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Automatic Mapping Clinical Notes to Medical Terminologies

Jon D. Patrick, Yefeng Wang, Peter Budd
2006 Australasian Language Technology Association Workshop  
Automatic mapping of key concepts from clinical notes to a terminology is an important task to achieve for extraction of the clinical information locked in clinical notes and patient reports.  ...  The present paper describes a system that automatically maps free text into a medical reference terminology.  ...  The present work proposes a system that automatically recognises medical terms in free text clinical notes and maps them into SNOMED CT terminology.  ... 
dblp:conf/acl-alta/PatrickWB06 fatcat:juwli4jknndgtj4oos2bfpa4su

Using Medical Text Extraction, Reasoning and Mapping System (MTERMS) to process medication information in outpatient clinical notes

Li Zhou, Joseph M Plasek, Lisa M Mahoney, Neelima Karipineni, Frank Chang, Xuemin Yan, Fenny Chang, Dana Dimaggio, Debora S Goldman, Roberto A Rocha
2011 AMIA Annual Symposium Proceedings  
The local medication terminology had 83.0% coverage compared to RxNorm's 98.0% coverage for free-text notes. 61.6% of mappings between the terminologies are exact match.  ...  Our goal is to develop a general natural language processing (NLP) system, called Medical Text Extraction, Reasoning and Mapping System (MTERMS), which encodes clinical text using different terminologies  ...  The gap in knowledge addressed is an automated approach to mapping terminologies that can be used to extract clinical concepts from notes to increase the interoperability and utility of clinical information  ... 
pmid:22195230 pmcid:PMC3243163 fatcat:ek7jm7rf4vbzthfurwrdg6gskq

Introduction of Enhancement Technologies into the Intensive Care Service, Royal Prince Alfred Hospital, Sydney

Angela Ryan, Jon Patrick, Robert Herkes
2008 Health Information Management Journal  
The Ward Round Information System (WRIS) has been designed to convert clinicians' clinical notes into the formal medical encoding ontology SNOMED-CT, thus enabling more consistent descriptions of patient  ...  terminology, such as Systematised Nomenclature of Medicine -Clinical Terms (SNOMED-CT).  ...  The inherent variation in the vocabulary of medical terminology is an obstacle to the efficient automatic analysis of electronic clinical notes.  ... 
doi:10.1177/183335830803700105 pmid:18245864 fatcat:giejld3akfgidebo2aoc2c2pym

A Lexical-Ontological Resource for Consumer Healthcare [chapter]

Elena Cardillo, Luciano Serafini, Andrei Tamilin
2010 Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering  
Furthermore, existing clinically-oriented terminologies cannot provide sufficient support when integrated into consumer-oriented applications, so there is a need to create consumer-friendly terminologies  ...  In Consumer Healthcare Informatics it is still difficult for laypeople to find, understand and act on health information, due to the persistent communication gap between specialized medical terminology  ...  directly read and interpret clinical notes or test results.  ... 
doi:10.1007/978-3-642-11745-9_21 fatcat:6lbzk6hkordclfbfcjkzc6hcia

Ontologizing Health Systems at Scale: Making Translational Discovery a Reality (Podium Abstract)

Tiffany J Callahan, Jordan M Wyrwa, Nicole A Vasilevsky, Peter R Robinson, Melissa A Haendel, Lawrence E Hunter, Michael G Kahn
2021 Zenodo  
This entry contains the podium abstract that was presented at the 2021 American Medical Informatics Association Virtual Informatics Summit (https://amia.org/education-events/amia-2021-virtual-informatics-summit  ...  To address these limitations, we have developed OMOP2OBO, the first health system-wide integration and alignment between Observational Medical Outcomes Partnership (OMOP) standardized clinical terminologies  ...  The ratio of automatic to manual mappings differed by clinical domain and ontology with conditions and drug ingredients having more automatic mappings than measurements.  ... 
doi:10.5281/zenodo.5716459 fatcat:nfmenf74oncjljfcqhrhsv4duu

