Oct 11th, 2016 Ontology Working Group Meeting: Difference between revisions

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* Date: Tuesday Oct 11th, 2016
* Date: Tuesday Oct 11th, 2016
* Time: 8:15am PDT (GMT-7)
* Time: 8:15am PDT (GMT-7)
* Connection details: Join from PC, Mac, Linux, iOS or Android:  
* Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/620296847
 
* Attendees:  
* Attendees:  
* Regrets: rest
* Regrets: PJ, DWS, EA


Recordings:
* Recordings:
** [[File:Planteome Ontology WG meeting 10-11-16 -audio only.m4a|thumb|Planteome Ontology WG meeting 10-11-16 -audio only]]
** [[File:Planteome Ontology WG meeting 10-11-16 video.mp4|thumb|Planteome Ontology WG meeting 10-11-16 video]]


=Agenda=
=Agenda=
==New Taxon constraints added to PO==
* Prototype taxon constraints have been added to the Plant Ontology
* This will be an area where the botanical expertise of the NYBG group will be very helpful
* Currently:
** whole plant (PO:0000003):  only_in_taxon NCBITaxon:33090 Viridiplantae {source="cjm"}
** plant ovary (PO:0000004): only_in_taxon NCBITaxon:3398 Magnoliophyta {source="GO:0035670"}
** microspore (PO:0020048):
* microspores are present in at least 5 different taxa (flowering plants, gymnosperms, some of the ferns, selaginella, and isoetes). Those taxa don’t have a common ancestor.
** DWS: Only, Marsilea, Regnellidium, Pilularia, Azolla, and Salvinia in the ferns.  A monophyletic group comprised of two families, Marsiliaceae (the first three genera) and Salvinaceae (the last two genera).
===How to deal with the ones that are in more than one taxa (that do not have a common ancestor)- two ways:===
*  In GO they name taxon unions (CM: but these are a real pain)
** id: GO:0009766
** name: primary charge separation
** namespace: biological_process
** def: "In the photosynthetic reaction centers, primary charge separation is initiated by the excitation of a molecule followed by the transfer of an electron to an electron acceptor molecule following energy transfer from light harvesting complexes." [ISBN:0792361431]
** is_a: GO:0022904 ! respiratory electron transport chain
** '''relationship: only_in_taxon NCBITaxon_Union:0000007 {id="GOTAX:0000169"} ! Viridiplantae or Bacteria or Euglenozoa'''
** relationship: part_of GO:0019684 ! photosynthesis, light reaction


* The other was is to use "X only_in_taxon (Y OR Z)", but this needs to be tested....


TBA....
* Suggestion: maybe we should be using the in_taxon relation, rather than the only_in_taxon relation


== Suggest adding a new relation between the morphology trait and a quality trait ==
Many of these are currently is_a children resulting in dual parentage, we also have some that are part_of, but this is technically not correct


e.g. pericarp texture (TO:0002623): 
* is_a pericarp morphology trait (TO:0000945)
* is_a fruit quality trait (TO:0002728)


