Unified Medical Language System

NLM Technical Bulletin, Nov-Dec 2020, UMLS 2020AB Release Available | National Institutes of Health | 11/2/2020

Wilder V. UMLS 2020AB Release Available. e1. 2020AB release of the Unified Medical Language System ¬Æ (UMLS) Knowledge Sources is as of November 2, 2020. The available downloads are: Full Release (UMLS Metathesaurus, Semantic Network, Specialist Lexicon and Lexical Tools, database load scripts, and MetamorphoSys for customizing your UMLS subset and browsing the data) UMLS Metathesaurus Files (complete Metathesaurus data without any customization) MRCONSO.RRF file (most widely used Metathesaurus file …

JAMIA Explores Self-Reported Covid-19 Symptoms On Twitter As Research Resource | Forbes | 7/14/2020

… tweets using Covid-19 keywords and performed semiautomatic filtering to monitor and collect self-reports of positive-tested Twitter users. The research extracted Covid-19 symptoms mentioned by the users, mapped them with the Unified Medical Language System , and compared the distributions to those reported in earlier studies from clinical settings. Once all of the data was precisely tabulated, JAMIA identified 203 positive-tested users who reported 1,002 symptoms with …

Estimating the efficacy of symptom-based screening for COVID-19 | Becker’s Hospital Review | 7/13/2020

… but added later in the course of documentation. All concepts were derived from the 2018AA SNOMED CT US vocabulary with the semantic group DISORDER 21 , maintained as part of the National Library of Medicine Unified Medical Language System . Extracted concepts were encoded as binary variables to indicate their presence or absence in a given patient’s clinical note, after filtering to keep only the non-historical, positive mentions about the patient …

Microsoft Azure launches medical data-mining tool | Becker’s Hospital Review | 7/8/2020

… treatments. Users can extract more than 100 types of personally identifiable information, including protected health information, in unstructured text. The AI tool also links entities to medical ontologies and coding systems, such as the Unified Medical Language System , to detect connections between medical concepts mentioned in text. For example, the tool can be used to find the relationship between a medication name and the dosage associated with it. Medical researchers …

Deeper Insights launches COVID-19 research app | Healthcare IT News | 5/28/2020

… 128,000 scientific research papers that have been produced on the virus since January 2020. It uses machine learning along a knowledge graph to establish the relevance of results. These are then aligned to the Unified Medical Language System (UMLS) Metaontolgy, ensuring full clinical understanding through a standardised medical language. Covid Insights can identify links between symptoms, drugs and other factors and supports the provision of top quality care by medical …

Study on Main Drugs and Drug Combinations of Patient-Controlled Analgesia Based on Text Mining | 5/23/2020

… program [ 12 ] of National Medical Library (NLM). MetaMap is a natural language processing program developed by NLM. It can match free words in the TXT format text to concepts in the Metathesaurus of the Unified Medical Language System (UMLS). It can compare words in titles and abstracts with concepts in the Metathesaurus and find matches through certain algorithms. A semantic type is assigned to each word. UMLS divided concepts into …

An Informatics Framework to Assess Consumer Health Language Complexity Differences: Proof-of-Concept Study | 5/21/2020

… term-level complexity of the health text, we first used the text processing and entity recognition tool MetaMap [ 45 ] to extract health terms that belong to 84 out of 127 semantic types in the Unified Medical Language System (UMLS, a compendium of over 190 medical controlled vocabularies) that are relevant to biomedicine, health, and nutrition [ 46 , 47 ]. Then we evaluated the density of professional terms and lay terms by mapping …

Identifying Emergency Department Symptom-Based Diagnoses with the Unified Medical Language System. | 12/13/2019

… follow-up plan. There is no well-defined method for identifying patients with a SBD without individual chart review. We describe a method for automated identification of SBDs from ICD-10 codes using the Unified Medical Language System (UMLS) Metathesaurus. METHODS: We mapped discharge diagnosis, with use of ICD-10 codes from a one-month period of ED discharges at an urban, academic ED to UMLS concepts and semantic types …

Applying a deep learning-based sequence labeling approach to detect attributes of medical concepts in clinical text | 12/5/2019

To detect attributes of medical concepts in clinical text, a traditional method often consists of two steps: named entity recognition of attributes and then relation classification between medical concepts and attributes. Here we present a novel solution, in which attribute detection of given concepts is converted into a sequence labeling problem, thus attribute entity recognition and relation classification are done simultaneously within one step. Methods A neural architecture combining bidirectional …

Text-mining clinically relevant cancer biomarkers for curation into the CIViC database | 12/3/2019

… Ontology [ 14 ]. All terms under the “cancer” (DOID:162) parent term were selected and filtered for nonspecific names of cancer (e.g., “neoplasm” or “carcinoma”). These cancer types were then matched with synonyms from the Unified Medical Language System (UMLS) Metathesaurus [ 29 ] (2019AA), either through existing external reference links in the Disease Ontology or through exact string-matching on the main entity names. The additional synonyms in the UMLS were then …

Will Artificial Intelligence Translate Big Data Into Improved Medical Care or Be a Source of Confusing Intrusion? A Discussion Between a (Cautious) Physician Informatician and an (Optimistic) Medical Informatics Researcher | 11/27/2019

… is more cautious. Dr Nelson was a practicing academic internist who became involved in informatics many years ago. He collaborated with Scott Blois on RECONSIDER (an early clinical decision support system) and on the Unified Medical Language System (UMLS) project. He eventually moved to the National Library of Medicine as Head of Medical Subject Headings. While at the National Library of Medicine, he fathered RxNorm, while continuing his work on …

