obophenotype / obophenotype/uberon

Deconvolute non-standard prefixes

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Description

The following prefixes show up in various places in UBERON but they are not in the Bioregistry, based on the OQUAT analysis in https://biopragmatics.github.io/oquat/unknowns/source/uberon and https://biopragmatics.github.io/oquat/invalids/source/uberon:

prefix count example_node example_val
OBOL 3401 http://purl.obolibrary.org/obo/UBERON_0000031 OBOL:automatic
GAID 814 http://purl.obolibrary.org/obo/UBERON_0000002 GAID:376
PHENOSCAPE 281 http://purl.obolibrary.org/obo/UBERON_4200008 PHENOSCAPE:wd
BM 246 http://purl.obolibrary.org/obo/UBERON_0000007 BM:Die-Hy-HY
FBC 121 http://purl.obolibrary.org/obo/UBERON_0000122 FBC:DOS
UBERONTEMP 105 http://purl.obolibrary.org/obo/UBERON_0016929 UBERONTEMP:0ea3066e-0c22-417b-8ac4-91c2aacba792
GOC 70 http://purl.obolibrary.org/obo/UBERON_0000017 GOC:GO
ABA 62 http://purl.obolibrary.org/obo/UBERON_0000955 ABA:Brain
UBERONREF 45 http://purl.obolibrary.org/obo/UBERON_0000075 UBERONREF:0000003
MURDOCH 38 http://purl.obolibrary.org/obo/UBERON_0011472 MURDOCH:2183
WikipediaVersioned 31 http://purl.obolibrary.org/obo/UBERON_8410000 WikipediaVersioned:Duodenojejunal_flexure&oldid=937307798
BSA 26 http://purl.obolibrary.org/obo/UBERON_0000020 BSA:0000121
FEED 20 http://purl.obolibrary.org/obo/UBERON_0001572 FEED:rd
Dorlands_Medical_Dictionary 16 http://purl.obolibrary.org/obo/UBERON_0000313 Dorlands_Medical_Dictionary:MerckSource
ANISEED 13 http://purl.obolibrary.org/obo/UBERON_0000160 ANISEED:1235303
OGES 13 http://purl.obolibrary.org/obo/UBERON_0000068 OGES:000022
NominaAnatomicaVeterinaria 12 http://purl.obolibrary.org/obo/UBERON_0001451 NominaAnatomicaVeterinaria:2005
LG 11 http://purl.obolibrary.org/obo/UBERON_0004889 LG:0012616
OldNeuroNames 9 http://purl.obolibrary.org/obo/UBERON_0002575 OldNeuroNames:-1761421113
BILS 9 http://purl.obolibrary.org/obo/UBERON_0000105 BILS:0000105
BilaDO 9 http://purl.obolibrary.org/obo/UBERON_0000066 BilaDO:0000004
BRAINSPAN 8 http://purl.obolibrary.org/obo/UBERON_0014736 BRAINSPAN:BRAINSPAN
NIFSTD_RETIRED 8 http://purl.obolibrary.org/obo/UBERON_0000966 NIFSTD_RETIRED:birnlex_1156
Geisha 7 http://purl.obolibrary.org/obo/UBERON_0003052 Geisha:syn
WikipediaCategory 7 http://purl.obolibrary.org/obo/UBERON_0000474 WikipediaCategory:Female_reproductive_system
XtroDO 7 http://purl.obolibrary.org/obo/UBERON_0000066 XtroDO:0000084
Bgee 5 http://purl.obolibrary.org/obo/UBERON_0018241 Bgee:AN
XB 5 http://purl.obolibrary.org/obo/UBERON_0003056 XB:curator
NeuroNamesCNID 5 http://purl.obolibrary.org/obo/UBERON_0015510 NeuroNamesCNID:177
BrainInfo 4 http://purl.obolibrary.org/obo/UBERON_8440010 BrainInfo:2102
NIF 4 http://purl.obolibrary.org/obo/UBERON_0009630 NIF:NIF
DHB 3 http://purl.obolibrary.org/obo/UBERON_0002739 DHB:MD
J 3 http://purl.obolibrary.org/obo/UBERON_0002233 J:77634
PhenoscapeRCN 3 http://purl.obolibrary.org/obo/UBERON_0012260 PhenoscapeRCN:Oct2012
CUMBO 2 http://purl.obolibrary.org/obo/UBERON_0001020 CUMBO:CUMBO
INCF 2 http://purl.obolibrary.org/obo/UBERON_0001880 INCF:Seattle_mtg_2010
