How Bio Ontologies Enable Open Science

How Bio-Ontologies enable Open Science Nigam Shah [email_address]

Key Points ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

[object Object],There are other uses of course, see Biomedical Ontologies: A functional perspective, Rubin et al, Briefings in Bioinformatics, Dec 2007, Vol 9:1 75-90

How does ontology help? ,[object Object],[object Object],[object Object],[object Object]

Ontologies and content acquisition ,[object Object],[object Object],[object Object],[object Object],[object Object]

Emerging trends in content acquisition ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Increasing Structure ,[object Object],[object Object],[object Object],[object Object]

Knewco: Concept Web and Wikiprofesional

The SWAN discourse ontology Ciccarese P, Wu E, Clark T (2007) 'An Overview of the SWAN 1.0 Ontology of Scientific Discourse‘ at the 16th International World Wide Web Conference Banff, Canada. May 8-12, 2007.

The SWAN Team and papers ,[object Object],[object Object],Copyright 2007 Alzheimer Research Forum and Massachusetts General Hospital [1] Gao Y, Kinoshita J, Wu E, Miller E, Lee R, Seaborne A, Cayzer S, Clark T (2006) ‘ SWAN: A Distributed Knowledge Infrastructure for Alzheimer Disease Research’. Journal of Web Semantics 4(3). [2] Ciccarese P, Wu E, Clark T (2007) 'An Overview of the SWAN 1.0 Ontology of Scientific Discourse'. 16th International World Wide Web Conference (WWW2007). Banff, Canada. May 8-12, 2007. [3] Clark T and Kinoshita J (2007) 'Alzforum and SWAN: The Present and Future of Scientific Web Communities'. Briefings in Bioinformatics 8(3). [4] Ciccarese, P, Wu E, Kinoshita J, Wong G, Ocana M, Ruttenberg A and Clark T (submitted for publication 9/4/2007) 'The SWAN Ontology of Scientific Discourse'. Photo not available

Integration of Text-mining + Curation ,[object Object],[object Object],[object Object],[object Object],[object Object]

Integration of Text-mining + Curation

Quick recap ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

NCBO’s efforts ,[object Object],[object Object],[object Object],[object Object]

NCBO ontology services Base URL: http://rest.bioontology.org/rest Documentation: www.bioontology.org/wiki/index.php/NCBO_REST_services Description REST URL List all ontologies ./ontologies Find a specific ontology ./ontologies/{ontology version id} Download ontology file ./ontologies/download/{ontology version id} Get versions of an ontology ./ontologies/version/{ontology id} Get concept ./concepts/{ontology version id}/{concept id} Search for concepts ./search/concepts/{query}?ontologies={ids} Get latest version of an ontology ./virtual/{ontology_id} Get concept for latest ontology version ./virtual/{ontology id}/{concept id} List all ontology categories ./categories

NCBO annotation services ,[object Object],[object Object],[object Object],[object Object],[object Object]

ANNOTATOR SERVICE ,[object Object]

Annotator: The Basic Idea ,[object Object]

Annotator: Usage ,[object Object],[object Object],[object Object],[object Object]

Open Biomedical Resources index ,[object Object],[object Object],[object Object]

NCBO services Ontology services (OBS) UMLS services BioPortal services Data service (OBR) Annotation service (OBA) Users UCSF Laboratree CollabRx PharmGKB, JAX HGMD Users BioPortal UI PDB/PLoS I2B2 NextBio IO informatics Users “ Resources” tab Knewco IO informatics

Uses of NCBO services ,[object Object],[object Object],[object Object],[object Object],[object Object]

BioLit web resource: automated recognition of ontology terms and database IDs after publication http://biolit.ucsd.edu

Automated recognition of ontology terms and database IDs before publication with manual curation by author Word 2007 add-in

Annotation: UCSF ,[object Object],[object Object],[object Object]

Annotation: CollabRx caTissue/TIES Specimen Banking Specimen management is based on ontologies developed by NCI Ontology-based integration to create a virtual specimen bank

Curation: JAX, UCHSC, PDB/PLoS ,[object Object],[object Object],[object Object]

Ontology Access: I2B2 ,[object Object],[object Object]

Ontology Access: IO-informatics

Ontology Access: NextBio ,[object Object]

Data Summarization: PharmGKB 1. CYP2C9 , 2. VKORC1 , 3. CYP2A6 , etc. 1. Hemorrhage , 2. Venous Thrombosis , etc. 1. warfarin , 2. coumarin , 3. phenoprocoumon , etc. 34 scored annotations: 5 scored annotations: 20 scored annotations:

Data Summarization: HGMD ,[object Object],[object Object]

How Bio Ontologies Enable Open Science

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