Conf. call with IDO 3-23-12

Friday, March 23, 2012, 2PM ET

Agenda/minutes for conference call with PO and IDO curators.

In attendance:

Back to Plant Disease Ontology main page.

Questions arising from reviews

Real data or problems in modeling disease

Is there an example/data set we can use as a test case?

e.g., Gene Associations for Trait Term "rice bacterial blight disease resistance" from species "Oryza sativa" in Gramene

access to ontology

Set up SVN site for draft on PO SVN?

Problematic terms from IDO

"The authors point out that the use of ‘clinical’ in OGMS / IDO and the definition of ‘symptom’ are problematic when building a plant disease ontology. This is (to me) one of the most interesting aspects of the paper. Have the authors tried to come up with more general definitions that would be universally applicable? Or is this not possible (why not)? It seems that the present structure works well for the plant ontology regardless, so I am not asking to revise the decision to build on OGMS / IDO. Rather I would be interested in a more detailed treatment of these problematic areas."

Examples of terms:

IDO:transition to clinical abnormality

IDO:subclinical infection

OGMS: symptom

Def. of symptom from IDO/OGMS: A quality of a patient that is observed by the patient and is hypothesized by the patient to be a realization of a disease. (note that "patient" is not in the IDO)

Def. of symptom from Roberts and Boothroyd "Fundamentals of Plant Pathology": A visible expression by a suscept of a pathologic condition.

Relations

"Several of the IDO-PD relations sound like they should be in IDO proper. Will they be communicated back? It also seems that these relations are “shortcut relations” for more complex constructs in BFO/RO. Have the authors explored making this connection explicit?"

has_causal_agent: This relation is used to indicate the causal agent of a disease or other stress. It has two subtypes: has_causal_biotic_agent and has_causal _abiotic_agent. In the IDO-PD, the domain is a plant infectious disease and the range is an organism that is bearer_of an infectious agent role.

primary/alternative_host_of: Two relations used to indicate whether a plant species is the primary or second-ary/alternative host of a disease, e.g., X. oryzae infected O. sativa primary_host_of X. oryzae infectious agent. The domain is an organism that is a subtype of Viridiplantae and is the bearer of a host role, and the range is an organism that is the bearer of an infectious agent role. Secondary hosts may be wild plant species that provide a place for the disease to survive when the crop host is not present or during a different part of the disease organism’s life cycle.

has_symptom: This relationship type is used to indicate the associated symptoms/traits that are evaluated to ascertain the manifestation of a stress or disease, e.g., rice bacterial leaf blight disease has_symptom leaf lesion.

found_in: This relationship is used to indicate the geograph-ical location of a host and/or pathogen species, e.g., X. oryzae found_in X. oryzae range. Instances of a disease or organisms also may have a found_in relation to an instance of a geographic region.

Other issues

Wiki page

Should this be part of the PO wiki, should we create a separate wiki for IDO-PO?

Versioning and release policies

(Probably don't need to worry too much about these yet)

• OWL versus OBO
• Pre-reasoned version