You are here

2014 ICBO Workshop: Starting an OBI-based Biobank Ontology


This workshop is collocated with the 2014 ICBO conference taking place in Houston, TX, USA

Objective and Scope

Biobanks are a critical resource for translational science. However, they often suffer from a lack of semantics in their ability to disseminate data and make it readily queryable. The OBO Foundry provides ontologies that are relevant to representing the structure and function of biobanks. Currently the OBO Foundry doesn't address many aspects of biobanks necessary for best utilization of their data. The organizers of this workshop have independently developed biobank ontologies [1-5] based on the Ontology of Biomedical Investigations (OBI) [6] and view this workshop as an opportunity to expand our collaboration with other ontologists interested in biobanks. We also wish to bring together people from the biobank world who are interested in bringing ontologies into this effort. The workshop will focus on problems and requirements of a biobank ontology, as well as potential solutions.

Topics of interest include, but are not limited to, the following:

  • Information models describing biobanks, their strengths, weaknesses, and competency criteria
  • Reports of biobank related ontologies
  • Case studies of applying ontologies to biobanks

All attendees will be expected to be interested in building an OBO Foundry compliant biobank ontology or providing use cases for a biobank ontology.


  1. Brochhausen M, Fransson M, Kanaskar N, Eriksson M, Merino-Martinez R, Hall RA, Norlin L, Kjellqvist S, Hortlund M, Topaloglu U, Hogan WR, Litton JE. Providing a semantically rich ontology for sharing biobank data based on Minimum Information About BIobank data Sharing. J Biomed Semantics. 2013 Oct 8;4(1):23.
  2. View OMIABIS:
  3. BioBank ontology homepage:
  4. View BioBank ontology:
  5. Essaid S, Torniai C and Haendel MA. Enabling semantic search in a bio-specimen repository. 2013 ICBO (pdf)
  6. Brinkman RR, Courtot M, Derom D, Fostel JM, He Y, Lord P, Malone J, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone SA, Soldatova LN, Stoeckert CJ Jr, Turner JA, Zheng J; OBI consortium. Modeling biomedical experimental processes with OBI. J Biomed Semantics. 2010 Jun 22;1 Suppl 1:S7

Oct. 6, 2014 Schedule
Introduction (30 min)

8:00 AM - 8:30 AM: OMIABIS and biobank.owl = a merged view of biobanks using OBI

The merged ontology can be obtained here:

Presentations (1.5 h)

8:30 AM -9:00 AM: Keynote - Dave Parrish "The Bio-Specimen Knowledge Bank - Enriching the specimen repository through ontology driven annotation and curation"

Dave Parrish is the Senior Director for Laboratory Informatics at Data in Motion and key driver of the sampleminded product strategy. He is currently fully engaged at the NIAID Integrated Research Facility (IRF) in Frederick Maryland establishing a unified research operation management system (ROMS). The IRF ROMS is a collection of commercial information management systems integrated through shared models of research data and the IRF operational workflows. The ROMS supports the complete study lifecycle from study design and review through study execution and data archive

Mr. Parrish has more than 20 years of experience developing knowledge-based solutions at the intersection of clinical research and data management. His expertise has evolved around three specific dimension of informatics: (1) Data Management and Data Warehousing, (2) Clinical Vocabularies and Controlled Terminologies, and (3) Development of Clinical Trials Ontologies, each focused on applying a pragmatic solution to clinical research. Over his career he has been at the forefront of adopting leading-edge information systems in support of clinical research. Mr. Parrish has supported a broad range information management activities—from software product development to clinical trials data center operations—that required skills to effectively involve users in the planning and implementation of client-directed, problem-oriented solutions.

9:00AM - 10:00 AM: Use case and related ontologies (15’ each plus 5’ discussion)
  • D. Birtwell & H. Williams, Penn Medicine Biobank Informatics OBI Influenced Software Design
  • R. Walls et al., A Specimen-based View of the World: Using the Biological Collections Ontology to Model Biodiversity Collections.
  • F. Manion et al., Towards a Common Semantic Representation of Informed Consent for Biobank Specimens

10:00 AM-10:15 AM Break

Discussion (1 h 45 min)

10:15 AM-11:40 AM: Joint development of the biobank ontology will take place using the OBI-based biobank ontology presented in the Introduction. Discussion of issues and needed extensions will be based on the presented use cases and existing ontologies.
  • Introduction of participants
  • Requirements and use cases
  • Extending the ontology

11:40 AM-12:00 PM: Wrap-up and future plans

Plans for further joint development and the generation of a manuscript describing the effort will be discussed.

Recommended installation before the workshop

Protege 4.3

Organizers (in alphabetical order)
Mathias Brochhausen

Division of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR

Mathias Brochhausen, PhD, MA is Assistant Professor in the Division of Biomedical Information, University of Arkansas for Medical Sciences. He has served as ontologist in multiple extramurally funded projects. He participates in the development and curation of multiple ontologies related to the Open Biomedical Ontologies Foundry, (OMRSE, IAO, d-acts, BFO). Since he joined UAMS in 2011 he has been involved in multiple funded projects as on ontologist. The focus of his research is ontology-driven medical information systems, ontology development, formal ontology, logical models in medical computation.

Melissa Haendel

Library and Department of Medical Informatics and Epidemiology, Oregon Health & Science University, Portland, OR

Dr. Haendel has led several previous ontology workshops and has participated in development of a number of other Open Bio-Ontology (OBO) standards for anatomy (CARO, Uberon, VAO, ZFA), phenotype (PATO), and biomedical resource ontologies (OBI, ERO). Her interest is in using ontologies for translational research to link human diseases to model organism data, and to infer experimental details relating to the use of organismally derived research resources.

Chris Stoeckert

Department of Genetics and Institute of Biomedical Informatics, Perelman School of Medicine University of Pennsylvania, Philadelphia, PA

Chris Stoeckert's research has focused on biomedical data integration. His group has worked on genomic databases including the EuPathDB project and the Beta Cell Genomics component of the Beta Cell Biology Consortium. Both projects involve the integration of genomes from multiple species, their annotation, and functional genomics datasets of various types. He is on the Board of the FGED Society which promotes data sharing. He is one of the founders and core developers of the Ontology for Biomedical Investigations. His work on data integration is motivated by biological discovery particularly in the area of transcriptional regulatory networks.

Jie Zheng

Department of Genetics and Institute of Biomedical Informatics, Perelman School of Medicine University of Pennsylvania, Philadelphia, PA

Jie Zheng is interested in ontology-based approaches to biomedical meta-data analysis and biomedical data integration including ontology development and data modeling. She has been involved in Ontology for Biomedical Investigation (OBI) development and building application ontologies based on OBI (e.g. , Biobank Ontology, Beta Cell Genomics Ontology (BCGO)). She is currently working on biosample metadata standardization based on ontology modeling and clinical data modeling for data integration from different resources with various representations and annotations.

Important Dates

July 15, 2014 - Paper submission deadline
August 15, 2014 - Notification of acceptance
September 15,2014 - Deadline for camera-ready copy
October 6,2014 - Workshop

Submission Guidelines

Papers are limited to 2-3 pages in the IEEE conference proceedings US Letter format:

Papers should be submitted electronically as a PDF file via the Easychair system at Scientific paper:

Submission Type: Scientific paper

Theme by Danetsoft and Danang Probo Sayekti inspired by Maksimer