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Biomedical subjects

William T Hole

Publications and source records attributed to William T Hole.

7 recordsLinked to original sources
PubMed2005

Integrating SNOMED CT into the UMLS: an exploration of different views of synonymy and quality of editing.

OBJECTIVE: The integration of SNOMED CT into the Unified Medical Language System (UMLS) involved the alignment of two views of synonymy that were different because the two vocabulary systems have different intended purposes and editing principles. The UMLS is organized according to one view of synonymy, but its structure also represents all the individual views of synonymy present in its source vocabularies. Despite progress in knowledge-based automation of development and maintenance of vocabularies, manual curation is still the main method of determining synonymy. The aim of this study was to investigate the quality of human judgment of synonymy. DESIGN: Sixty pairs of potentially controversial SNOMED CT synonyms were reviewed by 11 domain vocabulary experts (six UMLS editors and five noneditors), and scores were assigned according to the degree of synonymy. MEASUREMENTS: The synonymy scores of each subject were compared to the gold standard (the overall mean synonymy score of all subjects) to assess accuracy. Agreement between UMLS editors and noneditors was measured by comparing the mean synonymy scores of editors to noneditors. RESULTS: Average accuracy was 71% for UMLS editors and 75% for noneditors (difference not statistically significant). Mean scores of editors and noneditors showed significant positive correlation (Spearman's rank correlation coefficient 0.654, two-tailed p < 0.01) with a concurrence rate of 75% and an interrater agreement kappa of 0.43. CONCLUSION: The accuracy in the judgment of synonymy was comparable for UMLS editors and nonediting domain experts. There was reasonable agreement between the two groups.

Semantics↗
PubMed2004

Achieving "source transparency" in the UMLS Metathesaurus.

The UMLS Metathesaurus is a syntactically uniform, concept-based, semantically enhanced representation of many of the world's authoritative biomedical vocabularies. Released several times a year, the Metathesaurus is becoming a common, longitudinally maintained source of the current versions of these vocabularies. As vocabularies become standards for reimbursement, reporting, interoperation, and use by applications, the vocabulary obtained from the Metathesaurus must be consistent with that obtainable from each vocabulary's authority. Effective with the first 2004 release, the Metathesaurus represents new and updated sources "transparently"--both users and applications are able to "see" each vocabulary in the Metathesaurus without any of the small losses of information introduced by abstractions used in previous versions. Thus, the Metathesaurus can continue to provide its many semantic and lexical value-added features while guaranteeing that original sources will be "visible" in intact form. Vocabulary users and application developers will benefit from the enhancements and economies of scale offered by the Metathesaurus, while preserving distinctions between content provided by external authorities and content added as part of the Metathesaurus development and maintenance process.

Unified Medical Language System↗
PubMed2002

A semantic normal form for clinical drugs in the UMLS: early experiences with the VANDF.

A semantic normal form (SNF) for a clinical drug, designed to represent the meaning of an expression typically seen in a practitioner's medication order, has been developed and is being created in the UMLS Metathesaurus. The long term goal is to establish a relationship for every concept in the Metathesaurus with semantic type "clinical drug" with one or more of these semantic normal forms. First steps have been taken using the Veterans Administration National Drug File (VANDF). 70% of the entries in the VANDF could be parsed algorithmically into the SNF. Next steps include parsing other drug vocabularies included in the UMLS Metathesaurus and performing human review of the parsed vocabularies. After machine parsed forms have been merged in the Metathesaurus Information Database (MID), editors will be able to edit matched SNFs for accuracy and establish relationships and relationship attributes with other clinical drug concepts.

Algorithms↗
PubMed2002

Tracking meaning over time in the UMLS Metathesaurus.

The Unified Medical Language System(R) (UMLS) Metathesaurus contains records arranged by concept or meaning. Each concept contains a unique identifier (CUI) that can be used to track the concept over time. Since the January 2001 release, the Metathesaurus has included the file MRCUI that contains mappings for CUIs that disappear. This paper describes the processes that facilitated this effort and the ongoing effort to find suitable mappings for concepts whose meanings no longer exist in the Metathesaurus. This study highlights the need to identify missed synonymy prior to a release. It also shows a need to work more closely with source providers to identify the closest match in the Metathesaurus when they eliminate terms from their vocabularies.

National Library of Medicine (U.S.)↗
PubMed2002

Finding UMLS Metathesaurus concepts in MEDLINE.

The entire collection of 11.5 million MEDLINE abstracts was processed to extract 549 million noun phrases using a shallow syntactic parser. English language strings in the 2002 and 2001 releases of the UMLS Metathesaurus were then matched against these phrases using flexible matching techniques. 34% of the Metathesaurus names (occurring in 30% of the concepts) were found in the titles and abstracts of articles in the literature. The matching concepts are fairly evenly chemical and non-chemical in nature and span a wide spectrum of semantic types. This paper details the approach taken and the results of the analysis.

MEDLINE↗
PubMed2002

Integration of a standard gastrointestinal endoscopy terminology in the UMLS Metathesaurus.

MST(c), a standard terminology for gastrointestinal endoscopy reporting, was integrated in the January 2002 UMLS Metathesaurus in order to ease the practical interoperability of clinical data repositories in gastroenterology. The integration required full specification of names, resolution of discrepancies between English, French and Italian versions of MST, appropriate categorization with UMLS Semantic Types and MST-level Class attributes, assignment of explicit intra-table (and some useful inter-table) relationships mainly at concept level but also at the source level in order to retain and fully represent the original explicit and implicit MST organization. Main results, problems encountered and future plans are discussed.

Endoscopy, Gastrointestinal↗