Faculty of 1000 plans to launch a fully Open Access publishing program: F1000 Research

Faculty of 1000 today announces F1000 Research, a fully Open Access publishing program across biology and medicine that will launch later this year. The project is intended to address three major issues afflicting scientific publishing today: timely dissemination of research, peer review, and sharing of data.

Faculty of 1000 is also part of the BioSharing community!

[From their press release....]

Diverging from traditional journal publishing, F1000 Research will offer immediate publication; open, post-publication peer review; open revisioning of work including ongoing updates; and will encourage raw data deposition and publication. In addition, F1000 Research will accept a broad range of article formats and will encourage content types that are now routinely rejected such as negative results, case studies, thought experiments, preliminary analyses, and incomplete datasets.

Dr Rebecca Lawrence, who is leading the project at F1000 said: “Many questions remain as we fine-tune F1000 Research to break new ground in scholarly publishing. We therefore invite those working in the bioresearch community, institutions, funders, data centres and repositories, and data mining and informatics groups to join us in open discussion and debate about these many outstanding issues – via the RSS feed or by Twitter: @F1000Research.”

Oxford, Harvard Scientists Lead Data-Sharing Effort: ISA Commons and BioSharing

Led by researchers at University of Oxford (UK) and the Harvard Stem Cell Institute (HSCI) at Harvard University, (USA), more than 50 collaborators at over 30 scientific organizations around the globe have agreed on a common standard that will make possible the consistent description of enormous and radically different databases compiled in fields ranging from genetics to stem cell science, to environmental studies.

This collaborative effort provides a way for scientists in widely disparate life science fields to co-ordinate each other’s findings by allowing behind-the-scenes combination of the mountains of data produced by modern, technology driven science.

“We are now working together to provide the means to manage enormous quantities of otherwise incompatible data, ranging from the biomedical to the environmental,” says Dr. Susanna-Assunta Sansone, Team Leader of the project at the University of Oxford’s e-Research Centre.

An ecosystem of standard-compliant data curation and sharing solutions and the establishment of its on-line presence, the ISA Commons, is described in a Commentary published today in the journal Nature Genetics. The BioSharing initiatives is also introduced, extending on the MIBBI effort. 

The commentary is signed by all the collaborators.

"Sansone and colleagues also list a set of participant communities that can pioneer the approach and teach by example" says the Nature Genetics' Editorial. 

This emerging commons depends on its participants’ use of the ‘Investigation’, ‘Study’, and ‘Assay’ (ISA) metadata tracking framework. “The ISA system is the ideal solution for managing experimental metadata from diverse groups and is now a core solution at the NERC Environmental Bioinformatics Centre.  We look forward in the future to being able to exchange data with other ISA-compliant projects,” says Dawn Field, director of NERC NEBC, and visiting Professor at the Oxford e-Research Centre, noting that “this is the type of data sharing that should underpin ELIXIR”.

“An example of how this works at the Harvard Stem Cell Institute is that we can now find a relationship between experiments involving normal blood stem cells in fish and cancers in children”, says Winston Hide, director of HSCI’s new Center for Stem Cell Bioinformatics, and an associate Professor of Bioinformatics at the Harvard School of Public Health.

ISA Commons is also being used at Harvard Medical School (HMS) by the HMS LINCS (Library of Integrated Network-based Cellular Signatures) project led by Professors Peter Sorger and Timothy Mitchison.

“Understanding biology requires data from multiple fields, laboratories and experiments to work together. That not only requires commons standards, but tools that enable scientists to work with those standards without additional overheads. ISA is a great example of these principles in action" says Lee Harland, CTO at ConnectedDiscovery, London, UK

"One of the things that I find most empowering about this effort is that now small research groups can begin to store laboratory data using this framework, complying with community standards, without their own dedicated bioinformatics support. It is a bit like Facebook allowing everyone to create their own website pages - suddenly you don't need to be an expert in computing to get your data out to the rest of the world", says Jules Griffin, of the University of Cambridge.

"It also has the potential to work for large centers too”, says Scott Edmunds, editor of the journal published by open-access publisher BioMedCentral and BGI Shenzhen (previously known as the Beijing Genomics Institute) the world’s largest genomics institute, “We are working with this framework to help harmonizing and presenting may large-data types as possible in a common standardized and usable form, publishing it in the associated GigaScience journal.”

"What we like about the ISA framework is its unifying nature across different bioscience fields and institutions”, notes Dr. Christoph Steinbeck of the European Molecular Biology Laboratory, The European Bioinformatics Institute (EBI), who uses the ISA framework to power MetaboLights, the BBSRC-funded public repository for metabolomics experiments at EBI developed in collaboration with Griffin.

It was necessary to establish common data standards, say the commentary’s authors, because of the tsunami of data and technologies washing over the sciences. “There are hundreds of new technologies coming along but also many ways to describe the information produced” said Sansone, noting that "we can take a jigsaw puzzle of different sciences and now fit the many pieces together to form a complete picture".

The work was funded, by among others, the Harvard Stem Cell Institute, the U.S. National Institutes of Health, and the UK's Biotechnology and Biological Sciences Research Council (BBSRC) and Natural Environment Research Council (NERC).

Source article:

Sansone, S-A. et al. Toward interoperable bioscience data. Nature Genetics 44, 2 (2012). ISA Commons: isacommons.org

The Oxford e-Research Centre (http://www.oerc.ox.ac.uk) works across the University of Oxford, and at national and international level, to accelerate research through development of innovative computational and information technologies in multidisciplinary collaborations.

