UNIFIED MEDICAL LANGUAGE SYSTEMS (UMLS) The Unified Medical Language System (UMLS) is a long term research and development project that started in 1986 by the U.S. National Library of Medicine (NLM) The UMLS is not a gigantic and comprehensive medical vocabulary The UMLS is a relational database connecting “by concept” over 60 vocabularies, thesauri, medical problem lists etc. The UMLS project is development effort designed to facilitate the retrieval and integration of information from multiple machine-readable biomedical information sources, furthermore, helping to health professionals and researchers from using available machine-readable information in the way concepts are expressed in different machine-readable sources and by different users. The goal is to make it easier to develop systems that link information from patient record systems, bibliographic databases, factual databases, expert systems and the lexical programs in natural language processing and indexing research.

Purpose To aid the development of systems that help health professionals and researchers retrieve and integrate electronic biomedical information form a variety of sources, such as: Computer-based Patient Records Bibliographic databases Factual (full text) databases Administrative health data Expert systems

UMLS Uses Electronic patient records Natural language processing Information retrieval Thesaurus construction Automated indexing

UMLS COMPONENTS Metathesaurus Semantic Network Lexicon

UMLS Source “Vocabularies” Widely varying purposes, structures, properties that do not add up to single ontology or view of the world: Thesauri, e.g., MeSH (Medical Subject Headings) Statistical Classifications, e.g., ICD Billing Codes, e.g., CPT Clinical coding systems, e.g., SNOMED Lists of controlled terms, e.g., HL7 valid values

How to combine them? Not reallly ... Concepts, terms and attributes from many controlled vocabularies. New inter-source relationships, definitional information, use information. Scope determined by combined scope of source vocabularies.

METATHESAURUS Contains more than 60 vocabularies and classifications. 776.940 concepts 2,1 millions of concept names 11 millions of relationships between concepts Concepts, terms and attributes from many controlled “vocabularies” New inter-source relationships, definitional information, use information. Scope determined by combined scope of source vocabularies

Metathesaurus - Relations Preserves the structure of the original sources. Add news relationships between the concepts

METATHESAURUS Organization CUI Synonymous terms Preferred term

Metathesaurus structure CONCEPTs TERMs STRING CUI’s LUI’s SUI’s STRING Is organized by concept or meaning; its purpose is to link alternative names and views of the same concept together and to identify useful relationships between different concepts.. The Metathesaurus preserves the meanings, hierarchical connections, and other relationships between terms present in its source vocabularies, while adding certain basic information about each of its concepts and establishing new relationships between concepts and terms from different source vocabularies. STRING STRING

Metathesaurus structure example CONCEPTS (CUIs) TERMS (LUIs) STRING (SUIs) C0004238 L0004238 S0016668 (preferred) Atrial Fibrillation Atrial Fibrillations Auricular Fibrillation Auricular Fibrillations S0016669 L0004327 S0016899 (synonym) Auricular Fibrillation(preferred) S0016900 (plural variant)

Semantic Network All information about specific concepts is found in the Metathesaurus The Network provides information about the basic semantic types that are assigned to these concepts, and it defines the relationships that may hold between the semantic types It defines these types, both with textual descriptions and by means of the information inherent in its hierarchies

Semantic Network Example “BIOLOGIC FUNTION” HIERARCHY EXPERIMENTAL MODEL OF DISEASE The semantic types are the nodes in the Network, and the relationships between them are the link and that are assigned to concepts in the Metathesaurus. The current scope of the UMLS semantic types is quite broad, allowing for the semantic categorization of a wide range of terminology in multiple domains.

Relationship between Metathesaurus and Semantic Network

LEXICON It provide the lexical information needed for the SPECIALIST Natural Language Processing System It is a general English lexicon that includes many biomedical terms (commonly occurring English words and biomedical vocabulary) The lexicon entry for each word (or term) records the syntactic morphological orthographic information needed by the SPECIALIST natural language processing system The lexicon consists of a set of lexical entries with one entry for each spelling or set of spelling variants in a particular part of speech. Lexical items may be “multi-word” terms made up of other words if the multi-word term is determined to be a lexical item by its presence as a term in general English or medical dictionaries, or in medical thesauri. Expansions of generally used acronyms and abbreviations are also allowed as multi-word terms. The lexicon record format has one record per entry. When a base form has more than one part of speech there will be more than one record for that base form.

UNIFIED MEDICAL LANGUAGE SYSTEM - Summary Standard source of concepts and synonyms. Multilingual Broad extension. Allow integration between applications

REFERENCES http://www.nlm.nih.gov/pubs/factsheets/umls.html http://www.nlm.nih.gov/research/umls/META2.HTML http://www.nlm.nih.gov/research/umls/META3.HTML http://www.nlm.nih.gov/research/umls/META4.HTML http://www.nlm.nih.gov/pubs/cbm/umlscbm.html#6