SciBite - Role Of Ontologies (Pistoia Alliance Webinar)
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Transcript of SciBite - Role Of Ontologies (Pistoia Alliance Webinar)
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13 May 2023
Ontologies In The SciBite PlatformLee Harland | @SciBitely | www.scibite.com
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23 May 2023
80-90% of all potentially usable business information may originate in unstructured form
https://en.wikipedia.org/wiki/Unstructured_data
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33 May 2023
‘Semantics-as-a-Service’
Text ContentDocuments & Databases
Ontologies:Gene/Disease/Drug; Molecular; Chemical; Clinical; Adverse Event; PharmSci & Manufacturing; Business & Commercial; Regulatory; Geo-location; University/Company
Structured Data
+SciBite
API
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43 May 2023
Public Ontologies Are Vital
What They Are Great For• Providing a open, consistent, stable
identifier for a given “thing”• Developing community consensus as to
what that ”thing” is• Developing community consensus on what
all the things are • Powering Data Integration• Powering Scientific Analytics
Not Designed For Text Analytics/Mining
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3 Key Issues
53 May 2023
e.g. Human Phenotype Ontology (HPO) is a gold reference standard for phenotypes and many use cases start with “find all the phenotypes….”
But 6997 synonyms in current HPO over 11375 entities. Similar for many others as not their raison d'etre
1. Synonym Coverage
2. Coding Style 3. Ambiguity
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63 May 2023
Ontology Engineering
Raw Ontologies
Public SciBite
Customer
Expert Curation
Training, Testing, & Validation
TERMite
Feedback To Producers
Automated Learning, Enrichment & Curation
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SciBite Ontology Enrichment*
SciBite
HPO
MeSH
HGNC
Original
* Actual search space many fold larger due to adaptive matching
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83 May 2023
Ontology-Driven Search
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Ontology-Driven Search Everywhere!
93 May 2023
SciBite
Researchers (End User)
Information Management
(Content Awareness)
Informatics(Text Mining)
System Developers (3rd Party Integration)
Pharma’s Internal Apps
Commercial Content/Software
Providers
Competitor IntelligenceLiterature Awareness, Trends & AlertingAlign 3rd Party Content
Disease & Phenotype Networks, PPIs, Pharmacovigilance, Drug-Target/Biomarker MiningPatent MiningMachine Learning/AIDocument Management, Enterprise & Local Search,Ontology-XREFSemantic Auto-completeRDF & Integration
Customer-Provider IntegrationOntology-driven applicationsSmarter Apps!
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103 May 2023
Summary
• Text (Databases & Documents) accounts for large amount of corporate “knowledge”
• Public & Internal Ontologies have great potential in structuring this text into minable data
• But these ontologies require significant processing, both human and automated in order to make them “fit for purpose”
• Combine this with a fast, flexible, simple API and you can address a vast array of different use cases in– Software Vendors & Systems Developers– Content Providers– Data Scientists & Text Miners