View source for 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
== Agenda: ==
=== A. Introductions, as some people have not met yet.===
''See details on last months 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
* Ontology Repositories at GitHub- in progress
* Progress on opening new Planteome-related positions in the Jaiswal Lab (software developer, curator)

=== 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

=== C. 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, 
* 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

* 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