PAG 2015: Some Highlights

Contributions from Sushma Naithani, Kapeel Chougule and Yinping Jiao.

During the Gramene workshop at PAG 2015, participants were introduced to various resources and tools available at the Gramene database. Powerpoint slides used during these presentations are available in Gramene's Outreach FTP.

Dr. Joshua Stein (Cold Spring Harbor Laboratory) reviewed the 38 Ensembl/Gramene available genomes, and using case examples demonstrated how to browse a plant genome, access a region, show detailed gene structure and associated transcripts, ESTs and genetic diversity data. He also showed how to download various datasets using BioMart, and make cross-species comparison to obtain whole genome alignments, Compara gene trees to deduce phylogenetic and phylogenomic information, synteny maps, Orthologs/Paralogs.

Dr. Paul J. Kersey (EMBL - The European Bioinformatics Institute) demonstrated how advanced users who work with the bulk data could access plant genome data via programmatic interfaces (Web-based GUI, Public MySQL server, Perl and REST-ful API, FTP). The data mining tools for advanced used are constructed using BioMart framework but with its own set of interfaces. Dr. Kersey demonstrated how to access and download bulk data using examples using web GUI, web services, command line and local client interfaces.

Justin Preece (Dept. of Botany & Plant Pathology, Oregon State University) reviewed recent advances in the Plant Reactome, a resource for plant metabolic and regulatory pathways. Plant Reactome currently has curated metabolic and regulatory pathways from rice and Arabidopsis and orthology based projections of pathways for additional 33 other plant species including several Oryza species, and maize. He further showed upcoming development of expression data analysis tools and examples of orthology projections, and visualization of expression data.

Dr. Robert Petryszak (EMBL - The European Bioinformatics Institute) summarized recent development in Expression Atlas project that facilitates baseline and differential expression of genes for crop plants utilizing controlled vocabulary and hierarchical relationships derived from plant ontology, gene ontology, and experimental factor ontology. Currently, the Atlas project host 226 expression data sets for Arabidopsis and a few data sets for other species. Atlas supports searches for using one or more terms that include gene name, organism and conditions.

Dr. Sushma Naithani (Oregon State University) demonstrated how to upload, display and analyze genetic diversity data set and expression data set using Gramene/Ensembl browser. Using example of SNP data mapping on the barley genome browser, she showed how to users could obtain information about the consequences of genetic variation and relate this information with the expression profile of the gene, structure and function of gene product and phenotype data if available in a given species. She further used an example of microarray expression data that represented changes in gene expression during diurnal cycle to display this data on genome browser and how users can obtain important insight from this analysis.

During hands on session, Gramene curators assisted individual researchers on a one-to-one to analyze their data.

Together with another 11 databases, Gramene participated in the Plant Genomics Databases booth. During the exhibition time, we introduced our data and resources to the wider community and gave out brochures to the conference participants. Besides valuable feedback from current users, we got more people to learn about Gramene.

During the National Plant Genome Initiative (NPGI) workshop, Dr. Doreen Ware (Cold Spring Harbor Laboratory), Principal Investigator for the Gramene Project, presented a talk entitled: “Big Data: Challenges and Opportunities for Plant Sciences”, where she emphasized the need for interoperability between resources.

Gramene also participated in the USDA ARS Database meeting held on January 12, 2015. The purpose of this meeting was to bring together ARS scientists working on biological databases or as part of the ARS Big Data initiative to facilitate collaborations with each other, and with non-ARS database groups. At this meeting, Dr. Doreen Ware (Cold Spring Harbor Laboratory) presented : "The ARS Big Data Initiative; what it is and where we are going", and Kapeel Chougule (Cold Spring Harbor Laboratory) presented a report on the "Big data workshop on RNA seq" which was held at Cold Spring Harbor Laboratory, Dec 7-10, 2014. The meeting highlighted current data-related challenges facing databases and identified areas that databases can collaboratively work on to overcome these challenges. Of these, the group decided the four most important topics to address:

1. Metadata collection.
2. Data sharing and search
3. UI/Usability, and
4. Communication.

Gramene will be actively participating in this database conglomeration.