BioMed Central Blog

Journal of Biomedical Semantics publishes first articles

Journal of Biomedical Semantics was launched today, aiming to address the barriers to access and integration of data in the public domain that can hinder reanalysis. Semantics are essential for mining and analyzing data and the ability to manage semantic representations is vital for making computational approaches productive for a large community. The first articles published in the journal today reflect this.

In their introductory editorial ‘BioMedical Semantics: the hub for Biomedical Research’ Dietrich Rebholz-Schuhmann and Goran Nenadic discuss the importance and history of biomedical semantics as an emerging field and examine the aims of this timely new journal. Also  published today, Dr Nigel Collier addresses the issue of systematically evaluating online health news to support automatic alerting, and an article from Ms Kristina Hettne and colleagues highlights the importance of applying rewrite and suppression rules for the identification of terms in biomedical text mining and recommends a useful software tool for this.

“We aspire to provide authors and readers with opportunities to semantically enrich their publications so that they can become part of an integrated semantics network of biomedicine” say Editors-in-Chief Dietrich Rebholz-Schuhmann and Goran Nenadic.

For more details on the journal and its articles please visit the journal website. For information on submitting to the journal please see our instructions for authors.

Posted by Genevieve Horne at 16:24    Comments (2)

One hundred BioMed Central journals now indexed in Medline

Behavioral & Brain Functions, Molecular Brain and Particle and Fibre Toxicology have recently been accepted for inclusion in MEDLINE bringing the number of BioMed Central journals indexed in MEDLINE to a total of one hundred. This news is an endorsement of the success of each of these journals and reflects the strong reputations they have built in their respective fields.

In June of this year Behavioral & Brain Functions will also receive its first impact factor, which we eagerly anticipate. Particle and Fibre Toxicology is also tracked by Thomson Reuters and will be receiving its first impact factor in June 2011. Molecular Brain was launched just under two years ago with BioMed Central and has rapidly developed a strong readership with many articles receiving high access figures.

A full list of all one hundred BioMed Central journals indexed in MEDLINE is available from our website.

Posted by Charlotte Hubbard at 02:57    Comments (0)

BMC Research Notes will free [even more] dark data

BMC Research Notes was launched with the aim of reducing the loss suffered by science (and the potential for publication bias) when sound research goes unpublished. Now, with a welcomed change to our formatting criteria even more "dark data" will be freed.

Since the journal focuses on short reports, small-scale confirmatory studies, negative results, incremental updates to previous work and data-driven publications, we originally envisaged that the vast majority of articles published would be short, less than 2000 words long with up to 30 references.

As the popularity of the journal grows, researchers are increasingly considering BMC Research Notes for full research articles and we are keen to save a valuable resource – our authors’ time and effort. Anecdotally, authors have told us of hours wasted during the process of “doing the rounds” at different journals and publishers – submitting a  manuscript to a selective journal, making the manuscript conform to journal style, going through the review process, being rejected, and then starting over. Several times before being eventually published.  For this reason, we are changing our formatting criteria for the journal and no longer require BMC Research Notes authors to shorten their articles. Given the nature of much of the journal’s content to date we still encourage brevity, but by relaxing article formatting requirements we hope we are helping the journal better achieve its aims of completing the scientific record.

Similarly, we want to make the most effective use of another resource fundamental to science publishing – our peer reviewers’ time.  Authors whose work is not accepted for publication in other, more selective, journals published by BioMed Central may be offered the opportunity to publish in BMC Research Notes (see, for example, 'portability of peer review'). With consent of authors, editors and peer reviewers, reviewer reports can be shared between journals and an expedited peer-review process is possible when publishing in BMC Research Notes.

Posted by Iain Hrynaszkiewicz at 15:04    Comments (0)

The CONSORT 2010 statement – a “service history” for clinical trials

Posted by Victoria Thompson at 10:06    Comments (0)

Ethical approval - too strict on methodological research?

This week in Trials McKenzie and colleagues present their experience of obtaining ethical approval for a methodological study that planned to compare ethics committee applications with the published results of randomized controlled trials.

