Thursday March 5th, 2015

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

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:

• A test version of the AmiGO 2.2.3 browser is up and running at Amigo 2.0 on Planteome.dev.

- 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:

• http://purl.obolibrary.org/obo/go/extensions/go-plus.owl
• NCBI Taxonomy
• http://purl.obolibrary.org/obo/cl/cl-basic.owl \
• Evidence Code Ontology
• http://purl.obolibrary.org/obo/go/extensions/gorel.owl \
• http://purl.obolibrary.org/obo/ma.owl \
• http://purl.obolibrary.org/obo/pato.owl \
• http://purl.obolibrary.org/obo/po.owl \
• http://purl.obolibrary.org/obo/emap.owl \
• http://purl.obolibrary.org/obo/chebi.owl \
• http://purl.obolibrary.org/obo/uberon/basic.owl \
• http://purl.obolibrary.org/obo/go/extensions/go-modules-annotations.owl

• 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

• 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:

• Lead by Sinisa, with two graduate students, Image_Annotation_Working_Group_Meetings

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

• Oregon State University Advertisement: posted on various sites: http://aspb.site-ym.com/networking/apply_now.aspx?view=2&id=276580

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