Dear all,
currently, our proteins in CCO are linked to their respective
organisms by using the relationship "derives_from"; however, as Mathias
makes references in one of his articles [1], this relationship should be
carefully chosen and it seems that CCO is misusing it. In that sense, we
were wondering whether another relationship could be proposed? such as:
extracted_from?
comes_from?
occurs_in?
isolated_from?
appears_in_organism?
cheers,
Erick
[1] http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.pdf
--
==================================================================
Erick Antezana http://www.cellcycleontology.org
PhD student
Tel:+32 (0)9 331 38 24 fax:+32 (0)9 3313809
VIB Department of Plant Systems Biology, Ghent University
Technologiepark 927, 9052 Gent, BELGIUM
erant(a)psb.ugent.be http://www.psb.ugent.be/~erant
==================================================================
I see that you have invented and use a vocabulary for describing the
elements of OBO term specifications. An interesting piece of work, but
you may be unintentionally reinventing the wheel. Alternatively, you
could consider using the SKOS vocabulary, endorsed by W3C.
At a first glance, many of oboinowl resources correspond to skos ones,
though the mapping may not be obvious in some cases. For example, you
address definitions by means of the class called 'definition', while in
SKOS 'definition' is rather a property; where you have 'synonym' (a
class), SKOS provides 'altLabel' (a property); etc.
Have a look:
http://www.w3.org/2004/02/skos/
--
Wacek Kusnierczyk
------------------------------------------------------
Department of Information and Computer Science (IDI)
Norwegian University of Science and Technology (NTNU)
Sem Saelandsv. 7-9
7027 Trondheim
Norway
tel. 0047 73591875
fax 0047 73594466
------------------------------------------------------
Dear all,
A new version of the API has just been released (v 0.23).
Major changes consider the obo2owl conversion (though still under
discussion and development ) according to the mapping from:
http://www.bioontology.org/wiki/index.php/OboInOwl:Main_Page
On the other hand, the owl2obo conversion development has been
arrested temporally until the mapping described above reach a sound state.
enjoy it!
Erick Antezana
--
==================================================================
Erick Antezana Tel: 32 (0) 9 3313824
DEPARTMENT OF PLANT SYSTEMS BIOLOGY Fax:32 (0)9 3313809
GHENT UNIVERSITY/VIB, Technology Park 927, B-9052 Gent, Belgium
Vlaams Interuniversitair Instituut voor Biotechnologie VIB
mailto:erant@psb.ugent.be http://www.psb.ugent.be
==================================================================
Dear CCO friends,
I am pleased to announce the new release of the Cell Cycle Ontology
(Release 0.5: http://www.cellcycleontology.org/) In this release, more
terms have been integrated from the main sources (in particular from
BIND). Besides, the CCO upper level ontology
(http://www.sbcellcycle.org/cco/img/ulo.png) has also been enhanced.
Currently, the ontology has 44312 terms and 29 relationships. The
ontology is available in OBO, OWL, XML and DOT format. It is wroth
mentioning that the ontology in under constant improvement and still in
its infancy; therefore, any feedback is very welcome.
On the other hand, a new perl CCO API (Version 0.21) has also been
produced (http://www.sbcellcycle.org/cco/html/index.html#Download)
Finally, you'll also find in the web site some exports from the Gene
Ontology produced with the developed API.
Best regards,
Erick
==================================================================
Erick Antezana Tel: 32 (0) 9 3313824
DEPARTMENT OF PLANT SYSTEMS BIOLOGY Fax:32 (0)9 3313809
GHENT UNIVERSITY/VIB, Technology Park 927, B-9052 Gent, Belgium
Vlaams Interuniversitair Instituut voor Biotechnologie VIB
mailto:erant@psb.ugent.be
http://www.psb.ugent.be/~erant
==================================================================
