something strange with the UMLS Identifier dimethyl sulfoxide UMLS:DC0012403

[sstemann]

I'm not sure if this is a BTE issue or not but when I run the query, MVP1 What may treat Bethlem Myopathy, i get dimethyl sulfoxide twice, in in the UI

https://ui.test.transltr.io/main/results?l=Bethlem%20Myopathy&i=MONDO:0008029&t=0&r=0&q=a04bff0e-1b72-494c-ae67-6f1fbc7aa66e

Both say BTE

In the ARAX GUI > BTE > Result 40 shows dimethyl sulfoxide with CURIE UMLS:DC0012403, which I cannot find in the UMLS Metathesaurus

If I drop the D and search for UMLS:C0012403, I get dimethyl sulfoxide

Result 94 is CHEBI:28262 which seems normal

I'm sending to BTE first, I'm not sure if its really an NN issue given the CURIE looks non-existent

[andrewsu]

This partly has to do with us ingesting SuppKG, a resource that links dietary supplements to diseases. More details can be found in biothings/pending.api#55 and biothings/biothings_explorer#706, but the TLDR is that the resource invented these UMLS-like identifiers in cases where they didn't find a suitable UMLS identifier that already existed. We (internally) discussed the issue when we brought SuppKG on board and decided to just move forward since these are a relatively small proportion of suppKG as a whole, but we are certainly open to revisiting...

There is also something strange with the lack of EPC here, related to #831. We'll be looking into that one as well...

[sstemann]

in this Bethlem Myopathy query it looks like there's ~44 results with identifiers "UMLS:DC#######". On the plus side, these arent returned on the first page, but they are getting a sugeno .46 (0-1). On the other hand, some do have real CURIEs (Hawthorn Plant in UMLS is C1527346, Earthworms are C0086194). It seems odd to return results that do not have valid CURIES.

subjectNode_name	subjectNode_id
hawthorn	UMLS:DC1621401
earthworm	UMLS:DC1621389
4-hydroxyphenyl	UMLS:DC0912024
2-phenyl-benzopyrans	UMLS:DC0596577
ch'ih shen	UMLS:DC0377336
bac ngu vi tu	UMLS:DC0141729
bingpian	UMLS:DC0106916
apple polyphenol extract	UMLS:DC0071649
novasoy phytoestrogen extract	UMLS:DC0071011
2-hydroxy-4-methoxyacetophenone	UMLS:DC0069939
heparinoid	UMLS:DC0066923
acetate de d-alpha tocopheryle	UMLS:DC0042874
& vitamin palmitate	UMLS:DC0042839
n-octadecanoic acid	UMLS:DC0038229
atomic number 11	UMLS:DC0037473
5-alpha-furost-20-en-12-one-3 beta, 26-diol	UMLS:DC0036189
beta-d-ribofuranose	UMLS:DC0035549
b-2	UMLS:DC0035527
root	UMLS:DC0035509
epoprostanol	UMLS:DC0033567
fibersol-2	UMLS:DC0032594
24-beta-ethyl-delta-5-cholesten-3beta-ol	UMLS:DC0031866
activator	UMLS:DC0031610
flaxseed	UMLS:DC0023753
hesperidin methyl chalcone	UMLS:DC0019392
root	UMLS:DC0017987
bilberry fruit	UMLS:DC0016767
5-mthf	UMLS:DC0016410
1,200 mg	UMLS:DC0016157
additional omega-3 essential fatty acids	UMLS:DC0015689
acides gras cetylated	UMLS:DC0015684
eugenol	UMLS:DC0015153
acide docosahexaenoique	UMLS:DC0012968
dimethyl sulfoxide	UMLS:DC0012403
fiber	UMLS:DC0012173
bill henderson protocol	UMLS:DC0012155
beta-sitosterol-beta-d-glycoside	UMLS:DC0007158
acide butyrique	UMLS:DC0006523
berberina	UMLS:DC0005117
acide l-ascorbique, 6-palmitate	UMLS:DC0003968
anthocyanin	UMLS:DC0003161
alkaloid, nos	UMLS:DC0002062
acide gras essentiel	UMLS:DC0000545

[andrewsu]

Currently being evaluated by the chem-info group (slack link). tagging @vdancik to update feasibility/ideas when they have a chance to review...