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02 UMLS 004

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Published on November 20, 2007

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UMLS:  UMLS Mike Buck, Chengjian Che, Kevin Coonan, Vojtech Huser February 2004 Agenda:  Agenda Overview Metathesaurus Semantic Network Desiderata Application Discussion UMLS:  UMLS = Unified Medical Language System Created in 1986 3 parts Metathesaurus Database of concepts that appear in one or more constituent vocabularies Semantic Network Provides categorization of concepts in Metathesaurus and describes working relations between them. Specialist Lexicon Biomedical lexicon, associated tools used primarily for NLP Package: set of data files + tools (MetamorphoSys, lvg) + Java API UMLS Sub-agenda:  Sub-agenda Domain and intended use Maintenance organization Licensing requirements How it is distributed SNOMED-CT® inclusion Domain and intended use:  Domain and intended use DOMAIN Collection of terminologies Includes many domains, 100+ terminologies (MeSH, SNOMED, LOINC, ICD, RxNorm, First Databank, Gene Ontology) Same concepts are represented differently in many different vocabularies Absence of a standard format for distributing terminologies Bodenreider, O. (2004). "The Unified Medical Language System (UMLS): integrating biomedical terminology." Nucleic Acids Res 32 Database issue: D267-70 Current use:  Current use Almost nobody is using the whole UMLS as a production terminology (waiting for SNOMED) Most users extract only certain vocabularies (MeSH, RxNorm) Maintenance organization:  Maintenance organization National Library of Medicine (NLM) 8600 Rockville Pike Bethesda, MD 20894 Governmental agency Funded by Congress 2004 budget for NLM was $ 316M Approximately $3M for UMLS alone http://www.hhs.gov/budget/testify/b20030408_g.html Contact for help with UMLS Custserv@nml.nih.gov Licensing requirements and costs:  Licensing requirements and costs License Mail or fax signed license agreement to NLM http://www.nlm.nih.gov/research/umls/license.html No charge for UMLS license but many constituent vocabularies have their own license requirements if used outside the scope of the UMLS license Licensing restrictions:  Licensing restrictions Four progressive levels of use restriction in UMLS license (restrictions accumulate) 0- no restrictions 1- prohibited to translate or distribute derivative versions 2- cannot use in production environment 3- internal use for research and analysis only Examples MeSH (0) LOINC (0) First DataBank National Drug Data File (3) Micromedex DRUGDEX (3) How it is distributed:  How it is distributed Access via web browser UMLS Knowledge server (google UMLSKS) umlsks.nlm.nih.gov Files on your own computer Download 2 CD set Web services API available to query NLM server Web access:  Web access UMLS Files:  UMLS Files 4.9 GB when unzipped Quarterly updates AA, AB, AC, AD Not perfectly regular (2003AD does not exist) Not perfectly up to schedule (2004 AA does not exist yet) Manuals printed only once per year Text files, operating system independent, tools in Java MetamophoSys is a provided tool to extract portions of UMLS into separated data-files You get the files only - no “browser” included q.v. RELMA for LOINC or ClueBrowser for SNOMED New Distribution Format:  New Distribution Format Current format has not substantially changed between 2001AA – 2003AC releases Rich release (MR+) coming now White paper http://www.nlm.nih.gov/research/umls/white_paper.html Rich Release Format (Draft - January 29, 2004 ) http://umlsinfo.nlm.nih.gov/rich_release_format.html MetamorphoSys will have several additional file output options: the current relational ASCII file formats the new expanded relational file formats and (in 2004) XML formats. SNOMED-CT® will be released in the first 2004 release (2004AA), in the new Rich Release Format. World dimensions of UMLS:  World dimensions of UMLS UMLS is not meant to be just US project First extension was a Spanish version Other nations involved (part of distribution) French, Italian, Russian, Finish, Swedish, Norwegian, Hungarian, Basque, Hebrew, German UK (SNOMED, NHS, Read codes) UK: used Read Codes Incorporated into SNOMED-CT SNOMED inclusion:  SNOMED inclusion THIS AGREEMENT ("Agreement") is made as of June 30, 2003 by and between CAP (not-for-profit) and NLM (U.S. federal government agency) (licensee) $ 35,000,000 price tag 35K new concepts, 