d+\.\d+\.(n)?\d+$ |
^\d{1,2}(((\.\d{1,3}){1,3})|(\.\d+){2}\.[nB]\d{1,3})?$ |
eco |
Evidence and Conclusion Ontology | ECO:\d{7}$ |
^\d{7}$ |
empiar |
Electron Microscopy Public Image Archive | EMPIAR-\d{5,} |
^\d+$ |
envo |
Environment Ontology | ^ENVO:\d{7,8}$ |
^\d{7,8}$ |
eo |
Plant Environment Ontology | ^(P)?EO\:\d{7}$ |
^\d{7}$ |
fairsharing |
FAIRsharing | ^bsg-[dscp]?\d{6}$ |
^(bsg-[dscp]?\d{6})|(FAIRsharing\.\w+)$ |
fma |
Foundational Model of Anatomy | ^FMA:\d+$ |
^\d+$ |
foodon |
The Food Ontology | ^FOODON:[0-9]{8}$ |
^[0-9]{8}$ |
geogeo |
Geographical Entity Ontology | ^GEO_[0-9]{9}$ |
^\d{9}$ |
github |
GitHub username | ^[a-zA-Z0-9-_]+/[a-zA-Z0-9-_]+$ |
^[a-zA-Z0-9-_]+(/[a-zA-Z0-9-_]+)?$ |
gitlab |
GitLab | ^[0-9A-Za-z_][0-9A-Za-z-_()\. ]*/[0-9A-Za-z_][0-9A-Za-z-_\. ]*$ |
^.*/.*$ |
glyconavi |
GlycoNAVI | ^GN_[A-Za-z]*[_]*[A-Za-z0-9-:_]+$ |
^GN_[A-Za-z0-9_:]+$ |
go |
Gene Ontology | ^GO:\d{7}$ |
^\d{7}$ |
go.ref |
Gene Ontology Database references | ^GO_REF:\d{7}$ |
^\d{7}$ |
google.patent |
Google Patents | ^[A-Z]{2}\d+([A-Z])?$ |
^[A-Z]{2,4}\d+([A-Z])?([0-9])?$ |
gramene.growthstage |
Gramene Growth Stage Ontology | ^GRO:\d+$ |
^\d{7}$ |
gramene.taxonomy |
Gramene Taxonomy | ^GR\_tax\:\d+$ |
^\d+$ |
gsso |
Gender, Sex, and Sexual Orientation Ontology | ^GSSO:\d{6}$ |
^\d{6}$ |
hgnc |
HUGO Gene Nomenclature Committee | ^((HGNC|hgnc):)?\d{1,5}$ |
^\d{1,5}$ |
hp |
Human Phenotype Ontology | ^HP:\d{7}$ |
^\d{7}$ |
icd10 |
International Classification of Diseases, 10th Revision | ^[A-Z]\d+(\.[-\d+])?$ |
^(([XVI]+)|([A-Z][0-9]+((-[A-Z][0-9]+)|(\.[0-9]))?))$ |
ido |
Infectious Disease Ontology | ^[0-9]+$ |
^\d{7}$ |
iedb.reference |
Immune Epitope Database References | ^[0-9]+$ |
^\d+$ |
imex |
International Molecular Exchange | ^IM-\d+(-?)(\d+?)$ |
^\d+(-\d+)?$ |
ito |
Intelligence Task Ontology | ^.+$ |
^\d+$ |
lincs.cell |
LINCS Cell | (^LCL-\d+$)|(^LDC-\d+$)|(^ES-\d+$)|(^LSC-\d+$)|(^LPC-\d+$) |
^(LCL|LDC|ES|LSC|LPC)-\d+$ |
lrg |
Locus Reference Genomic | ^LRG_\d+$ |
^\d+$ |
ma |
Mouse adult gross anatomy | ^MA:\d+$ |
^\d+$ |
mamo |
Mathematical modeling ontology | ^MAMO_\d{7}$ |
^\d{7}$ |
maxo |
Medical Action Ontology | \d{7} |
^\d{7}$ |
mcro |
Model Card Report Ontology | ^MCRO:\d+$ |
^\d{7}$ |
mediadive.medium |
MediaDive Medium | ^[A-Z]?[0-9]{1,5}[a-z]?$ |
^\d+\w?$ |
merops.entry |
MEROPS Entry | ^I\d{2}\.\d{3}$ |
^[SCTAGMNUIX]{1,2}\d{2}\.([AB]\d{2}|\d{3})$ |
