RE: Antwort: RE: Semantic web article in Nature Biotechnology

Dear Luca,

Thank you for the input.  I know of (but not KNOW in the matter of detail)
about the ontologies you mentioned.  But a few reasons that "push" me off
about these ontologies for the use in the context of Semantic Web are:
(1) They do not comply to SW technology specifications.
If you go to OBO and check those developed ontology, most of them are not
coded in RDF/OWL.  Even for a few that have the "OWL-version", they are not
coded corrected.  For instance, GO has a presumed namespace
"http://www.geneontology.org/owl/", but access that URI leads to a 404.
Coding an ontology in RDF or OWL doesn't mean they are using the semantic
web ontology.
(2) Many of them are overlapping, for instance, GALEN and MSH, etc.
IMHO, ontology merging is no easier than schema integration.  It is a
transformation of the old problem but not the solution.
(3) All these ontologies are still developed in a monolithic manner. No
consideration about the granuality and practicality has been emphasized.  An
encyclopedic-like ontology is only useful as referece but not for other
"reasoning task".  I have used Jena before to play around the w3c's example
Wine Ontology.  Reasoning with subClass etc., is O.K. but once all other
axioms are considered, my computer always run of memory.

So, when I made the suggestion, I meant more from the technical perspective
than content. Particularly, I meant the application of ontology in the
context of semantic web.  If an ontology is designed in such that it can not
be executed in the context of SW, what good it does to us - at least in this
group? My own personal interest in ontologies are about experimental data,
like how to model gel, MS data etc.  Maybe, as a group, we can start from
this, I already have some prelimiary work done like a trivial top ontology
about scientific research - BOSS
(http://www.charlestoncore.org/ontology/boss), which I don't think overlap
with any of the ontologies you recommend?

Xiaoshu Wang  

> However I would like to prompt your attention on the work 
> which has already been done.
> The goal of creating biological and meaningful ontologies for 
> biology and for chemistry or medicine has a very long 
> history, thus by learning from "the past" one could save some 
> considerable time and also avoid repeating the same "design 
> flaws" (let's not call them mistakes).
> 
> If you have not yet done so, I would strongly suggest you to 
> add depth to your knowledge in the field of biomedical 
> ontologies before starting coding yourself "yet-another-ontology"
> if you want to have your effort being well rewarded (by 
> spread use of the ontology itself).
> 
> Few examples are:
>       Open Biological Ontologies (obo.sourceforge.net
>       Unified Medical Language System
>       GALEN Ontology
>       Medical Subject Headings
>       SWISS-PROT Keywords the SWISS-PROT keyword list now has 
> definitions
>       (in nat. lang.) associated with each keyword.
>       Edinburgh Anatomies Have whole or partial anatomy ontologies for
>       adult and developmental stages for several model organisms.
>       The Ingenuity company has a large knowledge base of experimental
>       findings in biology. Currently, their ontology is not viewable.
>       The MGED ontology working group aim to develop ontologies for
>       describing gene expression experiments and data.
>       Semiotes
>       Regulatory Networks Model
>       PharmGKB: Pharmacogenetics Knowledge Base.
>       the TAMBIS ontology (TaO) an ontology of bioinformatics 
> and molecular
>       biology.
>       RiboWeb an ontology describing ribosomal components, 
> associated data
>       and computations for processing those data.
>       EcoCyc an ontology describing the genes, gene product function,
>       metabolism and regulation within E. coli.
>       Molecular Biology Ontology (MBO)A general, reference 
> ontology for
>       molecular biology.
>       Gene Ontology (GO) an ontology describing the function, 
> the process
>       and cellular location of gene products from eukaryotes.
>       Mouse Genome Informatics GO browser
>       Mouse Anatomical Dictionary
>       ImMunoGeneTics (IMGT) Ontology
>       STAR/mmCIF Macromolecule structure ontology.
>       STAR/mmCIF Signal Transduction Knowledge #Environment (STKE).
>       GENAROM Ontology of gene product interactions.
>       GeneX Ontologies for comparing gene expression across species.
>       EpoDB Controlled Vocabulary function, cell and tissue type,
>       developmental stage and experimental type.
>       CBIL Controlled Vocabulary Terms for human anatomy.
>       Japan Bio-Ontology Committee including Signal 
> Transduction Ontology
>       flybase controlled vocabulary for fly anatomy used for 
> describing
>       phenotypes.
> 
> and certainly is a good idea to involve those which are 
> already 10+ years in the field:
> http://anil.cchmc.org/Bio-Ontologies.html
> http://www.cs.man.ac.uk/~stevensr/ontology.html
> 
> Good luck !
> luca
> 
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Received on Monday, 26 September 2005 14:54:13 UTC