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:
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 don’t 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
???