Thursday April 16th, 2015

• Who: LC, PJ, JP, JE, CM, JD
• Not available: EA, EZ, BS, GG, SN

Zoom Connection Details: Join from PC, Mac, iOS or Android: https://zoom.us/j/996259332

• Link to recording- Video: File:All-Hands Meeting 4-16-15.mp4
• Link to recording- Audio: File:All-Hands Meeting 4-16-15.m4a

A. General Comments and Updates:

Introductions:

• Leo Valette, New Crop Ontology curator and coordinator at the Bioversity, with Elizabeth Arnaud (for more info please see: Ontology_Working_Group_March_6th_2015

- Curating the trait dictionaries, used by plant breeders

• John Doonan, irector National Plant Phenomics Centre, at University of Aberystwyth, UK

- High throughput phenotyping - gene discovery and plant breeding. Integration of phenomic and genomic data

- Semi-automated phenotyping system, associated with Plant Breeding department - Background in developmental genetics, but works closely with George Gkoutos, expert in ontologies and bioinformatics

- George's news: postdoc position has been advertised, and BBSRC has agreed to extend it as part of the collaboration with CGIAR on tropical grasses (Need to check) - Hands on facilty for large scale phenotyping - Goal is integrate ontologies into phenotyping workflow.

Chris Mungall: - background in bioinformatics, involved with Gene Ontology, PATO with George Gkoutous, Uberon - Assist with deployment of AmiGO2 browser.

Xu Xu - In Sinisa's group, works on Image annotation - From Xu Xu : "hello all, I am Xu Xu. Sorry my mic is not working. Just an introduction here: I am Sinisa's student working in image annotation group, with Justin. I will be working on integrating AISO to BisQue. Happy to work with all of you!"

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

AmiGO2 install

AmiGO2 has been installed and loaded with our OWL files, includes some others that may not be needed. Also have around 200,000 annotations loaded from various ontologies. http://dev.planteome.org

Load times seem much better than the old AmiGO. At least for annotations. Loading the ontologies takes about 25 minutes, but does not include the ncbi taxon ontology. Inclusion of this takes too much memory and doesn't finish on palea. Looking at loading a small subset (plants?) of the taxon.

Test set of annotations loaded:

• /data/www/planteome_dev/amigo/assoc_files/eo_diversity_arabidopsis.assoc \
• /data/www/planteome_dev/amigo/assoc_files/eo_diversity_rice.assoc \
• /data/www/planteome_dev/amigo/assoc_files/eo_gene.assoc \
• /data/www/planteome_dev/amigo/assoc_files/eo_protein.assoc \
• /data/www/planteome_dev/amigo/assoc_files/eo_qtl.assoc \
• /data/www/planteome_dev/amigo/assoc_files/go_gramene_oryza.assoc \
• /data/www/planteome_dev/amigo/assoc_files/po_anatomy_gene_oryza_gramene.assoc \
• /data/www/planteome_dev/amigo/assoc_files/po_anatomy_gene_oryza_poc.assoc \
• /data/www/planteome_dev/amigo/assoc_files/po_anatomy_gene_vitis_poc.assoc \
• /data/www/planteome_dev/amigo/assoc_files/po_anatomy_gene_zea_MaizeGDB.assoc \
• /data/www/planteome_dev/amigo/assoc_files/po_anatomy_qtl_oryza_gramene.assoc \
• /data/www/planteome_dev/amigo/assoc_files/po_anatomy_stock_zea_MaizeGDB.assoc \
• /data/www/planteome_dev/amigo/assoc_files/po_growth_gene_oryza_gramene.assoc \
• /data/www/planteome_dev/amigo/assoc_files/po_growth_gene_vitis_poc.assoc \
• /data/www/planteome_dev/amigo/assoc_files/po_growth_qtl_oryza_gramene.assoc \
• /data/www/planteome_dev/amigo/assoc_files/po_ontology_IMP_gene_oryza_poc.assoc \
• /data/www/planteome_dev/amigo/assoc_files/to_diversity_arabidopsis.assoc \
• /data/www/planteome_dev/amigo/assoc_files/to_diversity_rice.assoc \
• /data/www/planteome_dev/amigo/assoc_files/to_Gene_association.assoc \
• /data/www/planteome_dev/amigo/assoc_files/to_Protein_association.assoc \
• /data/www/planteome_dev/amigo/assoc_files/to_QTL_association.assoc

D. Update from Ontologies Working group:

The OWG has been meeting roughly biweekly, around everyone's travel schedules

Updates on various collaborative projects:

• Panzea dataset annotation in collaboration with MaizeGDB

- large GWAS dataset 385,000 lines in MaizeGDB database - annotating with TO and PO terms - new interface at Maize GDB includes some of the PO terms, adding additional ontology terms and adding TO - working with their developers so their users can browse the ontology hierarchy

• Plant Diease ontology (will become part of Plant Stress Ontology)

- new undergrad helper working on adding diseases - will also tie into the Panzea dataset as they also have diseaes traits

- Working with new collaborating Database group PHI-Base Pathogen - Host Interaction database- Intiative from Rothamstad in England - large set of manually curated literature - covers wide range of plant species (and animals) - They are requesting terms and will make cross links to and from their database