Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Consider adding UMLS hasDbXrefs #16

Open
ndobb opened this issue Aug 17, 2023 · 6 comments
Open

Consider adding UMLS hasDbXrefs #16

ndobb opened this issue Aug 17, 2023 · 6 comments

Comments

@ndobb
Copy link

ndobb commented Aug 17, 2023 •
edited

Hello,

I utilized the SO for a recent project and needed to link various symptom entries to corresponding UMLS concepts. For quite a few, I noticed there were no UMLS DbXref values, so I ran their label values through MetaMapLite, then manually reviewed to make sure the UMLS concepts made sense and filtered for appropriate semantic types.

If these UMLS mappings would be of any value to the research community, please consider adding them.

SYMP_0000002 - abdominal distention
UMLS_CUI:C0000731

SYMP_0000005 - ataxia
UMLS_CUI:C0007758

SYMP_0000006 - backache
UMLS_CUI:C0004604

SYMP_0000007 - bleeding
UMLS_CUI:C0019080

SYMP_0000009 - blister
UMLS_CUI:C1579830

SYMP_0000016 - confusion
UMLS_CUI:C0009676

SYMP_0000020 - dehydration
UMLS_CUI:C0011175

SYMP_0000021 - delirium
UMLS_CUI:C0011206

SYMP_0000022 - depression
UMLS_CUI:C0011581

SYMP_0000023 - disorientation
UMLS_CUI:C0233407

SYMP_0000024 - drowsiness
UMLS_CUI:C0013144

SYMP_0000025 - dry cough
UMLS_CUI:C0850149

SYMP_0000030 - paralysis
UMLS_CUI:C0522224

SYMP_0000032 - flaccidity
UMLS_CUI:C0026825

SYMP_0000040 - hematuria
UMLS_CUI:C0018965

SYMP_0000041 - hemorrhage
UMLS_CUI:C0019080

SYMP_0000046 - hepatitis
UMLS_CUI:C0019158

SYMP_0000047 - hepatosplenomegaly
UMLS_CUI:C0019214

SYMP_0000054 - hypergammaglobulinemia
UMLS_CUI:C0020455

SYMP_0000058 - hyperreflexia
UMLS_CUI:C0151889

SYMP_0000059 - hypotension
UMLS_CUI:C0020649

SYMP_0000064 - joint pain
UMLS_CUI:C0003862

SYMP_0000075 - lethargy
UMLS_CUI:C0023380

SYMP_0000083 - lymphangitis
UMLS_CUI:C0024225

SYMP_0000086 - lymphopenia
UMLS_CUI:C0024312

SYMP_0000092 - skin lesion
UMLS_CUI:C0037284

SYMP_0000093 - muscle cramp
UMLS_CUI:C0026821

SYMP_0000094 - muscle weakness
UMLS_CUI:C0151786

SYMP_0000095 - myocarditis
UMLS_CUI:C0027059

SYMP_0000098 - nephritis
UMLS_CUI:C0027697

SYMP_0000099 - pain
UMLS_CUI:C0030193

SYMP_0000107 - pleural effusion
UMLS_CUI:C0032227

SYMP_0000114 - thrombocytopenia
UMLS_CUI:C0040034

SYMP_0000116 - prostration
UMLS_CUI:C0277794

SYMP_0000124 - seizure
UMLS_CUI:C0036572

SYMP_0000125 - liver inflammation
UMLS_CUI:C0019158

SYMP_0000128 - conjunctivitis
UMLS_CUI:C0009763

SYMP_0000136 - skin ulcer
UMLS_CUI:C0037299

SYMP_0000139 - sneezing
UMLS_CUI:C0037383

SYMP_0000141 - spasticity
UMLS_CUI:C0026838

SYMP_0000147 - steatorrhea
UMLS_CUI:C0038238

SYMP_0000153 - vasculitis
UMLS_CUI:C0042384

SYMP_0000162 - tremor
UMLS_CUI:C0040822

SYMP_0000177 - weakness
UMLS_CUI:C3714552

SYMP_0000186 - exhaustion
UMLS_CUI:C0392674

SYMP_0000187 - tiredness
UMLS_CUI:C0015672

SYMP_0000188 - abdominal discomfort
UMLS_CUI:C0232487

SYMP_0000208 - anemia
UMLS_CUI:C0002871

SYMP_0000210 - photophobia
