collaborating with the national center for biomedical ontology

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Collaborating with the Collaborating with the National Center for National Center for Biomedical Ontology Biomedical Ontology Mark Musen and the NCBO Team [email protected]

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Collaborating with the National Center for Biomedical Ontology. Mark Musen and the NCBO Team [email protected]. http://www.ncbcs.org. The National Center for Biomedical Ontology. One of three National Centers for Biomedical Computing launched by NIH in 2005 - PowerPoint PPT Presentation

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Page 1: Collaborating with the  National Center for  Biomedical Ontology

Collaborating with the Collaborating with the National Center for National Center for

Biomedical OntologyBiomedical OntologyMark Musen and the NCBO Team

[email protected]

Page 2: Collaborating with the  National Center for  Biomedical Ontology
Page 3: Collaborating with the  National Center for  Biomedical Ontology

http://www.ncbcs.org

Page 4: Collaborating with the  National Center for  Biomedical Ontology

The National Center for Biomedical The National Center for Biomedical OntologyOntology

• One of three National Centers for Biomedical Computing launched by NIH in 2005

• Collaboration of Stanford, Mayo, Buffalo, Washington University, Johns Hopkins, and the Medical College of Wisconsin

• Primary goal is to make ontologies accessible and usable• Research will develop technologies for ontology dissemination, use,

indexing, alignment, and peer review

Page 5: Collaborating with the  National Center for  Biomedical Ontology

NCBO: Key activitiesNCBO: Key activities

• We create and maintain a library of biomedical ontologies.

• We build tools and Web services to enable the use of ontologies.

• We collaborate with scientific communities that develop and use ontologies.

Page 6: Collaborating with the  National Center for  Biomedical Ontology

www.bioontology.orgwww.bioontology.org

Page 7: Collaborating with the  National Center for  Biomedical Ontology

http://bioportal.bioontology.org

Page 8: Collaborating with the  National Center for  Biomedical Ontology

BioPortal allows us to experiment BioPortal allows us to experiment with new models for with new models for

• Dissemination of knowledge on the Web• Integration and alignment of online content• Knowledge visualization and cognitive

support • Peer review of online content

Page 9: Collaborating with the  National Center for  Biomedical Ontology
Page 10: Collaborating with the  National Center for  Biomedical Ontology
Page 11: Collaborating with the  National Center for  Biomedical Ontology

Users can view and create mappingsUsers can view and create mappings

Page 12: Collaborating with the  National Center for  Biomedical Ontology

Biomedical Resource Ontology Biomedical Resource Ontology in BioPortalin BioPortal

Page 13: Collaborating with the  National Center for  Biomedical Ontology

““Notes” in BioPortalNotes” in BioPortal

Page 14: Collaborating with the  National Center for  Biomedical Ontology

Community-Based Annotation as Community-Based Annotation as Peer ReviewPeer Review

• Makes ontology evaluation a democratic process

• Assumes users’ application of ontologies will lead to insights not achievable by inspection alone

• Assumes end-users will be motivated to comment on and engage in dialog about ontologies in the repository

Page 15: Collaborating with the  National Center for  Biomedical Ontology

BioPortal is building an online BioPortal is building an online community of users whocommunity of users who

• Develop, upload, and apply ontologies• Map ontologies to one another• Comment on ontologies via “notes” to give

feedback • To the ontology developers• To one another

• Make proposals for specific changes to ontologies• Stay informed about ontology changes and

proposed changes via “push” technology• Incorporate BioPortal services into their own

technologies

Page 16: Collaborating with the  National Center for  Biomedical Ontology

http://ucsdbiolit.codeplex.comhttp://ucsdbiolit.codeplex.com

Page 17: Collaborating with the  National Center for  Biomedical Ontology

Automated recognition of ontology terms before publication

Page 18: Collaborating with the  National Center for  Biomedical Ontology

BioLit Web resource: automated recognition of ontology terms and database IDs after publication

Page 19: Collaborating with the  National Center for  Biomedical Ontology

IO informatics uses Ontology ServicesIO informatics uses Ontology Services

Page 20: Collaborating with the  National Center for  Biomedical Ontology

Wikipathways uses Ontology ServicesWikipathways uses Ontology Services

Page 21: Collaborating with the  National Center for  Biomedical Ontology
Page 22: Collaborating with the  National Center for  Biomedical Ontology