400K new strings Good until 2008 Text of the license http://www.nlm.nih.gov/research/umls/Snomed/snomed_license.html Agenda:  Agenda Overview Metathesaurus Semantic Network Desiderata Application Discussion Metathesaurus:  Metathesaurus DOMAIN Collection of terminologies Includes many domains, 100+ terminologies (MeSH, SNOMED, LOINC, ICD, RxNorm, First Databank) Statistics Concepts: 975,354 Strings: 2,361,983 Relationships: 12,071,232 Ref: http://www.nlm.nih.gov/research/umls/METAB3.HTML (number of concepts from each member terminology) Summary of Table Contents:  Summary of Table Contents Metathesaurus Concept Names (2.5.1) = MRCON Relationships between Different Concept Names (2.5.2) = MRREL, MRCOC, MRATX Attributes (2.5.3) = MRSAT, MRDEF, MRSTY, MRLO, MRRANK Source Information and contexts (2.5.4) = MRSO, MRCXT, MRSAB Indexes (2.6) = MRXW.BAQ, MRXW.DAN, MRXW.DUT, MRXW.ENG, MRXW.FIN, MRXW.FRE, MRXW.GER, MRXW.HEB, MRXW.HUN, MRXW.ITA, MRXW.NOR, MRXW.POR, MRXW.RUS, MRXW.SPA, MRXW.SWE, MRXNW.ENG, MRXNS.ENG Metathesaurus: Concepts:  Metathesaurus: Concepts Concept: Cluster of synonymous terms Identified by a CUI Term: Set of lexical variants Identified by a LUI String: Concept name Identified by a SUI CUIs, LUIs, SUIs:  CUIs, LUIs, SUIs CUI LUIs SUIs MRCON:  MRCON There is exactly one row in this file for each meaning of each unique string (CUI-SUI combination) in the Metathesaurus. Any difference in upper-lower case, word order, etc. creates a different unique string. Metathesaurus data for C0001403 (“Addison’s Disease”):  Metathesaurus data for C0001403 (“Addison’s Disease”) MRSO:  MRSO There is exactly one row in this file for each source of each string in the Metathesaurus. Metathesaurus data for C0001403 (“Addison’s Disease”):  Metathesaurus data for C0001403 (“Addison’s Disease”) MRREL:  MRREL There is one row in this table for each relationship between metathesaurus concepts known to the metathesaurus. Mrrel relationships:  Mrrel relationships MRSAT:  MRSAT There is exactly one row in this file for each concept, term and string attribute that does not have a sub-element structure. Attributes provide additional information about the meaning of a concept and explain how it is used in the source vocabulary. Mrsat concept attributes:  Mrsat concept attributes MRDEF:  MRDEF There is exactly one row in this file for each definition in the Metathesaurus. A few definitions approach 3,000 characters in length. Definitions:  Definitions Definitions MRSTY:  MRSTY There is exactly one row in this file for each semantic type assigned to each concept. MRSTY Semantic Types:  MRSTY Semantic Types Semantic Type Other Tables:  Other Tables mratx:  mratx mrcxt:  mrcxt mrlo:  mrlo mrrank:  mrrank mrcoc:  mrcoc Metathesaurus Change Files:  Metathesaurus Change Files There are six files or relations that identify key differences between entries in the previous and the current edition of the Metathesaurus. Deleted Concepts (File=DELETED.CUI) Merged Concepts (File=MERGED.CUI) Deleted Terms (File=DELETED.LUI) Merged Terms (File=MERGED.LUI) Deleted Strings (File=DELETED.SUI) Retired CUI Mapping (File=MRCUI) Future Changes:  Future Changes Effective with the 2004AA release of the UMLS Metathesaurus, the release file structure will be substantially expanded. Three existing relational files (MRCON, MRSO and MRATX) will be deprecated and merged into MRCONSO. Better version control for tracking changes to concepts and strings. And many more… Large Scale Vocabulary Test:  Large Scale Vocabulary Test Does the Metathesaurus cover the medical domain well? Participants searched 30 different terminologies in the 1996 UMLS for 32,679 normalized strings! 58% exact match 41% related concepts 1% not found Large Scale Vocabulary Test:  Large Scale Vocabulary Test Exact meaning match in constituent terminologies ranged from 45% to 71% Semantic types of missing matches: Findings 35% Disorders 20% Procedures 15% Concepts 15% Individual terminology match ranged from <1-63% of terms Only SNMI and RCD had >60% of terms Combined SNMI+RCD had 79% exact matches Conclusions: Combined vocabularies get greater coverage. Humphreys, B. L., A. T. McCray, et al. (1997). "Evaluating the coverage of controlled health data terminologies: report on the results of the NLM/AHCPR large scale vocabulary test." J Am Med Inform Assoc 4(6): 484-500. Agenda:  Agenda Overview Metathesaurus Semantic Network Desiderata Application Discussion UMLS Semantic