UMLS_CUI:C0085636

SYMP_0000225 - asthenia
UMLS_CUI:C0004093

SYMP_0000231 - bradycardia
UMLS_CUI:C0428977

SYMP_0000258 - double vision
UMLS_CUI:C0012569

SYMP_0000260 - dry mouth
UMLS_CUI:C0043352

SYMP_0000262 - endocarditis
UMLS_CUI:C0014118

SYMP_0000263 - epididymitis
UMLS_CUI:C0014534

SYMP_0000285 - flaccid paralysis
UMLS_CUI:C0085620

SYMP_0000289 - eczema
UMLS_CUI:C0013595

SYMP_0000292 - heart failure
UMLS_CUI:C0018802

SYMP_0000293 - hemiparesis
UMLS_CUI:C0018989

SYMP_0000295 - hepatic abscess
UMLS_CUI:C0023885

SYMP_0000298 - hoarse voice
UMLS_CUI:C0019825

SYMP_0000300 - hyperesthesia
UMLS_CUI:C0020453

SYMP_0000302 - hypothermia
UMLS_CUI:C0413252

SYMP_0000303 - hypoxemia
UMLS_CUI:C0700292

SYMP_0000313 - joint inflammation
UMLS_CUI:C0003864

SYMP_0000317 - leukopenia
UMLS_CUI:C0023530

SYMP_0000318 - loss of balance
UMLS_CUI:C0241981

SYMP_0000321 - loss of vision
UMLS_CUI:C3665346

SYMP_0000333 - muscle tenderness
UMLS_CUI:C0575064

SYMP_0000337 - night sweats
UMLS_CUI:C0028081

SYMP_0000346 - papule
UMLS_CUI:C1519353

SYMP_0000349 - paraplegia
UMLS_CUI:C0030486

SYMP_0000354 - pneumonitis
UMLS_CUI:C0032285

SYMP_0000356 - phlebitis
UMLS_CUI:C0031542

SYMP_0000360 - emaciation
UMLS_CUI:C0013911

SYMP_0000367 - proteinuria
UMLS_CUI:C0033687

SYMP_0000369 - ptosis
UMLS_CUI:C0005745

SYMP_0000372 - rhinorrhea
UMLS_CUI:C1260880

SYMP_0000376 - severe diarrhea
UMLS_CUI:C1443924

SYMP_0000383 - stiff neck
UMLS_CUI:C0151315

SYMP_0000389 - stupor
UMLS_CUI:C0085628

SYMP_0000393 - tinnitus
UMLS_CUI:C0040264

SYMP_0000399 - vertigo
UMLS_CUI:C0042571

SYMP_0000402 - cachexia
UMLS_CUI:C0006625

SYMP_0000404 - dyspareunia
UMLS_CUI:C0013394

SYMP_0000412 - anxiety
UMLS_CUI:C0003467

SYMP_0000414 - dysarthria
UMLS_CUI:C0013362

SYMP_0000420 - bloating
UMLS_CUI:C1291077

SYMP_0000421 - hematochezia
UMLS_CUI:C1321898

SYMP_0000422 - dyspepsia
UMLS_CUI:C0013395

SYMP_0000427 - impotence
UMLS_CUI:C0242350

SYMP_0000430 - pleuritic chest pain
UMLS_CUI:C0008033

SYMP_0000432 - itching
UMLS_CUI:C0033774

SYMP_0000434 - urticaria
UMLS_CUI:C0042109

SYMP_0000435 - paresthesia
UMLS_CUI:C0030554

SYMP_0000436 - abnormal vaginal bleeding
UMLS_CUI:C0578503

SYMP_0000440 - hair loss
UMLS_CUI:C0002170

SYMP_0000446 - bloodshot eye
UMLS_CUI:C0155169

SYMP_0000462 - symptom
UMLS_CUI:C1457887

SYMP_0000634 - leukocytosis
UMLS_CUI:C0023518

SYMP_0000636 - maculopapular rash
UMLS_CUI:C0423791

SYMP_0000654 - irritability
UMLS_CUI:C0022107

SYMP_0000666 - abnormal behavior
UMLS_CUI:C0233514

SYMP_0000672 - abscess
UMLS_CUI:C0000833

SYMP_0000682 - altered mental status
UMLS_CUI:C0278061

SYMP_0000686 - chronic cough
UMLS_CUI:C0010201

SYMP_0000689 - cramp
UMLS_CUI:C0026821

SYMP_0000715 - skin desquamation
UMLS_CUI:C0237849

SYMP_0000731 - renal failure
UMLS_CUI:C0035078

SYMP_0000734 - stroke
UMLS_CUI:C0038454

SYMP_0000744 - cervical lymphadenopathy
UMLS_CUI:C0235592

SYMP_0000756 - menorrhagia
UMLS_CUI:C0025323

