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cthoyt/bioregistry-text-mining-regexes.tsv

Created April 9, 2025 15:54
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Get first round of regexes from Bioregistry for Europe PMC/SIB accession mining support
Raw
bioregistry-text-mining-regexes.tsv
Prefix Resource Name RegEx Example
anzctr Australian New Zealand Clinical Trials Registry ACTRN\d+ ACTRN12623000498695
beetlebase Tribolium Genome Database -- Insertion TC\d+ TC010103
blastrule BlastRule NBR\d+ NBR016799
cellopub Cellosaurus Publication CLPUB\d+ CLPUB00496
chembl ChEMBL CHEMBL\d+ CHEMBL4303805
chembl.cell ChEMBL database of bioactive drug-like small [...] CHEMBL\d+ CHEMBL3307800
chembl.compound ChEMBL CHEMBL\d+ CHEMBL465070
chembl.target ChEMBL target CHEMBL\d+ CHEMBL3467
chempro.competitor ChemPro Competitor LDCM\d+ LDCM0160
chempro.probe ChemPro Probe LDPC\d+ LDPC0032
chempro.target ChemPro Target LDTP\d+ LDTP03903
clingen.allele ClinGen Allele Registry CA\d+ CA981206459
codelink GE Healthcare/Amersham Biosciences CodeLink [...] GE\d+ GE86325
cog Cluster of orthologous genes COG\d+ COG0001
comptox DSSTox substance DTXSID\d+ DTXSID2021028
dbsnp dbSNP Reference SNP number rs\d+ rs121909098
ddinter.drug Curated Drug-Drug Interactions Database - Drug DDInter\d+ DDInter20
dictybase.est dictyBase Expressed Sequence Tag DDB\d+ DDB0016567
drks German Clinical Trials Register DRKS\d+ DRKS00031815
drsc Drosophila RNAi Screening Center DRSC\d+ DRSC05221
drugbank.category DrugBank Drug Category DBCAT\d+ DBCAT000600
drugbank.condition DrugBank Condition DBCOND\d+ DBCOND0066902
drugbank.metabolite DrugBank Metabolite DBMET\d+ DBMET02292
echobase EchoBASE post-genomic database for [...] EB\d+ EB0170
ecmdb E. coli Metabolite Database ECMDB\d+ ECMDB00005
ecogene Database of Escherichia coli Sequence and Function EG\d+ EG10173
foodb.compound FooDB compound FDB\d+ FDB002100
foodb.food FooDB Food FOOD\d+ FOOD00020
fsnp F-SNP rs\d+ rs17852708
genetree GeneTree ENSGT\d+ ENSGT00550000074763
genprop Genome Properties GenProp\d+ GenProp0699
gold.meta GOLD metadata Gm\d+ Gm00047
gpmdb Global Proteome Machine Database GPM\d+ GPM32310002988
gwascentral.marker GWAS Central Marker HGVM\d+ HGVM15354
gwascentral.phenotype GWAS Central Phenotype HGVPM\d+ HGVPM623
gwascentral.study GWAS Central Study HGVST\d+ HGVST1828
hmdb Human Metabolome Database HMDB\d+ HMDB00001
hovergen Homologous Vertebrate Genes Database HBG\d+ HBG004341
ideal Intrinsically Disordered proteins with [...] IID\d+ IID00001
ihw International Histocompatibility Workshop [...] IHW\d+ IHW09326
integbio Integbio nbdc\d+ nbdc01071
isrctn International Traditional Medicine Clinical [...] ISRCTN\d+ ISRCTN10175490
itmctr International Traditional Medicine Clinical [...] ITMCTR\d+ ITMCTR2023000002
jcrb JRBC Cell Bank JCRB\d+ JCRB1355
kcris Korean Clinical Research Information Service KCT\d+ KCT0008394
kegg.dgroup KEGG Drug Group DG\d+ DG00301
kegg.rclass KEGG Reaction Class RC\d+ RC00001
lbctr Lebanon Clinical Trials Registry LBCTR\d+ LBCTR2023015204
massive MassIVE MSV\d+ MSV000082131
metabolights MetaboLights Compound MTBLS\d+ MTBLS1
mgnify.analysis MGnify Analysis MGYA\d+ MGYA00002270
