Difference between revisions of "The cROP (Common Reference Ontologies for Plants) Initiative"
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For ontologies labeled *, the Planteome group may adopt their development. | For ontologies labeled *, the Planteome group may adopt their development. | ||
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| + | == PRO-PO-GO Meeting == | ||
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| + | 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: | ||
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| + | 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: | ||
| + | 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), | ||
Revision as of 15:42, 5 October 2012
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.
The first proposed set of ontologies to be developed within the cROP Initiative is as follows:
- PO*: Plant Ontology
- GO: Gene Ontology
- PRO: Protein Ontology
- TO*: Plant Trait Ontology
- EO*: Environment Ontology (plant treatments) browse at Gramene
- ENVO: Ontology of environmental features and habitats
- PATO: Phenotype Quality Ontology
- Taxonomy: USDA-GRIN / NCBI / New?
- GAZ: An Ontologically-Informed Gazetteer (geographical locations)
- Plant IDO*: Plant Infectious Disease Ontology [1]
- Plant Diseases*: List of plant diseases
- CHEBI: dictionary of molecular entities
- PCO: Population and Community ontology
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: 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),
