Oct 31st, 2017 Ontology Working Group Meeting

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Planteome Ontology WG Zoom Meeting

  • Date: Tuesday Oct 31st, 2017
  • Time: 8:15am PDT (GMT-7)
  • Connection details:

Topic: Planteome Ontology Working Group Meeting Time: Oct 31, 2017 8:15 AM Pacific Time (US and Canada)

Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/442101652

Agenda and Notes

News:

  • Submitted the revisions on the NAR Paper- accepted for publication 10-30-17
    • See notes below on the changes implemented

Changes to the browser: (Currently on dev)

    • Can now search for an ECO term and see all the annotations that are associated with it
    • Eg.: New: There will only be the “link to annotations” on ontologies we specify where there are annotations (under ‘related options’)- GO, PECO, TO, PO
    • Can filter and bookmark the search for annotations

Evidence Type Filters

  • PJ: Is the ECO tree correctly capturing the annotations that are flowing from child terms to parent terms?
  • IAGP- does it have a mapping to the ECO terms?- see email from Seth and Justin
  • PJ: we need to append the ECO term label in the filter list with the actual ECO ID
    • How should this be done? We would have to modify the ECO ontology file
  • PJ: modify the facet to display the IDs- would take time
    • ECO ID could be appended to the ECO label- CM’s suggestion, but who would do this and where?
    • Could fork our own ECO, and modify but then we have the issue of maintaining it and staying in synch with the main file
    • Could the IDs and/or code be added by a script in the loading process?

LC: Would be great to have the three letter code be a link to the evidence code- but cannot do that right now as the mapping are not there.

  • Maybe we should be using the ECO ID in the annotations?
  • Need to display: Short code\ ECO ID\ ECO label are not shown together

Revisions to Base Statistics

  • Was only displaying GO annotations
    • Need to update the text at the top still- this is done on dev, still needs to be fixed on live
  • Three types of visualizations:
    • Shows annotations by ontology aspect, IEA annotations
    • PJ: can the axes be reversed? - It would make it easier to read the species, and aspects
    • The ‘Annotations by evidence’ are based on the ECO codes-
  • Annotations by species
  • Annotations by evidence
  • Ontology annotations by aspect/species by evidence
  • New AmiGO features:
    • Now can see all the annotations with different evidence codes
    • Will need to make the same changes on live and at CyVerse


Visit to BTI at Cornell last week

  • RTB Program of CGIAR crops: root, tuber and banana- also includes cassava, sweet potato, potato, and yam
    • Goal was to set up the synchronization between CO and GitHub
  • MAL attended all week, LC visited Thurs and Friday
  • Training on Protege to update the files in each repo
  • Migrated all ontologies to Plantoeme, Marie sorted out all the inconsistencies between files and got them straightened out
    • Issue to highlight problems with variable
    • Protected master branches in each repo- needs to be reviewed
    • Banana ontology file needs to be added once Guillaume returns
    • Clean up versions on the GitHub, need to add the mappings?
    • Changes pushed automatically to CO website- all done through Github API- uses webhook, then can be downloaded in the TD format
    • Eg. testing in the Sweet potato repo currently, still need to add the component for adding the terms to the CO database
  • Should be done by next week
  • Mapping for yam and banana next up
  • PJ: comments on the crop ontologies- curators don’t really need the hierarchy tree
    • Cassava does not have a large # of terms
    • Show them how they can use the TO- mapping of traits and variables
    • Can use the hierarchy to guide their work…
  • Obtaining data for TO-CO paper

Talked with Naama and Lukas, checking with data owners to be sure its ok, yield data

  • Displaying the TO on the ontology browser at the RTB site eg. Cassavabase?
    • Naama said they need to do some testing
    • Need a login to see the Variable Submission Form
  • Is the version of the cassava ontology on Cassavabase the same as the one on Planteome?
    • Maire says yes, need to check, has the hierarchy from CO

Variable Submission form

  • New Variable Submission form for breeders or users to request terms from curators: http://submit.rtbbase.org/
  • Opens an issue tracker in the appropriate repository, but how can they track the issue?
  • Curators:
    • Brian- BTI- which crop?
    • Afola- yam, cassava
    • Guillaume, Rhianon- banana
    • Dorcas- CIP- sweet potato and potato
  • This could be very useful for the TO for people to request terms for the TO- good for outside users
    • Designed to be used for requesting traits one by one
    • Do not need to supply all the info in the form
    • All fields are mandatory

Changes to Plant Experimental Conditions Ontology- PECO

  • Was formerly Plant Environment Ontology (EO)
  • The numbers have not changed, just the namespace has been changed
  • Need in the EO ids as an alt ID
    • Created release versions to link to from OBO Foundry and reorganized the repository, Editor’s version is peco-edit.obo
  • Should we have a conversion from peco-edit.obo to peco-edit.owl
    • MAL: we should be using the Makefile (although it’s not ready yet), to transform. run whenever a change is made in the edit file.

Repo is structured as recommended by CM

  • Note that the EO terms are still being imported with TO- what do we need to do the change those? MAL will change those
  • MAL: JE will need to change the catalog file...

What do we want to do on the renewal?

  • What preparations do we need to do?
  • Do we need to do some work to show how it will be pulled off?
  • Two weeks brainstorming sessions, then come back together and discuss
  • Kick off in December, follow up at PAG

Updates on papers in progress

  • PJ: GO annotations for reference genomes, sending back to Ensemble and Uniprot- JE, AM, PJ working on it. Starting with rice
  • AM adding references, putting them in the PO?

Upcoming Events

  • Phenoscape Hackathon in Dec
  • Plant and Animal Genome meeting January 2018
  • ICBO 2018- in Corvallis, possibly end of August

Next meeting: Nov 14th

Upcoming Events

  • Phenoscape Hackathon in Dec
  • Plant and Animal Genome meeting January 2018
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