#AccessToResearch & More! — Hashtags of the Week (HOTW): (Week of February 3, 2014)


I was pretty excited to see the announcement of the UK Access to Research initiative, a partnership of publishers and libraries across the United Kingdom, which will hopefully extend open access research in ways that may serve as a model for other countries. They made some interesting choices, including requiring people to visit their local library in order to get access.


Open Access and those Omnibus Bills


So last week, the Senate approved a Fiscal Year 2014 Omnibus Appropriations bill that will fund the government to October, and maybe that should make me happy enough, given how difficult it seems to have the government “do” anything these days.  But what you may not have known is that within this bill, the Department of Labor, the Department of Education and the Department of Health and Human Services is requiring that publications resulting from these agencies federal funds need to be made available online to the public no later than one year after its release in a peer-reviewed journal.  Similar to the National Institutes of Health Public Access Policy (NIHPAP), this act is a huge step in making information more available to the public.  NIHPAP was included in a December 2007 Omnibus bill and has made an incredible impact on making the full-text articles of NIH funded research available to the public.  Have you checked out PubMed Central recently?  While the FY 2014 Omnibus Appropriations Act does not clearly state where these articles should be made available, researchers who use federal funds from these agencies should talk with their librarians in order to ensure that they are complying with these new mandates.

It’s a great time to be a part of the Open Access Movement as we have seen really great strides in the past year toward information being available equitably.   Last year, we saw the introduction of the  Fair Access to Science and Technology Research Act (FASTR) bill, the OSTP Directive, and the Public Access to Public Science (PAPS) bill.  And I know these are not “technically” open access, but the fact that information is being required to be made available is still a great thing.

(In case you missed it, we had some great events for Open Access Week 2013 in October.  Here is the link to our closing keynote presentation, Redefining Impact, from Michael Buschman of Plum Analytics.)

So, I can honestly say that I’m happy with the government’s ability to “do” this past week.  I really hope this is a sign of things to come rather than a glitch.

Why You Should Care About Creative Commons 4.0

Creative Commons by Andres EM  CC BY 2.0

Creative Commons by Andres EM CC BY 2.0

Creative Commons, as many of you know, provides and promotes the sharing of material by creating licenses that allow authors to chose the conditions how their work can be reused. In the science community, Creative Commons is especially important because all scientific research is build on the reuse and re-analysis of other scientific works in an international and interdisciplinary world.

Creative Commons just released CC4 and claims to be the most “globally, legally robust licenses produced by CC to date.” There are many improvements that include internationalization, interoperability and durability, but the most exciting is the advances for data, PSI, science, and education. These exciting advances address the obstacles of adoption of CC by other governments, aka database rights in the EU. According to Puneet Kishor the implications for the change is great:

 That means a database creator in the EU, or any other jurisdiction where SGDR might exist, can use a CC4 license allowing use of the database without the user worrying about violating any database rights. In other words, using CC4 relieves the creator from separately licensing database rights, and it relieves the downstream database user – in particular if located in a region where SGDR apply– from worrying about violating any database rights

If you want to learn more about Creative Commons 4.0 check out this blog post or interview with Puneet Kishor. If you want to learn about applying a Creative Commons license, click here.

Open Access Publications Surge with NIH Mandate

from National Institutes of Health data, posted in the Nature News Blog

In November 2012 the National Institutes of Health announced that in spring 2013 it would be enforcing its 2008 Public Access Policy (PAP) by not awarding non-competing grant continuations to those grantees who were not in compliance with the PAP – that is, with publications resulting from NIH grants submitted to the open access repository, PMC (formerly known as PubMed Central).

Since the announcement, there has been a sizable spike in the number of PMC submissions, and the PAP seems to have a compliance rate now hovering somewhere between 75 and 80%. You can actually download the NIH manuscript submission data as a CVS file, or view monthly statistics here.

A tip of the hat to Kevin Read, NLM Fellow, who first pointed me to this Nature News Blog post.


BMJ’s Open Data Campaign

Attending Copyright Camp last week, I first heard about the BMJ’s Open Data Campaign.

Image from BMJ Open Data site

Image from BMJ Open Data site

On the campaign website, BMJ states that as of January of this year, it is not “publish[ing] any trial of drugs or devices where the authors do not commit to making the relevant anonymized patient level data available, upon reasonable request.” The previous system of “hidden clinical trial data,” where openness was not a requirement, results in “adverse outcomes.”

Part of the catalyst is attributed to the European Medicine Agency’s plan to share clinical trial data that is submitted by companies looking for approval across drugs and medical devices.

What’s more, BMJ is calling for your assistance. They have an online form where you can submit information on instances where drug data “has been hidden from public scrutiny.”

Trish Groves, BMJ’s deputy editor, has been blogging about the new(ish) campaign and why it is a necessary complement to the open access publishing movement, with specific attention to the trajectory for clinical trial data – a fascinating read!

