Sept 27th, 2016 Ontology Working Group Meeting: Difference between revisions

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=Planteome Ontology WG Zoom Meeting=
=Planteome Ontology WG Zoom Meeting=
* Date: Tuesday Aug 23rd, 2016
* Date: Tuesday Sept 27th, 2016
* Time: 8:15am PDT (GMT-7)
* Time: 8:15am PDT (GMT-7)


* Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/217118644
* Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/528884901


* Attendees: LC, AM, JE, CM, MAL, BS, DWS, BtSinn, Dario, GG
* Attendees: LC, MAL, AM, PJ, JE, BS, DWS,  
* Regrets: EA, PJ
* Regrets: rest


Recordings:
Recordings:
* [[File:Ontology WG Zoom Meeting 9-27-16 audio only.m4a|thumb|Ontology WG Zoom Meeting 9-27-16 audio only]]
* [[File:Ontology WG Zoom Meeting video 9-27-16.mp4|thumb|Ontology WG Zoom Meeting video 9-27-16]]


== Update on the Planteome Release 1.0, September 2016 ==
* Planteome 1.0 database includes 67,272 ontology terms with links to approximately 1.9 million (M) bioentities (data objects) including proteins, genes, RNA transcripts and gene models, germplasm, and QTLs.
* Bioentities were often annotated to more than one ontology term, resulting in approximately 17.2M annotations.


== Up date on the Release ==
* Reference ontologies for plants include the Plant Ontology (PO), Plant Trait Ontology (TO), and the Plant Environment Ontology (EO), and the Planteome portal also provides reference ontologies developed by collaborating groups: the Gene Ontology (GO), the Phenotypic Qualities Ontology (PATO), the Chemical Entities of Biological Interest (ChEBI), and the NCBI taxonomy.
* TBA


==PJ attending NSF meeting Sept 7-8th==
* Release 1.0 includes four species-specific trait ontologies for wheat, rice, lentil and cassava, developed by the Crop Ontology (http://www.cropontology.org/), a project of the CGIAR.
* The trait terms in these species-specific ontologies have been mapped to the relevant reference Trait Ontology terms for data integration. 


==Plant and Cell Physiology Database manuscript==
* Annotated data was sourced from 24 unique database resources and covers 86 different plant taxa.
* Addressing issues raised by the editors:
* Functional GO annotations are available for 62 species, which, for many of these species, the Planteome is a unique annotation resource.  
* [https://docs.google.com/document/d/1F36Ay3-NV890--Yfw7qMvcwFGAmeD_-E84XLvu2lFlM/edit?usp=sharing Response to Plant and Cell Physiology @ Planteome Database]
* deadline Sept 8th ish...
* draft will be circulated


==Fall workshop planning==
* Available at http://planteome.org/ and also at the CyVerse Mirror site: http://draco.cyverse.org/amigo
TBA...
 
* Link to http://planteome.org/blog
 
=== Comments and Discussion ===
* Planteome site:
** BS: Need a diagram or graphic that shows the relationship between the TO, the PO and the CO species- would add graphic appeal to the webpage
** PJ: From GODAN, People not aware of what an ontology is- should create a short video (can start with ppts); also need a new theme for the website- will work with JE on
 
* BS: working with the ISO http://www.iso.org/iso/home.html group to have BFO accepted as a standard. Creating an Industrial ontology foundry
** product manufacturing core, future extension to the Ag Industry
** suggests adding farmer friendly terms to the TO as synonyms- a "farmer slim" ?
 
* for next release, need to update the datasets, do incremental releases
 
===Comments from NSF meeting===
* PJ: Need to be on the forefront, prepare TO and PATO to capture new HTP algorithms
** for possible renewal, need proof of concepts, address traits in TO that are mathematical expressions
** Some are described as  a method and a description- e.g. PCA analysis, 2 axes, you know the first dimension
** These traits can be added to the CO maize ontology file ...???
 
