ArticleAMIA ... Annual Symposium proceedings. AMIA Symposium2010
Large-scale, Exhaustive Lattice-based Structural Auditing of SNOMED CT.
Article in AMIA ... Annual Symposium proceedings. AMIA Symposium, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- Identifying Missing IS-A Relations in SNOMED CT with Fine-Tuned Pre-trained Language Models and Non-lattice Subgraphs.AMIA ... Annual Symposium proceedings. AMIA Symposium · 2024Article
- Logical definition-based identification of potential missing concepts in SNOMED CT.BMC medical informatics and decision making · 2023Article
- Identifying Missing IS-A Relations in Orphanet Rare Disease Ontology.Proceedings. IEEE International Conference on Bioinformatics and Biomedicine · 2022Article
- Identification of missing hierarchical relations in the vaccine ontology using acquired term pairs.Journal of biomedical semantics · 2022Article
- Automated Identification of Missing IS-A Relations in the Human Phenotype Ontology.AMIA ... Annual Symposium proceedings. AMIA Symposium · 2022Article
- Using logical constraints to validate statistical information about disease outbreaks in collaborative knowledge graphs: the case of COVID-19 epidemiology in Wikidata.PeerJ. Computer science · 2022Article
- Leveraging non-lattice subgraphs for suggestion of new concepts for SNOMED CT.Proceedings. IEEE International Conference on Bioinformatics and Biomedicine · 2021Article
- A Comparison of Exhaustive and Non-lattice-based Methods for Auditing Hierarchical Relations in Gene Ontology.AMIA ... Annual Symposium proceedings. AMIA Symposium · 2021Article
- Detecting missing IS-A relations in the NCI Thesaurus using an enhanced hybrid approach.BMC medical informatics and decision making · 2020Article
- Extending import detection algorithms for concept import from two to three biomedical terminologies.BMC medical informatics and decision making · 2020Article
- Enhancing the Quality of Hierarchic Relations in the National Cancer Institute Thesaurus to Enable Faceted Query of Cancer Registry Data.JCO clinical cancer informatics · 2020Article
- Web-based Interactive Visualization of Non-Lattice Subgraphs (WINS) in SNOMED CT.AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science · 2020Article
- Leveraging Non-lattice Subgraphs to Audit Hierarchical Relations in NCI Thesaurus.AMIA ... Annual Symposium proceedings. AMIA Symposium · 2019Article
- Assessing the practice of biomedical ontology evaluation: Gaps and opportunities.Journal of biomedical informatics · 2018Review
- An efficient, large-scale, non-lattice-detection algorithm for exhaustive structural auditing of biomedical ontologies.Journal of biomedical informatics · 2018Article
- Auditing SNOMED CT hierarchical relations based on lexical features of concepts in non-lattice subgraphs.Journal of biomedical informatics · 2018Article
- Identifying Similar Non-Lattice Subgraphs in Gene Ontology based on Structural Isomorphism and Semantic Similarity of Concept Labels.AMIA ... Annual Symposium proceedings. AMIA Symposium · 2018Article
- Overlapping Complex Concepts Have More Commission Errors, Especially in Intensive Terminology Auditing.AMIA ... Annual Symposium proceedings. AMIA Symposium · 2018Article
- Mining non-lattice subgraphs for detecting missing hierarchical relations and concepts in SNOMED CT.Journal of the American Medical Informatics Association : JAMIA · 2017Article
- Can SNOMED CT Changes Be Used as a Surrogate Standard for Evaluating the Performance of Its Auditing Methods?AMIA ... Annual Symposium proceedings. AMIA Symposium · 2017Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
One criterion for the well-formedness of ontologies is that their hierarchical structure forms a lattice. Formal Concept Analysis (FCA) has been used as a technique for assessing the quality of ontologies, but is not scalable to large ontologies such as SNOMED CT (> 300k concepts). We developed a methodology called Lattice-based Structural Auditing (LaSA), for auditing biomedical ontologies, implemented through automated SPARQL queries, in order to exhaustively identify all non-lattice pairs in SNOMED CT. The percentage of non-lattice pairs ranges from 0 to 1.66 among the 19 SNOMED CT hierarchies. Preliminary manual inspection of a limited portion of the over 544k non-lattice pairs, among over 356 million candidate pairs, revealed inconsistent use of precoordination in SNOMED CT, but also a number of false positives. Our results are consistent with those based on FCA, with the advantage that the LaSA pipeline is scalable and applicable to ontological systems consisting mostly of taxonomic links.
Indexed as
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21347113PMC3041382What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.