Thursday April 16th, 2015

• Who: LC, PJ, JP, JE, CM, JD, XX
• 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 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, Director 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 facility for large scale phenotyping

- Goal is integrate ontologies into phenotyping workflow.

Chris Mungall, LBL - background in bioinformatics, involved with Gene Ontology, Phenotype ontology, PATO with George Gkoutous, human and mammalian systems, created Uberon anatomy ontology

- 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!"

Update on hires at OSU: PJ: Software Developer position has not had too many applicants, PJ met a potential candidate who is a spouse of a BPP department member, Biology Masters, recently from Yahoo.

Ontology curator position - will start evaluating applicants and will hopefully can offer to someone by mid May.

Marie Angelique Laporte has accepted the position, but will be joining the first week of May

No news on the position at NYBG.

B. Update from IT group- Data Store, AmiGO2

• Justin Elser, Chris Mungall, with Seth Carbon

AmiGO2 install

• A dev version of the AmiGO2 has been installed and loaded with a set of OWL files, includes some others that may not be needed. http://dev.planteome.org
• Still in progress, need to do a fair bit of configuration and organization of the ontology project files.
• Loading the ontologies takes about 25 minutes, but does not include the ncbi taxon ontology, which takes too much memory and doesn't finish on palea.
• Looking at loading a small subset (plants?) of the taxon

Ontologies loaded:

• ChEBI, GO, PATO, Cell, PO, TO, ECO, GOREL, also Uberon, Uberon/phenoscape-anatomy, ncbi_taxonomy (114)
• Need to include the Plant Experimental Conditions ontology (EO) and take out the CL and Uberon files
• Several of the features such as QuickGO are not working
• Filters are not being saved- compare with the GO version- It actually does not work there either, apparently designed this way.
• Mappings to SourceForge and other ontologies is not working

CM: In the future, we will have one uber file- "planteome.owl" that will contain all the planteome core and partner (PATO, ChEBI, GO etc) ontologies.

• Also could use only a slice of the GO, as there are a lot of non-plant relevant terms.

PJ: Could use the GR_tax-ontology.obo file that has many of the plant species, and should have all the pathogens- Note: GR_tax-ontology.obo has only green plants and red algae.

• GR_tax-ontology.obo should have refs to NCBI as well, would have to be maintained here, has not been worked on for over two years

CM: We could extract a slice of the NCBI taxonomy, if we can define our criteria e.g. everything that we have an annotation to, should have all the plants and the pests and pathogens.

Test set of annotations loaded

• Loaded around 200,000 annotations from various ontologies, out of a total of ~ 4 million
• Load times seem much better than the old AmiGO, at least for these annotations
• Problems were found in some of the files, specifically coming from the col 16- annotation extensions and also in column 5 (ontology ID), where spaces are causing problems
• JE corrected the issues he found in the files, but these revised files need to be committed back to the SVN

Ontology	Species	filename
PO-Anatomy	rice	po_anatomy_gene_oryza_gramene.assoc
PO-Anatomy	rice	po_anatomy_gene_oryza_poc.assoc
PO-Anatomy	rice	po_anatomy_qtl_oryza_gramene.assoc
PO-Anatomy	maize	po_anatomy_gene_zea_MaizeGDB.assoc
PO-Anatomy	grape	po_anatomy_gene_vitis_poc.assoc
PO-Anatomy	maize	po_anatomy_stock_zea_MaizeGDB.assoc
PO_Growth_Stage	rice	po_growth_gene_oryza_gramene.assoc
PO_Growth_Stage	rice	po_growth_qtl_oryza_gramene.assoc
PO_Growth_Stage	grape	po_growth_gene_vitis_poc.assoc
Plant_Ontology	rice	po_ontology_IMP_gene_oryza_poc.assoc
Trait_Ontology	?	to_diversity_arabidopsis.assoc
Trait_Ontology	?	to_Protein_association.assoc
Trait_Ontology	?	to_QTL_association.assoc
Trait_Ontology	Rice	to_diversity_rice.assoc
Trait_Ontology	?	to_Gene_association.assoc
Plant_EO	?	eo_protein.assoc
Plant_EO	rice	eo_diversity_rice.assoc
Plant_EO	?	eo_qtl.assoc
Plant_EO	arabidopsis	eo_diversity_arabidopsis.assoc
Plant_EO	?	eo_gene.assoc
Gene_Ontology	rice	go_gramene_oryza.assoc

Need to standardize the names of the annotation files

Browsing in AmiGO2

• Type term into search box on front page, autofill feature will be useful,
• Column sorting can be customized
• NCBI ids are not displayed correctly as the NCBI tree is not loaded
• Need to check on "Source"- where are it pulling that from?

• "Panther Gene Families"- We can customize this and can use our own Inparanoid gene families, as Panther does not have too many plants represented
• Inparanoid gene families- algorithm creates superclusters, based on ~70- 100 genomes, species by species comparison
• Can input any standard format such as New Hampshire, phyloXML, etc call it "Plant Gene Families" etc
• can try with a subset- e.g. Arabidopisis, rice and maize and associate with the GO annotations

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

Please fill in notes here....

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