Difference between revisions of "The cROP (Common Reference Ontologies for Plants) Initiative"

From Plant Ontology Wiki
Jump to navigationJump to search
m
m
 
(14 intermediate revisions by the same user not shown)
Line 1: Line 1:
 
The vision of the cROP initiative is to develop a reference set of ontologies for all plants, by analogy with, and in collaboration with, the [http://obofoundry.org OBO] (Open Biological and Biomedical Ontologies) Foundry.
 
The vision of the cROP initiative is to develop a reference set of ontologies for all plants, by analogy with, and in collaboration with, the [http://obofoundry.org OBO] (Open Biological and Biomedical Ontologies) Foundry.
 +
 +
For details see [http://www.planteome.org/ Planteome] website
  
 
The first proposed set of ontologies to be developed within the cROP Initiative is as follows:
 
The first proposed set of ontologies to be developed within the cROP Initiative is as follows:
Line 17: Line 19:
 
# PCO: [http://code.google.com/p/popcomm-ontology/ Population and Community ontology]
 
# PCO: [http://code.google.com/p/popcomm-ontology/ Population and Community ontology]
  
−
For ontologies labeled *, the Planteome group may adopt their development.
+
For ontologies labeled *, the Planteome group may adopt their development.  
−
 
 
−
== PRO-PO-GO Meeting ==
 
−
 
 
−
A first meeting on cROP from the perspective of basic biology ontologies will be held in Buffalo in May 2013 (probably May 15-16).  The goals of this meeting are to enhance coordination in ontology development and use in relation to plant genomics, proteomics and related fields. THe meeting is designed:
 
−
 
 
−
1. To inform members of the Protein, Plant and Gene Ontology communities of  developments in each of these ontologies, and in related ontologies such as the CL (Cell), TO (Plant Trait), ENVO (Environment), PATO (Phenotype) and IDO-Plant (Plant Infectious Disease) ontologies, . Specifically:
 
−
a. To enhance the PO treatment of plant-related proteins
 
−
b. To address issues concerning reuse of GO terms to describe plant-related proteins, for example as concerns treatment of plant life cycle and development stages
 
−
2. To contribute to the creation of the cROP (Common Reference Ontologies for Plants) initiative
 
−
3. To identify potentially fruitful applications which such enhanced coordination might bring 
 
  
−
Participants will include:
+
[[image:cROP.jpg | 600px ]]
−
PO Consortium members: Pankaj Jaiswal (Oregon), Barry Smith (Buffalo)
 
−
GO Consortium members: Judith Blake (JAX), Alex Diehl (Buffalo)
 
−
PRO Consortium members: Cathy Wu (Delaware), Alan Ruttenberg (Buffalo),
 

Latest revision as of 21:49, 21 October 2015

The vision of the cROP initiative is to develop a reference set of ontologies for all plants, by analogy with, and in collaboration with, the OBO (Open Biological and Biomedical Ontologies) Foundry.

For details see Planteome website

The first proposed set of ontologies to be developed within the cROP Initiative is as follows:

  1. PO*: Plant Ontology
  2. GO: Gene Ontology
  3. PRO: Protein Ontology
  4. TO*: Plant Trait Ontology
  5. EO*: Environment Ontology (plant treatments) browse at Gramene
  6. ENVO: Ontology of environmental features and habitats
  7. PATO: Phenotype Quality Ontology
  8. Taxonomy: USDA-GRIN / NCBI / New?
  9. GAZ: An Ontologically-Informed Gazetteer (geographical locations)
  10. Plant IDO*: Plant Infectious Disease Ontology [1]
  11. Plant Diseases*: List of plant diseases
  12. CHEBI: dictionary of molecular entities
  13. PCO: Population and Community ontology

For ontologies labeled *, the Planteome group may adopt their development.

CROP.jpg

Retrieved from "http://wiki.plantontology.org/index.php?title=The_cROP_(Common_Reference_Ontologies_for_Plants)_Initiative&oldid=26232"