Oct 31st, 2017 Ontology Working Group Meeting: Difference between revisions

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Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/442101652
Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/442101652
* Meeting Recordings:
** [[File:Ontology WG Meeting audio 10-31-17.m4a|thumb|Ontology WG Meeting audio 10-31-17]]
** [[File:Ontology WG Meeting video 10-31-17.mp4|thumb|Ontology WG Meeting video 10-31-17]]


=Agenda and Notes=   
=Agenda and Notes=   
==News:==
==News:==
* Submitted the revisions on the NAR Paper- accepted for publication 10-30-17
* 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===
** 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==
== 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
* 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
 
* 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 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...
 
* 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://archive.gramene.org/plant_ontology/ontology_browse.html#eo
** 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
 
== Updates on papers in progress==
* 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?
 
==After meeting by email:==
From CM: Invitation to submit cROP project description to WWW2018 International projects track
 
Dr. Pascal Hitzler
NCR Distinguished Professor, Director for Data Science
Data Semantics Laboratory, Wright State University, Dayton, OH
http://dssc.cs.wright.edu
http://www.pascal-hitzler.de
http://daselab.org
pascal@pascal-hitzler.de
http://www.semantic-web-journal.net
 
On 26 Sep 2017, at 11:54, Hitzler, Pascal wrote:
 
Chris,
I've been asked to be "international project track" track chair  (region: North America) for WWW2017 see: https://www2018.thewebconf.org/call-for-papers/international-project-c
 
My task is to solicit (a small number of) very prestigious multi-organization projects which concern "the web" in some way, and which are located in North America.  I think that a description of the NSF-sponsored cROP project may be an ideal candidate for this.
 
Would that be of interest?
 
The conference will be in Lyon, France, April 23-27, 2018. As you know, it is the primary academic event  on all things "World Wide Web".
 
Best Regards, Pascal.
 
From: Hitzler, Pascal
Sent: Tuesday, September 26, 2017 6:45 PM
To: 'Chris Mungall' <cjmungall@lbl.gov>
Subject: RE: invitation to submit cROP project description to WWW2017
projects track
 
There has been a semantic web research track at WWW for many years. Only
recently, as semantic web became more mainstream, they merged it into the
main track.
 
So yes, semantic web topics are (mostly) also www topics. An exception would be work which is completely independent of the Web, e.g. if somebody would make an off-line expert system powered by ontologies, then WWW would not be a good venue.
 
I was assuming you're taking advantage of data (and ontologies) published and distributed on the web, in the project. So yes I'd think that should suffice.


* MAL:
The international projects track was (and still is) rather competitive. Right now they are talking about a total of 9 slots (so probably 2 or 3 from North America), not more. But then WWW is a really big conference. I haven't been there for a while, but already 10 years ago it drew probably about at least 1,000 people each year. The international projects track is supposed to provide a few selected highlights on what's going on research-wise in research projects.
** 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


==Upcoming Events==
== Upcoming Events ==
* Phenoscape Hackathon in Dec
* Phenoscape Hackathon in Dec  
* Plant and Animal Genome meeting January 2018
* ICBO 2018- in Corvallis, possibly end of August


* Plant and Animal Genome meeting January 2018
Next meeting: Nov 14th

Latest revision as of 20:38, 10 February 2018

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?

After meeting by email:

From CM: Invitation to submit cROP project description to WWW2018 International projects track

Dr. Pascal Hitzler NCR Distinguished Professor, Director for Data Science Data Semantics Laboratory, Wright State University, Dayton, OH http://dssc.cs.wright.edu http://www.pascal-hitzler.de http://daselab.org pascal@pascal-hitzler.de http://www.semantic-web-journal.net

On 26 Sep 2017, at 11:54, Hitzler, Pascal wrote:

Chris, I've been asked to be "international project track" track chair (region: North America) for WWW2017 see: https://www2018.thewebconf.org/call-for-papers/international-project-c

My task is to solicit (a small number of) very prestigious multi-organization projects which concern "the web" in some way, and which are located in North America. I think that a description of the NSF-sponsored cROP project may be an ideal candidate for this.

Would that be of interest?

The conference will be in Lyon, France, April 23-27, 2018. As you know, it is the primary academic event on all things "World Wide Web".

Best Regards, Pascal.

From: Hitzler, Pascal 

Sent: Tuesday, September 26, 2017 6:45 PM
To: 'Chris Mungall' <cjmungall@lbl.gov>
Subject: RE: invitation to submit cROP project description to WWW2017
projects track

There has been a semantic web research track at WWW for many years. Only
recently, as semantic web became more mainstream, they merged it into the
main track.

So yes, semantic web topics are (mostly) also www topics. An exception would be work which is completely independent of the Web, e.g. if somebody would make an off-line expert system powered by ontologies, then WWW would not be a good venue.

I was assuming you're taking advantage of data (and ontologies) published and distributed on the web, in the project. So yes I'd think that should suffice.

The international projects track was (and still is) rather competitive. Right now they are talking about a total of 9 slots (so probably 2 or 3 from North America), not more. But then WWW is a really big conference. I haven't been there for a while, but already 10 years ago it drew probably about at least 1,000 people each year. The international projects track is supposed to provide a few selected highlights on what's going on research-wise in research projects.

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

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