Six plant species: Rice, Maize, Arabidopsis, soybean, Medicago, tomato ~ 4,193 new direct associations
New association data developed from MaizeGDB (Mary Schaeffer)
Based on data set from Scott Stelpfulg et al (Kaeppler group): "An expanded maize gene expression atlas based on RNA-sequencing and its use to explore root development"
Update of the Nimblegen Microarray data - more tissues, not so much background noise
2. Planteome.org Update:
3. Plant Trait Ontology:
Two questions from Barry about how to define the traits:
Anatomy and Morphology traits
The "anatomy and morphology trait
> Are there any traits which are not anatomy and morphology traits?
there are 8 different branches in the TO, anatomy and morphology trait is just one.
> the term 'anatomy and morphology trait' really means 'anatomy trait or morphology trait', right?
" Yes, I suppose it means 'or'. It is inclusive. 'anatomy trait or morphology trait' would be more correct."
> Is there a definition of 'anatomy trait' and of 'morphology trait'?
>Are they logically disjoint?
---> image of TO upper level with "anatomy and morphology traits":
Example child terms:
stem number (TO:0000953): A shoot system anatomy and morphology trait (TO:0000077) which is associated with the number of stems (PO:0009047).
Added Xrefs to: number (PATO:0001555); TO_GIT:157
stem size (TO:0000954):A stem anatomy and morphology trait (TO:0000361) which is associated with the size of a stem (PO:0009047).
Added Xrefs to: size (PATO:0000117); TO_GIT:157
Added narrow synonym: stalk size
Objection has been raised to: 'associated with' - BS: (a) it is vague (b) it will block reasoning
Suggestions:
stem number =def. a trait of a plant which is the number of stems of the plant"
and so on for the other cases
infructescence axis shape: An infructescence axis anatomy and morphology trait (TO:0000921) that describes the shape of the infructescence axis [or specify the 'of' further]
id: RO:0000086
name: has_quality
def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" []
property_value: IAO:0000112 "this apple has quality this red color" xsd:string
property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string
property_value: IAO:0000118 "has_quality" xsd:string
Possible solution using relations from RO:
ear shape (TO:0000964):
An infructescence anatomy or morphology trait (TO:0000920)
an ear infructescence (PO:0025597) has_quality shape.
