Dec 8th, 2015 Ontology Working Group Meeting

From Planteome.org
Jump to navigation Jump to search

Planteome Ontology WG Zoom Meeting:

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

  • 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.

- 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

From PJ: This is a leaflet tendril. looks like a rachis tendril (PO:0025366)?? -

Discussion about modified variables with scale info

- MAL has been working on implementing the suggestion from PJ to add additional variable ids which are specific to each of the categorical scales. That way there is a unique id to assign to a data annotation. From this you can determine the trait, method, and the scale. - ID scale- each scale has a specific ID, these IDs are not linked to TO, but to each specific CO-variables

- color: can be measured using a color wheel, or subjective 1-10, or whatever breeders have used. - The CO curators/breeders have their own system for quality control, somewhat subjective. Comparison within the crop species it is fine, but would be difficult to compare across species. At that point, we should just compare at the level of the TO trait term.

Trait Ontology changes

Planteome Curator Workshop at PAG

Updates and Agenda (PAG 2016 Planteome-CO workshop)


Next Meeting:

Retrieved from "https://wiki.planteome.org/index.php?title=Dec_8th,_2015_Ontology_Working_Group_Meeting&oldid=2265"