SYMP_0000760 - petechiae
UMLS_CUI:C0031256

SYMP_0000765 - sensory disturbance
UMLS_CUI:C0152027

SYMP_0000839 - acute pain
UMLS_CUI:C0184567

SYMP_0000867 - gastrointestinal bleeding
UMLS_CUI:C0017181

SYMP_0000868 - breathing problems
UMLS_CUI:C1260922

SYMP_0000876 - pericardial effusion
UMLS_CUI:C0031039

SYMP_0000895 - anaphylactic shock
UMLS_CUI:C0002792

SYMP_0000896 - exophthalmos
UMLS_CUI:C0015300

SYMP_0000900 - allergic reaction
UMLS_CUI:C0020517

SYMP_0019142 - lymphadenopathy
UMLS_CUI:C4282165

SYMP_0019145 - vomiting
UMLS_CUI:C0042963

SYMP_0019147 - hematemesis
UMLS_CUI:C0018926

SYMP_0019150 - pharyngitis
UMLS_CUI:C0031350

SYMP_0019151 - pulmonary edema
UMLS_CUI:C0034063

SYMP_0019153 - dyspnea
UMLS_CUI:C0013404

SYMP_0019155 - lymphadenitis
UMLS_CUI:C0024205

SYMP_0019160 - boil
UMLS_CUI:C0242301

SYMP_0019161 - muscle pain
UMLS_CUI:C0231528

SYMP_0019168 - pneumonia
UMLS_CUI:C0032285

SYMP_0019169 - arthritis
UMLS_CUI:C0003864

SYMP_0019173 - meningitis
UMLS_CUI:C0025289

SYMP_0019174 - chills
UMLS_CUI:C0085593

SYMP_0019176 - malaise
UMLS_CUI:C0231218

SYMP_0019177 - fatigue
UMLS_CUI:C0015672

SYMP_0019179 - lightheadedness
UMLS_CUI:C0220870

SYMP_0019180 - constipation
UMLS_CUI:C0009806

SYMP_0019181 - hoarseness
UMLS_CUI:C0019825

SYMP_0019183 - hyperactivity
UMLS_CUI:C0424295

SYMP_0020002 - anal abscess
UMLS_CUI:C0281778

SYMP_0020003 - acholic stool
UMLS_CUI:C2675627

SYMP_0020005 - acquired color vision deficiency
UMLS_CUI:C0155018

SYMP_0020006 - agitation
UMLS_CUI:C0085631

Thanks!
@ndobb ndobb changed the title Consider adding ULS hasDbXrefs Consider adding UMLS hasDbXrefs Aug 17, 2023
@lschriml
Copy link
Contributor

lschriml commented Aug 18, 2023 via email

@ndobb
Copy link
Author

ndobb commented Aug 18, 2023

Great! Please let me know if anything is unclear, etc., and thank you very much for your invaluable work.

@lschriml
Copy link
Contributor

lschriml commented Aug 18, 2023 via email

@allenbaron
Copy link
Collaborator

@ndobb I'd be interested in looking at your recent project using SO. Can you point me to a publication about it?

@allenbaron
Copy link
Collaborator

I found it:

Nicholas J Dobbins and others, LeafAI: query generator for clinical cohort discovery rivaling a human programmer, Journal of the American Medical Informatics Association, 2023;, ocad149, https://doi.org/10.1093/jamia/ocad149

We will add it as a use case of the Symptom Ontology on the Symptom Ontology information page (https://disease-ontology.org/resources/symptom-ontology).

Thanks again!

@ndobb
Copy link
Author

ndobb commented Aug 21, 2023

Yes, that's the one!

allenbaron added a commit to allenbaron/DO_dev that referenced this issue Aug 30, 2023
@allenbaron
Extract SYMP-UMLS suggested mappings for review
c609439 
Obtained using MetaMapLite; provided by @ndobb in
DiseaseOntology/SymptomOntology#16.

ONETIME SCRIPT
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
3 participants
@lschriml @ndobb @allenbaron