ISAcreator uses Ontology Services

Page 23: Collaborating with the  National Center for  Biomedical Ontology

ECG Gadget uses Ontology Services

Page 24: Collaborating with the  National Center for  Biomedical Ontology

Biositemaps Editor

Page 25: Collaborating with the  National Center for  Biomedical Ontology

Protégé BioPortal-reference plug-inProtégé BioPortal-reference plug-in

Page 26: Collaborating with the  National Center for  Biomedical Ontology

Simbios usesSimbios usesNCBO OntologyNCBO OntologyWeb WidgetsWeb Widgets

Page 27: Collaborating with the  National Center for  Biomedical Ontology

NCBO Annotator: The Basic IdeaNCBO Annotator: The Basic Idea

Process textual metadata to tag text automatically with as many ontology terms as possible.

Page 28: Collaborating with the  National Center for  Biomedical Ontology

NCBO Annotator NCBO Annotator http://bioportal.bioontology.org/annotatehttp://bioportal.bioontology.org/annotate

• Give your text as input

• Select your parameters

• Get your results … in text or XML

Page 29: Collaborating with the  National Center for  Biomedical Ontology

Resources Index: The Basic IdeaResources Index: The Basic Idea

• The index can be used for:• Search• Data mining

NCBO Annotator

Page 30: Collaborating with the  National Center for  Biomedical Ontology

Example: Indexing GEOExample: Indexing GEO

Page 31: Collaborating with the  National Center for  Biomedical Ontology
Page 32: Collaborating with the  National Center for  Biomedical Ontology

NCBO Indexed ResourcesNCBO Indexed Resources

Page 33: Collaborating with the  National Center for  Biomedical Ontology

Links to specific resourcesLinks to specific resources

Page 34: Collaborating with the  National Center for  Biomedical Ontology

GMiner uses NCBO Annotation Services

Page 35: Collaborating with the  National Center for  Biomedical Ontology

See our wiki to learn more!See our wiki to learn more!

www.bioontology.org/wiki/index.php/Using_NCBO_Technology_In_Your_Project

Page 36: Collaborating with the  National Center for  Biomedical Ontology

Ways to collaborate with NCBOWays to collaborate with NCBO

• Be a user!• Propose a Driving Biological Project (DBP)• Get a collaborating research grant (NIH

R01)• Initiate an industrial or academic joint

projects

Page 37: Collaborating with the  National Center for  Biomedical Ontology

Current Driving Biological ProjectsCurrent Driving Biological Projects

• caNanoLab: Workers at Stanford and Wash U developing searchable catalog of therapeutic nanoparticles

• Cardiovascular Research Grid: Workers at Hopkins developing ontology of ECGs and electrophysiological studies

• Rat Genome Database: Workers at MCW use ontologies to annotate genomic data

Page 38: Collaborating with the  National Center for  Biomedical Ontology

Current “Collaborating R01” grantsCurrent “Collaborating R01” grants

• UW: Creating views of ontologies• UCSD: Using ontologies to annotate

neuroimaging data• UC Denver: Ontology enrichment through

published literature• Pittsburgh: Ontology enrichment through

EMR data• Wright State: Semantic data integration

Page 39: Collaborating with the  National Center for  Biomedical Ontology

Some other collaborative activitiesSome other collaborative activities

• CollaboRx, Inc. — Resource annotation• NextBio, Inc. — Ontology-based search• Google, Inc. — Web of Trust• University of Karlsruhe — Use of OMV in

BioPortal metadata• World Health Organization — Ontology

support for ICD11

Page 40: Collaborating with the  National Center for  Biomedical Ontology

Other NCBO componentsOther NCBO components

• Education and training• Graduate students• Post docs• Visiting researchers

• Outreach and dissemination• Specialized workshops• Support for conferences

• ISMB Bio-ontologies SIG• International Conference on Biomedical Ontology

Page 41: Collaborating with the  National Center for  Biomedical Ontology

NCBO needs HCLS!NCBO needs HCLS!

• To push on our technology• To drive our requirements• To help disseminate ontology-based

methods in biomedicine• To help promote W3C recommendations in

biomedicine• To help us in our mission to educate the

community and to encourage best practices

Page 42: Collaborating with the  National Center for  Biomedical Ontology

http://bioontology.org