Dec 8th, 2015 Ontology Working Group Meeting: Difference between revisions

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From PJ: [http://www.prota4u.org/plantphotos/Lens%20culinaris%201.gif lentil tendrils image]
From PJ: [http://www.prota4u.org/plantphotos/Lens%20culinaris%201.gif lentil tendrils image]
From PJ: This is a leaflet tendril.  ''looks like a rachis tendril (PO:0025366)??''
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== Discussion about modified variables with scale info ==
== Discussion about modified variables with scale info ==

Revision as of 20:50, 8 December 2015

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.

Trait Ontology changes

Planteome Curator Workshop at PAG

Updates and Agenda (PAG 2016 Planteome-CO workshop)


Next Meeting:

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