Feb 21st, 2017 Ontology Working Group Meeting

Planteome Ontology WG Zoom Meeting

• Date: Tuesday Feb 21st, 2017
• Time: 8:15am PST (GMT-8)
• Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/370267127

• Attendees: LC, PJ, AM, JE, CM, BS, DWS, BSinn, DC, EA, Mal

• Regrets: none

• Recordings:
  • File:Ontology WG Zoom Meeting-video 2-21-17.mp4
  • File:Ontology WG Zoom Meeting- audio 2-21-17.m4a

• Link to notes on Gdoc: https://docs.google.com/document/d/1DZur5ivCsAa5mFLs3vBKL1sZitt8txVsTLu9i1h2iZ0/edit?usp=sharing

You can preview the latest ontology and database release here: Planteome Release 2.0 on http://dev.planteome.org/amigo

Agenda: Discuss Workplan for Year 3 for the Ontologies group What are the goals for the coming months? Review what we listed in the last annual report...

PJ: We need to review what we proposed doing in the grant, and see what is still pending

Building community interfaces and engagement on adding ontology terms and annotations

Plant Stress Ontology

Enrichment of TO for terms where we do not have a one-to-one match, in the mappings, for example from CO to TO Enrich TO and other ontologies for terms for crops- should have 1-1 mappings

CM: the ontologies need to be more integrated in annotations and need to be pulling in more annotations, like we are doing with GRIN- this will bring in more ontology terms (?)

PJ: Issues with PATO as well- need to address some of the outstanding problems... Should we continue to use it? Yes Some definitions need major revisions Who can make changes- CM and George are the main editors right now Need to make sure we have open tickets for the issues…. Need appropriate terms to describe leaf morphology, shapes, margin types Need big effort in making sure these are in PATO- https://github.com/pato-ontology/pato/issues

Need to set a platform for next round- proof of concept

Field is moving into the HPT phenotyping- lessons from Phenome 2017.. Automated learning, deep learning...finding new terms HPT phenotyping traits are mathematical expressions, remote sensing data How to engage with the HPT phenotyping community? EA has met with Jesse Poland (KSU) - he is happy to discuss with us how to adapt the ontologies to the needs of the HTP community Advances in the area towards farm to fork-- working with Industry partners, storage and management, processing plants, Need vocabs and data standards on that side what is the major impact of this work on the community Data collection by sensors- alert farmers to water, App Guiding automated processes EBI meeting in April: industrial partnerships- food, quality, measurements , analytics

CM: Need to also address the issue with EO ?? (difficult to hear on the recording…)

Vision for wider focus and impact- idea for new grant? Discussions with private start up company: Ripe.io - manages quality, measures

USDA NIFA - RFPs for RCN type projects... Community workshops, take inputs, generate white papers, develop standards and analytics

Involve Matthew Lang- food ontology difficulties getting response from him… Vision and deliverables for industry, ontologies on back end Applying for PhenRCN type grant,

BS: involved with NIST? NIH grant MOTORPAK: Biochemistry of exercise/ ontology of physical activity, food relevant dimensions, looking for partners to get involved or contribute

What activities will be left to do by November 2017?

Possibility of a 1 year no cost extension? Have to have the $ All the partners should review their budgets Need to have a clear plan Review goals in grant - see annual report 2016

CM: need to get Triple store up and running Tools for viewing the ontologies APIs

From CO: new crops coming: Brassica, sorghum, yam, sugarcane

   - Goal should be to use automated mappings and follow up with manual check
   - At what stage should the mappings take place?
   - Can we have the automated mappings when the TDs are created?

Areas of TO need to be addressed: canopy/population traits Eg. Yam ontology- differences in size of tubers …… They want to have different classes for the weight of small, medium and large tubers- how to do this in TO? Issue of overlapping equivalence axioms...

Need to flesh out the EA in the TO- agree on the patterns Roseae traits coming up

From PJ: Semi automated approach should work, need to have people to contribute in an open way, understand what an ontology is, Manual creation of terms Need automated way to introduce new terms, bottlenecks NYBG contribute to TO??

MAL: We have started to do the mappings in a semiautomatic way, followed by manual checking Based on EQ statements Sorting out how to automatically add the terms to the TO Issues with the TO is making the EQ patterns difficult By instituting the design patterns, then the format of the definitions will change- no long will be genus differentia format and will not include the term IDs as we have been doing. Why is this the case? Can’t we set up the design patterns to formulate them however we wish? - A given trait can be classified under different super classes and using the genus differentia format, you have to make a choice which one to use. Using the DPs, the classification is automatic.

