A talk about the merger and refactoring of the eagle-i and VIVO ontologies presented by myself, Brian Lowe, Janos Hajagos, and Erich Bremer at the VIVO2013 conference in St. Louis

1. Integrated Semantic Framework:
launching the next generation
VIVO ontology
Erich Bremer, Jon Corson-Rikert,
Melissa Haendel,
Janos Hajagos and Brian Lowe
@ontowonka
net w o r k

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People and Resources
techniques
training
protocols
affiliation
roles
grants
credentials
genes
anatomy
manufacturer
publications
disease

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CTSAConnect Project
Connecting 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

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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-i
Resources
VIVO
People
Coordination
eagle-i
VIVO
Semantic
Clinical
activities

5. ISF Content and modularization
eagle-i
Research resources
VIVO
Person profiling
CTSA ShareCenter
Discussions, requests,
share documents
ISF
Contact Organizations
Affiliations
Services Events
Clinical
Expertise
Reagents
Organisms
Credentials
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Original Ontologies
eagle-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

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A first approach
Goals:
 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

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Preferred 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

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What the ISF means for VIVO
 Fewer object properties
 hasRole
 hasAttendeeRole
 hasClinicalRole
 hasPartnerRole
 hasOrganizerRole
 hasOutreachProviderRole
 hasTeacherRole
 …

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What the ISF means for VIVO
 Fewer object properties
 hasRole
 hasAttendeeRole
 hasClinicalRole
 hasPartnerRole
 hasOrganizerRole
 hasOutreachProviderRole
 hasTeacherRole
 …

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Original Motivation

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Original Motivation

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New Approach
 Consistently query for type of related resource
 Configure application behavior for property and class
combinations, not properties alone
Person
Teacher
Role
hasRole
Presenter
Role
hasRole
“teaching activities”
“presentations”

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Reified Relationships
Thing Thing
vivo:
Relation-
ship
time
interval

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Reified Relationships
foaf:Person
bibo:
Document
vivo:
Authorship
author
rank
vivo:authorInAuthorship vivo:linkedInformationResource

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Reified Relationships
foaf:Person
bibo:
Document
vivo:
Authorship
author
rank
vivo:authorInAuthorship vivo:linkedInformationResource

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Reified Relationships
foaf:Person
bibo:
Document
vivo:
Authorship
author
rank
vivo:relates vivo:relates

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Reified Relationships
Thing Thing
time
interval
vivo:relates vivo:relates
AdvisingRelationship
Authorship
AwardedDegree
AwardReceipt
Editorship
Grant
IssuedCredential
Position

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Relationships and Roles Together
Person Person
Mentoring
Relationship
mentor
role
mentee
role
Mentoring
Process

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Relationships and Roles Together
Person
Funding
Organiza-
tion
Grant
PI
role
funder
role

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Fewer Person Subclasses
 Most Person subclasses removed from ISF
 Retained in VIVO application until 1.7+
 Person
 FacultyMember
 NonFacultyAcademic
 Postdoc
 Librarian
 Archivist
 …

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Fewer Person Subclasses
 Better to query for people by positions and roles
 Person
 FacultyMember
 NonFacultyAcademic
 Postdoc
 Librarian
 Archivist
 …

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Three examples of merging and
refactoring
 Tackle an open design/representation issue proposing
a new design pattern (position of a person over time)
 Reference/incorporation of external vocabularies or
taxonomies
 Merging two different design approaches (Person and
Contacts) using existing standard (Vcard)

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Merging person and contact representation

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eagle-i ontology browser with ISF

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Inclusion of external vocabularies in
the ISF

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Including vocabularies in ISF
ISF ontology Vocabularies

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Using external vocabularies together

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 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

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UMLS Integration
The Unified Medical Language System (UMLS) Metathesaurus is a
long term project of the National Library of Medicine

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Additional vocabularies
RxNorm
SNOMED CT CPT
ICD9CM, MeSH, and NCIt are made available in the initial CTSAconnect release

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Expressed as a SKOS Vocabulary

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Cross vocabulary concept mapping

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Connect to the full UMLS

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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

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ISF/VIVO Ontology Working Group
 Extending and building on the ISF going forward
• Collaborating with other VIVO working groups to assure
the ISF evolves as it needs it to
• Synergies with ShareCenter, eagle-i, Plumage from UCSF
 Engaging as a community with SciENCV, CASRAI,
euroCRIS LOD group, CTSA Ontology Affinity Group,
and others
 Biweekly calls, mailing list, documentation – all on
wiki.duraspace.org/display/vivo

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ISF/ShareCenter Drupal Integration
1) Mapping Drupal Node Fields with corresponding ISF
Predicates
2) Integration Issue #1 – Drupal creates it’s own URIs for
mappings.
3) Importing of custom RDF augmentation to Drupal
RDF Store (ARC2)
4) Integration Issue #2 – ARC2 store wiped clean on
each re-indexing

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Team
CTSA 10-001: 100928SB23
PROJECT #: 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-
Waldegg
Sophia Cheng
Share Center:
Chris Kelleher, Will
Corbett, Ranjit Das,
Ben Sharma
University at Buffalo:
Barry Smith, Dagobert
Soergel
CTSAconnect project
ctsaconnect.org
ISF ontology
sourcehttp://code.google.com/p/connect-
isf/
ISF 1.0 Documentation
http://connect-
isf.googlecode.com/svn/release/2013-07-
31/isf-1.0-documentation.pdf
New Duraspace Ontology Working Group
https://wiki.duraspace.org/pages/viewpage.
action?pageId=34656953
Resources