The Harvard Stem Cell Institute (http://www.hsci.harvard.edu) is a collaboration of more than 100 Harvard and Harvard-affiliated scientists dedicated to using the power of stem cell biology to advance basic understanding of human development in order to develop treatments and cures for a host of degenerative conditions and diseases.

GigaScience, GigaDB and BioSharing

Revolutionizing data collection, dissemination and use, GigaScience launches the new integrated journal and database in collaboration with BGI and BioMed Central, and working closely with the BioSharing and the ISA commons communities to maintain the highest data and metadata standards.

The novel format of publishing integrates manuscript publication with  the GigaDB public database, where dataset (i) gets a DOI to make them discoverable, trackable and citable, and (ii) are structured according to community standards, via the ISA tools.

Synergy force - The BioSharing community grows

The BioSharing community keeps growing steadily!


In the last few months the BioCatalogue, Dryad, DataCite, the Digital Curation Centre (DCC), COMBINE, the National Cancer Research Institute (NCRI) Informatics Initiative have joined the BioSharing community. 


These groups are recognized stakeholders with strong ties with their respective communities. A link with/among them is pivotal for the BioSharing mission and it will be essential also to continue developing and enriching the catalogue of standards. 

Alsheikh-Ali et al Data Availability study published in PloS One

Public Availability of Published Research Data in High-Impact Journals

Full Article


Alawi A. Alsheikh-Ali1,2#, Waqas Qureshi3#, Mouaz H. Al-Mallah4,5, John P. A. Ioannidis2,6,7,8,9*

Abstract

Background
There is increasing interest to make primary data from published research publicly available. We aimed to assess the current status of making research data available in highly-cited journals across the scientific literature.

Methods and Results
We reviewed the first 10 original research papers of 2009 published in the 50 original research journals with the highest impact factor. For each journal we documented the policies related to public availability and sharing of data. Of the 50 journals, 44 (88%) had a statement in their instructions to authors related to public availability and sharing of data. However, there was wide variation in journal requirements, ranging from requiring the sharing of all primary data related to the research to just including a statement in the published manuscript that data can be available on request. Of the 500 assessed papers, 149 (30%) were not subject to any data availability policy. Of the remaining 351 papers that were covered by some data availability policy, 208 papers (59%) did not fully adhere to the data availability instructions of the journals they were published in, most commonly (73%) by not publicly depositing microarray data. The other 143 papers that adhered to the data availability instructions did so by publicly depositing only the specific data type as required, making a statement of willingness to share, or actually sharing all the primary data. Overall, only 47 papers (9%) deposited full primary raw data online. None of the 149 papers not subject to data availability policies made their full primary data publicly available.

Conclusion
A substantial proportion of original research papers published in high-impact journals are either not subject to any data availability policies, or do not adhere to the data availability instructions in their respective journals. This empiric evaluation highlights opportunities for improvement.

BioSharing at COMBINE meeting - Community Standards for Systems Biology

The 2nd COMBINE meeting was held on 2-7 September in gorgeous Heidelberg.

"The 'COmputational Modeling in BIology' NEtwork (COMBINE) is an initiative to coordinate the development of the various community standards and formats for computational models, initially in Systems Biology and related fields. By doing so, it is expected that the federated projects will develop a set of interoperable and non-overlapping standards covering all the aspects of modeling in biology."

During the live streamed meeting, the core COMBINE community gave overview talks on the latest updates on the popular standards, SBML, SED-ML, BioPAX, SBGN and CellML. Brilliant keynote talks by Peer Bork (EMBL Heidelberg) and Michael White (University of Manchester) on their 20+ years of research in systems biology added to the memorability of the meeting.

A lecture on BioSharing was also given by Prof. Dawn Field, titled as "BioSharing: standards, policies and communication in bioscience".

All slides and posters are published in a Nature Precedings collection for COMBINE 2011.

Pistoia Alliance - Vocabulary Services Initiative and Information Ecosystem workshop

BioSharing team works to engage closely with the Pistoia Alliance as new R&D business models demand successful integration of heterogeneous data from multiple providers and scientific domains. Here described are the Pistoia Alliance's activities BioSharing team is part of.

The Vocabulary Services Initiative (VSI) is the latest working group launched by the Pistoia Alliance to tackle the heterogeneous terminological landscape that makes expensive and hard to share, correlate and integrate data. VSI aims to address the issues and possible solutions around the precompetitive development of open research vocabularies will benefit information producers and consumers. The VSI working group, lead by Lee Harland (Connected Discovery) and Ian Dix (AstraZeneca), has developed a paper describing the need for shared services around vocabularies. Titled "Empowering Industrial Research with Shared Biomedical Vocabularies", the paper is to be published in Drug Discovery Today - most likely in the November 2011 issue. 

Going one step further, Pistoia Alliance will explore the concept of the "Information Ecosystem" at a highly interactive workshop on 10 October 2011 in Hannover, Germany (the site of the Bio-IT World European meeting). "Delegates will describe the evolving information ecosystem in biomedical and pharmaceutical research and determine strategies for collaboratively shaping this ecosystem to maximum advantage... Even if you can't attend the meeting, we invite you to send use cases describing what scientists expect and need from this highly changeable environment".