Thursday March 5th, 2015

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Who: EA, LC, JE, JP Not available: PJ, BS, GG, EZ, ST

Link to recording: File:AllHands 3-5-15.mp4

A. General Comments and Updates:

  • Schedule for Monthly All-Hands meetings

- We will do a new doodle poll- LC

  • 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

- EA- It would be very useful to have a copy of the 'official abstract' to share with partners or colleagues. See link to award on NSF site: http://www.nsf.gov/awardsearch/showAward?AWD_ID=1340112

- LC will send EA the NSF logos to use with the announcement on the Crop Ontology page

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

- position is open, being advertised on various sites: Planteome blog, ASPB Careers

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

- It currently just has a standard set of ontologies and a small subset of annotations.

- To navigate: go to http://dev.planteome.org/amigo/search/ontology

  • 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.

Possibly amy be better to just load a branch of the NCBI taxonomy, for the plants- we do not really need the whole thing.

  • Next steps are to work on the theming and to clean up the list of the ontologies:

Currently, this is the list of ontologies that are loaded:

AmiGO2 Planteome dev.png

Links:

  • Priority for us will be refining the list of the ontologies: Do not need the following:
    • Mouse_ontology
    • adult_mouse_anatomy
  • Need to include the Trait Ontology
  • Also need to check on the versions of the ontologies being loaded from the purls above- may be able to modify to use our verisons.
  • Load time for the ontologies is about 2 hours and the test set of annotations loaded in a few minutes.
  • 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.
  • For more information, please see the notes at: Data_storage_and_AmiGO2_Working_Group

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

  • Bisque (http://bioimage.ucsb.edu/bisque) is the Image Annotation (IA) of iPlant, and is the platform we will be using for the Planteome
  • Last group meeting was Feb 12th, Image_Annotation_Working_Group_Meetings
  • Setting up development environment for the two graduate students who work with Sinisa
  • Starting to work on the IA modules with in Bisque
  • Bisque has some aspects of segmentation, but it is limited, compared to the AISO desktop tool
  • Initial focus is to build a basic user interface that allows single segmentation input- it sends it out to the Bisque server and returns a segmented image. Not interactive- done over the network
  • Bisque lacks the software architecture to do interactive segmentation, over the network.
  • Bisque developers are working on a more synchronous interactive mode (independent of our project)



From last month's meeting:

  • 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

  • Next meeting is Friday Mar 6th, 2015 8:30am PST (GMT-8)

Update on Position advertisements:

  • Crop Ontology position is closed, interviews are March 19-20th

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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