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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