ISB’s Response to NEJM’s editorial on the subject of Data Sharing

One of the primary goals of biocuration is to provide an accurate and comprehensive representation of biological knowledge and easy access to these data for working scientists, whether they be computational scientists, basic researchers, or clinicians. This and other goals of our field are achieved thanks to the convergent endeavors of biocurators, software developers, bioinformaticians, and many other researchers. Biocurators provide essential resources to the biological community such that a number of databases have become an integral part of the tools researchers use on a daily basis for their work. Much of our work is accomplished through the use and citation of publicly available datasets as well as data generated in our institutions. In addition, the results of our analyses and the datasets we generate are very commonly used by other researchers.

As members of the Executive Committee for the International Society for Biocuration (ISB) we express our deep concern about the grave statements made in the recently published editorial from the New England Journal of Medicine (NEJM) [1] regarding the principles behind data sharing in the context of scientific research. The notion that rapid and unrestricted sharing of data and research resources can undermine the advancement of research itself is in direct contrast to the many initiatives being promoted by research institutions around the world. Two examples of this are the Big Data to Knowledge initiative (BD2K) [2], which highlights that sharing software and data are key elements to help solving outstanding healthcare problems [3], and an initiative from the Office of Science and Technology Policy of the United States Government to expand public access to the results of federally funded research [4]. Requirements from both granting agencies and journals state a need for sharing, accompanied by policies that address and protect privacy concerns where necessary.

Like many of our colleagues, we also think that NEJM’s additional commentary on the editorial [5] falls short in the attempt to address the statements at the center of the controversy that the initial piece incited from the wider scientific community.

The consequences of conducting research in an environment that restricts rather than encourages prompt access to data can only result in slowing the progress of discovery. The practices of openness and collaboration lie at the core of the mission of ISB, and we will continue to do everything in our power to promote these principles within our membership and with our collaborators.

Respectfully,

The International Society for Biocuration Executive Committee,

J. Michael Cherry – President,
Monica Munoz-Torres – Secretary,
Sandra Orchard – Treasurer,
Cecilia Arighi,
Melissa Haendel,
Suzanna Lewis,
Claire O’Donovan,
Sylvain Poux,
Zhang Zhang.

1. Longo, D.L. and J.M. Drazen, Data Sharing. N Engl J Med, 2016. 374(3): p. 276-7
2. Big Data to Knowledge initiative (BD2K). https://datascience.nih.gov/bd2k
3. Bourne, P. Data Science @ NIH – The Year in Review. INPUT|OUTPUT. 2016. https://datascience.nih.gov/DataScienceYearinReview2015
4. Expanding Public Access to the Results of Federally Funded Research. 2013.
https://www.whitehouse.gov/blog/2013/02/22/expanding-public-access-results-federally-funded-research
5. Drazen, J.M. N Engl J Med, 2016. DOI: 10.1056/NEJMe1601087

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Travel fellowships for the Biocuration 2016 Conference

The International Society for Biocuration and The Ninth International Biocuration Conference are pleased to provide current ISB members with travel fellowships for students, junior curators, curators from low-income countries, and from countries suffering from natural disasters.

We intend to support a total of twelve (12) applicants.

Please note that applying for a fellowship does not guarantee that you will receive funding.

Award:

– A total of twelve travel awards will be issued. Eight (8) awards of up to CHF1,000 and four (4) with up to CHF500 as micro-grants.
– The Amount per travel fellowship will depend on registration and travel costs. Funds will be transferred on a reimbursement basis and receipts will be required.

Requirements and procedures:
Each applicant for a travel fellowship must satisfy the following conditions:

– The applicant must be a current ISB member. To sign up, go to http://biocuration.org/membership/membership-levels/
– The applicant must have been selected for a poster or oral presentation at the 9th International Biocuration Conference.
– Only the presenting author from a multi-author abstract may apply for a fellowship.
– The applicant must submit an accompanying letter explaining why s/he is requesting travel funds: please remember we are encouraging junior curators, curators originating from low-income countries, and curators from countries suffering from natural disasters.
– Application materials should be sent to intsocbio@gmail.com with the subject ‘Travel Fellowships to Biocuration 2016‘.

Note: The applicant should review visa requirements and make any necessary arrangements of her/his own.

Application deadline: 4 March, 2016
Notification of acceptance: 11 March, 2016
Conference Dates: 10-14 April, 2016

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CTD turned 10!

