Oct 31st, 2017 Ontology Working Group Meeting

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

• Meeting Recordings:
  • File:Ontology WG Meeting audio 10-31-17.m4a
  • File:Ontology WG Meeting video 10-31-17.mp4

Agenda and Notes

News:

• Submitted the revisions on the NAR Paper- accepted for publication 10-30-17

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

• • Displays the ECO term label, but not the ECO IDS
  • ECO terms need to be linked to the short codes- they have been mapped by GOC
  • Mapping is not displayed, done by GOC http://geneontology.org/page/guide-go-evidence-codes

• 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

• Planteome Evidence codes page: http://planteome.org/evidence_codes
  • Needs to be updated, make consistent with the http://wiki.geneontology.org/index.php/Evidence_Code_Ontology_(ECO)
• Could we display the ECO tree in the DD browser?
  • No, it would mess up other things, only displays the internal ontologies

Revisions to Base Statistics

• Link to: http://dev.planteome.org/amigo/base_statistics
• Can get to it from here: http://browser.planteome.org/amigo/software_list

• 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

• MAL attended all week, LC visited Thurs and Friday
• 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,
• Training on Protege to update the file

• 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

• WDIWG paper is out- needs planteome reference and cite the funding source.
  • https://f1000research.com/articles/6-1843/v1
  • http://datastandards.wheatis.org
  • http://ist.blogs.inra.fr/wdi/

Changes to Plant Experimental Conditions Ontology- PECO

• Was formerly Plant Environment Ontology (EO)
• The numbers have not changed, just the namespace has been chnged
• 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...

• BS: Need to send out notifications about the change from EO to PECO, check who is using EO

https://www.ebi.ac.uk/ols/ontologies/eo

• Gramene archive site
• http://agroportal.lirmm.fr/ontologies/EO
• https://bioportal.bioontology.org/ontologies/PECO
• http://aber-owl.net/ontology/EO
• http://www.ontobee.org/ontology/EO
• http://semanticportal.esipfed.org/ontologies/PEO
• https://arapheno.1001genomes.org/ontology/PECO/EO:0001001
• http://elixir-portugal.org/peao-ontology-plant-experimental-pipelines
• http://identifiers.org/registry
• http://vest.agrisemantics.org/content/plant-environment-ontology
• http://gensc.org/the-plant-specimen-contextual-data-consensus/
• http://ontofox.hegroup.org/tutorial/lists.php
• http://terraref.org/articles/existing-data-standards-and-tools/#vocabularies-and-ontologies
• http://www.phenotypercn.org/?page_id=1483

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
• AM: Outline has been shared with CM and Jorrit, focusing on the Samara germplasm one first, avoiding overlap with ICBO paper
• In the Planteome Publications folder: https://drive.google.com/drive/folders/0B71O1Y7eIKhsQ3VtTDhqTkxRUnM?usp=sharing

• 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

Visit to BTI at Cornell last week

- MAL attended all week, LC visited Thurs and Friday

• 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, Need to be trained on Protege to update the file

• New Variable Submission form for curators:

Changes to Plant Experimental Conditions Ontology- PECO

• Was formerly Plant Environment Ontology (EO)

Upcoming Events

• Phenoscape Hackathon in Dec

• Plant and Animal Genome meeting January 2018