Network--overview:  UMLS Semantic Network--overview Purpose is to provide a consistent categorization of all UMLS concepts. Purpose is to provide a set of useful relationships between concepts 135 semantic types entity or event 54 relationships isa or associated_with Semantic type 3d map:  Semantic type 3d map UMLS Semantic Network—structure:  UMLS Semantic Network—structure Semantic types are nodes Each metathesuarus concept (CUI) has a semantic type (TUI) located in MRSTY Eg COOO1403|T047|Disease or Syndrome Relationships are links Most specific semantic type possible is assigned Parent-child—linked by isa (primary link) Large set of non-hierarchical links as well Slide67:  Semantic types are nodes: either entity or event Slide68:  Entity Slide69:  Entity and Event UMLS Semantic Network—structure:  UMLS Semantic Network—structure Semantic types are nodes Each metathesuarus concept (CUI) has a semantic type (TUI) located in MRSTY Relationships are links Most specific semantic type possible is assigned Parent-child—linked by isa (primary link) Large set of non-hierarchical links as well UMLS Semantic Network—structure:  UMLS Semantic Network—structure Semantic types are nodes Each metathesuarus concept (CUI) has a semantic type (TUI) located in MRSTY Relationships are links Most specific semantic type possible is assigned Parent-child—linked by isa (primary link) Large set of non-hierarchical links associated_with Non-hierarchical links:  Non-hierarchical links Associated_with Physically related to Spatially related to Temporally related to Functional related to Affects Manages Treats Etc. Brings about Etc…. Conceptually related to Attributes of links (relationship) is hierarchical Slide76:  Sample hierarchy of non-hierarchical relationships Distributions:  Distributions Unit record format (one file) SU contains all attributes for any given semantic type or relationship ASCII relational tables similar to meta-thesaurus distribution Flat (text) delimited file ASCII relational format files:  ASCII relational format files SRDEF contains definitions for semantic types and relations. SRSTR contains the structure of the semantic network Pairs of semantic types/relationship Relation of second to first Status of relationship (defined for argument and children, defined for argument only, blocked SRSTRE1/2 allowed relationships in semantic network Pairs of either encoded (1) or text name (2) with relationship (either coded or text) Slide79:  :::::::::::::: SRDEF :::::::::::::: STY|T020|Acquired Abnormality|A1.2.2.2|An abnormal structure,or one that is abnormal in size or location, found in or deriving from a previously normal structure. Acquired abnormalities are distinguished from diseases even though they may result in pathological functioning (e.g., "hernias incarcerate").|Abscess of prostate; Hemorrhoids; Hernia, Femoral; Varicose Veins||||| ASCII relational format:  ASCII relational format SRDEF contains definitions for semantic types and relations. SRSTR contains the structure of the semantic network Pairs of semantic types/relationship Relation of second to first Status of relationship (defined for argument and children, defined for argument only, blocked SRSTRE1/2 allowed relationships in semantic network Pairs of either encoded (1) or text name (2) with relationship (either coded or text) Slide81:  :::::::::::::: SRSTR :::::::::::::: Acquired Abnormality|cooccurs_with|Injury or Poisoning|D|Acquired Abnormality|isa|Anatomical Abnormality|D| Acquired Abnormality|result_of|Behavior|D| Activity|isa|Event|D| Age Group|isa|Group|D| Alga|isa|Plant|D| ASCII relational format:  ASCII relational format SRDEF contains definitions for semantic types and relations. SRSTR contains the structure of the semantic network Pairs of semantic types/relationship Relation of second to first Status of relationship (defined for argument and children, defined for argument only, blocked SRSTRE1/2 allowed relationships in semantic network Pairs of either encoded (1) or text name (2) with relationship (either coded or text) Slide83:  :::::::::::::: SRSTRE2 :::::::::::::: Acquired Abnormality|isa|Anatomical Abnormality| Acquired Abnormality|isa|Anatomical Structure| Acquired Abnormality|isa|Physical Object| Acquired Abnormality|isa|Entity| Acquired Abnormality|affects|Alga| Acquired Abnormality|affects|Amphibian| Acquired Abnormality|affects|Animal| Slide90:  Descendants (first generation) Chemicals & Drugs 5-HT3-receptor