Plant Disease Ontology (PDO)

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.