Difference between revisions of "CL:Aligning species-specific anatomy ontologies with CL"

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(Replacing page with 'http://obofoundry.org/wiki/index.php/CL:Aligning_species-specific_anatomy_ontologies_with_CL')
 
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http://obofoundry.org/wiki/index.php/CL:Aligning_species-specific_anatomy_ontologies_with_CL
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The OBO Cell ontology is intended to be a species-neutral reference ontology.
 
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Species-centric anatomy ontologies may want to 'extend' CL with subtypes of cells that are specific to certain types of organism - the discussion on where the dividing line between what goes in a SCA (species-centric anatomy) ontology and CL is still open.
 
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In addition, SCA ontology maintainers may wish to 'replicate' CL terms in their own ontology. Why? The canonical example here is:
 
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  Purkinje_cell part_of cerebellum
 
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This assertion is universally true (all Purkinje cells are part_of some cerebellum at all times). The fact that not all organisms have a cerebellum is irrelevant. See [[RO:part_of]] for details.
 
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Here is the problem. We have a species-neutral cell ontology with Purkinje_cell (CL:0000121), but we have no species-neutral anatomy ontology with brain parts. We do have for example the zebrafish anatomy [[ZFA:Main_Page]] which has ZFA:0000100 cerebellum. So we can say:
 
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  CL:0000121 part_of ZFA:0000100
 
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However, this is incorrect as not all Purkinje cells are part of fish cerebellums. Whilst it is not explicitly stated whether the definition of ZFA:0000100 is scoped to any particular organism type, we get into problems if we assume the definitions apply to all organisms in which the type is instantiated, as there will be other links in ZFA that do not hold for all organisms.
 
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If ZFA were to include a term for Purkinje cell, say ZFA:9999999, we could say:
 
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  ZFA:999999 part_of ZFA:0000100
 
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SCA curators may have other reasons for replicating CL terms (or terms from other species-neutral reference ontologies like GO) in their ontology.
 
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It's important that SCAs stay in sync with species neutral resources like CL and CARO [[CARO:Main_Page]]
 

Latest revision as of 09:02, 8 June 2009

http://obofoundry.org/wiki/index.php/CL:Aligning_species-specific_anatomy_ontologies_with_CL

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