Biomedical Ontologies

Mary Chitty, Cambridge Healthtech mchity@healthtech.com
ASIST Annual Meeting, Oct. 22, 2003, Long Beach CA 

"The first layer of the semantic Web consists of ontologies and taxonomies ... "A huge amount of this is being done very desperately in the realm of biotech, for the human genome and new drug development." Tim Berners Lee, August 30, 2001 keynote at Software Development East in Boston. Alexandra Weber Morales "Web founder seeks simplicity" Show Daily Online, 2001 http://www.sdgnews.com/sd2001es_006/sd2001es_006.htm

What is an ontology?, W3C, Requirements for a web ontology language, [work in progress] http://www.w3.org/TR/webont-req/#onto-def

Similar to a dictionary or glossary, but with greater detail and structure that enables computers to process its content. An ontology consists of a set of concepts, axioms, and relationships that describe a domain of interest. An upper ontology is limited to concepts that are meta, generic, abstract and philosophical, and therefore are general enough to address (at a high level) a broad range of domain areas. IEEE, Standard Upper Ontology (SUO) Working Group, 2003 http://suo.ieee.org/

The word "ontology" seems to generate a lot of controversy in discussions about AI [artificial intelligence]. It has a long history in philosophy, in which it refers to the subject of existence. ... In the context of knowledge sharing, I use the term ontology to mean a specification of a conceptualization … Ontologies are often equated with taxonomic hierarchies of classes, but class definitions, and the subsumption relation, but ontologies need not be limited to these forms. Tom Gruber, Stanford Univ. "What is an ontology?" 2001
http://www-ksl.stanford.edu/kst/what-is-an-ontology.html

Glossary of Ontology Terminology, KSL Network Services, Stanford Univ., US, 2001, 20+ terms. http://www-ksl-svc.stanford.edu:5915/doc/frame-editor/glossary-of-terms.html

Terminology of methods and techniques for defining, sharing, and merging ontologies, John F. Sowa, 2001. Based on discussions in the ontology working group of the NCITS T2 Committee on Information Interchange and Interpretation. 18 definitions. http://users.bestweb.net/~sowa/ontology/gloss.htm

Information Management & Interpretation glossary, Mary Chitty http://www.genomicglossaries.com/content/Informationmgt.ASP#ontology,%20ontologies

Life Sciences Ontologies
Gene Ontology, EBI European Bioinformatics Institute http://www.geneontology.org/ Molecular function, biological process, cellular component

LOINC Logical Observation Identifiers Names and Codes, Regenstrief Institute Inc. Germany http://www.loinc.org/

MedDRA Medical Dictionary for Regulatory Activities http://www.meddramsso.com/ 

MGED Microarray Gene Expression Data ontology group, http://mged.sourceforge.net/ontologies/index.php

OBO Open Biological Ontologies http://obo.sourceforge.net/

Protégé Ontologies Library, Stanford Medical Informatics, Stanford Univ. School of Medicine https://protegewiki.stanford.edu/wiki/Protege_Ontology_Library

SNOMED Systematized Nomenclature of Medicine, College of American Pathologists http://www.snomed.org/

UMLS Unified Medical Language System, National Library of Medicine, US http://www.nlm.nih.gov/research/umls/

Gene nomenclature
HUGO Gene Nomenclature Committee http://www.genenames.org/ 
We have approved symbols for nearly one half of the genes in the human genome and, with an estimated 15,000 more genes to name, we still have plenty to do!

There is "currently no official nomenclature for human genes, however, the Human Gene Nomenclature Committee (part of HUGO) is currently trying to establish a nomenclature standard and does have a recommended format. The Human Gene Nomenclature Committee is the accepted authority for establishing these standards. … There is no enforcement of this suggested nomenclature method and investigators are free to name a gene as they wish. dbSNP FAQ # 6, NCBI, US http://www.ncbi.nlm.nih.gov/SNP/get_html.cgi?whichHtml=faq#hum%20gen%20nomen

Plant and animal gene nomenclature
Other Nomenclature Guidelines (for non-human species), HUGO  http://www.gene.ucl.ac.uk/nomenclature/moreguides.html   Includes plants (Arabadopsis, rice) model organisms, cows and chickens.

IUPAC Nomenclature and Terminology, International Union of Pure and Applied Chemistry http://www.chem.qmul.ac.uk/iupac/

IUPAC Chemical Identifier Project, International Union of Pure and Applied Chemistry http://www.iupac.org/projects/2000/2000-025-1-800.html

Bibliography
Oliver Bodenrieder, Joyce Mitchell, Alexa MacCray, "Biomedical Ontologies", Pacific Symposium on Biocomputing, Jan. 2003  http://psb.stanford.edu/psb03/cfp-ontologies.html 

Robin Cover, XML Cover Pages: Resource Description and Classification, 2003
http://www.oasis-open.org/cover/classification.html Covers standard industry taxonomies and ontologies, library cataloging, news industry and metadata initiatives

FIPA Foundation for Intelligent Physical Agents, Standards Committee http://www.fipa.org/subgroups/AWSI-WG-docs/AWSI_WG_Charter.pdf

Jim Hendler "Introduction to ontologies on the semantic web", 2001 http://www.cs.umd.edu/users/hendler/ontologies.html

Michael Krauthammer, Brief review of clinical vocabularies, MGED Microarray Gene Expression Data Society, Ontology Working Group, 2002 http://www.cbil.upenn.edu/Ontology/MKreview.html

Mark Mandel, Resources for Biomedical Terminology and Ontology, Univ. of Pennsylvania, 2003 http://www.cis.upenn.edu/~mamandel/term.html

Natalye Fridman Noy and Deborah McGuinness, Ontology 101: A guide to creating your first ontology, Knowledge Systems Laboratory, Stanford University, Mar. 2001. http://ksl.stanford.edu/people/dlm/papers/ontology-tutorial-noy-mcguinness-abstract.html

Deborah L. McGuinness in Dieter Fensel, Jim Hendler, Henry Lieberman, and Wolfgang Wahlster, editors. Spinning the Semantic Web: Bringing the World Wide Web to Its Full Potential. MIT Press, 2002.  See "Ontology Spectrum" for variations in meanings of "ontology http://www.ksl.stanford.edu/people/dlm/papers/ontologies-come-of-age-mit-press-(with-citation).htm

Peter Morville, Bottoms up: Designing Complex, Adaptive Systems, New Architect, Dec. 2002 http://www.newarchitectmag.com/documents/s=2452/na1202b/  Creating usable and sustainable taxonomies

Semantic Web.org, Markup Languages and Ontologies http://www.semanticweb.org/knowmarkup.html

Chris Stoeckert, Microarray Databases: Standards and Ontologies, Chipping Forecast II, Nature Genetics 32: supplement, 469 – 473, Dec. 2002 [requires free registration]
http://www.nature.com/cgi-taf/dynapage.taf?file=/ng/journal/v32/n4s/index.html