metatlas |
Metabolic Atlas | ^MA[MR]\d{5}[a-z]?$ |
^(MAM\d{5}\w)|(MAR\d{5})$ |
mge |
Aclame | ^mge:\d+$ |
^\d+$ |
mgi |
Mouse Genome Informatics | ^MGI:\d+$ |
^\d+$ |
mi |
Molecular Interactions Controlled Vocabulary | ^MI:\d{4}$ |
^\d{4}$ |
mint |
Molecular Interaction Database | ^MINT\-\d{1,7}$ |
^\d{1,7}$ |
mir |
Identifiers.org Registry | ^MIR:\d{8}$ |
^\d{8}$ |
miriam |
Identifiers.org namespace | ^[a-z_\.]+$ |
^[0-9a-z_:\.-]+$ |
miriam.collection |
MIRIAM Registry collection | ^MIR:000\d{5}$ |
^000\d{5}$ |
miriam.resource |
MIRIAM Legacy Registry Identifier | ^MIR:001\d{5}$ |
^001\d{5}$ |
mod |
Protein modification | ^MOD:\d{5} |
^\d{5}$ |
mp |
Mammalian Phenotype Ontology | ^MP:\d{7}$ |
^\d{7}$ |
ms |
Mass spectrometry ontology | ^MS:\d{7}$ |
^\d{7}$ |
mzspec |
Universal Spectrum Identifier | ^mzspec:(PDX|USI|PXD)[0-9]{6}:[^:]+:(scan|index|nativeId):[0-9]+(:.*)?$ |
^.+$ |
nando |
Nanbyo Disease Ontology | ^NANDO:[0-9]+$ |
^\d+$ |
neurolex |
NIF Standard Ontology: Neurolex | ^([Bb]irnlex_|Sao|nlx_|GO_|CogPO|HDO|nifext_)\d+$ |
^\d+$ |
nmdc |
National Microbiome Data Collaborative | ^[A-Za-z0-9._~\-\:]+$ |
^.{2,}$ |
nmr |
NMR-instrument specific component of metabolomics investigations | ^NMR:\d+$ |
^\d+$ |
obcs |
Ontology of Biological and Clinical Statistics | ^OBCS:\d+$ |
^\d{7}$ |
obi |
Ontology for Biomedical Investigations | (^OBI:\d{7}$)|(^OBI_\d{7}$) |
^\d{7}$ |
ocid |
Ontology Concept Identifiers | ocid:[0-9]{12} |
^[0-9]{12}$ |
oma.hog |
OMA HOGs | ^HOG:[0-9]{7}(\.[0-9a-z.]+)?(_[0-9]+)?$ |
^[0-9]{7}(\.[0-9a-z.]+)?(_[0-9]+)?$ |
omia |
Online Mendelian Inheritance in Animals | ^\d+$ |
^\d{6}(-\d+)?$ |
omim |
Online Mendelian Inheritance in Man | ^[*#+%^]?\d{6}$ |
^\d+$ |
opb |
Ontology of Physics for Biology | ^OPB_\d+$ |
^\d+$ |
opl |
Ontology for Parasite LifeCycle | ^OPL:\d+$ |
^\d{7}$ |
orphanet.ordo |
Orphanet Rare Disease Ontology | ^Orphanet(_|:)C?\d+$ |
^C?\d+$ |
panther.pthcmp |
PANTHER Pathway Component | ^[GPUCS]\d{5}$ |
^(G|P|U|C|S)\d{5}$ |
pato |
Phenotype And Trait Ontology | ^PATO:\d{7}$ |
^\d{7}$ |
pid.pathway |
NCI Pathway Interaction Database: Pathway | ^\w+$ |
^\b[0-9a-f]{8}\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\b[0-9a-f]{12}\b$ |
pmc |
PubMed Central | PMC\d+ |
^PMC\d+(\.\d+)?$ |
po |
Plant Ontology | ^PO:\d+$ |
^\d+$ |
pr |
Protein Ontology | ^PR:P?\d+$ |
^(?:\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+)?)$ |
pride |
