RTXteam / RTX-KG2

Build system for the RTX-KG2 biomedical knowledge graph, part of the ARAX reasoning system (https://github.com/RTXTeam/RTX)
MIT License
38 stars 8 forks source link

Orphanet Curie Prefix Should Be Lowercase #400

Closed ecwood closed 2 months ago

ecwood commented 4 months ago

From Amy:

Question for the KG2pre team: I noticed that in KG2pre (e.g., KG2.10.0pre), the ORPHANET prefix is uppercase, but in the SRI NodeNormalizer, it appears to be lowercase (i.e., orphanet - see: https://nodenormalization-sri.renci.org/get_normalized_nodes?curie=ORPHANET:220493). Do we know if we’re right to use uppercase?

This appears to be the case in Biolink as well: https://github.com/biolink/biolink-model/blob/master/biolink-model.yaml#L111

ecwood commented 2 months ago

Running

match (n) where n.provided_by contains "infores:ordo" return n.id, n.name limit 50

on KG2.10.1pre returns

n.id n.name
"OBO:ordo.owl" "ORPHANET Rare Disease Ontology v4.3"
"orphanet:88630" "Terminal osseous dysplasia - pigmentary defects"
"orphanet:88632" "Familial ocular anterior segment mesenchymal dysgenesis"
"orphanet:88635" "Vacuolar myopathy with sarcoplasmic reticulum protein aggregates"
"orphanet:88637" "Hypomyelination - hypogonadotropic hypogonadism - hypodontia"
"orphanet:88639" "Neurodegeneration due to 3-hydroxyisobutyryl-CoA hydrolase deficiency"
"orphanet:88642" "Channelopathy-associated congenital insensitivity to pain"
"orphanet:88643" "Obesity - colitis - hypothyroidism - cardiac hypertrophy - developmental delay"
"orphanet:88644" "Autosomal recessive ataxia, Beauce type"
"orphanet:88659" "Autosomal dominant progressive nephropathy with hypertension"
"orphanet:88660" "Hypertension due to gain-of-function mutations in the mineralocorticoid receptor"
"orphanet:88661" "Amelogenesis imperfecta"
"orphanet:887" "VACTERL/VATER association"
"orphanet:888" "Van der Woude syndrome"
"orphanet:88917" "X-linked Alport syndrome"
"orphanet:88918" "Autosomal dominant Alport syndrome"
"orphanet:88919" "Autosomal recessive Alport syndrome"
"orphanet:88924" "Autosomal dominant polycystic kidney disease type 1 with tuberous sclerosis"
"orphanet:88938" "Pseudohypoaldosteronism type 2A"
"orphanet:88939" "Pseudohypoaldosteronism type 2B"
"orphanet:88940" "Pseudohypoaldosteronism type 2C"
"orphanet:88949" "MUC1-related autosomal dominant tubulointerstitial kidney disease"
"orphanet:88950" "Autosomal dominant medullary cystic kidney disease with hyperuricemia"
"orphanet:88993" "Esophageal malformation"
"orphanet:891" "Familial exudative vitreoretinopathy"
"orphanet:892" "Von Hippel-Lindau disease"
"orphanet:893" "WAGR syndrome"
"orphanet:894" "Waardenburg syndrome type 1"
"orphanet:895" "Waardenburg syndrome type 2"
"orphanet:896" "Waardenburg syndrome type 3"
"orphanet:897" "Waardenburg-Shah syndrome"
"orphanet:898" "Wagner disease"
"orphanet:89838" "KRT14-related epidermolysis bullosa simplex"
"orphanet:401874" "Fatal multiple mitochondrial dysfunction syndrome type 2"
"orphanet:401901" "Huntington disease-like syndrome due to C9ORF72 expansions"
"orphanet:401911" "AXIN2-related attenuated familial adenomatous polyposis"
"orphanet:401923" "9q31.1q31.3 microdeletion syndrome"
"orphanet:401935" "14q24.1q24.3 microdeletion syndrome"
"orphanet:401942" "Familial median cleft of the upper and lower lips"
"orphanet:401945" "Moyamoya disease with early-onset achalasia"
"orphanet:401948" "Hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency"
"orphanet:401953" "Episodic ataxia with slurred speech"
"orphanet:401959" "Partial corpus callosum agenesis-cerebellar vermis hypoplasia with posterior fossa cysts syndrome"
"orphanet:401964" "Autosomal dominant Charcot-Marie-Tooth disease type 2 with giant axons"
"orphanet:401973" "MEND syndrome"
"orphanet:401979" "Autosomal recessive spondylometaphyseal dysplasia, Mégarbané type"
"orphanet:401986" "1p31p32 microdeletion syndrome"
"orphanet:401993" "Cold-induced sweating syndrome-hyperthermia spectrum"
"orphanet:401996" "Karyomegalic interstitial nephritis"
"orphanet:402003" "Autosomal dominant focal non-epidermolytic palmoplantar keratoderma with plantar blistering"

which confirms this fix. Closing this issue