“Desiderata” for Controlled Medical Vocabularies http://bit.ly/desider1. Content – formal editorial policy and methodology; provide breadth and depth; don’t just add terms2. Concept orientation – exactly one meaning per concept and exactly one concept per meaning3. Concept permanence – old concepts cant be deleted; names can be changed as long as meaning doesnt change
“Desiderata” for Controlled Medical Vocabularies http://bit.ly/desider4. Nonsemantic identiﬁers – use a meaningless integer5. Polyhiearchy – employ multiple hierarchies to support need for tree walking and inferencing6. Formal Deﬁnitions – structured descriptions that invoke relationships within the terminology
“Desiderata” for Controlled Medical Vocabularies http://bit.ly/desider7. Reject “not elsewhere classiﬁed” – terminology changes induce semantic drift8. Graceful evolution – ﬁx mistakes; account for changes in medical knowledge9. Recognize redundancy – redundant expressions are inevitable, but redundant concepts are bad
Is Roz Chast’s ice cream ontology desiderata compliant?
What is the license of the controlled vocabulary?• Are the ontology codes copyrighted and can they be used in an open source application?• Need to account for the possibility that the data is reused for a commercial interest
Externally maintained vocabularies are more sustainable Who will maintain and host the vocabulary?
The Ontology Team isconsidering serving vocabularies for select domains“The VIVO community might be able to buildservices to serve controlled vocabularies for organizations and journals.” http://bit.ly/J7Vd8w
Food and Agriculture Organization (FAO) geopolitical ontology • master reference for geopolitical information in multiple languages • provides relations among territories (land borders, group membership, etc) • tracks historical changes Ships with VIVO application
Types of Specialty All Specialties Board-Certiﬁed Specialties Board-Certiﬁed Subspecialties
Types of Medical Expertise Feigned Clinical Research < < GLG-20s Performed Board-certiﬁed Invented amasquerading 100+ ECGs in Cardiology better ECGas doctors for comic eﬀect
We use Intelligent Medical Objects (IMO)’s interface terminology• Maps medical expertise terms to SNOMED CT• Useful for returning relevant results to patients searching for a doctor• Enables the physician to enter more arcane areas of expertise (e.g., Asian American Community Health)• A commercial application
Physician Admin View:Search for “chemotherapy” in IMO
Physician Admin View:Search for “that” yields manyterms not in SNOMED CT.
Expertise exists in POPS.Board certiﬁcation dataexists in POPS, Intellicred.
Export from PhysiciansProﬁle System containsspecialty and expertise
Board CertiﬁcationsProblem #1: No indication of certifying board. At least 13 certiﬁcations including geriatric medicine,pain medicine, and urology are given by at least one ABMS board.
Board Certiﬁcations Problem #2: Names ofcertiﬁcations are ambiguous.Colon and rectal surgery is listed in the following alternate ways: Surgery, Colon and Rectal Colon-Rectal Surgery Colorectal Surgery
Board CertiﬁcationsProblem #3: No given date of certiﬁcation.
The National Uniform Claim Committee(NUCC) maintains a list of health careprovider taxonomy codes, but this listseems to be exclusively for non-MDs.
Change in number of ABMSSubspecialties/Specialties 145 84 66 74 20 10 70 79 92 96 99 0 12 re- 19 70 -19 - 19 By 19 By 19 2P 19 1980
Cosmetic Dentistry Geriatric Psychotherapy Neuro Critical CareCosmetic Dermatology Gynecologic Endocrinology Neuro RadiologyCosmetic Surgery Gynecologic Pathology Neuro-OphthalmologyCritical Care Neurology Gynecology Neuro-PathologyDermatology, General Hand Surgery NutritionEar, Nose, and Throat, Heart Surgery Oral and MaxillofacialPediatric Hematology/Oncology PathologyEchocardiography Hepatobiliary Surgery Oral and Maxillofacial SurgeryElectrodiagnostic Medicine Hepatology OrthodonticsEmergency Neurology High Risk Obstetrics Orthopedic SurgeryEndocrinology Hospitalist Orthopedics ollowing 135 boardFacial Plastic and Immunopathology Pain Medicine/Pain The fReconstructive SurgeryFacial Plastic Surgery Infant Psychiatry Intensive Care Management Pathology ns in our systemFamily Psychology Internal Medicine, General Pediatric Allergy and certiﬁcatioFetal CardiologyFoot and Ankle Surgery International Medicine International Travel Medicine Immunology Pediatric Behavior and cognized by ABMS.Foot Surgery Interventional Neuroradiology Development are not reGastroenterology PathologyGastrointestinal PathologyGastrointestinal Surgery Interventional Oncology Interventional Pain Management Pediatric Dentistry Pediatric Neurological Surgery Prior to 1970 1970-1979 1970-1979 Pediatric NeurologyGeneral Anesthesiology Interventional Radiology Pediatric NeurosurgeryGeneral Cardiology Invasive Cardiology Pediatric Orthopedic SurgeryGeneral Dentistry Laboratory Medicine Pediatric OrthopedicsGeneral Dermatology Laryngology PeriodonticsGeneral Internal Medicine Liver Pathology Plastic and ReconstructiveGeneral Neurology Maternal-Fetal Medicine SurgeryGeneral Neurosurgery Medical Genetics PsychologyGeneral Obstetrics and Molecular Genetics Pulmonary Disease MedicineGynecology Molecular Hematopathology RadiologyGeneral Ophthalmology Molecular Infectious Disease Radiology, Vascular/General Pediatrics Molecular Pathology InterventionalGeneral Psychiatry Musculoskeletal Oncology Reproductive EndocrinologyGeneral Surgery Musculoskeletal Radiology Surgery, Critical CareGeneral Urology Neonatal Neurology Surgery, HandGenetics, Medical Neonatal Surgery Surgery, Oral and MaxillofacialGeriatric Cardiology Neonatal Thoracic Surgery Thoracic SurgeryGeriatric Dermatology Neonatology Vascular and Interventional