Creation of an Interface Terminology of Abdominal Ultrasonography Pathologies Using a SNOMED CT to Automate the Process of Ultrasound Note Creation

Shvyrev S, Surin M, Rodionov V
2012 European Journal for Biomedical Informatics  
Conclusions: SNOMED CT has shown high eciency in the encoding of specialized clinical terminology. The methodology used allowed us to extract the necessary terms for a given domain.  ...  A lack of common principles of coding of health information leads to diculties of interpretation and automatic processing of ultrasound ndings, as well as the inability to ensure interoperability.  ...  Considering that dierent clinicians use dierent terminology to describe the same medical concept, the interpretation of medical reports and automatic processing becomes more dicult.  ... 
doi:10.24105/ejbi.2012.08.3.9 fatcat:n4m57htflndjre5bzluserveme

Using SNOMED CT in combination with MedDRA for reporting signal detection and adverse drug reactions reporting

Olivier Bodenreider
2009 AMIA Annual Symposium Proceedings  
This approach has the potential to enable the collection of adverse events related to drugs directly from clinical repositories. The quality of the mapping needs to be evaluated.  ...  Through the descendants in SNOMED CT, 108,305 additional SNOMED CT concepts can be linked to MedDRA. Fine-grained SNOMED CT concepts can be mapped automatically to MedDRA.  ...  A MedDRA license was provided to the author for research purposes by MedDRA MSSO / Northrop Grumman Corporation.  ... 
pmid:20351820 pmcid:PMC2815504 fatcat:xvioyc5q6jafnatez5pdzs5gnu

Coverage of patient safety terms in the UMLS metathesaurus

Aziz A Boxwala, Qing T Zeng, Anthony Chamberas, Luke Sato, Meghan Dierks
2003 AMIA Annual Symposium Proceedings  
Terms from three proprietary patient safety terminologies were mapped to the concepts in UMLS by an automated mapping program developed by us.  ...  The integration and large-scale analyses of medical error databases would be greatly facilitated by the use of a standard terminology.  ...  Table 3 . 3 Performance of the automatic mapping tool. Note that the program did not match 39 terms to any concepts. Keys: C=Correct, PC=Partially Correct, IC=Incorrect.  ... 
pmid:14728144 pmcid:PMC1479991 fatcat:563cu6dwdbf7fi6gxi2xibrqzy

SNOMED CT for processing of free text in healthcare: a systematic scoping review (Preprint)

Christophe Gaudet-Blavignac, Vasiliki Foufi, Mina Bjelogrlic, Christian Lovis
2020 Journal of Medical Internet Research  
However, currently, there is no easy solution for mapping free text to this terminology and to perform automatic postcoordination.  ...  In total, 12 different software packages were used to map text to SNOMED CT concepts, the most frequent being Medtex, Mayo Clinic Vocabulary Server, and Medical Text Extraction Reasoning and Mapping System  ...  MCVS: Mayo Clinic Vocabulary Server. b MTERMS: Medical Text Extraction Reasoning and Mapping System. c MedLEE: Medical Language Extraction and Encoding System. d cTAKES: clinical Text Analysis and Knowledge  ... 
doi:10.2196/24594 pmid:33496673 fatcat:vjrifdnmy5et5gdujfcvwnjntq

Cross-terminology mapping challenges: A demonstration using medication terminological systems

Himali Saitwal, David Qing, Stephen Jones, Elmer V. Bernstam, Christopher G. Chute, Todd R. Johnson
2012 Journal of Biomedical Informatics  
We found that three methods were required to accurately map the majority of actively prescribed medications. Only 62.5% of source medication codes could be mapped automatically.  ...  Compound drugs were especially difficult to map: only 7.5% could be mapped using the automatic method.  ...  One limitation is that we used fairly simple approaches to mapping medications that we could not map automatically.  ... 
doi:10.1016/j.jbi.2012.06.005 pmid:22750536 pmcid:PMC4398308 fatcat:3nflp44my5huzghtyxs3bu3riu

Integrating Consumer-Oriented Vocabularies with Selected Professional Ones from the UMLS Using Semantic Web Technologies [chapter]

