Conf. call with IDO 3-23-12 - Revision history

Rwalls: /* Versioning and release policies */

2012-03-23T20:28:02Z

Versioning and release policies

Rwalls: /* Wiki page */

2012-03-23T20:26:32Z

Wiki page

Rwalls: /* IRI's */

2012-03-23T20:24:50Z

IRI's

Rwalls: /* Scope */

2012-03-23T20:24:07Z

Scope

Rwalls: /* Trait Ontology */

2012-03-23T20:23:38Z

Trait Ontology

Rwalls: /* Trait Ontology */

2012-03-23T20:16:59Z

Trait Ontology

Rwalls: /* Relations */

2012-03-23T20:15:40Z

Relations

Rwalls: /* Relations */

2012-03-23T20:13:34Z

Relations

Rwalls: /* Relations */

2012-03-23T20:12:24Z

Relations

Rwalls: /* Potentially problematic terms from IDO */

2012-03-23T19:59:33Z

Potentially problematic terms from IDO

@@ Line 204: / Line 204: @@
 *OWL versus OBO
 *Pre-reasoned version
 *How to include imported ontologies with downloads.

@@ Line 195: / Line 195: @@
 ==Wiki page==
 Should this be part of the PO wiki, should we create a separate wiki for IDO-PO?
 ==Versioning and release policies==

← Older revision		Revision as of 20:24, 23 March 2012
Line 162:		Line 162:

	Is there a temporary alternative to use until the ontology is ready for submission to OBO Foundry?		Is there a temporary alternative to use until the ontology is ready for submission to OBO Foundry?
		+
		+	''We should use the obo purls. Can ask Chris or someone else to create directory for us.''

	==Syncing with other ontologies==		==Syncing with other ontologies==

@@ Line 155: / Line 155: @@
 ==Scope==
 Do we want to cover all green plants or just land plants?
 ==IRI's==

← Older revision		Revision as of 20:23, 23 March 2012
Line 148:		Line 148:

	''A trait is something you observe - a sign or symptom. Leaf lesion is a trait (this is an entity). Leaf lesion yellow or leaf lesion brown is a phenotype.''		''A trait is something you observe - a sign or symptom. Leaf lesion is a trait (this is an entity). Leaf lesion yellow or leaf lesion brown is a phenotype.''
		+
		+	==PAMGO==
		+	''In manuscript, we should say that when we begin to describe the specific biological processes for interactions between plants and disease organism, we will link out to PAMGO terms in GO.''

	=Other issues=		=Other issues=

@@ Line 147: / Line 147: @@
 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.
+''A trait is something you observe - a sign or symptom. Leaf lesion is a trait (this is an entity). Leaf lesion yellow or leaf lesion brown is a phenotype.''
 =Other issues=

@@ Line 115: / Line 115: @@
   m instanceOf bfo:material entity AND
-−
   i instanceOf bfo:independed continuant AND
@@ Line 129: / Line 129: @@
 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==

@@ Line 98: / Line 98: @@
 ==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.
+''Developing for OGMS - a 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 but the material basis for the disease.''
-has_material_basis - does not imply a causal relation so much as a
+ Definition (under development):
-not invertible
+i instanceOf bfo:independed continuant AND
-−
-d has_material_basis m iff for all times t
+          i has_disposition d at t implies i has_part m at t
-          i has_disposition d at t implies i has_part m at t
+''IDO is working on a relation for "has_infectious_agent".''
-has_infectious_agent
+''For example, could say that malaria has_infectious_agent Plasmodium, and also that malaria has_material_basis Plasmodium.''
-disease versus disease course
+''The reason has_causal_basis was developed, is because you cannot use "has_infectious_agent" for non-infectious diseases (e.g., abiotic stressors) in plants. However, we may still be able to use has_material_basis in this case.''

@@ Line 41: / Line 41: @@
 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.
+This treatment of ‘abnormal’ is distinct from those statistical treatments which do not take account of the overlap in the distribution of test results between
-''Could we call this asympomatic infection, with "subclinical infection" as a synonym?
+normal and abnormal populations or of normal distribution extremes. What are standardly called ‘normal variants’ (for example a left lung with three lobes) do not satisfy criteria ii) and iii).
@@ Line 57: / Line 75: @@
 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 Roberts and Boothroyd: Harmful physiological processes caused by continuous irritation of a plant by a primary causal agent. 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==