Thursday March 5th, 2015

From Planteome.org
Jump to navigation Jump to search
The printable version is no longer supported and may have rendering errors. Please update your browser bookmarks and please use the default browser print function instead.

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

<html5media height="720" width="1280">File:AllHands 3-5-15.mp4</html5media>

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.

- 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:

Priority for us will be refining the list of the ontologies: Currently, this is the list of ontologies that are loaded:

AmiGO2 Planteome dev.png

Links:


  • 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:

From last week:

  • 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
Retrieved from "https://wiki.planteome.org/index.php?title=Thursday_March_5th,_2015&oldid=707"