BIODBCORE.ORG. Database of Protein and Genetic Interactions. Persistence and Availability of Web Services in Computational Biology. Introduction In 2003, the journal Nucleic Acids Research (NAR) published its first Web Server Issue in an open-access format.
This special issue on Web services that perform “useful computations” was described in its editorial as the “natural companion” to the annual, then already decade-old Database Issue [1]. The peer-reviewed contributions consisted of 131 of the most widely known, freely accessible Web services from the years before 2003, which is why the services in this issue are of an exceptional quality. There are many benefits to studying this rather compact but very well-defined collection of services. Authors are expressly allowed to re-publish their service in the Web Server Issue after a hiatus of two years, if they can give the number of citations or other measures of community impact for their service, to support its re-publication [2].
In the minds of most computational biologists, Web services are unreliable at best. Table 1. Doi:10.1371/journal.pone.0024914.t001. Open-source human genomes. On target: A public repository for large-scale RNAi experiments : Nature Cell Biology. My data are your data : Nature Biotechnology. Relic of the past?
Data are trying to jump off shelves. (istockphoto). In January, over 50 researchers from 30 academic and commercial organizations agreed on a standard for describing data sets. The BioSharing initiative, comprising both researchers and publishers, launched the Investigation-Study-Assay (ISA) Commons, which promises to streamline data sharing among different databases1. Life scientists have thousands of databases, over 300 terminologies and more than 120 exchange formats at their disposal, says BioSharing co-founder Susanna-Assunta Sansone of the University of Oxford. Although increased data sharing is central to scientific progress and is attracting attention from many quarters2, standards are only some of the stars that must align to make it possible.
Share and share alike? Oversharing is embarrassing in social media but sharing is always a virtue for scientists. Box 1: Letting data speak Fair share? Expanding the outlook Tune into my network Sharing a special sauce. Open-data project aims to ease the way for genomic research. Last summer, biologist Andrew Kasarskis was eager to help decipher the genetic origin of the Escherichia coli strain that infected roughly 4,000 people in Germany between May and July.
But he knew it that might take days for the lawyers at his company — Pacific Biosciences of Menlo Park, California — to parse the agreements governing how his team could use data collected on the strain. Luckily, one team had released its data under a Creative Commons licence that allowed free use of the data, allowing Kasarskis and his colleagues to join the international research effort and publish their work1 without wasting time on legal wrangling. The project received approval from ethics reviewers on 23 April; as soon as May, anyone will be able to sign the consent and begin contributing their own data to the database.
Honest approach Sharing the wealth But, Butte says, Portable Legal Consent could benefit researchers without the means to assemble large data sets. Dealing with data. Hello there!
If you enjoy the content on PLOS Biologue, consider subscribing for future posts via email or RSS feed. PLoS Biology aspires to drive openness in data use and re-use, not just open access to the literature. We are pleased to announce a partnership with Dryad that helps our authors make their data re-useable and accessible by providing a home for data linked to publications. Source: Wikimedia attributed to Victorgrigas It is not news to say that the current handling of research data within the life sciences is rather chaotic. Even when data is shared – which is not always – where it should be housed remains a matter for discussion. The publishers of research output – journals – are uniquely well-placed to help researchers ensure that all data underlying a study are made available alongside any published articles. A step towards resolving the data problem: PLoS Biology partners with Dryad.
BioSharing. BioLOD.org, The Download Hub of Biological Linked Open Databases for Phenomes.