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: Albert Goldfain, Lindsay Cowell, Pankaj Jaiswal, Justin Elser, Ramona Walls
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?
Perhaps mine GO annotations for a specific pathogen.
We can use the data in Gramene as a test case, and PJ could curate some papers for pathogen expression if we need them. We don't need to worry about this too much for the ICBO paper, but it will be important going forward.
Albert: IDO-PD is a reference ontology, not an application ontology, so having a specific use in mind is less important. Application ontologies can be built off of the IDO-PD.
access to ontology
RW set up SVN folder for draft on PO SVN: http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/collaborators_ontology/plant_disease/
Should we put a link to this in the paper?
Set up link for SVN externals.
Potentially 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 : A process by which a part of an organism or something contained in an organism becomes clinically abnormal.
What does clinically abnormal mean? Can we apply this same concept to a plant?
IDO:subclinical infection: An infection that is part of an asymptomatic host.
Could we call this asympomatic infection, with "subclinical infection" as a synonym?
OGMS:symptom: 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.
OGMS:disease: A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
Def. of disease from Roberts and Boothroyd: Harmful physiological processes caused by continuous irritation of a plant by a primary causal agen. It results in morbific cellular activity and is expressed in characteristic pathological responses called symptoms; continuous malfunctioning.
Def. of disease from Manners "Principals of Plant Pathology": harmful deviation from normal functioning of physiological processes. This definition allow malfunctions caused by non-living agencies such as mineral deficiency to be classed as diseases: such diseases are sometimes known as disorders...
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.
Developing for OGM - way to link dispostions with material entities that produce those dispositions to link a disease to its underlying disorder.
has_material_basis - does not imply a causal relation so much as a
not invertible
d has_material_basis m iff for all times t
d instanceOf bfo:disposition AND
m instanceOf bfo:material entity AND
i instanceOf bfo:independed continuant AND
i has_disposition d at t implies i has_part m at t
has_infectious_agent
disease versus disease course
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.
Trait Ontology
"While most ontologies mentioned are introduced a bit, the ‘trait ontology’ is only explained as “describing traits” (manuscript text) and dealing with “plant traits” (Table 1), which is not helpful to someone like me who is unsure what the scope of that ontology is."
Can PJ provide a one sentence description of the scope of the TO?
A trait is something you observe - a sign or symptom. Like a phenotype. Leaf lesion is a trait.
The thing that you observe, not your observation.
PAMGO
Other issues
Scope
Do we want to cover all green plants or just land plants?
IRI's
RW set up Protege so that IRIs follow the OBO Foundry (http://purl.obolibrary.org/obo/idopd.owl/IDOPD_0000000) but we have no special permission from OBO to do this, and right now these links are meaningless.
Is there a temporary alternative to use until the ontology is ready for submission to OBO Foundry?
Syncing with other ontologies
IDO
Multiple comments in IDO could cause problems with working with OE.
Can we create a subset of IDO with only terms that are relevant to plants?
TO
The main issue will be from TO -- using IDOPD terms to logically define TO terms.
Mireoting
Could Lindsay or Albert provide some help to RW on how to import terms using Mireot or other techniques.
How did you import terms from NCBI? Just re-use them/enter by hand?
Importing organisms
NCBItaxon ontology versus UBio id
What exactly do each of those stand for?
"A taxonomic classification of living organisms and associated artifacts for their controlled description within the context of databases."
From UBio: "NameBank is a biological name server. It stores and serves NameBankIDs via Life Science Identifiers, a persistent and distinct identifier. Each NameBank LSID returns a NameBank object which contains information about the NameBank record."
Neither of these resources say anywhere that their ids represent organisms of a particular class.
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
- How to include imported ontologies with downloads.
