Difference between revisions of "Plant Disease Ontology (PDO)"
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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] | ||
| − | * | + | Conversion of ontology file to owl from OBO: At the Protege Short Course: |
| + | *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. | ||
| + | *need to figure out how to do it again, maybe redo the import and replicate? | ||
| + | *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??? | ||
| + | |||
| + | * The PDO:Ids are not showing up in the annotations- how do I get them to display? | ||
| + | eg. causal agent PDO:0000015 | ||
| + | |||
| + | |||
| + | =What else did we did:= | ||
| + | *Created object properties: inverse of each other: | ||
| + | -'causal agent of' and has_causal_agent | ||
| + | - has_part and part_of | ||
| + | *Also created: | ||
| + | - isa_primary_host | ||
| + | **probably should make the naming consistent with underscores | ||
| + | |||
| + | |||
| + | ==Fixing problem of spp. as causal agents== | ||
| + | *fungal spp. (PDO:0000070) made it a subclass of fungal biotic causal agent (PDO:0000026) with the class restrictions (?correct term?),: | ||
| + | * has_part only 'fungal species' | ||
| + | * has_part some 'fungal species' | ||
| + | |||
| + | *Pythium spp. (PDO:0000064) | ||
| + | -made this class Equivalent to 'fungal spp.' and (has_part only 'Pythium sp.') | ||
| + | |||
| + | *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. | ||
| + | |||
| + | Can do the same with the other two classes: Curvularia spp. and Fusarium spp. | ||
Revision as of 23:07, 9 June 2012
This page will hold notes on the Plant Disease Ontology (PDO) being developed by the PO
Issues under discussion:
- use of common names to describe the diseases and are caused by a variety of pathogens: e.g. Pecky Rice
Conversion of ontology file to owl from OBO: At the Protege Short Course:
- 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.
- need to figure out how to do it again, maybe redo the import and replicate?
- 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???
- The PDO:Ids are not showing up in the annotations- how do I get them to display?
eg. causal agent PDO:0000015
What else did we did:
- Created object properties: inverse of each other:
-'causal agent of' and has_causal_agent - has_part and part_of
- Also created:
- isa_primary_host
- probably should make the naming consistent with underscores
Fixing problem of spp. as causal agents
- fungal spp. (PDO:0000070) made it a subclass of fungal biotic causal agent (PDO:0000026) with the class restrictions (?correct term?),:
- has_part only 'fungal species'
- has_part some 'fungal species'
- Pythium spp. (PDO:0000064)
-made this class Equivalent to 'fungal spp.' and (has_part only 'Pythium sp.')
- 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.
Can do the same with the other two classes: Curvularia spp. and Fusarium spp.
