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| − | This page will hold notes on the Plant Disease Ontology (PDO) being developed by the PO
| + | Notes on the Plant Disease Ontology (PDO) being developed by the PO |
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| − | Issues under discussion:
| + | The ontology is based on the information here: [[Plant Diseases of the Important Plant Species in the Plant Ontology]] |
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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]
| + | Link to [http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/collaborators_ontology/plant_disease/ PDO on the svn] |
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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?
| + | Issues under discussion: |
| − | eg. causal agent PDO:0000015
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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] |
| − | ==What else did we did:==
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| − | *Created object properties: inverse of each other: | |
| − | -'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.
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