Elena Cardillo, Genaro Hernandez, Olivier Bodenreider
2011 Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering  
Our work leverages the Italian consumer-oriented medical vocabulary and its mapping to the ICPC2 terminology.  ...  professionals (i.e., mapped to terms from existing medical vocabularies).  ...  Mapping to several terminologies. Among the 336 ICPC2 concepts mapped to the other resources, 90 map to two terminologies (e.g. A71 -Measles), 130 map to 3 terminologies (e.g.  ... 
doi:10.1007/978-3-642-23635-8_7 fatcat:a7qwq7x3wfg6jmdbjyroyhq7mi

Normalization and standardization of electronic health records for high-throughput phenotyping: the SHARPn consortium

Jyotishman Pathak, Kent R Bailey, Calvin E Beebe, Steven Bethard, David S Carrell, Pei J Chen, Dmitriy Dligach, Cory M Endle, Lacey A Hart, Peter J Haug, Stanley M Huff, Vinod C Kaggal (+20 others)
2013 JAMIA Journal of the American Medical Informatics Association  
These resources were used to demonstrate semi-automatic execution of MU clinical-quality measures modeled using the Quality Data Model (QDM) and an open-source rules engine.  ...  Extracted information was standardized and normalized to meaningful use (MU) conformant terminology and value set standards using Clinical Element Models (CEMs).  ...  All authors contributed to and approved the final manuscript.  ... 
doi:10.1136/amiajnl-2013-001939 pmid:24190931 pmcid:PMC3861933 fatcat:k4l6a7laqvbfthjoz7twmqkm6i

Extracting clinical cases from XML-based electronic patient records for use in web-based medical case based reasoning systems

S Manickam, S S Abidi
2001 Studies in Health Technology and Informatics  
Development and usage of Case Based Reasoning (CBR) driven medical diagnostic system requires a large volume of clinical cases that depict the problem-solving methodology of medical experts.  ...  To address this constraint we present a strategy to pro-actively transform generic Electronic Patient Records (EPR) to Operable CBR-oriented Cases (OCC) that are compliant to specialised CBR-based medical  ...  of the CBR system (i.e. case structure); and (v) terminological and conceptual standardisation of heterogeneous clinical cases to a common information standard.  ... 
pmid:11604816 fatcat:dbciov75srclzm7a6qnpjhtr5u

Leveraging XML-based electronic medical records to extract experiential clinical knowledge

Syed Sibte Raza Abidi, Selvakumar Manickam
2002 International Journal of Medical Informatics  
In practical terms, procurement of CBRcompliant cases is quite challenging, as this requires medical experts to map their experiential knowledge to an unfamiliar computational formalism.  ...  We present a methodology to autonomously transform XML-based EMR to specialized CBR-compliant cases for CBRdriven medical diagnostic systems.  ...  equivalence EMR content Terminological mapping OCC content (after terminological mapping) . . . . . .  ... 
doi:10.1016/s1386-5056(02)00076-x pmid:12467802 fatcat:2swqsw72cnexlalkxavovab6se

Standardizing Heterogeneous Annotation Corpora Using HL7 FHIR for Facilitating their Reuse and Integration in Clinical NLP

Na Hong, Andrew Wen, Majid Rastegar Mojarad, Sunghwan Sohn, Hongfang Liu, Guoqian Jiang
2018 AMIA Annual Symposium Proceedings  
The framework contains two main modules: 1) an automatic schema transformation module, in which the annotation schema in each corpus is automatically transformed into the FHIR-based schema; 2) an expert-based  ...  We demonstrated that it is feasible to leverage FHIR as a standard data model for standardizing heterogeneous annotation corpora for their reuse and integration in advanced clinical NLP research and practices  ...  Due to that the SHARPn corpora contain all the common sections in clinical notes, we call it the General Clinical Corpora in the following illustration, and list a number of example mappings.  ... 
pmid:30815098 pmcid:PMC6371380 fatcat:hjvggnpvnja65pgpkkebvvejhe
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