Thursday Feb 6th, 2015

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

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

Link to audio recording: File:Planteome all 2-5-15.m4a

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

• Member of editorial board of the OBO Foundry, Ontology Consultant
• Guidance on ontology development, consistent structure for PO and can be extended to other ontologies
• Setting standards and identifying and disseminating best practices for ontology development and use
• Website

Georgios Gkoutos, University of Aberystwyth, UK:

• Roles- As laid out in the Phoebe (ERA-CAPs) and cROP proposal
• Create logical definitions for plant phenotype ontology
• Expand Plant PhenomeNet, along with Phenotype RCN and integrate it into the Planteome interface
  • Developed out of http://phenomebrowser.net/index.html
• 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

• Recent AVATOL grant meeting: http://avatol.org/; http://currents.plos.org/treeoflife/avatol/; http://currents.plos.org/treeoflife/article/next-generation-phenomics-for-the-tree-of-life/
  • Sinisa and Thomas G Dietterich are involved, machine learning direction is planned for later developemnts
• Their goal is automatically filling cells in data matrices for phylogenetic analysis, based on the images
• Our goal is integrating the ontologies, anatomy first, then the qualities, ultimately connect to the GO
• New AISO-BisQue tool will be online and version controlled,

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: Bioversity HR does not want to advertise too widely in order to avoid too many Cvs to be screened between now and end of February as they are quite busy at the moment for the Bioversity programme restructuring, due end of March, so please just advertise on your web site and specialized ones.

• 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-

• 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

Discussion:

• Nature's Scientific Data is calling for data descriptors/paper on plant phenotype: http://blogs.nature.com/scientificdata/2015/01/30/call-for-submissions-describing-plant-phenotype-data
• This could be another place; http://currents.plos.org/treeoflife/
• See the related paper on the site: http://currents.plos.org/treeoflife/article/next-generation-phenomics-for-the-tree-of-life/