antagonist  ¤ alizapride  ¤ alpha-fluoromethylhistidine  ¤ azasetron  ¤ benzquinamide  ¤ benzquinamide 50 MG Intravenous Solution  ¤ buclizine  ¤ Chlorpromazine  ¤ Chlorprothixene  ¤ clebopride  ¤ Cyclizine  ¤ Dexamethasone  ¤ DEXTROSE/FRUCTOSE/PHOSPHORIC ACID SOLN,ORAL  ¤ Diazepam  ¤ diorylate  ¤ Diphenhydramine  ¤ diphenidol  ¤ dixyrazine  ¤ DOLASETRON 100 MG Oral Tablet  ¤ (69 first generation descendants) [direct children and narrower concepts] Slide92:  Co-occurring Concepts Anatomy middle ear  [10]  ¤ Chemicals & Drugs Analgesics  [11]  ¤ Analgesics, Non-Narcotic  [11]  ¤ Analgesics, Opioid  [38]  ¤ Anesthetics, Inhalation  [8]  ¤ Concepts & Ideas Practice Guidelines  [8]  ¤ Quality of life  [15]  ¤ Disorders Abnormalities, Drug-Induced  [12]  ¤ Akathisia, Drug-Induced  [15]  ¤ Basal Ganglia Diseases  [9]  ¤ Physiology Gastric Emptying  [11]  ¤ Procedures Adenoidectomy  [7]  ¤ Ambulatory Surgical Procedures  [28]  ¤ Analgesia, Epidural  [7]  ¤ Analgesia, Patient-Controlled  [17]  ¤ Antineoplastic Combined Chemotherapy Protocols  [107]  ¤ Number of pairs (shown/all) = 99/850 (12%) Frequency (shown/all) = 5356/6610 (81%) Agenda:  Agenda Overview Metathesaurus Semantic Network Desiderata Application Discussion Desiderata…:  Desiderata… Content Not intended to be an independent terminology but rather a collection and mapping of constituent terminologies. Extension is dependent upon contributing terminologies Concept Orientation Concepts (CUIs) are unique, defined, and specific. Inter-concept relationships are either inherited from the source vocabularies or generated specifically by the editors of the Metathesaurus …Desiderata …:  …Desiderata … Concept Permanence CUIs are never reused, and deprecated CUIs with mapping to current CUIs is maintained (MRCUI). Nonsemantic Concept Identifier CUIs, LUIs, SUIs, TUIs are non-hierarchal ...Desiderata…:  ...Desiderata… Polyhierarchy While CUIs, etc. are not hierarchical, some hierarchical relationships from source terminologies are preserved (e.g. MeSH) Semantic network allows for multiple isa and inverse_isa relationships Membership in one hierarchy does not preclude membership in another …Desiderata…:  …Desiderata… Formal Definitions. No UMLS definitions for CUIs CUI definitions are available from source vocabularies for some (4.6%) terms Semantic types are defined …Desiderata…:  …Desiderata… Reject “Not Elsewhere Classified” Depends upon source vocabularies who often have NEC Multiple Granularities Semantic network provides abstraction and aggregation of concepts. Some source terminologies include/are hierarchal (e.g. MeSH tree) Multiple Consistent Views Defined in SRSTRE, MRCTX and MRREL …Desiderata:  …Desiderata Representing Context Semantic Network provides relationships and the context. Graceful Evolution Totally dependent upon contributions of constituent vocabularies. Deprecated concepts are well handled, mapped and documented. Recognize Redundancy Some undesirable redundant CUIs Clearly ambiguous terms are catalogued and are Agenda:  Agenda Overview Metathesaurus Semantic Network Desiderata Application Discussion Some applications of UMLS:  Some applications of UMLS Primary user is NLM for indexing Medline Semantic network used to clean up metathesaurus NCI uses for classification of precancers Used for NLP Used to generate Medline queries by mapping concepts to MeSH Used as template for DSS ontology Has not been used as internal terminology for CDR, but SNOMED-CT may change that Vanderbilt University WizOrder Decision Support/Order Entry System:  Vanderbilt University WizOrder Decision Support/Order Entry System WizOrder uses the UMLS as a dictionary to encode free-text entries into controlled vocabularies. The UMLS provides mapping between vocabularies, allowing to translate patient-specific information to MeSH terms and perform automated literature retrieval. WizOrder uses the tables of co-occurring concepts and the Semantic Network to provide sensible lists of potential drug interactions and adverse drug reactions, and generate fully-formed MEDLINE queries for PubMed. Geissbuhler, A. and R. A. Miller (1998). "Clinical application of the UMLS in a computerized order entry and decision-support system." Proceedings / AMIA: 320-4. MAOUSSC A French coding system:  MAOUSSC A French coding system MAOUSSC, a multiaxial coding system, was used for the representation of 1500 procedures from 15 clinical specialties, using UMLS concepts and relationships