Blog posts

We just heard the news that the recent Plant Ontology Paper is available online from Plant and Cell Physiology: http://pcp.oxfordjournals.org/content/early/2012/12/05/pcp.pcs163.abstract?keytype=ref&ijkey=y8ieoOz5Ec5iIaT Right now it is just the abstract with a link to the full text accepted proof. But it has been assigned a DOI, in case you would like to cite it.

Matt Geniza, Molecular and Cellular Biology PhD graduate student in the Jaiswal lab has been awarded the Anita S. Summers Graduate Student Travel Award for his work involving Triticum monococcum (wheat) transcriptome assembly and annotation. He will be presenting his work at the upcoming Plant and Animal Genome Conference (January, 2013) in San Diego.

Plant breeders, biologists and bioinformatics specialists from ten countries, seven US states and two plant agribusinesses gathered in Corvallis, Oregon, September 13th-15th, 2012 for a Crop Plant Trait Ontology Workshop. The workshop was hosted by the Plant Ontology and the Trait Ontology, and co-organized by TransPlant, European Bioinformatics Institute, GARNet, Generation Challenge Program, Sol Genomics Network, and SoyBase.

Oregon State University has been named a partner on a grant that aims to further the understanding of the molecular interactions and genes in crops that include rice and corn. Over the course of the next five years, OSU will receive the grant, which was awarded by the National Science Foundation. OSU will develop an online database, called a plant reactome, with information about the molecular and genetic interactions in the cells of corn, rice and Arabidopsis, a small flowering plant that's used as a research model.

Source: American Journal of Botany | Aug, 20, 2012 New search tools give scientists better ways of managing data Botany is plagued by the same problem as the rest of science and society: our ability to generate data quickly and cheaply is surpassing our ability to access and analyze it. In this age of big data, scientists facing too much information rely on computers to search large data sets for patterns that are beyond the capability of humans to recognize—but computers can only interpret data based on the strict set of rules in their programming. New tools called ontologies provide the rules computers need to transform information into knowledge, by attaching meaning to data, thereby making those data retrievable by computers and more understandable to human beings. Ontology, from the Greek word for the study of being or existence, traditionally falls within the purview of philosophy, but the term is now used by computer and information scientists to describe a strategy for representing knowledge in a consistent fashion. An ontology in this contemporary sense is a description of the types of entities within a given domain and the relationships among them. A new article in this month’s American Journal of Botany by Ramona Walls (New York Botanical Garden) and colleagues describes how scientists build ontologies such as the Plant Ontology (PO) and how these tools can transform plant science by facilitating new ways of gathering and exploring data (http://www.amjbot.org/content/99/8/1263.full).

First draft of the pigeonpea (Cajanus cajan) genome of the variety ‘Asha’ was recently published by two reports. Singh et al. A 510.81 Mbp genome size and 47,004 protein coding genes were identified from a 10x sequence coverage of the genome. According to the lead author this is the first plant genome sequencing project that was completed entirely by a network of Indian institutions supported by the Indian Council of Agricultural Research.

Justin Preece and Mamatha Hanumappa have written a Perl utility application designed to map homologous genes from one species onto the PathVisio pathway diagram of another species. Requires only a GPML PathVisio document, a CSV file of homolog mappings, and a configuration file. The source code and documentation may be found here. Further enhancements and/or a collaboration with the PathVisio group on a plug-in version are likely forthcoming.

The Gramene database team is happy to announce the 34th major release of the database and the website. http://news.gramene.org/?p=760. The Jaiswal lab is a co-investigator on the Gramene project and several lab members contributed to this effort. Salient features of this release include:

• Updates on Ensembl genome browser for six genomes

A new publication on the QlicRice just came online (Smita et al. 2011). The Jaiswal lab contributed to this collaborative effort lead by Dr. KC Bansal's lab at the National Bureau of Plant Genetic Resources (NBPGR), Indian Agricultural Research Institute (ICAR), New Delhi, India.