PRIDE Controlled Vocabulary | ^\d+$ |
^\d{7}$ |
probonto |
Probability Distribution Ontology | ^PROB_c\d+$ |
^(c|k)\d{7}$ |
psipar |
Protein Affinity Reagents | ^PAR:\d+$ |
^\d+$ |
pw |
Pathway ontology | ^PW:\d{7}$ |
^\d{7}$ |
reactome |
Reactome | (^R-[A-Z]{3}-\d+(-\d+)?(\.\d+)?$)|(^REACT_\d+(\.\d+)?$) |
^R-[A-Z]{3}-\d+(-\d+)?(\.\d+)?$ |
refseq |
Reference Sequence Collection | ^(((WP|AC|AP|NC|NG|NM|NP|NR|NT|NW|XM|XP|XR|YP|ZP)_\d+)|(NZ\_[A-Z]{2,4}\d+))(\.\d+)?$ |
^(((AC|AP|NC|NG|NM|NP|NR|NT|NW|WP|XM|XP|XR|YP|ZP)_\d+)|(NZ_[A-Z]{2,4}\d+))(\.\d+)?$ |
ro |
Relation Ontology | ^RO_\d{7}$ |
^(HOM)?\d{7}$ |
rrid |
Research Resource Identification | ^RRID:[a-zA-Z]+.+$ |
^[a-zA-Z]+.+$ |
sbo |
Systems Biology Ontology | ^SBO:\d{7}$ |
^\d{7}$ |
sio |
Semanticscience Integrated Ontology | ^SIO_\d{6,6}$ |
^\d{6}$ |
slm |
SwissLipid | ^SLM:\d+$ |
^\d+$ |
so |
Sequence types and features ontology | ^SO:\d{7}$ |
^\d{7}$ |
stato |
The Statistical Methods Ontology | ^STATO:\d+$ |
^\d{7}$ |
storedb |
Store DB | ^STOREDB:(STUDY|FILE|DATASET)\d+$ |
^(STUDY|FILE|DATASET)\d+$ |
swh |
Software Heritage | ^swh:[1-9]:(cnt|dir|rel|rev|snp):[0-9a-f]+(;(origin|visit|anchor|path|lines)=\S+)*$ |
^[1-9]:(cnt|dir|rel|rev|snp):[0-9a-f]+(;(origin|visit|anchor|path|lines)=\S+)*$ |
tair.gene |
TAIR Gene | ^Gene:\d{7}$ |
^\d{7}$ |
tair.locus |
The Arabidopsis Information Resource | ^\d{7}$ |
^\d+$ |
tair.protein |
TAIR Protein | ^AASequence:\d{10}$ |
^\d{10}$ |
uberon |
Uber Anatomy Ontology | ^UBERON:\d+$ |
^\d+$ |
uo |
Units of measurement ontology | ^UO:\d{7}? |
^\d{7}$ |
uspto |
United States Patent and Trademark Office | ^(D|PP|R|T|H|X|AI)?\d+$ |
^(\d{1,2},?\d{3},?\d{3}|(PP|RE|AI|RX)\d{2},?\d{3}|(D|T|H|X)\d{3},?\d{3})$ |
vario |
Variation Ontology | ^VariO:\d+$ |
^\d+$ |
vgnc |
Vertebrate Gene Nomenclature Committee | ^((VGNC|vgnc):)?\d{1,9}$ |
^\d{1,9}$ |
wikidata |
Wikidata | ^(Q|P)\d+$ |
^(Q|P|E)\d+$ |
wikipedia.en |
Wikipedia | ^[A-Za-z-0-9_]+$ |
^\S+$ |
wormbase |
WormBase | ^WB[A-Z][a-z]+\d+$ |
^(CE[0-9]{5}|WB[A-Z][a-z]+\d+)$ |
Embedding of Namespace in LUI
The following entries have an incorrect value in the namespaceEmbeddedInLui
field.
| Prefix | Name | Pattern | MIRIAM | Correct |
|---|
Prefix Mismatch when Namespace Embedded in LUI
When the namespace is embedded in the LUI, it’s expected that the prefix should be uppercased. This is often not the case.
| Prefix | Name | Pattern | Correct Prefix |
|---|