whenever possible. After UMLS was used for five years as a knowledge source for representing 1500 complex medical procedures in MAOUSSC, its value is considered significant. Bodenreider, O., A. Burgun, et al. (1998). "Evaluation of the Unified Medical Language System as a medical knowledge source." Journal of the American Medical Informatics Association 5(1): 76-87. National Cancer Institute (NIH):  National Cancer Institute (NIH) Terms in the UMLS (Unified Medical Language System) related to precancers were extracted in the first attempt to create a comprehensive listing of precancers. The CDSS::  The CDSS: Designed to let mere mortals encode medical knowledge sans Protégé Created a rule-based templates encoded in Arden Syntax for transfusion medicine based on UMLS entities However only 73% of highly specific, specialized terms were found in UMLS (e.g. didn’t find a CUI for “transfusion of red blood cell plasma depleted”) Expert selects elements (CUIs) and relationships (RELs) from metathesuarus and semantic network Allows for interchange with other DSS Avoids having to describe ontology de novo Removes idiosyncratic terms Hierarchy of terms/concepts, high level concepts, semantic types are combined to form ontology after expert selects specific relevant relationships Concepts are then linked to MLM via a relationship “has as rule” A UMLS-based Knowledge Acquisition Tool for Rule-based Clinical Decision Support System Development:  A UMLS-based Knowledge Acquisition Tool for Rule-based Clinical Decision Support System Development Transfusion according to current best practices, guidelines and governmental regulations is crucial. Body of knowledge is rapidly changing. Data driven (alert) and consultation modes Clinician and DSS agreed 40% Experts in transfusion medicine and DSS agreed 100% Difference was attributable to gaps in clinicians knowledge of current practices SAPHIRE v2:  SAPHIRE v2 Goal: enhance encoding of structured (CDA/XML) radiography reports Question: Optimal combination of terminology for different sections? Procedure, history, technique, findings and impression Method: Comparison w/ 50 reports indexed by hand 10 CXR, 10 head CT, 10 abdominal CT, 10 chest CT, 5 head MR, 5 bone scans 19 source vocabularies used in comparison (including SNOMED, CCPSS, COSTAR, ICD10, DXP, MSH, UWDA, RCD) Huang, Y., H. J. Lowe, et al. (2003). "A pilot study of contextual UMLS indexing to improve the precision of concept-based representation in XML-structured clinical radiology reports." Journal of the American Medical Informatics Association 10(6): 580-7. history:  history findings:  findings impression:  impression Unresolved issues of UMLS:  Unresolved issues of UMLS NLM UMLS websites 2 info pages knowledge server There is no good browser for UMLS Import into RDBMS Protégé (UMLS Plugin) Semantic network browser is fairly close Use of UMLS as source terminology (HDD for CDR) Future of UMLS Will people use? Will SNOMED-CT be continued Role of internationalization What is the optimal combination of constituent terminologies to describe a particular clinical domain Conclusions:  Conclusions The UMLS describes the relationships between constituent terminologies via mapping to independent concepts Production use of some of the terminologies requires additional licenses from the vendors Addition of SNOMED-CT Semantic network may support a range of ontology creation methods and tools The optimal terminology or collection of terminologies for any given domain remain to be determined Due to it’s size, the UMLS metathesaurus requires special treatment and tools (e.g. UMLSKS) Agenda:  Agenda Overview Metathesarus Semantic Network Desiderata Application Discussion Slide116:  NLM. UMLS Knowledge Sources 2003AC Documentation. NIH. 11-01-2003. Available at: http://www.nlm.nih.gov/research/umls/UMLSDOC.HTML. Accessed 2-23-2004, 2004. Humphreys BL, McCray AT, Cheh ML. Evaluating the coverage of controlled health data terminologies: report on the results of the NLM/AHCPR large scale vocabulary test. J Am Med Inform Assoc. Nov-Dec 1997;4(6):484-500. Geissbuhler A, Miller RA. Clinical application of the UMLS in a computerized order entry and decision-support system. Proceedings / AMIA. 1998:320-324. Bodenreider O, Burgun A, Botti G, Fieschi M, Le Beux P, Kohler F. Evaluation of the Unified Medical Language System as a medical knowledge source. Journal of the American Medical Informatics Association. Jan-Feb 