Massive Open Online Course (MOOC) on Data Management for Biomedical Big Data

The Countway Library of Medicine at the Harvard Medical School has received funding from the NIH Big Data to Knowledge (BD2K) Initiative for Research Education, to develop a Massive Open Online Course (MOOC) on Data Management for Biomedical Big Data. This MOOC is is built upon and expands the training materials of the New England Collaborative Data Management Curriculum (NECDMC), developed by several libraries in the New England region. 

The Best Practices for Biomedical Research Data Management course is hosted by the Canvas Network and provides training to librarians, biomedical researchers, undergraduate and graduate biomedical students, and other individuals interested on best practices for discoverability, access, integrity, reuse value, privacy, security, and long term preservation of biomedical research data. The course is free and self-paced….”

Best Practices for Biomedical Research Data Management – Canvas Network | Free online courses | MOOCs

“Biomedical research today is not only rigorous, innovative and insightful, it also has to be organized and reproducible. With more capacity to create and store data, there is the challenge of making data discoverable, understandable, and reusable. Many funding agencies and journal publishers are requiring publication of relevant data to promote open science and reproducibility of research.

In order to meet to these requirements and evolving trends, researchers and information professionals will need the data management and curation knowledge and skills to support the access, reuse and preservation of data.

This course is designed to address present and future data management needs….”

Horton: Planetary health is worth fighting for | Stanford Daily

Richard Horton, editor-in-chief of The Lancet (published by Elsevier), “suggested that journals like The Lancet “need to be advocates for open science — we need to believe in tearing down the barriers that stop people from accessing that information, generating that information and disseminating it. We need to be strong voices; in a sense, the moral conscious of our community, holding us accountable.” …”

Extracting research evidence from publications | EMBL-EBI Train online

“Extracting research evidence from publications Bioinformaticians are routinely handling big data, including DNA, RNA, and protein sequence information. It’s time to treat biomedical literature as a dataset and extract valuable facts hidden in the millions of scientific papers. This webinar demonstrates how to access text-mined literature evidence using Europe PMC Annotations API. We highlight several use cases, including linking diseases with potential treatment targets, or identifying which protein structures are cited along with a gene mutation.

This webinar took place on 5 March 2018 and is for wet-lab researchers and bioinformaticians who want to access scientific literature and data programmatically. Some prior knowledge of programmatic access and common programming languages is recommended.

The webinar covers: Available data (annotation types and sources) (1:50) API operations and parameters and web service outputs (8:08) Use case examples (16:56) How to get help (24:16)

You can download the slides from this webinar here. You can learn more about Europe PMC in our Europe PMC: Quick tour and our previous webinar Europe PMC, programmatically.

For documentation, help and support visit the Europe PMC help pages or download the developer friendly web service guide. For web service related question you can get in touch via the Google group or contact the helpdesk [at]”>help desk.”

Can the automatic posting of preprints increase the pace of medical research? – The Publication Plan for everyone interested in medical writing, the development of medical publications, and publication planning

“Preprints — versions of research papers made publicly available prior to formal publication in a peer reviewed journal — continue to be a topic of much discussion within the medical publications community. As the industry looks at ways to improve and advance the transparent and timely dissemination of research, preprints offer a potential route to achieving these aims. Already commonly used in fields such as physics, the launch of the medical publications preprint server medRxiv, expected later this year, is awaited with interest.

Meanwhile, Public Library of Science (PLOS) announced last month that all articles submitted to PLOS journals will now automatically be published on the biology preprint server bioRxiv as preprints, ahead of ‘traditional’ publication in a PLOS journal. Following initial top-line checks by PLOS, to ensure adherence to things like ethical standards and the journal’s scope, articles will be posted to bioRxiv while undergoing peer review at PLOS in parallel.

PLOS and Cold Spring Harbor Laboratory, which operates bioRxiv, hope this collaboration will help advance data dissemination and ultimately increase the speed of research. The potential of preprints has also been explored by other groups, including the possibility for preprints to improve online article engagement and for journals to use preprint servers to identify potential articles for publication.”

