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:
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
- 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":
Examples:
Created new child term:
- 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 to: 'associated with' - (a) it is vague (b) it will block reasoning
To improve I need to know what will the entity which has the corresponding trait? If it is plant, then just say
stem number =def. a trait of a plant which is the number of stems of the plant and so on for the other cases
2. Update from Bioversity:
- Progress on mapping the CO vocabularies