Obstacles to researching the researchers: A case study of the ethical challenges of undertaking methodological research investigating the reporting of randomised controlled trials
Joanne E McKenzie, G PETER Herbsion, Paul Roth, Charlotte Paul
Trials 2010, 11:28 (21 March 2010)

The authors aimed to assess the prevalence of selective outcome reporting - where significant results are more likely to be reported than those that are not significant - but approval was denied on the grounds that they did not plan to obtain informed consent from trialists to view their applications. The committee’s response is not an unusual one, but McKenzie et al consider it to be symptomatic of weaknesses in the system, including a failure to recognize the nature and importance of methodological research of this kind.

Posted by Victoria Thompson at 16:32    Comments (0)

Stem Cell Research & Therapy - advancing the pathway to the clinic

The publication of the first articles in Stem Cell Research & Therapy today marks the launch of a major forum for translational research into stem cell therapies.

Stem cell research has progressed to the clinic and has enormous potential for treating  incurable diseases such as Parkinson’s disease and Alzheimer’s disease, and potential for alleviating suffering in chronic conditions such as diabetes and osteoarthritis.

This new journal is edited by Profs Rocky Tuan (University of Pittsburgh School of Medicine) and Timothy O’Brien (National University of Ireland, Galway), who welcome contributions in their lead editorial.

“The journal provides an important avenue of publication in translational aspects of stem cell therapy spanning preclinical studies, clinical research and commercialization. The critical pathway to the clinic is complex and advancing towards commercialization for stem cell therapies is challenging. The journal will focus on cutting edge research which contributes to this process. I look forward to working with Rocky Tuan and other editorial board members to ensure the journal meets the needs of the stem cell research community with an emphasis on translation,” said Prof O’Brien.

President Barack Obama last year removed barriers to responsible stem cell research in the USA and this executive order could become law, but national legislation on stem cells varies. By providing open access to rigorous research Stem Cell Research & Therapy will help the international science community rapidly disseminate new ideas.

One of the journal’s first research articles identifies a potential new source of mesenchymal stem cells for autoimmune dieases such as systemic lupus erythematosus. Reviews, commentaries and reports will accompany research articles; in this issue Djuric and Ellis highlight advancements in the understanding of dynamic epigenetic changes occurring in the cell reprogramming process.

To stay informed about the latest content, sign-up to receive article alerts. Stem cell-related research published across BioMed Central's journal portfolio is available on the Stem Cell Gateway.

Posted by Iain Hrynaszkiewicz at 15:59    Comments (2)

Alzheimer genetics in the post-GWAS era

Genome-wide association studies (GWASs) published in the last two years have confirmed the role of APOE as a genetic risk-factor for late-onset Alzheimer’s disease as well as proposing a host of other potential candidate genes. However, despite their success in revealing common genetic factors for complex diseases, it is unclear whether GWASs are able to identify the underlying genetics of Alzheimer’s disease.

In a review published recently in Alzheimer’s Research & Therapy, Ertekin-Taner summarises genetic studies in Alzheimer’s disease carried out before the GWAS era as well as findings from recent GWASs and suggests that alternative approaches are necessary in order to identify the remaining genetic susceptibility factors associated with the disease. In particular, reassessing GWAS results using novel approaches, such as combining biologically relevant quantitative phenotype and GWAS data, may lead to the identification of genetic factors that influence Alzheimer’s disease risk and possible biological pathways, something which could translate into therapeutic potential.

Alex Kroll - Senior Assistant Editor, Alzheimer's Research & Therapy

Posted by Frances Mulvany at 09:28    Comments (0)

False duplications in genome assemblies

David Kelley and Steven Salzberg at the University of Maryland have developed a pipeline to correct misassembles due to false duplications, in a study published today in Genome Biology. Diploid genomes harbour a significant amount of variation between homologous chromosomes. This causes problems for genome assembly algorithms which may construct two DNA sequences corresponding to one divergent region and incorporate both into an assembly as a false segmental duplication.