Exploring semantic deep learning for building reliable and reusable one health knowledge from PubMed systematic reviews and veterinary clinical notes | 11/12/2019

… based resources is lack of “grounding” or “normalisation” [ 13 ], i.e. the fact that biomedical/clinical terms appearing in the NICE CPGs or BMJ Best Practice are not mapped to specific terminological entries like the Unified Medical Language System (UMLS) [ 14 ] Metathesaurus. Normalisation may help with periodic updates of evidence-based resources from the biomedical literature, as PubMed/MEDLINE articles are indexed with Medical Subject Headings (MeSH) [ 15 ], which is included …

NLM Technical Bulletin, Nov-Dec 2019, UMLS 2019AB Release Available | National Institutes of Health | 11/5/2019

Wilder V. UMLS 2019AB Release Available. NLM Tech Bull. 2019 Nov-Dec;(431):e1. 2019 November 05 [posted] The 2019AB release of the Unified Medical Language System (UMLS) Knowledge Sources is available for download as of November 4, 2019. The available downloads are: Full Release (UMLS Metathesaurus, Semantic Network, Specialist Lexicon and Lexical Tools, database load scripts, and MetamorphoSys for customizing your UMLS subset and browsing the data) UMLS Metathesaurus …

scispacy 0.2.3 | 8/23/2019

… 33 , 34 ) Spinal and bulbar muscular atrophy SBMA ( 6 , 7 ) Spinal and bulbar muscular atrophy AR ( 29 , 30 ) androgen receptor UmlsEntityLinker (Alpha feature) The UmlsEntityLinker is a SpaCy component which performs linking to the Unified Medical Language System . Note that this is currently an alpha feature. The linker simply performs a string overlap search on named entities, comparing them with a knowledge base of 2.7 million concepts using an approximate …

BioWordVec, improving biomedical word embeddings with subword information and MeSH | Nature | 5/10/2019

… domain knowledge with the text corpora can be beneficial to improve the quality of word embeddings. In the biomedical domain, there are abundant biomedical knowledge data such as the medical subject headings (MeSH) and unified medical language system (UMLS), which could be explored to complement the textual information in the literature. Intuitively, integrating such biomedical domain knowledge should help improve the quality of word embedding such that it better captures …

NLM Technical Bulletin, May-Jun 2019, UMLS 2019AA Release Available | National Institutes of Health | 5/9/2019

Wilder V. UMLS 2019AA Release Available. NLM Tech Bull. 2019 May-Jun;(428):e1. 2019 May 09 [posted] The 2019AA release of the Unified Medical Language System (UMLS) Knowledge Sources is available for download as of May 6, 2019. Metathesaurus The 2019AA Metathesaurus contains approximately 3.85 million concepts and 14.6 million unique concept names from 210 source vocabularies. Three new NCI sub-sources: NCI_CPTAC (Clinical Proteomic Tumor Analysis Consortium …

IRIS Announces FHIR® Enablement of VSAC Resources | PR Newswire | 12/21/2017

… service was delivered through IRIS’ support of the Federal Health Architecture (FHA) , and FHA’s partnership with National Library of Medicine ‘s (NLM) Value Set Authority Center (VSAC) . This RESTful API provides users holding a Unified Medical Language System ® Metathesaurus License access to the current VSAC value sets and supported code systems. The VSAC provides downloadable access to all official versions of vocabulary value sets drawn from standard vocabularies contained in …

IRIS Announces FHIR® Enablement of VSAC Resources | PR Newswire | 12/21/2017

… service was delivered through IRIS’ support of the Federal Health Architecture (FHA) , and FHA’s partnership with National Library of Medicine ‘s (NLM) Value Set Authority Center (VSAC) . This RESTful API provides users holding a Unified Medical Language System ® Metathesaurus License access to the current VSAC value sets and supported code systems. The VSAC provides downloadable access to all official versions of vocabulary value sets drawn from standard vocabularies contained in …

Charles E. Barr, MD, MPH, Appointed Chief Science Officer of Biologics and Biosimilars Collective Intelligence Consortium | PR Newswire | 12/6/2017

… and policy makers with the best research and data to inform decisions and achieve the best outcomes. In addition, Dr. Barr participated in the original design and development of the National Library of Medicine’s Unified Medical Language System (UMLS) project, served on an advisory committee to NCQA on HEDIS audits and was on the planning committee for the Observational Medical Outcomes Partnership (OMOP). He was a consultant to the Society …

Charles E. Barr, MD, MPH, Appointed Chief Science Officer of Biologics and Biosimilars Collective | PR Newswire | 12/6/2017

… and policy makers with the best research and data to inform decisions and achieve the best outcomes. In addition, Dr. Barr participated in the original design and development of the National Library of Medicine’s Unified Medical Language System (UMLS) project, served on an advisory committee to NCQA on HEDIS audits and was on the planning committee for the Observational Medical Outcomes Partnership (OMOP). He was a consultant to the Society …

Semantics-Powered Healthcare Engineering and Data Analytics | 10/26/2017

… commonly used in pharmacy management [ 4 ]. Moreover, with rich concepts linked by semantic relationships, they have also been widely used in natural language processing, data mining, machine learning, semantic annotation, and automated reasoning. The Unified Medical Language System (UMLS), developed and maintained by the United States National Library of Medicine, is a compendium of over 190 controlled vocabularies and biomedical ontologies, including ICD, SNOMED CT, and RxNorm. In the renaissance …