Sept 15th, 2015- Ontology Working Group Meeting
Time: 8:15am PDT (GMT-7:00) Pacific Time (US and Canada)
Connection details: Join from PC, Mac, iOS or Android: https://zoom.us/j/655429261
- In attendance: LC, MAL, AM, PJ
- Regrets:
- 09/15/15 Meeting minutes
Agenda
1. Upcoming Plant Ontology Release #21
For more information: [Plant_Ontology_Release_#21]
- New association data developed from the Plant Phenotype Pilot Project paper published in Feb 2015: http://www.plantmethods.com/content/11/1/10/abstract
- Six plant species: Rice, Maize, Arabidopsis, soybean, Medicago, tomato
- 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"
- The Plant Genome doi:10.3835/plantgenome2015.04.0025
- Accepted paper, posted 08/07/2015.
- Update of the Nimblegen Microarray data - more tissues, not so much background noise
- Many updated Xrefs and links
- Browser updated for the transition to GitHub with links to the new Issue Tracker and association repository on the SVN
- Timeline- within the next 2 weeks
2. Plant Trait Ontology:
Questions from Barry about how to define the traits:
---> 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]
synonym: cob shape
Vertebrate Trait Ontology: http://www.berkeleybop.org/ontologies/vt.owl -- “related to”
Animal Trait Ontology: http://147.99.159.184:8080/webprotege/#ATOL -- “related to”
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
ossible 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.
Added dXrefs: shape (PATO:0000052);
Example from BATTO:
[Term] id: TO:0000431 ! ear length intersection_of: BATTO:0000001 ! biological attribute intersection_of: affects_quality PATO:0000122 ! length intersection_of: attribute_of PO:0020136 ! ear (sensu Zea)
> 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'?
>Is there a definition of 'morphology trait'?
>Are they logically disjoint?
3. Update from Bioversity:
- Progress on mapping the CO vocabularies and creating cross products
4. Proposed Meeting in Corvallis early November-
Goals of the meeting: Strategic planning and ontology curation
Who should attend: Medicago, soybean, legume