Thursday March 5th, 2015

Who: PJ, EA, LC, JE, JP Not available: BS, JD

A. General Comments and Updates:

• Schedule for Monthly All-Hands meetings

- do we need to do a new doodle poll or is this time good?

• Planteome Wiki page has been set up with password protection (if you are reading this, it must be working :-))

From last meeting... * PJ will circulate final version of the proposal in a cleaned-up format

• Progress on opening new Planteome-related positions in the Jaiswal Lab (software developer, curator)

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

• AmiGO 2.2.3 site up and running at dev.planteome.org. It currently just has GO and a small subset of annotations.
• Note: I was unable to get it to load with the ncbi taxon ontology like GO has because the loading program ran out of memory.
• JE is working with Chris Sullivan to figure out a way to be able to do the load from one of the compute nodes in the cluster as they have much more RAM.

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

• Lead by Sinisa, with two graduate students, Image_Annotation_Working_Group_Meetings

• 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 Mar 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