ONTOLOGY RESOURCES FOR THE BIOMEDICAL COMMUNITY

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ONTOLOGY RESOURCES FOR THE BIOMEDICAL
COMMUNITY Daniel L. Rubin, Nigam Shah, Kaustubh
Supekar, Archana Vembakam, Lynn Murphy, Natalya
Noy, Mark A. Musen Stanford University,
Stanford, CA, USA
INTRODUCTION The National Center for biomedical
Ontology is producing resources and tools to
enable researchers to effectively access, manage,
and use biomedical knowledge in electronic form.
Two key resources that the Center is producing
include the Open Biomedical Ontologies (OBO)
library of biomedical ontologies and BioPortal, a
Web application enabling human users and
computer-based agents access OBO knowledge
resources.
ONTOLOGY TOOLS, APPLICATIONS, AND RESEARCH

• Ontology Metadata and Peer-Review
• Capture structured representation of user
  critiques on ontology design
• Enumerate and summarize types of ontology
  evolutionary changes
• Create peer review platform for ontologies based
  on Web of Trust
• Provide tools to enable community to evaluate and
  improve ontology quality

• Ontology Alignment and Diff
• PROMPT compares two ontologies or versions
• PROMPT provides visual summary of differences in
  terms and structure

• OPEN BIOMEDICAL ONTOLOGIES
• Ontology library containing ontologies from broad
  range of biomedical domains
• Ontology content includes important medical
  terminologies, such as SNOMED and NCI Thesaurus
• Ontology categories (anatomy, development,
  chemical entities, etc)
• Public access, regularly updated

Metadata Ontology
Web-based tools to enter ontology metadata, to
post reviews, and to rate reviewers

• Pictorial-Guided Ontology Navigation
• Allows multi-scale images to be annotated using
  ontology terms
• Supports view subsets of ontologies pertinent to
  biological scale of the data
• Permits ontology-annotated data to be browsed
  according to image scale

• Ontology Processing Pipeline
• Maintains versions of ontologies collect
  ontology metadata
• Validates newly submitted files classify
  ontologies
• Provides processing checkpoints to support
  complex workflows
• Supports an Ontology Librarian supervisory role

• Tools for Ontology Applications
• Indexing and search of ontology contents (which
  ontologies contain a term?)
• Tools to map databases and text to ontology terms
• Ontology-based navigation of annotated data

Modified after illustration by Carol Goble

• BIOPORTAL
• A Web application providing public access to OBO
  ontologies
• Permits users to upload and browse OBO ontologies
• Provides workflow for processing newly submitted
  ontologies
• Permits search for terms across ontologies
• Provides access tools for ontologies (alignment,
  diff, visualization)
• Includes ontology ratings, editing support, and
  metadata
• Provides Web services for integrating BioPortal
  functionality into applications