Sept 15th, 2015- Ontology Working Group Meeting

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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, BS, CM

Agenda

1. Upcoming Plant Ontology Release #21

- Many changes and updates to the PO which will accompany the PSDS paper submission

  • Transition to GitHub complete, and working well- required many updated Xrefs and links in the various browsers, ontology files and pages.
  • PO Live 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
  • For more information: Plant_Ontology_Release_#21


  • 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"

2. Planteome.org Update:

  • Once the Plant Ontology update is pushed out, we will be rolling all the data files and updated ontologies to the Planteome web page: Planteome.org for our Planteome 1.0 release.
  • This is important as we are getting ready to submit our first annual report and people are using the Planteome site, so we want to make sure it is all working well.
  • We are diligently working to make sure all the dbxrefs and links are updated, so if you find any issues, please let us know.

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.

TO top level.jpg

> 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?


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

Examples from other from OBO_Foundry_Ontologies that cover traits:

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

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.

Added dXrefs: shape (PATO:0000052);


Example from BATTO: http://www.ontobee.org/browser/index.php?o=oba

[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)

4. Update from Bioversity:

  • Progress on mapping the CO vocabularies and creating cross products
  Please fill in details...

5. Proposed: Ontology Development Meeting in Corvallis early November-

Please see the notes here: Planteome_Curator_workshop_Fall_2015

5. TermGenie Demo

Tabled for next meeting


Next meeting: Sept 29th

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