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

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
  • 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 CGIARS 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:http://wiki.planteome.org/index.php/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

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
• Build a community consensus on widespread acceptance and availability, invite discussions
• Possible places: Plant Methods, Nature Plants, Nature Methods, New Phytologist
• Will help us crystallize our ideas, goals and plans

Goals:

• 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