* Suggest to invite Edgar Spalding to attend a future conference call - see page Phytomorph: http://phytomorph.wisc.edu/
** PJ will invite him...; link to publications: http://www.botany.wisc.edu/spalding.htm
 
* Example traits from PJ presentation eg: aerenchyma formation under drought to remobilize carbon
** New program manager is from modelling - AGMIP
** NSF want to see how we fit in with the modelling community- need list of traits to start modelling
 
* NSF Annual report now due:
** LC will send out template from last year
** Need paragraph of accomplishments since last year; list of people on the project, monthly hour commitment etc
 
* NSF wants to see community engagement
** PJ: contracted with private company, Sanmita Inc, to create an app or online data submission platform for freelance curation and to maintain their own gene nomenclature
** Compare with functionalities of Noctua tool from GO
 
== Marie-Angelique visits in Corvallis for next five weeks ==
* Goals for Marie's visit:
** Enriching the Trait Ontology and integrating the maize trait dictionary
 
* Other sources of maize traits for integration:
** Panzea traits (including the NAM population- annotations to this)
** Underground root traits from Johnathan Lynch's group (dropbox folder of papers)
** GRIN global traits (Either Samara scrape, or excel spreadsheet from PJ)
 
* Enrich TO for tuber/underground traits
** look at YAML pattern application to curate large chunks of missing morphology traits.
** CIMMYT: sweet potato TD and potato TD
   
* Second priority: paper
** write a brief paper about mapping traits to the TO, expand on MAL's ICBO proceedings paper
** Goal: try and get a draft done while MAL is stateside
 
* Samara tool for web scraping: https://github.com/jhpoelen/samara
** Using for scraping the GRIN Global data and Yorik
** Yorik is contracted to help with the APS scrape
 
== Recent meetings and Conferences==
===NSF meeting Sept 7-8th, 2016===
* PJ attended, presented Planteome- see notes above
 
=== GODAN Summit, New York City, Sept 15-16th, 2016 ===
* http://summit.godan.info/
* Shared exhibit booth:
** Planteome- ''PJ  attended''
** Crop Ontology- ''Bioversity- EA''
** Gramene
** Agronomy Ontology- Medha
** IC3-FOODS at UC Davis for Food Ontology
** Agricultural Nutrition and Technology Ontology (ANT)


== Other items?==
=== Scientific Advisory Board===
=== Scientific Advisory Board===
* List of possible people:  
* List of possible people:  
Line 34: Line 103:
** others?
** others?


 
* ''DWS: Suggested  David Spooner, USDA potato researcher''
* LC will draft a letter and discuss with PJ
* Goals review progress, help improve, recommend us to funders
* Goals review progress, help improve, recommend us to funders
* Could have a meeting with them at the fall workshop
* Could have a half day online meeting with them later in the fall, maybe could also meet at PAG


== Other items?==
===Fall workshop planning===
Problem of lack of affordable housing at OSU this fall


= Upcoming Meetings and Workshops=
= Upcoming Meetings and Workshops=
== GODAN Summit, New York City, Sept 15-16th, 2016 ==
==IC-FOODS Conference November 7-9,2016 Davis, California ==
* http://summit.godan.info/
* http://www.ic-foods.org/conference
* Who is involved- will present an exhibit booth together:
* Matthew Lange is organizing
** Planteome- ''PJ will attend''
* BS cannot attend, will be at ISO meeting in Europe
** Crop Ontology- ''Bioversity- EA will attend''
* MAL and PJ will atend
** Gramene
** Agronomy Ontology- Medha
** IC3-FOODS at UC Davis for Food Ontology
** Agricultural Nutrition and Technology Ontology (ANT)
* Materials for booth are being collected in DropBox folder:
** Project logo in high resolution
** Short slide show (~ 5 slides) to show your project's impact and applications
** Any handouts like brochures
 
* Also can bring swag gifts such as tote bags, coffee mugs,pens,jump drives with your project materials on it, etc


== 4th International Plant Phenotyping Symposium, CIMMYT, December 13 – 15, 2016 ==
== 4th International Plant Phenotyping Symposium, CIMMYT, December 13 – 15, 2016 ==
Line 70: Line 130:
== Phenome 2017, Feb 10th to 14th, 2017==
== Phenome 2017, Feb 10th to 14th, 2017==
http://www.phenome2017.org/#homepage
http://www.phenome2017.org/#homepage
* DWS will attend- evo devo presentation
* CM will attend and present Planteome and pheno-BLASTing


== [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

Latest revision as of 21:43, 7 February 2017

Planteome Ontology WG Zoom Meeting

  • Date: Tuesday Sept 27th, 2016
  • Time: 8:15am PDT (GMT-7)
  • Attendees: LC, MAL, AM, PJ, JE, BS, DWS,
  • Regrets: rest

Recordings:

