The Human Protein Atlas

“The Human Protein Atlas is a Swedish-based program initiated in 2003 with the aim to map all the human proteins in cells, tissues and organs using integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics and systems biology. All the data in the knowledge resource is open access to allow scientists both in academia and industry to freely access the data for exploration of the human proteome….The Human Protein Atlas program has already contributed to several thousands of publications in the field of human biology and disease and it is selected by the organization ELIXIR (www.elixir-europe.org) as a European core resource due to its fundamental importance for a wider life science community. The Human Protein Atlas consortium is funded by the Knut and Alice Wallenberg Foundation….”

The Human Protein Atlas

“The Human Protein Atlas is a Swedish-based program initiated in 2003 with the aim to map all the human proteins in cells, tissues and organs using integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics and systems biology. All the data in the knowledge resource is open access to allow scientists both in academia and industry to freely access the data for exploration of the human proteome….The Human Protein Atlas program has already contributed to several thousands of publications in the field of human biology and disease and it is selected by the organization ELIXIR (www.elixir-europe.org) as a European core resource due to its fundamental importance for a wider life science community. The Human Protein Atlas consortium is funded by the Knut and Alice Wallenberg Foundation….”

Laura and John Arnold Foundation contributes funding to launch Vivli, the Center for Global Clinical Research Data – Vivli

“Vivli, a Massachusetts-based nonprofit, has received $2 million from the Laura and John Arnold Foundation to build a first-of-its-kind data sharing platform for clinical trial research. The innovative platform will include a data repository, analysis tools and a dynamic search engine. It will provide transparency and access to clinical research data from around the globe, break data out of existing silos, and accelerate scientific discovery to improve human health.”

Addgene Depositors Get More Citations

“Professor Feng Zhang’s original 2013 gene editing paper on CRISPR/Cas amassed nearly 2,400 citations in its first four years (1). In addition to publishing in Science, Professor Zhang deposited the associated plasmids with Addgene. Since then, Addgene has filled over 6,500 requests for these plasmids. While clearly an outlier, this story had us wondering: is there a larger trend here? Do papers associated with Addgene deposits accumulate more citations than those without Addgene deposits? Even more interestingly, could we tell if depositing a plasmid with Addgene causes a paper to get cited more? …So what do we find [from Web of Science]? Lots more citations for the papers with plasmids deposited at Addgene – typically about four times as many as papers without plasmids deposited with Addgene….”

If funders and libraries subscribed to open access: The case of eLife, PLOS, and BioOne [PeerJ Preprints]

“Following on recent initiatives in which funders and libraries directly fund open access publishing, this study works out the economics of systematically applying this approach to three biomedical and biology publishing entities by determining the publishing costs for the funders that sponsored the research, while assigning the costs for unsponsored articles to the libraries. The study draws its data from the non-profit biomedical publishers eLife and PLOS, and the nonprofit journal aggregator BioOne, with this sample representing a mix of publishing revenue models, including funder sponsorship, article processing charges (APC), and subscription fees. This funder-library open access subscription model is proposed as an alternative to both the closed-subscription model, which funders and libraries no longer favor, and the APC open access model, which has limited scalability across scholarly publishing domains. Utilizing PubMed filtering and manual-sampling strategies, as well as publicly available publisher revenue data, the study demonstrates that in 2015, 86 percent of the articles in eLife and PLOS acknowledged funder support, as did 76 percent of the articles in the largely subscription journals of BioOne. Twelve percent of the articles identified the NIH as a funder, 8 percent identifies other U.S. government agencies. Approximately half of the articles were funded by non-U.S. government agencies, including 1 percent by Wellcome Trust and 0.5 percent by Howard Hughes Medical Institute. For 17 percent of the articles, which lacked a funder, the study demonstrates how a collection of research libraries, similar to the one currently subscribing to BioOne, could cover publishing costs. The goal of the study is to inform stakeholder considerations of open access models that can work across the disciplines by (a) providing a cost breakdown for direct funder and library support for open access publishing; (b) positing the use of publishing data-management organizations (such as Crossref and ORCID) to facilitate per article open access support; and (c) proposing ways in which such a model offers a more efficient, equitable, and scalable approach to open access than the prevailing APC model, which originated with biomedical publishing.”