1998;5(1):76-87. Hersh W, Mailhot M, Arnott-Smith C, Lowe H. Selective automated indexing of findings and diagnoses in radiology reports. Journal of Biomedical Informatics. Aug 2001;34(4):262-273. Huang Y, Lowe HJ, Hersh WR. A pilot study of contextual UMLS indexing to improve the precision of concept-based representation in XML-structured clinical radiology reports. Journal of the American Medical Informatics Association. Nov-Dec 2003;10(6):580-587. Bodenreider O, Hole WT, Humphreys B, L., Roth L, A., Srinivasan S. Customizing the UMLS Metathesaurus for your Applications. November, 2002. Available at: http://umlsinfo.nlm.nih.gov/powerpoint/T13-color.pdf. Accessed 2-23-2004, 2004. Bodenreider O. The Unified Medical Language System (UMLS): integrating biomedical terminology. Nucleic Acids Res. Jan 1 2004;32 Database issue:D267-270. Achour SL, Dojat M, Rieux C, Bierling P, Lepage E. A UMLS-based knowledge acquisition tool for rule-based clinical decision support system development. Journal of the American Medical Informatics Association. Jul-Aug 2001;8(4):351-360. References:  References http://www.nlm.nih.gov/research/umls/umlsmain.html (basic information) http://umlsinfo.nlm.nih.gov/ (presentations) http://umlsks.nlm.nih.gov/ Knowledge server, login required http://www.nlm.nih.gov/research/umls/UMLSDOC.HTML Documentation http://www.nlm.nih.gov/research/umls/METAB3.HTML (number of terms from each terminology) http://meow.nlm.nih.gov/cgi-public/concept-history.pl concept history (leukemia C0023418) References:  References The Unified Medical Language System An Informatics Research Collaboration Betsy L. Humphreys, MLS, Donald A. B. Lindberg, MD, Harold M. Schoolman, MD, and G. Octo Barnett, MD Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=9452981 The UMLS project: making the conceptual connection between users and the information they need. B L Humphreys and D A Lindberg Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=8472002 The Unified Medical Language System (UMLS): integrating biomedical terminology Olivier Bodenreider1 Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=14681409 Slide119:  Other articles that may be of interest: Planned NLM/AHCPR large-scale vocabulary test: using UMLS technology to determine the extent to which controlled vocabularies cover terminology needed for health care and public health. B L Humphreys, W T Hole, A T McCray, and J M Fitzmaurice Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=8816351 Evaluating the Coverage of Controlled Health Data Terminologies Report on the Results of the NLM/AHCPR Large Scale Vocabulary Test Betsy L. Humphreys, MLS, Alexa T. McCray, PhD, and May L. Cheh, MS Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=9391936 Making the Conceptual Connections The UMLS after a Decade of Research and Development Alexa T. McCray, PhD and Randolph A. Miller, MD Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=9471340 New release format:  New release format WHAT: create and distribute robust, purpose-specific mappings between different source vocabularies and classifications within the Metathesaurus. In the new release format, the Associated Expressions file (MRATX) will be deprecated in favor of a new mappings file (MRMAP), which will have a more robust structure for representing simple, complex, and rule-based mappings using Metathesaurus or source-asserted unique identifiers. WHY: current Metathesaurus release format can represent one-to-one, one to many, and one-to-Boolean expression mappings, the more complex mappings are cumbersome to maintain and to use and the format does not accommodate rule-based mappings. Slide121:  2.3.1: CAP owns and shall retain ownership of the copyright and patent in SNOMED and in the trademark SNOMED 4.3: Release schedule.  CAP shall provide updated versions of the U.S. English edition of SNOMED CT Core Content at least annually or on the then current release schedule, whichever is more frequent. 4.4 Procedures for Suggesting Enhancements.  CAP shall publish on its Website procedures for submitting suggested enhancements and extensions to SNOMED, including an explicit statement of the subject scope of SNOMED and its relationship to the scope of LOINC and RxNorm and any current priorities for SNOMED development. Agreement:  Agreement 6.1 Term.  The term of this agreement is five years commencing from the award effective date of Contract NO1-LM-3-3503. CAP hereby grants to the NLM a perpetual non-exclusive license to all versions of SNOMED provided under this agreement. 