PJ: need to make sure the TO terms are consistent with the EQ LC: Need to work with PATO and make sure we are using the qualities in a consistent manner CM: TermGenie will be replaced with a new better tool this year. IncaTools is the foundation for that

EA: Need guidelines for people developing the trait dictionaries- eg Elixir project, developing TD for tree species What are the recommended best practices? Guidelines are in place for TD development, but need the next steps Key step is the mapping to TO… One TD per tree species

PJ: Species specific traits should be added to the appropriate TD for folks from outside the CG system, then can be consumed by the planteome

Are they open to contributions from outside groups via GH? Same TD file for everyone would be best EA- would not be acceptable by project managers, project specificity needed Select level of granularity PJ: suggest adding new column for comments- which project added specific terms, with different IDs for these Keeping them project specific Private companies do not want to share their info- need tools that they can use for the mapping

PJ: Concern that versions of TDs on GH are not the same as ones used in field?? Recommended: Use the same platform? Work from GH..? Demonstration of community involvement and buy-in

EA: Example issue the Brassica group- want to have their own GitHub

Separate group, separate project

Need written guidelines for the mapping part Need to agree on the workflow

Make a few 5 minute videos to explain best practices and what an ontology is Start at the beginning to collaborate

PJ: TO needs lots of work, would be great to have input from the NYBG group Need to expand the fruit types into TO Need to make sure the CO terms have a i:i mapping in the TO NYBG group: Focus should be on the inflorescence and the grain fruit Higher granularity in the CO vocabs

Site visit in 2017? Probably not, PJ will follow up with the NSF folks By Aug/Sept should be thinking about new proposal in 2018- PI? Proposal should be ready to go in Jan

Possible Workshop in fall? Or come to

GO meeting in Corvallis https://sites.google.com/view/goc2017 GO meeting June 1-5 Protein Ontology sub meeting- BS organizing, will let PJ know Possibility of having GC folks come

DWS: what should the next project be - seeds? Inflorescence types for next meeting Commercial application- seed qualities Quality measures of inflorescences as well

Deep learning app- leaf shape recognition- Being developed by Sinisa and Dimitri etc -

Phenome 2017 update:

HTP traits- how to address in TO Think about bringing in the PCO Prepare a short summary of the traits- couple of slides Share google doc of notes Send PJ a short summary

Meeting update: Phenome 2017, Feb 10th to 14th, 2017

• http://www.phenome2017.org/#homepage
• LC , received a travel grant, and presented Planteome presentation
• AM presented Samara poster
• DWS and BtSinn decided not to attend

Upcoming Meetings and Workshops

Biocuration 2017, March 26-29, 2017

• Stanford University, Palo Alto, California, United States
• http://biocuration2017.org
• Upcoming deadlines:
• Abstract submission for poster ONLY February 17, 2017
• Early conference registration February 17, 2017
• Online conference registration March 10, 2017
  • 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.

2017 Gene Ontology Consortium Meeting, June 1-5th, 2017, Corvallis

• GO Meeting Corvallis
• Registration
• Travel plans

• Dates: June 1-5, 2017 (Details)
  • Arrive (May 31) View travel directions
  • GOC meeting (June 1-3)
  • Noctua gene annotation jamboree (June 4)
  • Reactome Pathway curation jamboree (June 5)
  • Depart (June 5 late evening / June 6 anytime)

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

• Workshop proposal accepted-

• T5-06:Ontologizing botanical knowledge (two sessions)
  • Organizer: Hong Cui (University of Arizona, USA)
  • James Macklin (Agriculture Agri-Food Canada, Canada)
  • Pankaj Jaiswal (Oregon State University, USA)

• T5-18: Bioinformatics resources for comparative functional and phylogenetic analysis of plant genomes, pathways and diversity
  • Organizer: Pankaj Jaiswal (Oregon State University, USA)
  • Sushma Naithani (Oregon State University, USA)

• Deadline for the abstract submission for oral presentations has been extended for 39 of the 212 general symposia where one or a few speaker slots are available
• New deadline: February 15, 2017 for those 39 symposia and for posters only

• Abstract submitted? Not yet

ICBO 2017, Sept 12th-15th, 2017

• Newcastle, GB
• http://icbo.buffalo.edu/
• Important dates:
  • Mar 29, 2017: Workshops and tutorials proposals submission deadline
  • Apr 19, 2017: Notification of acceptance of workshops and tutorials
  • Jun 02, 2017: Paper and Poster Deadline
  • Jun 16, 2017: Paper Reviews Due