[Taxacom] Nomenclature vs taxonomy et al.

Neil Sarkar sarkar at amnh.org
Sat Aug 19 11:12:11 CDT 2006

Nomenclatures are just the names themselves, without regard to how  
the named entities are related to each other. This is how the terms  
are used in biomedical informatics as well as in biodiversity  
studies. However, as you rightly point out the terms are "lumped"  
together by ASTM -- very inconsistent with how the terms are used by  
informaticians (probably a reflection that many informaticians don't  
really know the difference...).

Anyway, Taxonomies posit how entities are related to each other. The  
biomedical informatics domain has many more taxonomies -- which have  
evolved into "ontologies" -- than the biodiversity domain. Our  
taxonomies are now referred to as "Alpha-taxonomies," probably  
because the first taxonomies that were ever described had to do with  
organizing life.

Jim Cimino's chapter in the recent edition of the text book (chapter  
7), "Biomedical Informatics Computer Applications in Health Care and  
Biomedicine," has a good description of the distinction between  
terminologies, vocabularies, and ontologies. Also, Jim recently  
edited an issue in the Journal of Biomedical Informatics that covers  
a lot of the distinctions:

Journal of Biomedical Informatics
Volume 39, Issue 3, Pages 249-378 (June 2006)
Biomedical Ontologies
Edited by James J. Cimino and Barry Smith

Anita Burgun and Olivier Bodenreider also have an article that you  
might find informative:

Aspects of the taxonomic relation in the biomedical domain
Formal Ontology in Information Systems  archive
Proceedings of the international conference on Formal Ontology in  
Information Systems - Volume 2001
Ogunquit, Maine, USA
Pages: 222 - 233
Year of Publication: 2001

Hope the above helps.


On 2006 Aug 19, at 07:13 EDT, Una Smith wrote:

> Can any TAXACOMer recommend reading material (preferably
> published) that may help to explain what is a taxonomy and
> what is a nomenclature?

Indra Neil Sarkar, PhD
Bioinformatics Associate
Divisions of Invertebrate Zoology
   & Library Services
American Museum of Natural History
Central Park West at 79th Street
New York, NY 10024 USA
+1 212 769 5571
email: sarkar at amnh.org
www  : genomeCurator.org/people/sarkar
skype: ligerWeb
Eastern Daylight Time Zone (Z-4)
**** PSB 2007 Biodiversity Informatics Track ****

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