MorphoBank 2 http://purl.obolibrary.org/obo/UBERON_0013614 MorphoBank:177
NominaAnatomica 2 http://purl.obolibrary.org/obo/UBERON_0010356 NominaAnatomica:NA
Obol 2 http://purl.obolibrary.org/obo/UBERON_0003281 Obol:obol
PAPUB 2 http://purl.obolibrary.org/obo/UBERON_2001162 PAPUB:0000142
Phenoscape 2 http://purl.obolibrary.org/obo/UBERON_4000164 Phenoscape:PM
Swanson 2 http://purl.obolibrary.org/obo/UBERON_0001893 Swanson:2004
NIF_Organism 2 http://purl.obolibrary.org/obo/UBERON_0007221 NIF_Organism:birnlex_695
NOID 2 http://purl.obolibrary.org/obo/UBERON_0018367 NOID:1
OGEM 2 http://purl.obolibrary.org/obo/UBERON_0000307 OGEM:000006
BioMart 1 http://purl.obolibrary.org/obo/UBERON_0000363 BioMart:BioMart
CHECKME 1 http://purl.obolibrary.org/obo/UBERON_0003997 CHECKME:CHECKME
Giesha 1 http://purl.obolibrary.org/obo/UBERON_0005421 Giesha:syn
Hymans 1 http://purl.obolibrary.org/obo/UBERON_0010260 Hymans:Hymans
MTB 1 http://purl.obolibrary.org/obo/UBERON_0002145 MTB:379
AOO 1 http://purl.obolibrary.org/obo/UBERON_3000406 AOO:LAP
ASD 1 http://purl.obolibrary.org/obo/UBERON_3010449 ASD:BJB
Fast_Health_Medical_Dictionary 1 http://purl.obolibrary.org/obo/UBERON_0008230 Fast_Health_Medical_Dictionary:http://www.fasthealth.com/dictionary/
NCBI 1 http://purl.obolibrary.org/obo/UBERON_0001471 NCBI:matt
OMD 1 http://purl.obolibrary.org/obo/UBERON_0003075 OMD:neural+plate
PATOC 1 http://purl.obolibrary.org/obo/UBERON_0005160 PATOC:MAH
PLB 1 http://purl.obolibrary.org/obo/UBERON_0013730 PLB:plb
Renal_Physiology 1 http://purl.obolibrary.org/obo/UBERON_0008404 Renal_Physiology:Section_7
WA 1 http://purl.obolibrary.org/obo/UBERON_0003049 WA:dh
Wiktionary 1 http://purl.obolibrary.org/obo/UBERON_7500117 Wiktionary:opisthocranion
bgee 1 http://purl.obolibrary.org/obo/UBERON_0036219 bgee:ANN
ref 1 http://purl.obolibrary.org/obo/UBERON_0004870 ref:Stedmans
DrerDO 1 http://purl.obolibrary.org/obo/UBERON_0004707 DrerDO:0000052
MAP 1 http://purl.obolibrary.org/obo/UBERON_0001155 MAP:0000001
TA2 1 http://purl.obolibrary.org/obo/UBERON_8410000 TA2:2952
Talairach 1 http://purl.obolibrary.org/obo/UBERON_0035933 Talairach:1047

Generated by the following code:

from tabulate import tabulate
from collections import Counter

import requests


def main():
    url = "https://raw.githubusercontent.com/biopragmatics/oquat/main/results/uberon.json"
    data = requests.get(url).json()

    counter = Counter()
    examples = {}
    for data in data["results"].values():
        for key in ["synonym_pack", "prov_pack", "xref_pack"]:
            for prefix, uri_to_value_dict in data[key]["unknown_prefixes"].items():
                counter[prefix] += len(uri_to_value_dict)
                examples[prefix] = list(uri_to_value_dict.items())[0]

    rows = [(prefix, count, *examples[prefix]) for prefix, count in counter.most_common()]

    print(
        tabulate(
            rows, headers=["prefix", "count", "example_node", "example_val"], tablefmt="github"
        )
    )


if __name__ == "__main__":
    main()

Any help figuring out what these are and how they're used would be appreciated!

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