“Patent-Based Open Science” by Lee Petherbridge

Abstract:  The contemporary approach to innovation in the life sciences relies on a patent-based proprietary model. Limitations on patent rights and business concerns often focus innovation to markets where the near-term monetary rewards are highest. This is “efficient” under an austere understanding of the term, but the proprietary model can be problematic from a practical perspective because it may not focus innovation to certain deserving markets. This Article contends that the property rights conferred by patent law may still serve as a positive base for innovation directed to underserved markets. The comparatively strong rights conferred by patent law provide upstream or pioneering innovators the power to establish some of the environmental conditions in which subsequent innovation takes place. This includes a power to create an environment of relatively open access to rights, which in appropriate cases may foster efficiency gains, reduce innovation suppressive costs, and achieve production for ultimate consumers at closer to marginal cost. In several parts, this paper discusses the topography of law and innovation in the life sciences, the characteristics of innovation in the life sciences that may support the use of patents to impose an “open science” framework, a legal means of imposing such a framework using servitudes, and some of the legal and economic implications of using patents in this manner. This Article concludes that there are reasons why universities and research-oriented medical schools should sometimes favor this approach and that limited testing should be performed to determine the efficacy of the approach.

MedPix

“MedPix® is a free open-access online database of medical images, teaching cases, and clinical topics, integrating images and textual metadata including over 12,000 patient case scenarios, 9,000 topics, and nearly 59,000 images. Our primary target audience includes physicians and nurses, allied health professionals, medical students, nursing students and others interested in medical knowledge….We are actively seeking new case contributions – which become a digital publication of MedPix® at the National Library of Medicine. Please join us in supporting one of the world’s largest open-access teaching files….”

Q&A: An open-data evangelist preaches creative cooperation to speed drug development

“When Dr. Atul Butte thinks data, the word “big” can’t do it justice. He was honored by President Barack Obama’s administration as an “open science champion of change” in 2013 for his work at Stanford University to sift 400 trillion molecular, clinical, and epidemiological data points to find new medicines and disease-fighting insights — and to speed the process by making the data as public as possible.”

Global Access in Action

“Global Access in Action, a project of the Berkman Klein Center for Internet & Society at Harvard University, seeks to expand access to lifesaving medicines and combat the communicable disease burden that disproportionately harms the world’s most vulnerable populations. We accomplish this by conducting action-oriented research, supporting breakthrough initiatives, facilitating stakeholder dialogue, and providing policy advice to pharmaceutical firms on best practices to increase impact.  GAIA uses its pragmatic and neutral viewpoint to enable dialogue across traditional boundaries between government, industry, nonprofits, and academia, and to promote new, innovative solutions amongst these parties to create better outcomes.”

An artificial future | Research Information

“One of the most exciting data projects we [Elsevier] are working on at the moment is with a UK based charity, Findacure. We are helping the charity to find alternative treatment options for rare diseases such as Congenital Hyperinsulinism by offering our informatics expertise, and giving them access to published literature and curated data through our online tools, at no charge.

We are also supporting The Pistoia Alliance, a not-for-profit group that aims to lower barriers to collaboration within the pharmaceutical and life science industry. We have been working with its members to collaborate and develop approaches that can bring benefits to the entire industry. We recently donated our Unified Data Model to the Alliance; with the aim of publishing an open and freely available format for the storage and exchange of drug discovery data. I am still proud of the work I did with them back in 2009 on the SESL project (Semantic Enrichment of Scientific Literature), and my involvement continues as part of the special interest group in AI….”