[Obo-discuss] CMO: Colony Morphology Ontology

[Anália M. G. L. <an...@de...>]

Hello all,
 
 
regarding the lastest discussion about CMO and PATO overlap, here are our (remaining) concerns:
 
When we start to construct CMO, we have analysed the ontologies available to the scientific community and we did not find any that fully and comprehensively encompasses the terms we have defined as crucial to describe colony morphology.

We don't have any objection in using PATO terms instead of our CMO terms in colony description. However, in the scope of bacterial colony morphology, PATO should be extended since some colony phenotypic features do not exist in PATO, such as "margin", "sheath", "irregular form", "entire", "homogeneous surface", "heterogeneous surface, etc.  Are PATO authors available to discuss such extension?

 

In addition, as mentioned in previous e-mails, some definitions of PATO terms are not suitable in the scope of colony morphology as "shape" and "size". How can it be managed?  These terms and their concepts are of general use by scientific community and of great importance in colony morphology description. 

 

We appreciate the use of an ontology already well structured as PATO, however, in our opinion, the inclusion of new terms and the "modification" of others seems crucial to enable the use of PATO by a larger community of biologists, microbiologists and clinicians focus on colony morphology studies.

 
 
Although some some of you have suggested the use of PATO before, we are not sure if our concerns/needs can be indeed met. So, it would be of great help if PATO authors be so kind to bring light into this dicussion.
 
Hope to hear from you soon!
 
Cheers,
Anália

-- Anália Lourenço, PhD Faculty Researcher CEB - Centre of Biological Engineering IBB - Institute for Biotechnology and Bioengineering Campus de Gualtar, University of Minho 4710-057 Braga, Portugal Email: an...@de... URL: http://biopseg.deb.uminho.pt/AnaliaLourenco Tel: +351 253 604 423 Fax: +351 253 678 986