Agenda
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Presentation regarding terminology services –
Ergin/Cui
Discuss Tech team timelines and deliverables
– All /Anu
Come up a with a high level technology view
of the architecture for guidance of prototype
development (architecture diagram) Claudiu
Brief updates from others
Supported by the NIH grant 1U24 AI117966-01 to the University of California, San Diego
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Terminology Services (Ergin)
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Requirements?
Supported by the NIH grant 1U24 AI117966-01 to the University of California, San Diego
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ngram
Input
Query Entry
Terminology
Server
ontology
Prepare
Identify
Entities
Organize
results
Expand
(synonyms,
hyponyms)
Run
Execute
query
Presentation
Format and
List
Apply Filter
Categorization
Refine
Terminology in search
Query Entry
ngram
Input
Query Entry
Terminology
Server
ontology
Prepare
Identify
Entities
Organize
results
Expand
(synonyms,
hyponyms)
Run
Execute
query
Presentation
Categorization
Refine
Format and
List
Apply Filter
ngram
Input
Query Entry
Terminology
Server
ontology
Prepare
Identify
Entities
Organize
results
Expand
(synonyms,
hyponyms)
Run
Execute
query
Presentation
Categorization
Refine
Format and
List
Apply Filter
Terminology Server in Search
Search string à Phrases and operators
v  Phrases à Term
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Term identification (NER)
Term à Term class (entity type, semantic
type)
v  Term à Related terms (synonyms,
hyponyms)
v  Term à Semantic links (?)
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Terminology Server in Indexing
Document à Phrases
v  Phrases à Terms
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Term identification (NER)
Term à Related terms
Terminology – other
Organize/customize search results based
on datasource
v  Terminology Management functionality
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Import (owl, rdf), Update, Map, List, view
meta information(date create, update, who,
when?, is active, …)
NIF – OntoQuest
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List all ontologies
Display information about a particular ontology:
Download an ontology file: Download the file (.owl)
corresponding to the given ontology.
Get defined categories in an ontology
Get Concept
Search Concepts
Get parents/children of a given concept
Get subclasses/superclasses, parts/whole of a given
concept
Get siblings of a given concept
Search terms starting with the query
Search term properties
Terminology
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Primary
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Disease (Condition)
Drug (Chemical, Substance, Compound)
Omic: Gene – Protein
Auxillary
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Body Structure
Procedure
•  Laboratory
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Organism
Maybe
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Physical object
Terminology Content
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MeSH
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Backbone
Supported by
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Gene ontology/nomenclature
•  GO, HGNC, NCBI
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SNOMED CT
NCI Thesaurus
PubChem
UMLS CUIS as the glue
Maybe
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Protein db
•  HPRD, NCBI
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ICD9, ICD10
RxNorm
LOINC
OpenGALEN
GRAIL language
v  Not free
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CTS-R2 implementations
Draft Standard, submitted by Mayo Clinics
v  http://wiki.hl7.org/index.php?
title=Common_Terminology_Services__Release_2_%28Normative%29
v  NCBO Bioportal – REST
v  NCBO Bioportal – RDF
v  eXist – An XML database
v  LexEVS
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Graph DB
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Search string à Phrases and operators
Phrases à Term
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Term à Term class (entity type, semantic type)
Term à Related terms (synonyms, hyponyms)
Term à Semantic links (?)
Organize/customize search results based on datasource
Terminology Management functionality
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Term identification (NER)
Import (owl, rdf), Update, Map, List, view meta
information(date create, update, who, when?, is active, …)
Small data: 20-30 million entires
Conclusion
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Start with a graph db
Populate
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MeSH
SNOMED CT
NCIT
…
Implement REST services for
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Normalize a phrase
Find Term
Find related term
•  parent/child
•  Synonyms
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Management (add, list, view, …)
Timeline & deliverables
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Discuss from excel spreadsheet + Jeff’s
comments
Architecture Diagram
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From Claudiu
Updates from Others
Other issues
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Any other issues?
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Thank You