[Gramene-announce] From our blog: Gramene @ PAG 2015

Fri Feb 6 13:20:59 EST 2015

PS: The slides used during the Gramene workshop are available at Gramene's
Outreach FTP, see ftp://ftp.gramene.org/pub/gramene/outreach/pag_2015/

On Fri, Feb 6, 2015 at 12:46 PM, Monaco, Marcela <mmonaco at cshl.edu> wrote:

> Gramene blog  -- Gramene @ PAG 2015
>
> 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.
>
> 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<
> http://de.iplantcollaborative.org/dl/d/EE96C006-2D74-4CB0-84E6-4FE4CD7A4E24/PAG_RNA_Seq_workshop_presnt.pptx>
> 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.
>
> [
> http://www.gramene.org/sites/default/files/styles/large/public/739FDC03-04B9-4B28-B1A5-A0C59B3A59D8.jpg?itok=4VIuCk8s
> ]<
> http://www.gramene.org/sites/default/files/739FDC03-04B9-4B28-B1A5-A0C59B3A59D8.jpg
> >
>
>
> ==
>
> Marcela K. Monaco, PhD
> Cold Spring Harbor Laboratory
> Williams Building #5
> Cold Spring Harbor, NY 11542
>
>
>
>
>
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