Update on the Planteome Release 1.0, September 2016

  • Planteome 1.0 database includes 67,272 ontology terms with links to approximately 1.9 million (M) bioentities (data objects) including proteins, genes, RNA transcripts and gene models, germplasm, and QTLs.
  • Bioentities were often annotated to more than one ontology term, resulting in approximately 17.2M annotations.
  • Reference ontologies for plants include the Plant Ontology (PO), Plant Trait Ontology (TO), and the Plant Environment Ontology (EO), and the Planteome portal also provides reference ontologies developed by collaborating groups: the Gene Ontology (GO), the Phenotypic Qualities Ontology (PATO), the Chemical Entities of Biological Interest (ChEBI), and the NCBI taxonomy.
  • Release 1.0 includes four species-specific trait ontologies for wheat, rice, lentil and cassava, developed by the Crop Ontology (http://www.cropontology.org/), a project of the CGIAR.
  • The trait terms in these species-specific ontologies have been mapped to the relevant reference Trait Ontology terms for data integration.
  • Annotated data was sourced from 24 unique database resources and covers 86 different plant taxa.
  • Functional GO annotations are available for 62 species, which, for many of these species, the Planteome is a unique annotation resource.

Comments and Discussion

  • Planteome site:
    • BS: Need a diagram or graphic that shows the relationship between the TO, the PO and the CO species- would add graphic appeal to the webpage
    • PJ: From GODAN, People not aware of what an ontology is- should create a short video (can start with ppts); also need a new theme for the website- will work with JE on
  • BS: working with the ISO http://www.iso.org/iso/home.html group to have BFO accepted as a standard. Creating an Industrial ontology foundry
    • product manufacturing core, future extension to the Ag Industry
    • suggests adding farmer friendly terms to the TO as synonyms- a "farmer slim" ?
  • for next release, need to update the datasets, do incremental releases

Comments from NSF meeting

  • PJ: Need to be on the forefront, prepare TO and PATO to capture new HTP algorithms
    • for possible renewal, need proof of concepts, address traits in TO that are mathematical expressions
    • Some are described as a method and a description- e.g. PCA analysis, 2 axes, you know the first dimension
    • These traits can be added to the CO maize ontology file ...???
  • Example traits from PJ presentation eg: aerenchyma formation under drought to remobilize carbon
    • New program manager is from modelling - AGMIP
    • NSF want to see how we fit in with the modelling community- need list of traits to start modelling
  • NSF Annual report now due:
    • LC will send out template from last year
    • Need paragraph of accomplishments since last year; list of people on the project, monthly hour commitment etc
  • NSF wants to see community engagement
    • PJ: contracted with private company, Sanmita Inc, to create an app or online data submission platform for freelance curation and to maintain their own gene nomenclature
    • Compare with functionalities of Noctua tool from GO

Marie-Angelique visits in Corvallis for next five weeks

  • Goals for Marie's visit:
    • Enriching the Trait Ontology and integrating the maize trait dictionary
  • Other sources of maize traits for integration:
    • Panzea traits (including the NAM population- annotations to this)
    • Underground root traits from Johnathan Lynch's group (dropbox folder of papers)
    • GRIN global traits (Either Samara scrape, or excel spreadsheet from PJ)
  • Enrich TO for tuber/underground traits
    • look at YAML pattern application to curate large chunks of missing morphology traits.
    • CIMMYT: sweet potato TD and potato TD
  • Second priority: paper
    • write a brief paper about mapping traits to the TO, expand on MAL's ICBO proceedings paper
    • Goal: try and get a draft done while MAL is stateside

Recent meetings and Conferences

NSF meeting Sept 7-8th, 2016

  • PJ attended, presented Planteome- see notes above

GODAN Summit, New York City, Sept 15-16th, 2016

  • http://summit.godan.info/
  • Shared exhibit booth:
    • Planteome- PJ attended
    • Crop Ontology- Bioversity- EA
    • Gramene
    • Agronomy Ontology- Medha
    • IC3-FOODS at UC Davis for Food Ontology
    • Agricultural Nutrition and Technology Ontology (ANT)

Scientific Advisory Board

  • List of possible people:
    • Sandy Knapp
    • Lynn Schriml (Lynn Schriml- Google Scholar)
    • Sarah Mathews - Was at Harvard, but she has moved to CSIRO in Canberra, Australia
    • Ruth Bastow
    • others?
  • DWS: Suggested David Spooner, USDA potato researcher
  • Goals review progress, help improve, recommend us to funders
  • Could have a half day online meeting with them later in the fall, maybe could also meet at PAG

Other items?

Fall workshop planning

Problem of lack of affordable housing at OSU this fall

Upcoming Meetings and Workshops

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

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

  • International Maize and Wheat Improvement Center (CIMMYT)
  • El Batan, Texcoco, México (Near Mexico City)
  • Early bird registration deadline: October 16, 2016

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

http://www.intlpag.org/

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

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

Workshop proposal accepted

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