Their approach is to align DNA sequence fragments to the surrounding sequence, using mate pair information, to determine whether duplicated segments should be merged into one copy. Mate pairs are two sequence reads derived from the same region of DNA and this study is the first time in which mate pair reads have been used to detect duplications. Kelley and Salzberg apply their pipeline to the cow, chimpanzee, dog and chicken genomes and they identify many single copy regions that have been falsely incorporated as segmental duplications in these genome assemblies, which also allows previously undetected polymorphisms to be identified.  This promises to be a valuable method for correcting existing errors in many genome assemblies and to control for misassembly errors in future genome sequencing efforts.

Posted by Emma Ralph at 11:50    Comments (0)

Highlights from the latest issue of Arthritis Research & Therapy

In each print edition of Arthritis Research & Therapy the Editors-in-Chief, Profs Ravinder Maini and Peter Lipsky, highlight articles that are of special interest to the journal's readership – the Editors’ choice.

In the latest issue, a feasibility trial by Ng and colleagues found that a combination of glucosamine sulphate supplementation and walking for approximately 30 minutes a day, three times a week, significantly reduced pain and improved physical function in osteoarthritis patients.

Another selection by the Editors is a study by Schurgers et al which highlights the discrepancy between the in vitro and in vivo effects of mesenchymal stem cells.  The team of researchers from Katholieke Universiteit Leuven, Belgium, demonstrated that murine bone marrow-derived mesenchymal stem cells dose-dependently suppress T cell proliferation in vitro, but are unable to influence the disease course in a mouse model of collagen-induced arthritis.

Also making the Editors' choice is a comprehensive review article examining the contribution of genetic variation and infection to the pathogenesis of anti-neutrophil cytoplasmic antibody-associated systemic vasculitis, with a focus on the role of autoantibodies to the membrance protein LAMP-2.

All research published in Arthritis Research & Therapy is open access; reviews published within the previous 6 months require a subscription. Visit the journal website to view the latest articles published in the journal.

Abigail Jones

Senior Assistant Editor - Arthritis Research & Therapy

Posted by Frances Mulvany at 09:41    Comments (0)

Wiki-based integration of genomic data

A new Wiki portal for collaborative annotation and analysis of congenital heart defects, recently described in Genome Medicine, highlights the potential of this technology for systems biology studies of other complex biological processes.

Inspired by the well-known Wikipedia, Barriot and colleagues describe CHDWiki, a Wiki knowledge base for congenital heart defects (CHDs), which integrates gene prioritisation strategies and allows browsing of gene interaction networks.  Their article 'Collaboratively charting the gene-to-phenotype network of human congenital heart defects' appears in the March issue of Genome Medicine.

CHDs are a major cause of mortality in newborns, but the origin and outcome of such disorders is complex, being the result of many possible genetic abnormalities and/or pre- and post-natal environmental and behavioural components.  CHDWiki aims to bridge the gap between the complex analyses necessary to understand these factors, and the wet-lab researchers and clinical geneticists whose work can benefit from this knowledge.  The Wiki will not only act as a community repository of up-to-date information on CHDs, but is the first specialised portal to include tools for annotation and analysis of gene-phenotype relationships.  The authors anticipate that such portals will be important for systems biology studies of many other medical conditions and biological processes.

Rebecca Furlong
Assistant Editor, Genome Medicine

Posted by Rebecca Furlong at 14:45    Comments (0)

Orphanet Journal of Rare Diseases ranked highly by new 'SNIP' citation metric

Henk Moed at the Centre for Science and Technology Studies (CWTS) at Leiden University has recently developed a new journal indicator, the Source Normalized Impact per Paper (SNIP), based on citation data from Scopus. A journal’s SNIP can be thought of as similar to a normalized Impact Factor, which weights citations to adjust for the fact that some fields are more citation-rich than others. The intention is that SNIPs will allow more effective comparison of journals between different fields.  More information about SNIPs and how they are calculated can be found  in Moed’s recent article and at www.journalindicators.com.