* maybe we can use [http://www.ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/RO_0002326 contributes_to]
* if and only if exists c', p' c part_of c' and c' capable_of p and c capable_of p' and p' part_of p then c contributes_to p
== Harmonization between TO and PO ==
* The PO defines classes with sometimes a lot of synonyms (broad and narrow)
** e.g. PO fruit (http://browser.planteome.org/amigo/term/PO:0009001)
* In TO, the classes 'fruit weight' and 'kernel weight' exist. How to harmonize that?
* Options:
# Add the fruit types to the PO as separate terms
# Keep only 'fruit weight' in the TO, and then 'kernel weight' will become a synonym of 'fruit weight'
# Keep 'fruit weight' in the TO and move 'kernel weight' to appropriate the Crop Ontologies and then these can be imported in TO. The CO class 'kernel weight' will use the same design pattern as 'fruit weight' with a taxon constraint.
# Use the fields: subClassOf instead of equivalentClass for the design pattern (DP) when narrow synonyms
* Related question: should all the CO classes have a taxon constraint? Or only the classes with a species-specific entity (i.e. synonyms narrow or broad) should have one?
* ''discussion with PJ after the call: we will go with the first option- Add the fruit types to the PO as separate terms.  Ideally we should reinstate the alt ids as their original term, but that may be lost in history.  First SVN entry is  Apr 25th 2005, and at that point they were already merged.''
== CO mappings ==
* Eight crops have been mapped to TO so far: lentil, cassava, wheat, and rice are part of the current Planteome release 1.0
* New crops mapped: sweet potato, maize, soybean, and pigeonpea
** These are not on the browser yet, but mappings have been completed
* Statistics are available here: [https://docs.google.com/spreadsheets/d/1BbM5QT7idUr8MTbSd9SGnJlJRl7OaLUlrkjKQJzJ3fI/edit?usp=sharing TO-CO Mappings Stats]
* Attempt of a visualization: [http://mariealaporte.github.io CO-TO mappings image] (avoid this if you have ocean sickness!). Feedback is welcome
** Suggest removing the nodes which have no mappings to clean it up and make it simpler to view
== Redirect from old Plant Ontology Site==
* The old Plant Ontology PO site is not maintained anymore and is going into archive
* All traffic on http://plantontology.org to has been redirected to http://planteome.org
* The main drupal site has been renamed http://archive.plantontology.org/ including the Amigo browser, so you can still visit it
* the former dev and beta sites redirect to http://dev.planteome.org/amigo
* For updates, follow http://planteome.org
=== Review of Content- what needs to be saved?===
* PO anatomy glossary- can this be set up on the Planteome site?
From CM (by email):
* I think it may be worthwhile doing a quick alignment of content and figuring out what is worth preserving and what is not
* For example in http://archive.plantontology.org/node/5
** Plant Ontology development guidelines -- mostly out of date. Point to README-editors instead
** Ontology relationship types -- this is not useful for most users, it's redundant with what is in RO. You could point to the RO view in AmiGO here
** Instructions for submitting annotations -- sounds useful but it just goes to the top level of the wiki!
** Annotation file format -- this is just a duplication of what is on the GO side with s/GO/PO/...
** Mulitimedia files -- one video, which is cool. Maybe set up a vimeo channel instead
** Release Notes -- out of date
* As a general rule, a lot of content becomes stale quickly, and we have limited resources for keeping everything fresh. It's usually better to be minimal and point to github markdown docs (which are generally better updated as they are close to the source) or dynamic content, eg. from golr/amigo. And to publish lots of papers too....


= Upcoming Meetings and Workshops=
= Upcoming Meetings and Workshops=
==IC-FOODS Conference November 7-9,2016 Davis, California ==
==IC-FOODS Conference November 7-9, 2016 Davis, California ==
* http://www.ic-foods.org/conference
* http://www.ic-foods.org/conference
* Matthew Lange is organizing
* Matthew Lange is organizing
Line 41: Line 119:
* DWS will attend- evo devo presentation
* DWS will attend- evo devo presentation
* CM will attend and present Planteome and pheno-BLASTing
* CM will attend and present Planteome and pheno-BLASTing
* If you would like to be considered for a talk please submit your abstract by November 1, 2016
* early bird registrations till Nov. 15th- [https://ww2.eventrebels.com/er/Registration/StepRegInfo.jsp?ActivityID=18283&StepNumber=1 Registration Link]
==Biocuration 2017, March 26-29, 2017==
* Stanford University, Palo Alto, California, United States
* http://biocuration2017.org
* Call for Workshops:
** Submission deadline: November 11, 2016
** Submission email: biocuration2017@lists.stanford.edu
* Biocuration 2017 will bring together hundreds of leading curation scientists, bioinformaticians, and developers from all over the world to discuss their work, promote collaboration and foster a sense of community in this very active and growing area of research.
* The purpose of a workshop is to provide an opportunity for participants from academia and industry to present and discuss novel ideas on current and emerging topics relevant to biocuration.  Workshops are an excellent forum for exploring emerging approaches and task areas, for bridging the gaps between the curation and technology subfields of biocuration, and for critiquing existing approaches. This is a great opportunity to discuss specific topics with so many colleagues and working scientists gathered in the same location. 
* For the best opportunity for consideration, proposals should be received by November 11, 2016.  Please submit a short paragraph (or two) describing the following:
* Proposed scope and main objective, and their relation to biocuration
* Brief discussion of why the topic is of particular interest at this time
* Suggested format (talks, panel discussion, etc.)
* Potential speakers, panels, or other activities