mirnest miRNEST MNEST\d+ MNEST029358
molbic.cellline MolBiC Cell Line CL\d+ CL000025
molbic.compound MolBiC Compound CP\d+ CP0041613
molbic.protein MolBiC Protein PT\d+ PT00819
ncbibook NCBI Bookshelf NBK\d+ NBK331
nif.std NIF Standard Ontology BAMSC\d+ BAMSC981
norine Nonribosomal Peptides Database NOR\d+ NOR00681
npass Natural Product Activity and Species Source [...] NPC\d+ NPC139585
nrfc National Repository of Fish Cell Lines NRFC\d+ NRFC051
pactr Pan African Clinical Trials Registry PACTR\d+ PACTR202304525632216
pdc.study Proteomic Data Commons PDC\d+ PDC000351
pfam.clan Pfam Clans CL\d+ CL0192
pharmgkb.disease PharmGKB Disease PA\d+ PA447218
pharmgkb.drug PharmGKB Drug PA\d+ PA448710
pharmgkb.pathways PharmGKB PA\d+ PA146123006
pharmgkb.variant PharmGKB Variant PA\d+ PA166156302
piroplasma PiroplasmaDB TA\d+ TA14985
ppr Europe PMC Preprints PPR\d+ PPR103739
prodom ProDom PD\d+ PD10000
radlex RSNA Informatics RadLex RID\d+ RID1
rcb RIKEN Bioresource Center Cell Bank RCB\d+ RCB0002
rdbsb Registry and database of bioparts for [...] OENC\d+ OENC205
rpcec Cuban Registry of Clinical Trials RPCEC\d+ RPCEC00000423
rtecs Registry of Toxic Effects of Chemical Substances AB\d+ AB1925000
seed.compound SEED Compound cpd\d+ cpd15380
seed.reaction SEED Reactions rxn\d+ rxn00001
skip Stemcell Knowledge and Information Portal SKIP\d+ SKIP001214
smpdb Small Molecule Pathway Database SMP\d+ SMP0000219
subtilist Bacillus subtilis genome sequencing project BG\d+ BG11523
synbip.bts Synthetic Binding Proteins Binding Target st\d+ st00576
synbip.epitope Synthetic Binding Protein Epitope mt\d+ mt002305
synbip.pss Synthetic Binding Protein Protein Scaffold ps\d+ ps048
synbip.sbp Synthetic Binding Protein sbp\d+ sbp000002
tctr Thai Clinical Trials Registry TCTR\d+ TCTR20230429001
tigrfam TIGR protein families TIGR\d+ TIGR00010
tsc Tetrahymena Stock Center SD\d+ SD00043
ttd.drug TTD Drug DAP\d+ DAP000773
ttd.target TTD Target TTDS\d+ TTDS00056
umbbd.rule EAWAG Biocatalysis/Biodegradation Database bt\d+ bt0001
uniprot.arba Association-Rule-Based Annotator ARBA\d+ ARBA00000001
virsirna VIRsiRNA virsi\d+ virsi1909
wwf.ecoregion World Wildlife Fund Ecoregion AT\d+ AT1402
ymdb Yeast Metabolome Database YMDB\d+ YMDB00001
Raw
get-bioregistry-text-mining-regexes.py
import bioregistry
from tabulate import tabulate
import click
from textwrap import shorten
import pandas as pd
def main():
rows = []
for resource in bioregistry.resources():
pattern = resource.get_pattern()
if pattern is None:
continue
stripped = pattern.removeprefix("^").removesuffix("$")
if not stripped.endswith("\\d+"):
continue
if stripped == "\\d+":
continue
sstripped = stripped.removesuffix("\\d+")
if len(sstripped) == 1 or sstripped == "\\w" or not sstripped.isalpha():
continue
rows.append((
resource.prefix,
shorten(resource.get_name(), 50),
stripped,
resource.get_example()
))
df = pd.DataFrame(rows, columns=['Prefix', 'Resource Name', "RegEx", "Example"])
print(df.to_markdown(index=False))
df.to_csv("bioregistry-text-mining-regexes.tsv", index=False, sep='\t')
if __name__ == '__main__':
main()
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