6.2 Survival of Certain Rights and Obligations.  Upon completion of this agreement for any reason, LICENSEE may retain and continue to distribute and continue to use the versions of SNOMED provided under this agreement in research and in NLM production applications. SUBLICENSEEs may continue to use the versions of SNOMED provided under this agreement after the expiration thereof. UMLS and SNOMED:  UMLS and SNOMED Already part of Methathesaurus: SNOMED SNOMED, 2nd Edition [1979,1982] SNOMED International, Version 3.5 [1998]) NHS Clinical Terms Version 3 of the NHS Clinical Terms SNOMED inclusion:  SNOMED inclusion June 30, 2003 - the day that NLM received the files from the CAP Source: http://www.nlm.nih.gov/research/umls/Snomed/snomed_faq.html#is http://www.snomed.org/NLM_Agreement/CAP_NLM_main.html Incorporation of subsequent updates should become available in the UMLS much more rapidly. Already part of Metathesaurus: SNOMED SNOMED, 2nd Edition [1979,1982] SNOMED International, Version 3.5 [1998]) NHS Clinical Terms Version 3 of the NHS Clinical Terms US and non-US:  US and non-US …for no cost use within the U.S. by both U.S. government (federal, state, local, and territorial) and private organizations. U.S. commercial organizations may include SNOMED as obtained via the UMLS within products sold to U.S. customers. U.S. commercial organizations that wish to include SNOMED in products vended in other countries need to obtain an additional license from the CAP for that purpose. Non-U.S. users of the UMLS still need a separate license agreement with the CAP for production uses of SNOMED Mike’s References:  Mike’s References UMLS Information at NLM: http://www.nlm.nih.gov/research/umls/ UMLS Homepage: http://umlsinfo.nlm.nih.gov/ UMLS Knowledge Source Server: http://umlsks4.nlm.nih.gov/kss/servlet/Turbine;jsessionid=06d5i05xz1 Mike’s References:  Mike’s References UMLS Documentation: http://www.nlm.nih.gov/research/umls/UMLSDOC.HTML UMLS Tutorials/Presentations: http://umlsinfo.nlm.nih.gov/presentations.html Mike’s References:  Mike’s References Bodenreider, Olivier; Hole, William T.; Humphreys, Betsy, L.; Roth, Laura, A.; Srinivasan, Suresh Customizing the UMLS Metathesaurus for your Applications. Proc AMIA Symp; Nov. 2002. http://umlsinfo.nlm.nih.gov/powerpoint/T13-color.pdf Mike’s References:  Mike’s References Metathesaurus Basics article: http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=14681409 History of UMLS: http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=9452981 Roberto’s References:  Roberto’s References The Unified Medical Language System An Informatics Research Collaboration Betsy L. Humphreys, MLS, Donald A. B. Lindberg, MD, Harold M. Schoolman, MD, and G. Octo Barnett, MD Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=9452981 Roberto’s References:  Roberto’s References The UMLS project: making the conceptual connection between users and the information they need. B L Humphreys and D A Lindberg Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=8472002 Roberto’s References:  Roberto’s References The Unified Medical Language System (UMLS): integrating biomedical terminology Olivier Bodenreider1 Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=14681409 SPECIALIST Lexicon:  SPECIALIST Lexicon Lexical information needed for the SPECIALIST Natural Language Processing System (NLP) Added to the UMLS project in the 1994 version Covers both commonly occurring English words as well as biomedical vocabulary Organized on a lexical and not a semantic basis Lexical entries may contain more than one sense of a word 119,000+ lexical records Lexical tool programs - Used to help incorporate a new vocabulary into the Metathesaurus and for NLP research Example of a Lexical Record for the lexical item “Anaesthetic”:  Example of a Lexical Record for the lexical item “Anaesthetic” base = anaesthetic spelling_variant=anesthetic entry = E008769 cat = noun variants = reg entry = E008770 cat = adj variants = inv position = attribute Oregon Health and Science University SAPHIRE Radiology System:  Oregon Health and Science University SAPHIRE Radiology System The SAPHIRE system matches text to concepts in the UMLS Metathesaurus for the automated indexing of image reports http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11977808&dopt=Abstract

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