Weill Game Plan for Board Certiﬁcations• Explore ingest from Intellicred (fewer certiﬁcations, less variability, may include certifying agency?)• Explore external vocabularies• Failing that, create our own
Expertise term from Weill Cornell Physician Proﬁle 3% of terms from the source system System (n = 2578) lack or have an unclear equivalent in UMLS How does a term of local clinical expertise map to UMLS using Stony Brooks API? Weill → UMLS – In Vitro Fertilization Counseling → V Unclear Fertilization | Counseling – Adjustable Band → Band – Bowel-Sparing Strictureplasty → No Identical Subtype Compound term Equivalent preserving Union of two concepts original meaning53% of terms from 3% of terms from 2% of terms from the source systemcorrespond exactly to 5% of terms from the source system the source systemsome representation 34% of terms from the source system can be represented by the joining (not can only be represented as a in UMLS the source system have some equivalent in UMLS that is intersection) of two subtype of a can only be lexically different but concepts in UMLS concept in UMLS represented as a– Polycystic Ovary Syndrome semantically identical combination of terms– Anaphylaxis Weill → UMLS Weill → UMLS– Aortic Dissection from UMLS – Billing and Coding → Billing | – Bipolar 1 Disorder → Bipolar– Chemoembolization– Dental Implant Weill → UMLS Coding Disorder – Biopsy of Skin → Skin biopsy – Bone and Mineral Metabolism – FAA Medical Exam → Medica– Echocardiogram Weill → UMLS → Bone Metabolism | Mineral – Aneurysm of Popliteal Artery → Exam – Asian American Community Health Metabolim Aneurysm Popliteal → Asian American | Community – Bladder and Prostate Cancer – Charcot-Marie-Tooth Disease → Health → Bladder Cancer | Prostate Charcot-Marie-Tooth – Endoscopic Ultrasound of Cancer – Cirrhosis of Liver → Cirrhosis Esophagus → Endoscopic Ultrasound – Coarctation of the Aorta → | Esophagus Coarctation – Chronic Pelvic Pain In Female → Chronic Pelvic Pain | Female – Bronchoscopy With Biopsy →
Pre-coordination Post-coordinationDeﬁnition Terms combined by a developer to denote a Terms combined at the time of search and speciﬁc concept and its retrieval using Boolean attributes more or other operators. precisely.Beneﬁts Users who are not Lazy or “busy” totally familiar with a developers controlled vocabulary and its structure.Examples avian hypersensitivity avian AND pneumonitis hypersensitivity AND pneumonitis carrier sense multiple access carrier sense AND multiple access
How do we semantically model post-coordinated terms?1. Do not mess with post-coordination. User adds term from lookup service. Thats it. (Existing method.)2. User adds term from lookup service. Machine makes basic inferences based on similarity. (Everything is "related term.")3. User adds term from lookup service. Administrator models terms.4. User adds term from lookup service. User interface enables and guides end user.
Option #3: User adds term from lookup service. Administrator models terms.Can we build on others work?• The International Health Terminology Standards Development Organization (IHTSDO) in Denmark is working to develop and promote SNOMED to support sharing of modelling.• IMO, our terminology service, may help model coordinated terms.
Need for post-coordination is widespread For example, many global health terms require coordination.
Why SNOMED CT may be better at representing medical terms compared to UMLS• No formal conceptual model (near-synonymy)• No hierarchy• Lots of redundancy• Lots of ambiguity
UMLS is good for helping you ﬁnd termsin a speciﬁc terminology because allmany-to-one term-to-concept mappingsexpand the synonyms you can matchagainst. I recommend you use UMLS toﬁnd terms from a very limited set ofterminologies - maybe SNOMED plusLOINC plus RxNorm, for example.Jim Cimino
Proposed Role of SKOSClassesskos:Concept snomedct:Procedure snomedct:Disorder rxnorm:Drug ...Propertiesskos:related snomedct:equivalentTo ...skos:broaderskos:narrower
Read MoreGuidelines for the Construction, Format, andManagement of Monolingual ControlledVocabularieshttp://bit.ly/niso-standardDesiderata for Controlled MedicalVocabularieshttp://bit.ly/desider
Practice Robot Courtesy with Local Extensions Use classes/properties that are subclasses/subproperties of existing classes/properties in VIVO’s core ontology.