== [http://www.ibc2017.cn XIX International Botanical Congress], July 23-29, 2017, Shenzhen, China ==
== [http://www.ibc2017.cn XIX International Botanical Congress], July 23-29, 2017, Shenzhen, China ==
Workshop proposal accepted
Workshop proposal accepted
==ICBO 2017, Sept 12th-15th, 2017==
* Newcastle, GB
* http://icbo.buffalo.edu/

Latest revision as of 22:06, 24 October 2016

Planteome Ontology WG Zoom Meeting

  • Date: Tuesday Oct 11th, 2016
  • Time: 8:15am PDT (GMT-7)
  • Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/620296847
  • Attendees:
  • Regrets: PJ, DWS, EA

Agenda

New Taxon constraints added to PO

  • Prototype taxon constraints have been added to the Plant Ontology
  • This will be an area where the botanical expertise of the NYBG group will be very helpful
  • Currently:
    • whole plant (PO:0000003): only_in_taxon NCBITaxon:33090 Viridiplantae {source="cjm"}
    • plant ovary (PO:0000004): only_in_taxon NCBITaxon:3398 Magnoliophyta {source="GO:0035670"}
    • microspore (PO:0020048):
  • microspores are present in at least 5 different taxa (flowering plants, gymnosperms, some of the ferns, selaginella, and isoetes). Those taxa don’t have a common ancestor.
    • DWS: Only, Marsilea, Regnellidium, Pilularia, Azolla, and Salvinia in the ferns. A monophyletic group comprised of two families, Marsiliaceae (the first three genera) and Salvinaceae (the last two genera).

How to deal with the ones that are in more than one taxa (that do not have a common ancestor)- two ways:

  • In GO they name taxon unions (CM: but these are a real pain)
    • id: GO:0009766
    • name: primary charge separation
    • namespace: biological_process
    • def: "In the photosynthetic reaction centers, primary charge separation is initiated by the excitation of a molecule followed by the transfer of an electron to an electron acceptor molecule following energy transfer from light harvesting complexes." [ISBN:0792361431]
    • is_a: GO:0022904 ! respiratory electron transport chain
    • relationship: only_in_taxon NCBITaxon_Union:0000007 {id="GOTAX:0000169"} ! Viridiplantae or Bacteria or Euglenozoa
    • relationship: part_of GO:0019684 ! photosynthesis, light reaction
  • The other was is to use "X only_in_taxon (Y OR Z)", but this needs to be tested....
  • Suggestion: maybe we should be using the in_taxon relation, rather than the only_in_taxon relation

Suggest adding a new relation between the morphology trait and a quality trait

Many of these are currently is_a children resulting in dual parentage, we also have some that are part_of, but this is technically not correct

e.g. pericarp texture (TO:0002623):

  • is_a pericarp morphology trait (TO:0000945)
  • is_a fruit quality trait (TO:0002728)
  • maybe we can use contributes_to
  • if and only if exists c', p' c part_of c' and c' capable_of p and c capable_of p' and p' part_of p then c contributes_to p

Harmonization between TO and PO

  • In TO, the classes 'fruit weight' and 'kernel weight' exist. How to harmonize that?
  • Options:
  1. Add the fruit types to the PO as separate terms
  2. Keep only 'fruit weight' in the TO, and then 'kernel weight' will become a synonym of 'fruit weight'
  3. Keep 'fruit weight' in the TO and move 'kernel weight' to appropriate the Crop Ontologies and then these can be imported in TO. The CO class 'kernel weight' will use the same design pattern as 'fruit weight' with a taxon constraint.
  4. Use the fields: subClassOf instead of equivalentClass for the design pattern (DP) when narrow synonyms
  • Related question: should all the CO classes have a taxon constraint? Or only the classes with a species-specific entity (i.e. synonyms narrow or broad) should have one?
  • discussion with PJ after the call: we will go with the first option- Add the fruit types to the PO as separate terms. Ideally we should reinstate the alt ids as their original term, but that may be lost in history. First SVN entry is Apr 25th 2005, and at that point they were already merged.

