bioportal as (the only functional) oor sandbox (so far) natasha noy, michael dorf stanford...
TRANSCRIPT
![Page 1: BioPortal as (the only functional) OOR SandBox (so far) Natasha Noy, Michael Dorf Stanford University](https://reader035.vdocuments.mx/reader035/viewer/2022062511/55149a4a550346f06e8b56ff/html5/thumbnails/1.jpg)
BioPortal as (the only functional)
OOR SandBox(so far)
Natasha Noy, Michael Dorf
Stanford University
![Page 2: BioPortal as (the only functional) OOR SandBox (so far) Natasha Noy, Michael Dorf Stanford University](https://reader035.vdocuments.mx/reader035/viewer/2022062511/55149a4a550346f06e8b56ff/html5/thumbnails/2.jpg)
BioPortal: A Community-Based Ontology Repository
http://bioportal.bioontology.org
![Page 3: BioPortal as (the only functional) OOR SandBox (so far) Natasha Noy, Michael Dorf Stanford University](https://reader035.vdocuments.mx/reader035/viewer/2022062511/55149a4a550346f06e8b56ff/html5/thumbnails/3.jpg)
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
![Page 4: BioPortal as (the only functional) OOR SandBox (so far) Natasha Noy, Michael Dorf Stanford University](https://reader035.vdocuments.mx/reader035/viewer/2022062511/55149a4a550346f06e8b56ff/html5/thumbnails/4.jpg)
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
![Page 5: BioPortal as (the only functional) OOR SandBox (so far) Natasha Noy, Michael Dorf Stanford University](https://reader035.vdocuments.mx/reader035/viewer/2022062511/55149a4a550346f06e8b56ff/html5/thumbnails/5.jpg)
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
![Page 6: BioPortal as (the only functional) OOR SandBox (so far) Natasha Noy, Michael Dorf Stanford University](https://reader035.vdocuments.mx/reader035/viewer/2022062511/55149a4a550346f06e8b56ff/html5/thumbnails/6.jpg)
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)
![Page 7: BioPortal as (the only functional) OOR SandBox (so far) Natasha Noy, Michael Dorf Stanford University](https://reader035.vdocuments.mx/reader035/viewer/2022062511/55149a4a550346f06e8b56ff/html5/thumbnails/7.jpg)
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)
![Page 8: BioPortal as (the only functional) OOR SandBox (so far) Natasha Noy, Michael Dorf Stanford University](https://reader035.vdocuments.mx/reader035/viewer/2022062511/55149a4a550346f06e8b56ff/html5/thumbnails/8.jpg)
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
![Page 9: BioPortal as (the only functional) OOR SandBox (so far) Natasha Noy, Michael Dorf Stanford University](https://reader035.vdocuments.mx/reader035/viewer/2022062511/55149a4a550346f06e8b56ff/html5/thumbnails/9.jpg)
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 (
http://protegewiki.stanford.edu/index.php/WebProtege)
– We are about to start the work on integrating BioPortal and WebProtégé to enable a tight link between editing and library functions
![Page 10: BioPortal as (the only functional) OOR SandBox (so far) Natasha Noy, Michael Dorf Stanford University](https://reader035.vdocuments.mx/reader035/viewer/2022062511/55149a4a550346f06e8b56ff/html5/thumbnails/10.jpg)
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
![Page 11: BioPortal as (the only functional) OOR SandBox (so far) Natasha Noy, Michael Dorf Stanford University](https://reader035.vdocuments.mx/reader035/viewer/2022062511/55149a4a550346f06e8b56ff/html5/thumbnails/11.jpg)
Discovery
• Metadata search is a weak point– Will be addressed in the next few months– Will enable search of comments,
mappings, reviews
![Page 12: BioPortal as (the only functional) OOR SandBox (so far) Natasha Noy, Michael Dorf Stanford University](https://reader035.vdocuments.mx/reader035/viewer/2022062511/55149a4a550346f06e8b56ff/html5/thumbnails/12.jpg)
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
![Page 13: BioPortal as (the only functional) OOR SandBox (so far) Natasha Noy, Michael Dorf Stanford University](https://reader035.vdocuments.mx/reader035/viewer/2022062511/55149a4a550346f06e8b56ff/html5/thumbnails/13.jpg)
Metadata in BioPortal
![Page 14: BioPortal as (the only functional) OOR SandBox (so far) Natasha Noy, Michael Dorf Stanford University](https://reader035.vdocuments.mx/reader035/viewer/2022062511/55149a4a550346f06e8b56ff/html5/thumbnails/14.jpg)
Knowledge Domain
• BioPortal itself is a repository of biomedical ontologies
• However, its technology is domain-independent and will remain so
![Page 15: BioPortal as (the only functional) OOR SandBox (so far) Natasha Noy, Michael Dorf Stanford University](https://reader035.vdocuments.mx/reader035/viewer/2022062511/55149a4a550346f06e8b56ff/html5/thumbnails/15.jpg)
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
![Page 16: BioPortal as (the only functional) OOR SandBox (so far) Natasha Noy, Michael Dorf Stanford University](https://reader035.vdocuments.mx/reader035/viewer/2022062511/55149a4a550346f06e8b56ff/html5/thumbnails/16.jpg)
Long-Term Plans
• Federation
• Triplestore as storage mechanism
• Generation of custom-tailored values sets and dictionaries
• ???