Finding common ground: integrating the eagle-i and VIVO ontologies

Finding common ground:integrating the eagle-i and VIVO ontologies

Carlo Torniai, Shahim Essaid, Brian Lowe, Jon Corson-Rikert, and Melissa Haendel

@[email protected]

ICBO 2013

www.ctsaconnect.org CTSAconnectReveal Connections. Realize

Potential.

People and Resources

techniques

training

protocols

affiliation

roles

grants

credentials

genes

anatomy

manufacturer

publications

disease


Potential.

CTSAConnect ProjectConnecting people and resources

Needs: Identify potential collaborators, relevant resources, and expertise across scientific disciplines

Assemble translational teams of scientists to address specific research questions

Goal is to create a semantic representation of clinician and basic science researcher expertise to enable:

More effective linking of information about clinicians and basic science researchers

Computation and publication of clinical expertise data as Linked Data (LD) for use in other applications


Potential.

Integrated Semantic Framework Ontology (ISF) suite

Merge the eagle-i and VIVO ontologies into one single ontology suite (the ISF)

Extend their coverage to include representation of clinical encounter

Modularize the ISF such that it can be made available in a set of files that can be reused independently

eagle-iResources

VIVO

People

Coordinationeagle-i

VIVO

Inte

grat

ed

Framework

Semantic

Clinical activities

ISF Content and modularization

eagle-IResearch resources

VIVOPerson profiling

CTSA ShareCenterDiscussions, requests,

share documents

ISF

Contact OrganizationsAffiliations

Services EventsClinical Expertise

ReagentsOrganisms

Credentials

CTSAconnectReveal Connections. Realize

Potential.

7/8/13 6www.ctsaconnect.org CTSAconnectReveal Connections. Realize

Potential.

Original Ontologieseagle-i resource ontology VIVO ontology

BFO as upper Ontology No upper Ontology

Has OBO Foundry principles as guiding design principles

Adopts ontologies already in wide use across the Linked Data community such as FOAF and BIBO

Aimed at driving an application as well as develop an interoperable core domain ontology

Aimed mostly at supporting data validation and data entry through the VIVO application and to produce Linked data

Active application and ontology development and live data

Active application and ontology development and live data

Somewhat unconventional scenario: Usually creating ontologies from scratch or reusing existing ontologies without above constraints


Potential.

A first approachGoals: Identify overlapping and duplicated entities in the eagle-i and VIVO ontologies Avoid severe disruptions in application compatibility Minor incremental additions to the ISF and push significant changes back to the

source ontologies

Good for: Referencing existing entities while developing new ISF-specific modules Performing initial alignments on classes in some portion of the overlapping

hierarchies

Limits: Lengthy process of identifying necessary alignments and implementing changes

in the source ontologies With no disruption to the applications, development was slow and low impact


Potential.

“Current” approach Implement the refactoring and merging disconnected from application and

data constraints Impact on the application and data migration assessed after refactoring Better balance of impact on apps and data migration versus total redesign of approach

Refactoring of source files based on content coverage


Potential.

Three examples of merging and refactoring

Merging two different design approaches (Person and Contacts) using existing standard (Vcard)

Tackle an open design/representation issue proposing a new design pattern (position of a person over time)

Reference/incorporation of external vocabularies or taxonomies


Potential.

Merging person and contact representation


Potential.

Person and their roles over time

Carlo

Travis

OHSU DMICE

Time

student

mentor

Assignment of mentor


Potential.

Assigning a relationship between people


Potential.

Semantically refining assignments


Potential.

Inclusion of external vocabularies in the ISF


Potential.

Including vocabularies in ISFISF ontology Vocabularies


Potential.

Using external vocabularies together


Potential.

Annotation view with approved or pending approval. Module view shows pending axiom changes per module and has ability to save the

changes with a log comment, and generate the spreadsheet summary

Protégé refactoring plugin


Potential.

So what? Now that eagle-i and VIVO are “on the same page,” future

development can leverage better consensus and ontologically rigorous solutions

CTSAs have a new research profiling data standard for exchange

Applications such as Vivo, eagle-i, LOKI, Profiles, SciVal, and ScienCV are working on generating ISF compliant data

We can profile people based on a much larger diversity of their activities and products of research

There is still a lot of work to do – this was a short term project and ISF could be better generalized for other use cases


Potential.

Team

CTSA 10-001: 100928SB23PROJECT #: 00921-0001

OHSU:Melissa Haendel, Carlo Torniai, Nicole Vasilevsky, Shahim Essaid, Eric Orwoll

Cornell University:Jon Corson-Rikert, Dean Krafft, Brian Lowe

University of Florida: Mike Conlon, Chris Barnes, Nicholas Rejack

Stony Brook University: Moises Eisenberg, Erich Bremer, Janos Hajagos

Harvard University:Daniela Bourges-WaldeggSophia Cheng

Share Center:Chris Kelleher, Will Corbett, Ranjit Das, Ben Sharma

University at Buffalo:Barry Smith, Dagobert Soergel

CTSAconnect project ctsaconnect.org

CTSAconnect ontology sourcehttp://code.google.com/p/connect-isf/

Resources

http://www.ctsaconnect.org/

http://code.google.com/p/connect-isf/




Date post:	20-Aug-2015
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Finding common ground: integrating the eagle-i and VIVO ontologies

Education