The Comparative Toxicogenomics Database (CTD) recently celebrated its 10-year anniversary on the web. Since its beginnings, CTD has been devoted to centralizing and harmonizing information about genes responding to environmental toxic agents across diverse species. The database has now evolved into a premier toxicology resource, allowing scientists to discover information and develop testable hypotheses about the biological consequences of chemical exposure (both environmental and drug). Today, CTD includes over 24 million toxicogenomic connections relating chemicals/drugs, genes/proteins, diseases, taxa, phenotypes, Gene Ontology annotations, and pathways.

This celebratory milestone was recently published in the journal Nucleic Acids Research, which summarized the history and evolution of CTD, including descriptions of curation processes, new content, and enhanced visualization and analysis tools. The article also detailed a new “Pathway View” tool that leverages gene interaction data from BioGRID to allow users to build unique toxicogenomic interaction modules connecting chemical exposure to disease events.

As it was ten years ago, CTD today is still managed by a small team of biologists and software engineers who work with both the toxicology and biocuration communities to advance understanding of chemical-gene-disease data and how best to extract and code this information from the published literature. All CTD data are freely available to the public. As well, CTD content has been disseminated further into the scientific community via more than 55 other databases that routinely incorporate CTD’s annotations. If interested in establishing links to CTD data, please notify us and follow these instructions.

CDT_10yearsCDT

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CTD curates 88K articles for drug-induced events

Understanding chemical toxicity is a common goal shared between environmental health scientists and pharmaceutical drug makers. Now, the Comparative Toxicogenomics Database (CTD, http://ctdbase.org/), which has historically focused on environmental chemicals, has completed a unique curation project coding therapeutic drug-induced disease and phenotype events from more than 88,000 articles published over the last seven decades. The results were recently reported in the journal Database (http://database.oxfordjournals.org/content/2013/bat080.full).

CTD artwork:logo

In the study, five CTD biocurators reviewed and manually curated 88,629 articles in just one year, coding information via controlled vocabularies for pharmaceutical compounds and their potential toxicity in cardiovascular, neurological, renal, and hepatic systems. Over 250,000 interactions were ultimately curated, linking 5,500 chemicals, 9,100 genes, 2,700 diseases, and 120 phenotypes. In the paper, CTD provided details about their curation strategy, performance metrics, and enhanced data content. As well, a new module for capturing chemical-phenotype data was introduced to curate drug-induced events at the molecular and cellular level before a disease developed.

One key finding was the discovery of 360 pharmaceutical drugs with overlapping adverse effects for four physiological systems-of-interest to drug makers resulting in cardiotoxicity, neurotoxicity, renal toxicity, and hepatotoxicity. Integrated into the CTD framework, these results are now combined with other datasets to make novel predictions and help generate testable hypotheses about drug-induced events.

The data are freely available from CTD. As well, the curation has been disseminated further into the scientific community via more than 55 other databases that routinely incorporate CTD’s annotations. If interested in establishing links to CTD data, please notify us (http://ctdbase.org/help/contact.go) and follow these instructions (http://ctdbase.org/help/linking.jsp).

Submitted by Allan Peter Davis.

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DATABASE, The Journal of Biological Databases and Curation, is now the official journal of the International Society for Biocuration.

The International Society for Biocuration (ISB) was created to promote biocuration, the product of multidisciplinary teams of database curators, software developers and bioinformaticians. Biocurators, whose work facilitates research and education across the life sciences, create and maintain a wide variety of online tools and databases essential to the biological community in their daily work. Such important efforts now have a rightful home at DATABASE.

DATABASE, The Journal of Biological Databases and Curation, supports the growing need of the research community to discuss a range of issues related to the creation, development and maintenance of biological databases, and to strengthen communication between database developers, curators and users. As this resonates strongly with the mission of the ISB, we are delighted to announce that DATABASE has now become the Society’s official journal. DATABASE has published more than 250 papers, 50 of which have appeared in the Biocuration Virtual Issue, a special collection of articles describing work presented at the annual International Biocuration Conference.

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2013/2014 ISB Executive Committee

The term of the 2013/2014 ISB Executive Committee (EC) starts on November 1st, 2013. We are delighted to welcome Melissa Haendel and Jennifer Harrow to the ISB EC, joining Teresa Attwood, Alex Bateman, J. Michael Cherry, Pascale Gaudet, Monica Munoz-Torres, Claire O’Donovan, and Marc Robinson-Rechavi. We are grateful to Renate Kania and Chisato Yamasaki for having served on the committee since 2011.

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