Dec 8th, 2015 Ontology Working Group Meeting

Planteome Ontology WG Zoom Meeting:

Date: Tuesday Dec. 8th, 2015 Time: 8:15am PST (GMT-8)

• Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/600315375

• Attendees: LC, AM, PJ, DWS, BS

Updates

- DWS is working on a plant anatomy glossary- images can be linked to the PO terms in the digital version. Main interest in terms for spines, prickles, stipules, LC: should use the purl rather than the PO webpage or planteome page.

• Prickle- http://purl.obolibrary.org/obo/PO_0025169
• Spine- two options:
  • spine leaf: http://purl.obolibrary.org/obo/PO_0025173
  • spine stipule: http://purl.obolibrary.org/obo/PO_0025174
• Thorn: http://purl.obolibrary.org/obo/PO_0025172
• Stipule: http://purl.obolibrary.org/obo/PO_0020041 (see also spine stipule above)
• Leaflet: http://purl.obolibrary.org/obo/PO_0020049

- DWS recently attended a meeting with the Center for Open Science, Univ. of Virginia

• making experiments repeatable in ecology and psychology, what kind of metadata needs to be captured- using ontologies can help
  • e.g. problem of repeatibility

• BS: developing an ontology for biological and clinical statistics- make pipeline repeatable
• in Evolutionary biology- all the steps are defined and documented
• From BS: Related effort: Force 11/Force 2016- Open Science Initiative (Melissa Haendel, Maryanne Martone)

Mapping of TO terms to trait dictionaries for lentil, soybean, cassava, rice:

lentil plant height on the TO hierarchy

• Overview of Progress: CO curators are used to using the spreadsheets
• Afola requested access so he could fill in the mappings to cassava
• Link to mapping spreadsheet: CO Mappings to TO
• If you want to edit it, you have to request access
• Goal- matching to ref Trait Ontology Terms from the more granular CO terms. Can be an exact match or a match to a higher level
  • Can create a composite tree as shown in the graphic for lentil plant height. We would like to avoid massive term inflation.
  • Idea is to prefix the CO term with the species name e.g. lentil plant height (this can be added programmatically?)
• The TO terms would be linked to the PO and PATO terms through the equivalence axioms (formerly called cross products)

From PJ: lentil tendrils image

Planteome Curator Workshop at PAG

Updates and Agenda (PAG 2016 Planteome-CO workshop)

Next Meeting: