Business case reviewOntology equivalence mapping

John Wise and Carmen Nitsche

March 2015

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Problem statement

Ontologies are critical to manage life sciences data.  

Within each domain we often find multiple ontologies being applied not just between organizations, but even within a single organization.  

This makes information access and retrieval across the varied and silo'ed data repositories very difficult.  What is not needed is another ontology, but rather a better understanding of what applicable ontologies are used, ways to improve the existing ontologies, and ways to interchange between these ontologies.  As part of such an effort, it might be helpful to establish a generic template for conversion of one ontology to another.  

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Proposal / Value PropositionFacilitate the application and consumption of ontologies by Pistoia Alliance Members and the wider Life Science community.

Distill a consensus-based opinion from Pistoia Alliance Members to influence and support providers of ontological resources in commercial organisations and academic institutions.

Establish an expert community to:

1. focus on a particular ontological theme,

2. understand and represent member needs,

3. define guidelines for best practise,

4. define requirements for an ontology mapping tool

5. devise and create a sustainable ontology mapping service.

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Ontology Equivalence Mapping leadership

• Champion: Martin Romacker, Roche• Project Lead: Gordon Baxter, Instem• Project Manager: Ian Harrow

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Expert Community Group

Formation of an Expert Community Group (possible name: Applied Ontologies Expert Community?). This group will be instrumental for the operation of this project.

Formal Survey of Needs

Conduct a formal survey to understand the needs of Pistoia members for the successful application of ontologies and to enable selection of a content deliverable by the Expert Community Group. This process will also give opportunity to recruit more members to the expert community group.

Guidelines for Minimal Standards

Develop guidelines for minimal standards to enable the application of ontologies. This will encourage best practise and serve as a reference for ontology providers (open source and commercial).

Process Deliverables - Foundational

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The following ontology themes emerged from interviews, conducted by the author, with representatives from ten Pistoia Member organisations (as listed in Appendix a.).

It is expected that the expert community group will select one theme, making use of the survey results.

Ontology themes to be considered

• Human Disease and Mammalian Phenotype

• Biomarkers

• Macromolecules

• Assays

• Pathways

Content Deliverables

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Ontologies Mapping Tool

Better tools are required by ontology users to map and visualise ontologies to understand potential overlaps and identify equivalence. Survey the existing ontology tools to show their capabilities, target user and define the user requirements for an Ontologies Mapping Tool. This would lead to an open competition to attract solutions with suitable incentives. One useful way to articulate the user requirements could be to define relevant use cases, the implementation of which can then be attempted in the evaluated tools.

Ontologies Mapping Maintenance Service

This service could be developed from a strategic road map defined by the Expert Community with initial focus on the selected theme for content delivery. The maintenance service would show case the guidelines for minimal standards. The Expert Community would set up a request for proposal (RFP) to attract proposals from academic consortia..

Process Deliverables - Advanced

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2016Q2 Q3 Q4 Q12016 Q2 Q3

Establish team and launch kick-off meeting5/15/2015

Define guidelines for minimum standards & select ontology theme for first mapping exercise9/15/2015

Phase 2: Define and create ontology mapping service8/15/2016

Conduct user survey6/15/2015

Develop ontology mapping tool (e.g. competition, shared risk funding, RFP, etc.)

3/15/2016

Proposed timelines

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9

Estimated resource requirement

February 23, 2015 Advancing the emerging portfolio

DELIVERABLES PHASE ESTIMATED COST

Project management 1&2 $100,000

Communications 1&2 $50,000

Ontology Equivalence Mapping tool 1 $80,000

Ontology Mapping Service 2 $70,000

TOTAL $300,000

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Interest community:

Organisation

Eagle Genomics Ltd.

GSK

Instem

The Jackson Laboratory

J&J

Merck

NCBI

Organisation

Novartis

Osthus

Roche

Sanofi

Takeda

Thomson Reuters

UCB

The following companies contributed to the business case and/or have indicated interest:

@pistoiaalliance www.pistoiaalliance.org