Difference between revisions of "Plant Disease Ontology (PDO)"

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This page will hold notes on the Plant Disease Ontology (PDO) being developed by the PO
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Notes on the Plant Disease Ontology (PDO) being developed by the PO
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The ontology is based on the information here: [[Plant Diseases of the Important Plant Species in the Plant Ontology]]
  
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Link to [http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/collaborators_ontology/plant_disease/ PDO on the svn]
  
  
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*use of common names to describe the diseases and are caused by a variety of pathogens: e.g. [http://www.apsnet.org/publications/commonnames/Pages/Rice.aspx Pecky Rice]
 
*use of common names to describe the diseases and are caused by a variety of pathogens: e.g. [http://www.apsnet.org/publications/commonnames/Pages/Rice.aspx Pecky Rice]
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=Conversion of ontology file to owl from OBO: At the Protege Short Course:=
 
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*Imported the plant_disease_ontology.obo file, version 1553.  Had to do something to make the names appear as the labels, rather than the PDO:id. At the time Tim Redmond said there was some sort of bug, but he worked around it.
 
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*need to figure out how to do it again, maybe redo the import and replicate?
 
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*We also set the numbering system so we could add terms (entities) and have them be assigned a PDIO:id- how did we do that???
 
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* The PDO:Ids are not showing up in the annotations- how do I get them to display?
 
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eg. causal agent PDO:0000015
 
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==What else did we did:==
 
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*Created object properties: inverse of each other:
 
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-'causal agent of' and has_causal_agent
 
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- has_part and part_of
 
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*Also created:
 
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- isa_primary_host
 
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**probably should make the naming consistent with underscores
 
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===Fixing problem of spp. as causal agents===
 
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*fungal spp. (PDO:0000070) made it a subclass of fungal biotic causal agent (PDO:0000026) with the class restrictions (?correct term?),:
 
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* has_part only 'fungal species'
 
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* has_part some 'fungal species'
 
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*Pythium spp. (PDO:0000064)
 
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-made this class Equivalent to 'fungal spp.' and (has_part only 'Pythium sp.')
 
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*Created the new class 'Pythium sp.' and made the two individual Pythium sp.subclasses of it: Pythium dissotocum and Pythium spinosum.  Not sure how to see the new PDO:id.
 
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Can do the same with the other two classes: Curvularia spp. and Fusarium spp.
 

Latest revision as of 17:12, 10 April 2013

Notes on the Plant Disease Ontology (PDO) being developed by the PO

The ontology is based on the information here: Plant Diseases of the Important Plant Species in the Plant Ontology

Link to PDO on the svn


Issues under discussion:

  • use of common names to describe the diseases and are caused by a variety of pathogens: e.g. Pecky Rice
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