W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > December 2007

RE: Experiment Ontology

From: Miller, Michael D (Rosetta) <Michael_Miller@Rosettabio.com>
Date: Mon, 3 Dec 2007 07:50:21 -0800
To: "Matthias Samwald" <samwald@gmx.at>, "Susie M Stephens" <STEPHENS_SUSIE_M@LILLY.COM>
cc: public-semweb-lifesci@w3.org
Message-ID: <E1IzDaH-0003gw-2z@aji.w3.org>

hi all,

i agree with much of what matthias has to say, including 

> Many of the datatype properties in this ontology look very 
> interesting and 
> might provide requirements for other ontologies.

having been one of the editors of FuGE, i'm wondering if there are any
tools that can translate UML to RDF or OWL?

the problem i see in this Experiment Ontology is one of the issues that
occurred in creating MAGE and lead to refinements in FuGE.  that is, the
choose of terms in life sciences always seems directed at a particular
type of experiment, here, things like chip type (which is more than just
a species, consider the differences between Affymetrix and Agilent way
of creating the chip and Illumina's bead type reporters) or wells as
opposed to spots/features, gene list, calling out particular gene and
protein databases.  also, Protocol in the Experiment Ontology is a very
restricted usage.

what FuGE tries to do is describe the backbone of a life sciences
investigation/experiment (other overloaded terms) in a generic way.  UML
models derived from FuGE bring in more domain specific details (such as
GelML and, still under development, MAGEv2) but still try and leave much
of the annotation to OntologyTerm elements which are designed to come
from other ontologies.

cheers,
michael

http://www.psidev.info/index.php?q=node/125
http://fuge.sourceforge.net/
https://www.cbil.upenn.edu/magewiki/index.php/magev2

> -----Original Message-----
> From: public-semweb-lifesci-request@w3.org 
> [mailto:public-semweb-lifesci-request@w3.org] On Behalf Of 
> Matthias Samwald
> Sent: Sunday, December 02, 2007 2:25 PM
> To: public-semweb-lifesci@w3.org; Susie M Stephens
> Subject: Re: Experiment Ontology
> 
> 
> Hi Susie,
> 
> Susie wrote:
> > It would be great if you could take a look at it and 
> provide comments. The
> > ontology is available at:
> > 
> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Tasks/Experimen
> t_Ontology
> 
> * Some of the entities/properties are missing a rdfs:label or 
> have an empty 
> label (a string with lenght 0).
> * Some of the entities could be taken from existing 
> ontologies like OBI, RO 
> or some of the OBO Foundry ontologies. This would save work and makes 
> integration with other data sources and ontologies much 
> easier. By the way, 
> there seem to be several groups working on ontologies for mircoarray 
> experiments, or are at least planning to do that. It would be 
> great if these 
> groups could work together.
> * The class 'Chip type' should be removed and be replaced by 
> subclasses of 
> 'chip', e.g., 'chip (human)', 'chip (mouse)' etc.
> * Some of the object properties appear like they are intended 
> to be datatype 
> properties (e.g., 'has proteome id').
> * Many of the datatype properties could be replaced with 
> object properties, 
> possibly referring to third party ontologies -- of course 
> this would require 
> a richer ontology and more work spent on creating mappings. 
> 'has molecular 
> function' could refer to entities from the gene ontology, 
> 'has associated 
> organ' could refer to an ontology about anatomy and so on.
> * Object properties and their ranges are quite redundant. 
> Property 'has 
> reagent' has range 'Reagent', property 'has treatment' has 
> range'Treatment' 
> and so on. Maybe the ontology could be designed in such a way 
> that there are 
> only some generic properties such as 'has part'. This would make the 
> ontology much easier to maintain, query and understand in the 
> long term.
> * It is unclear how 'Gene list' is intended to be used.
> * 'Hardware' and 'Software' should not be subclasses of 'Protocol'.
> 
> 
> Many of the datatype properties in this ontology look very 
> interesting and 
> might provide requirements for other ontologies. It would be 
> great if some 
> of them could be described/commented in more detail so that 
> we know more 
> about the requirements that motivated the creation of these 
> properties.
> 
> I hope that was somewhat helpful.
> 
> cheers,
> Matthias Samwald
> 
> 
> 
> 
> 
Received on Monday, 3 December 2007 15:52:04 UTC

This archive was generated by hypermail 2.3.1 : Wednesday, 7 January 2015 14:52:34 UTC