Orphanet Journal of Rare Diseases is BioMed Central’s highest-ranking journal based on the SNIP metric, with a value of 1.31 (the median SNIP for the ~17,000 journals in Scopus is 0.52). This places the journal in the top 4% of all journals listed in Scopus. For comparison, the journal's Impact Factor of 3.14 makes it the 22nd most highly-rated BioMed Central journal by Impact Factor. The contrast between these two rankings demonstrates that caution is needed when interpreting citation metrics, as much depends on the algorithm used. The SNIP provides a valuable new means to identify high quality journals in fields which may not in general be highly cited. 

Other BioMed Central journals which are ranked particularly highly by the SNIP metric include:

Posted by Charlotte Hubbard at 03:39    Comments (0)

Normalizing RNA-seq data

Genome Biology recently published an article from Alicia Oshlack and colleagues in which they describe an approach for performing Gene Ontology analysis on RNA-seq data. RNA-seq is an emerging technology for monitoring gene expression levels by directly sequencing the mRNA molecules in a sample, and is likely to overtake microarrays as the technique of choice for gene expression profiling.   Now, Genome Biology has published another innovative method, this time for normalizing RNA-seq data. This method is much needed and will be embraced by the genomics community as, until now, methods for normalizing RNA-seq data have often relied on tools that were based on those developed for microarray data.

A common approach for normalizing RNA-seq data has been to consider the expression of an individual gene relative to the global gene expression levels. In her latest paper, Oshlack, at the Walter and Eliza Hall Institute in Melbourne, Australia, shows that this is not always appropriate.  In particular, if one tissue has a small number of genes that are significantly differentially expressed compared with another tissue then these can affect whether or not other genes in the sample are determined as being differentially expressed, often leading to implausible results. The paper demonstrates again the need for new statistical techniques to fully exploit the powerful RNA-seq technology, as well as providing a useful tool for doing this.

Posted by Andrew Cosgrove at 17:32    Comments (0)

Technology and the developing world

In a four-part series, Afrinnovator interviews Ken Banks of FrontlineSMS and Kiwanja.net founder, about FrontlineSMS and mobile technology.

Meanwhile, eLearning Africa 2010’s 5th International Conference on ICT for Development, Education and Training is still taking registrations for its event in Zambia late May.

In a Public Service article, Jeff Waage, Director of the London International Development Centre, discusses why policy, local knowledge and new innovations are critical in enhancing the capacity of science and technology to deliver in the developing world. He concludes that whilst building new science and technology with development will be a challenge we must help developing country partners to improve their national scientific capacity so that they may participate in global science and innovation.

Computer Aid International recently published a case study entitled ‘Preserving African history: Bamoun King's Palace’.  Computer Aid International has provided over 500 PCs to the project which are being used for educational purposes as well as to document the history of the Bamoun people online.

 Finally, Computer Aid International is still seeking participants for its Cycle Nepal Challenge. This once in a lifetime 10 day cycle challenge begins on the 30th October 2010 and lasts until the 8th November 2010. You will be cycling a land of diverse landscapes, peoples, customs, cultures and languages, from snow capped peaks to green sub tropical forests and paddy fields. For more information please contact Maurizio Borgatti.

Posted by Charlotte Webber at 12:04    Comments (0)

Calculating genetic risk from multiple loci

Research recently published in Genome Medicine shows that a widely-accepted model for predicting genetic risk of disease is not realistic when it is applied to current human disease data. Three other models provide a better fit to these data but are indistinguishable from each other.

Naomi Wray and Michael Goddard, from Queensland Institute of Medical Research and the University of Melbourne, examined mathematical models which integrate the disease risks from several genomic loci to determine the overall risk to an individual. 
The unconstrained Risch model, which is commonly used in theoretical studies, was rejected as being unrealistic according to current human complex disease parameters.  However, the CRisch, Odds, and Probit models were all compatible with these observed data. 

The authors suggest that it will not be possible to distinguish between these last three models until more of the genetic variance causing human traits can be understood.  As we learn more about the many kinds of mutations that are associated with genomic disease, so we can evaluate and model the ways that they interact to cause a phenotype.

Rebecca Furlong
Assistant Editor, Genome Medicine

Posted by Rebecca Furlong at 16:07    Comments (0)