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BioPortal as (the only functional) OOR SandBox (so far) Natasha Noy, Michael Dorf Stanford University.

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Presentation on theme: "BioPortal as (the only functional) OOR SandBox (so far) Natasha Noy, Michael Dorf Stanford University."— Presentation transcript:

1 BioPortal as (the only functional) OOR SandBox (so far) Natasha Noy, Michael Dorf Stanford University

2 BioPortal: A Community- Based Ontology Repository

3 The National Center for Biomedical Ontology One of the five National Centers for Biomedical Computing launched by NIH Collaboration of Stanford, Mayo, Buffalo, Victoria, Medical College of Wisconsin, Washington University, John Hopkins Primary goal is to make ontologies accessible and usable Research will develop technologies for ontology dissemination, indexing, alignment, and peer review

4 Key Technology: BioPortal Web accessible repository of ontologies for the biomedical community: –http://bioportal.bioontology.org Online support for ontology –Peer review –Notes (comments and discussion) –Versioning –Mapping –Search –Resources

5 The BioPortal Technology BioPortal is a library of biomedical ontologies All BioPortal data is accessible through REST services –BioPortal user interface accesses the repository through REST services as well The BioPortal technology is domain- independent –There are installations of BioPortal for libraries in other domains –BioPortal code is open-source –Technology stack includes mySQL, J2EE, Spring, Hibernate, Ruby-on-Rails

6 OOR and BioPortal The OOR sandbox currently runs the BioPortal code The assumption is that it will diverge Some of the OOR requirements contribute to the setting of directions for BioPortal But BioPortal has its user base that primarily drives the requirements (and of course, the funders)

7 OOR Requirements (not addressed -- yet) in BioPortal Persistence –No triplestore-based storage (planned) Rules –Unlikely in the next year Policies –Will have some support (private areas of BioPortal)

8 Representation Languages Not trivial to add support for Common Logic and other expressive formalisms A simple data model drives the user interface –Hence, you cannot easily adapt what will show up in the class form You can add an ontology in CL, for example, and make it available for download, but not for browsing, etc. –Perhaps not that useful

9 Ontology Services Syntax validation and consistency checking –May add, but many biomedical ontologies dont have enough expressive power to check consistency Editing and creation of ontologies –Not in BioPortal, but supported by WebProtégé ( –We are about to start the work on integrating BioPortal and WebProtégé to enable a tight link between editing and library functions

10 Auditing We have rudimentary auditing, quality control of contributed ontologies We hope to get more community involvement in this task –The infrastructure for reviewing and ranking is mostly set up –Need users to contribute to these areas of BioPortal

11 Discovery Metadata search is a weak point –Will be addressed in the next few months –Will enable search of comments, mappings, reviews

12 Metadata Representation in BioPortal As of September 2009, BioPortal uses ontology-based representation of metadata The following are part of the metadata and are represented as instances in the BioPortal metadata ontology: –Ontology details –notes and comments (soon) –mappings (soon) –reviews (soon) –ontology views

13 Metadata in BioPortal

14 Knowledge Domain BioPortal itself is a repository of biomedical ontologies However, its technology is domain- independent and will remain so

15 Short- to Mid-Term Plans Migration of the rest of the metadata to ontology-based representation Structured notes to collect term proposals Integration of BioPortal and WebProtégé Ontology evaluation metrics Access controls; private areas of BioPortal myBioPortal

16 Long-Term Plans Federation Triplestore as storage mechanism Generation of custom-tailored values sets and dictionaries ???

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