CO mappings

  • Eight crops have been mapped to TO so far: lentil, cassava, wheat, and rice are part of the current Planteome release 1.0
  • New crops mapped: sweet potato, maize, soybean, and pigeonpea
    • These are not on the browser yet, but mappings have been completed
  • Attempt of a visualization: CO-TO mappings image (avoid this if you have ocean sickness!). Feedback is welcome
    • Suggest removing the nodes which have no mappings to clean it up and make it simpler to view

Redirect from old Plant Ontology Site

Review of Content- what needs to be saved?

  • PO anatomy glossary- can this be set up on the Planteome site?

From CM (by email):

  • I think it may be worthwhile doing a quick alignment of content and figuring out what is worth preserving and what is not
  • For example in http://archive.plantontology.org/node/5
    • Plant Ontology development guidelines -- mostly out of date. Point to README-editors instead
    • Ontology relationship types -- this is not useful for most users, it's redundant with what is in RO. You could point to the RO view in AmiGO here
    • Instructions for submitting annotations -- sounds useful but it just goes to the top level of the wiki!
    • Annotation file format -- this is just a duplication of what is on the GO side with s/GO/PO/...
    • Mulitimedia files -- one video, which is cool. Maybe set up a vimeo channel instead
    • Release Notes -- out of date
  • As a general rule, a lot of content becomes stale quickly, and we have limited resources for keeping everything fresh. It's usually better to be minimal and point to github markdown docs (which are generally better updated as they are close to the source) or dynamic content, eg. from golr/amigo. And to publish lots of papers too....

Upcoming Meetings and Workshops

IC-FOODS Conference November 7-9, 2016 Davis, California

4th International Plant Phenotyping Symposium, CIMMYT, December 13 – 15, 2016

Plant and Animal Genome 2017, Jan 14-18, 2017, San Diego, CA, USA

http://www.intlpag.org/

  • October 31 early registration deadline
  • Deadline for workshop abstract submissions is December 2, 2016.
  • Deadline for changes to program (posting speakers) is November 30, 2016
  • Poster Abstracts Submission Deadline is October 28, 2016

Phenome 2017, Feb 10th to 14th, 2017

http://www.phenome2017.org/#homepage

  • DWS will attend- evo devo presentation
  • CM will attend and present Planteome and pheno-BLASTing
  • If you would like to be considered for a talk please submit your abstract by November 1, 2016
  • early bird registrations till Nov. 15th- Registration Link

Biocuration 2017, March 26-29, 2017

  • Stanford University, Palo Alto, California, United States
  • http://biocuration2017.org
  • Call for Workshops:
    • Submission deadline: November 11, 2016
    • Submission email: biocuration2017@lists.stanford.edu
  • Biocuration 2017 will bring together hundreds of leading curation scientists, bioinformaticians, and developers from all over the world to discuss their work, promote collaboration and foster a sense of community in this very active and growing area of research.
  • The purpose of a workshop is to provide an opportunity for participants from academia and industry to present and discuss novel ideas on current and emerging topics relevant to biocuration. Workshops are an excellent forum for exploring emerging approaches and task areas, for bridging the gaps between the curation and technology subfields of biocuration, and for critiquing existing approaches. This is a great opportunity to discuss specific topics with so many colleagues and working scientists gathered in the same location.
  • For the best opportunity for consideration, proposals should be received by November 11, 2016. Please submit a short paragraph (or two) describing the following:
  • Proposed scope and main objective, and their relation to biocuration
  • Brief discussion of why the topic is of particular interest at this time
  • Suggested format (talks, panel discussion, etc.)
  • Potential speakers, panels, or other activities

XIX International Botanical Congress, July 23-29, 2017, Shenzhen, China

Workshop proposal accepted

ICBO 2017, Sept 12th-15th, 2017

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