Using SNOMED CT with the UMLS - Medical Ontology Research

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MetaMap • Developed by NLM http://metamap.nlm.nih.gov/ • To map biomedical text to UMLS concepts • Target can be restricted to specific vocabularies • Mapping algorithm ◦ parsing – noun phrases identified ◦ variant generation ◦ candidate retrieval – retrieve all Metathesaurus strings containing at least one of the variants ◦ candidate evaluation – based on centrality, variation, coverage and cohesiveness ◦ mapping construction – complete mappings constructed by combining candidates
Inter-terminology mapping • Make use of the concept structure of the UMLS to identify equivalence between terminologies • Utilize the relationships between UMLS concepts to improve yield
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Using SNOMED CT with the UMLS IHTSD
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Outline • Overview of the UMLS
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Overview of the UMLS Introduction
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Motivation • Started in 1986 •
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Overview of the UMLS Overview throu
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Adrenal insufficiency Clinical vari
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AD in medical vocabularies • Syno
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MeSH Disease Endocrine system disea
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SNOMED International Disease/Diagno
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SNOMED CT (UMLS view) Disorder of e
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ICD-10 Endocrine, nutritional and m
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organize concepts Disease Endocrine
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UMLS view Immune system diseases Di
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Categorize concepts • High-level
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Lexical knowledge Adrenal gland dis
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Additional knowledge: UMLS editors
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Overview of the UMLS UMLS Knowledge
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UMLS Metathesaurus
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Source Vocabularies (2011AA) • 16
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Biomedical terminologies (cont’d)
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Integrating subdomains Clinical rep
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Addison’s Disease: Concept Diseas
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Metathesaurus Evolution over time
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Symbolic relations • Relation ◦
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Everything else • Co-occurrence i
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UMLS Semantic Network
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Semantic Network • Semantic netwo
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Associative (non-isa) relationships
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Relationships may inherit semantics
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SPECIALIST Lexicon • Content ◦
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Orthography • Spelling variants
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Lexical tools • To manage lexical
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Normalization Example Hodgkin Disea
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Indexes • Word index ◦ word to
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Overview of the UMLS Conclusions
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Trans-namespace integration Addison
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Dr. Kin Wah Fung SNOMED CT integrat
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Different views of synonymy • In
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UMLS editing process • Analysis o
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Examples of split SNOMED CT synonym
Page 81 and 82: SNOMED CT Concept View Acetaminophe
Page 83 and 84: Common types of cross-hierarchy mer
Page 85 and 86: Extent of disagreement • Splittin
Page 87 and 88: Dr. Kin Wah Fung Representing SNOME
Page 89 and 90: SNOMED CT is more complex than othe
Page 91 and 92: Rich Release Format (RRF) • Also
Page 93 and 94: SNOMED CT Concepts SNOMED CT Concep
Page 95 and 96: SNOMED CT Relationships SNOMED CT R
Page 97 and 98: Dr. Olivier Bodenreider Applying UM
Page 99 and 100: Beta-blocker in SNOMED CT
Page 101 and 102: Finding variants in other sources S
Page 103 and 104: Ms. Janice H. Willis Applying UMLS
Page 105 and 106: SNOMED CT QA What we learn from mai
Page 107: UTS browser • https://uts.nlm.nih
Page 110 and 111: Search options include limiting by
Page 112 and 113: Metathesaurus Browser Tree search t
Page 114 and 115: SNOMED CT-centric display Click CUI
Page 116 and 117: Metathesaurus Browser Tree search d
Page 118: http://www.nlm.nih.gov/research/uml
Page 121 and 122: Getting started with the UTS API
Page 123 and 124: Getting a proxy granting ticket pri
Page 125 and 126: Getting a single-use proxy ticket p
Page 127 and 128: Mapping • ‘Mapping’ generally
Page 129 and 130: Mapping terms to a terminology •
Page 131: Example of synonym substitution •
Page 135 and 136: The IntraMap algorithm (2) 2. A tar
Page 137 and 138: Use of MetaMap for inter-terminolog
Page 139 and 140: Motivation • Translation ◦ Seed
Page 141 and 142: Multi-lingual vocabularies in the U
Page 143 and 144: Finding terms in other languages
Page 145 and 146: Addison’s disease in UMLS
Page 147 and 148: C0001403 in Dutch Source Term type
Page 149 and 150: Dr. James T. Case Use case: The rol
Page 151: Access to the USCRS
Page 154 and 155: Dentistry SNOMED CT International 1
Page 156 and 157: Why integrate UMLS with a SCT brows
Page 158 and 159: No SNOMED CT Description Informs yo
Page 160 and 161: UMLS Concept Concept exists in ICD9
Page 162 and 163: References: UMLS home page • UMLS
Page 164 and 165: References • UMLS as a research p
Page 166 and 167: References • SNOMED CT and UMLS
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Using SNOMED CT with the UMLS - Medical Ontology Research

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