Thursday Feb 6th, 2015

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Planteome All-Hands Monthly Meeting- Thursday Feb 6th, 2015

Who: PJ, EA, LC, JE, JP, DWS, GG, EZ, BS; Not available: ST, CM, JD

A. Introductions, as some people have not met yet.

See details on last month's page: Tuesday_Jan_6th,_2015

Barry Smith, University at Buffalo

  • Head of the OBO Foundry, Ontology Consultant
  • Guidance on ontology development, consistent structure for PO and can be extended to other ontologies
  • Setting standards for ontologies

Georgios Gkoutos, University of Aberystwyth, UK:

  • Roles- As laid out in the proposal, (Fibi? was this referring to the ERA-CAPs proposal??)
  • create logical definitions for plant phenotype ontology
  • Expand Plant Phenoment , along with Phenotype RCN
  • Contribute to expanding the reference ontologies as need
  • PATO partially funded from this project, will need to address needs of the Planteome as we move forward
  • Should have an acknowledgment on the PATO web site:http://wiki.obofoundry.org/wiki/index.php/PATO:Main_Page
  • Will be hiring a postdoc once the contracts are set up, somewhat of a lengthly procedure, will keep us posted
  • Will be working with the ontology group and closely with John Doonan

John Doonan, University of Aberystwyth, UK (not present on the call)

  • Senior person, collaborator- Director National Plant Phenomics Centre for the UK (http://www.plant-phenomics.ac.uk/en/)
  • Tools and workflows developed in the project will be integrated into the NPPC, for the phenotype evaluation

Elizabeth Arnaud: CGIAR Centers

Crop Ontologies (http://www.cropontology.org/)

  • Applied ontologies, crop specific ontologies and vocabularies for plant breeders communities traits, methods and scales
  • Align concepts with PO, TO, GO, PDO and expand the list of traits
  • Integrating descriptors for annotating germplasm=m and genetic experiments in the various CGIAR campuses
  • List of 8-10 crops and or clades, and will add additional ones
  • Build common references and cross links
  • Contribute to development of the reference ontologies
  • Outreach to users on CGIAR campuses
  • Key crops for the initial pilot cases: wheat, maize, rice
  • Will also test alignment tools and annotation tools

B. General Comments and Updates:

  • Schedule will be: Monthly All-Hands meetings and the working groups will meet and report back to the group.
  • PJ will circulate final version of the proposal in a cleaned-up format
  • Contracts work on an invoice system
  • Planteome-Internal Mailing list has been set up, this will be a useful way to share information among the key people in the team.
  • Planteome Wiki page has been set up with password protection (if you are reading this, it must be working :-))
  • Ontology Repositories at GitHub- in progress
  • Progress on opening new Planteome-related positions in the Jaiswal Lab (software developer, curator)
  • LC will look into using Zoom (https://www.zoom.us/) for calls, possibly will get a speaker phone

C. Update from IT group- Data Store, AmiGO2, Justin Elser:

  • Justin E has been working with Seth Carbon and Chris Mungall on installing the SolR (http://en.wikipedia.org/wiki/Apache_Solr) system to run the AmiGO2 browser
  • Index based, dynamic, flexible and adaptable
  • Call last Friday- ideas for data visualizations,
  • Running, but needs some extension from the GO Schema for the new relations we use in the PO etc
  • Background: Plant Ontology has been run on MySQL database in the past, but now we are transitioning to the new NoSQL platform.
  • Has some visualization tools, for the ontologies rather than the data
  • Need some use cases for demonstration
  • Development version will be run from OSU, then eventually will be ported to the new Live site at iPlant
  • Also involves contributions from Eugene Zhang and his two grad students- who will share tasks, one main one secondary
  • JE can add the needed access for the people involved
  • JE will document steps in progress- see link to wiki page:AmiGO2_install

D. Update from AISO/BisQue group- Justin Preece:

  • Lead by Sinisa, with two graduate students, 3 meetings in last two weeks Image_Annotation_Working_Group_Meetings
  • AISO is a desktop software- Annotation of Images with Ontologies: http://www.plantontology.org/software/AISO
  • Based on segmentation of images and labeling those with ontology terms
    • Initially done with the Plant anatomy terms from the PO
  • Goal is to expand the work done for AISO to the BisQue online platform
  • BisQue Platform: http://bioimage.ucsb.edu/bisque;
  • Advanced image manipulation, storage, and annotation platform, hosted on the iPlant
  • Lacks interactive segmentation functions and ontology annotation for metadata
  • Annotated images will also be stored at iPLant
  • Generation of Sample Images - DWS
    • Need to generate the labeled images- initially using AISO
  • Priorities would be images of leaf types, flowers, root and stem sections
  • DWS has a large number of images from the plant anatomy textbook - will send us the link
  • DWS owns them so it is not a problem, part of the laboratory exercises on a CD for the book
  • Will go along with the glossary of anatomy terms based on the PO

E. Update from Ontologies Working group:

Who is involved: EA, BS, DWS, LC, PJ, others TBA

  • We have had three meetings so far, including a face-to-face meeting with many of the CO curators at PAG.
  • Next meeting is Tuesday Feb 10th, 2015 8:30am PST (GMT-8)

EA: Ad for postdoc position has been advertised, as of Friday Jan 30th, and open till end of February. Anticipate having the person in place by Mid-March. VA_PostDoc_CropOntology_NSF_MPL_Final.pdf

  • PJ: we can help advertise the position advertisement- by posting on Planteome.org and the PO Facebook page. EA asked
  • First steps for Ontologies WG is to decide on which of the species-specific Crop Ontologies we will focus on initially. Previously we had discussed wheat, rice and maize as the initial targets.
  • The Plant Ontology should be fairly mature as a source of the entity terms, for the plant parts and stages, but need to assess what needs to be done from the CO side for the species specific trait ontologies.
  • Additional terms can be added to the PO as needed
  • BS can look over the TO and provide guidance as to the structure-
    • Comments from email, after the call:
  • EA met with Ruaraidh Sackville-Hamilton (Head of Genetic Resources, IRRI)- They are working on updating the rice trait dictionary and they are interested in making sure the terms are cross-referenced with the TO terms.
    • Need to make sure they have access to the latest version of the TO, and may need some assistance to ensure the links are done correctly.

- LC will follow up with EA to coordinate it

  • Initial efforts will need to be focused on maturing the Trait Ontology and filling in the gaps.

Links: http://www.cropontology.org/

F. Position Paper or "White Paper"

  • In order to state our plans and cultivate our ideas, we should move quickly to produce a Position Paper or "White Paper".
  • We do not want to lose out on ideas and concepts that we have proposed- others may take the credit and publish it first
  • We should put forward our plans and stance, and what we expect to produce, rather than discussing it later in the project
  • Possible places: Plant Methods, Nature Plants, Nature Methods, New Phytologist
  • Will help us crystallize our ideas, goals and plans

Goals:

  • Build a community consensus on widespread acceptance and availability, invite discussions
  • Define the vocabularies and terms such as phenotypes, etc
  • What level of phenotypes are we looking at: molecular aspects, function, processes, location, etc
  • Any evaluated characteristic of an entity can considered a phenotype
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