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ICBO 2016 Workshop #W09


OBI-ECO Interactions & Evidence

Workshop type

Project Workshop (Project specific talks + Discussions)


Marcus Chibucos, University of Maryland

Co-organizer(s) Chris Stoeckert
Jie Zheng
Workshop Abstract

Both the Ontology for Biomedical Investigations (OBI) and the Evidence & Conclusion Ontology (ECO) are being used to model aspects of scientific investigations, including research methods/results, data interpretation, and conclusions. OBI models methods and instruments relevant to an investigation in a very detailed way, whereas ECO represents evidence in a broad way in order to support database annotations.

ECO and OBI developers have had an ongoing dialogue for several years, and there is general agreement that further alignment of ECO and OBI will benefit both resources. ECO had previously taken some preliminary steps to utilize OBI/IAO. For example, considering ECO evidence classes as information artifacts (i.e. IAO:conclusion) about the results of OBI:planned processes has helped preliminary attempts at clarifying the central axis of ECO. And OBI has added relevant classes in the realm of evidence such as "drawing a conclusion based on data" (OBI:0000338). Such developments are a good start, but much more must be done in the area of modeling evidence.

ECO development and outreach have increased recently thanks to support by the National Science Foundation (award number 1458400). Coordination with other ontologies, and OBI in particular, is one aim of the grant. So we now have the opportunity to explore evidence in the context of multiple ontologies to the benefit of all.

A workshop will be held in Baltimore in May, 2016 to bring together OBI and ECO developers, as well as engaged users interested in approaches to modeling evidence, provenance, confidence, and so on. The specific agenda will be driven by real-world examples and use cases, such as those often described on our issue trackers.

Anticipated topics for the ICBO 2016 workshop will include the following that will build upon earlier discussions at the Baltimore workshop:

  • Current status of evidence within the scope of ECO/OBI.
  • Establishing a framework for cross-ontology coordination between ECO-OBI.
  • Assessing how OWL logic supports use cases that arise in OBI-ECO data interaction.
  • Defining different types of evidence and apply them to real world examples.
  • Fitting conclusions and propositions into a discussion of evidence.
  • Accommodating different models of assertion be by ECO & OBI.
  • Reasoning involved in evidence.
  • Evaluating entities like statistical effects in experimental design (e.g. if we measure gene expression, how do we assess whether a drug is effective or ineffective?)
  • The meaning of evidence as connoted by context of specific experimental design.
  • Using ontological representation of evidence in the cycle of knowledge (from hypothesis generation to drawing conclusions and back to new hypotheses) in scientific investigations.

The goal of this workshop is to bring people together who are working on practical problems involving evidence. Interactive discussions amongst people interested in evidence is the only way to effectively achieve community consensus on how to represent evidence. Progress on some of the agenda topics will require actual editing of OBI & ECO at the meeting and creation of tracker issues/individual action items. We will identify key priorities for ECO/OBI development over the coming months. Comprehensive and openly accessible documentation of workshop discussions and agreed upon outcomes will be generated.

This workshop is part of an ongoing dialogue that we are trying to foster within the ontology community and will lead to further discussions and workshops. It will demonstrate how community efforts can work together and provide an opportunity to involve young researchers in critical standards development. We anticipate the efforts of this workshop to lead to advancements resulting in presentations and discussions at future ICBO meetings. This workshop will also serve as an opportunity to involve young researchers in critical standards development at the ICBO meeting.

Funding source (if any) National Science Foundation (award number 1458400)