How EHRs [Electronic Health Records] Facilitate Clinical Research

“The data in electronic health records overlaps with the types of data collected for clinical research. This provides opportunities for data sharing and reuse without reentry or transcription, thus supporting open science and learning health systems. Building better bridges between research and health care offers limitless possibilities for facilitating research and improving health care delivery….”

Can patents ever be as popular as papers? | Sponsored | Chemistry World

“The value and usefulness of patents should, in fact, not only demand an increase in their popularity but make them a first-choice source for those seeking chemical information….

A final, unavoidable truth is that research papers aren’t always free. When you try to access a highly relevant paper from a website, you may be greeted by a paywall.

The emergence of open access journals does present the synthetic chemist with a free method of acquiring chemical information. However, in general, medicinal chemists will not deviate from the staple intellectual diet of JACS, JOC, BMCL, Tet. Letts., Tetrahedron, Synthesis and Synlett. These are widely considered to be the best sources of the medicinal and synthetic organic chemistry but these titles are not very supportive of open access. Any serious chemical research entity will have to foot a large annual subscription bill to gain access to them.

In stark contrast, patents are freely available from the World Intellectual Property Organisation (WIPO)….The most important thing that a research chemist needs to know is that all patents are freely accessible to the public. All 55 million of them. Clearly, this is a data repository that rivals any journal title, especially when the cost to access this wealth of chemical information is zero….”


This website, originally created in a collaboration between The British Pharmacological Society (BPS) and the International Union of Basic and Clinical Pharmacology (IUPHAR) and now developed jointly with funding from the Wellcome Trust, is intended to become a “one-stop shop” portal to pharmacological information. One of the main aims is to provide a searchable database with quantitative information on drug targets and the prescription medicines and experimental drugs that act on them….The Guide to PHARMACOLOGY database is licensed under the Open Data Commons Open Database License (ODbL). Its contents are licensed under the Creative Commons Attribution-ShareAlike 3.0 Unported license….”

Pharmaceutical companies’ policies on access to trial data, results, and methods: audit study | The BMJ

“Objectives To identify the policies of major pharmaceutical companies on transparency of trials, to extract structured data detailing each companies’ commitments, and to assess concordance with ethical and professional guidance….

Results Policies were highly variable. Of 23 companies eligible from the top 25 companies by revenue, 21 (91%) committed to register all trials and 22 (96%) committed to share summary results; however, policies commonly lacked timelines for disclosure, and trials on unlicensed medicines and off-label uses were only included in six (26%). 17 companies (74%) committed to share the summary results of past trials. The median start date for this commitment was 2005. 22 companies (96%) had a policy on sharing CSRs, mostly on request: two committed to share only synopses and only two policies included unlicensed treatments. 22 companies (96%) had a policy to share IPD; 14 included phase IV trials (one included trials on unlicensed medicines and off-label uses). Policies in the exploratory group of smaller companies made fewer transparency commitments. Two companies fell short of industry body commitments on registration, three on summary results. Examples of contradictory and ambiguous language were documented and summarised by theme. 23/42 companies (55%) responded to feedback; 7/1806 scored policy elements were revised in light of feedback from companies (0.4%). Several companies committed to changing policy; some made changes immediately.

Conclusions The commitments made by companies to transparency of trials were highly variable. Other than journal submission for all trials within 12 months, all elements of best practice were met by at least one company, showing that these commitments are realistic targets.”

Nebula Genomics: Blockchain-enabled genomic data sharing and analysis platform

“The first human genome was sequenced in 2001 at a cost of $3 billion. Today, human genome sequencing costs less than $1000, and in a few years the price will drop below $100. Thus, personal genome sequencing will soon be widely adopted as it enables better diagnosis, disease prevention, and personalized therapies. Furthermore, if genomic data is shared with researchers, the causes of many diseases will be identified and new drugs developed. These opportunities are creating a genomic data market worth billions of dollars….The Nebula peer-to-peer network will enable data buyers to acquire genomic data directly from data owners without middlemen. This will enable data owners to receive sequencing subsidies from data buyers and profit from sharing their data….”