Rewarding Open Access – Nominations for the Accelerating Science Award Program

A new award, with major sponsorship from Google, the Public Library of Science (PLoS) and the Wellcome Trust, seeks to reward pioneers for the social good byawarding $30,000 to three people who have “applied scientific research published through open access” – in ANY field – for the benefit of society.

Open Access Logo

The official award site is here, and the application period closes June 15th, 2013 – so hop to it!

Nominees should be people and/or teams that have:

  • Used
  • Applied
  • or remixed scientific research published through open access.

Examples of nominees (so far) include:

bioinformatics team repurposes existing source codes used for searching genomic data associated with individual cancer tumors to create a new open source algorithm and web tool that can search multiple tumor types simultaneously, enabling faster and more comprehensive searches by oncologists for use in clinical treatment of cancer patients.


patient advocate creates a new web community for individuals with a rare genetic disorder and their families; this website curates existing and newly available open access research about causes and treatment protocols, and offers interpretative science articles and a user forum to help nonscientist readers better understand the science presented.

Some rules*:

  • Teams are eligible
  • Self-nominations are totally kosher

Nomination forms are here, and there is an award FAQ as well.

*NOT the full suite of rules – see the entire set of guidelines here.

Follow the conversation at #SciASAP.

The award is also supported by:


Public Comment Meetings on Access to Federally Supported Data & Publications

The National Academy of Sciences is holding 4 sessions over May 14-17 to gain public input on making available and accessing the results of federally funded efforts (both publications and data). Webinars will feature brief remarks by experts in each field, but the bulk of the time is reserved for public input. These sessions are all in response to the memo from the Office of Science and Technology Policy that we’d blogged about earlier in the year. Huzzah!

The sessions are broken out as follows:


  • Tuesday, May 14, 9 am – 5pm (EST)
  • Wednesday, May 15, 9 am – 12 pm (EST)
  • Read the full agenda here.
  • View the webcast here.


  • Thursday, May 16, 9 am – 5 pm (EST)
  • Friday, May 17, 9 am – 12 pm
  • Read the full agenda here.
  • View the webcast here.

The sessions are sponsored by the following veritable bevy of organizations:

NAS webinar sponsors

Escaping the Paywall: Taxpayer-funded research will be free

Open Access LogoOver the summer I wrote about a We the People petition asking the White House to mandate measures similar to the NIH Public Access Policy (in place since 2008)for more Federal agencies.  A quick review, the NIH PAP  has results from NIH-funded projects (eventually) published in open access journals and repositories.

That petition has gotten a response (from Dr. John Holdren, the Director of the Office of Science and Technology Policy)! One paragraph from Dr. Holdren’s response is particularly salient:

The logic behind enhanced public access is plain. We know that scientific research supported by the Federal Government spurs scientific breakthroughs and economic advances when research results are made available to innovators. Policies that mobilize these intellectual assets for re-use through broader access can accelerate scientific breakthroughs, increase innovation, and promote economic growth. That’s why the Obama Administration is committed to ensuring that the results of federally-funded scientific research are made available to and useful for the public, industry, and the scientific community.

But what does that actually do? The Office of Science and Technology Policy also issued a memo to the heads of federal agencies to the effect that those spending over $100 million on research & development should make the results of that research publicly available 12 months after publication (the standard embargo time).

Ah – democracy in action!

It’s not just about open access publication either – there are provisions regarding the “management and sharing of scientific data produced with Federal funding,” which I have a feeling may be the next version of the open access movement we see, if the 2012 Medical Library Association meeting is any indication.

Most of the coverage I’ve seen online is pretty positive regarding the measure – the Association of Research Libraries issued a press release supporting the action; the Huffington Post linked the move to Internet activist & programmer wunderkind Aaron Swartz; and the Chronicle of Education noted that even publishers were OK with the shift and that certain agencies, notable the National Science Foundation, had already rolled out timelines to implement open access publications. Now, not all of the coverage was entirely glowing – some argued that the measure doesn’t go far enough (full disclosure – that’s my alma mater there [Go Bears!] but I have no affiliation with the department or author). But all seem to agree that it is at least a series of steps in the right direction.

To top it all off, the House and Senate have recently introduced legislation (FASTR, or the Fair Access to Science and Technology Research Act) that would reduce that embargo period to 6 months! Our fearless open access soapbox librarian Jean recommends this site to follow FASTR’s developments in Congress.

Free Cytoscape Training Sessions in February

Cytoscape is an open source network visualization tool.  Cytoscape allows the exploration of molecular interactions and biological pathways and integrates these networks with annotations, gene expression profiles and other data.


Interested in learning more about Cytoscape?  Attend one or both of the following hands-on workshops:

Cytoscape:  Going from Raw Data to a Publishable Image

During this workshop, we will utilize a raw experimental data set to visualize functional relationships of gene fusion partners in cancer as a case study to produce publication-quality images.  Participants will learn how to import network and attribute data, change visual properties to easily distinguish biologically significant relationships, create a legend for the image, and more.

This training will be held on Monday, February 4 from 9:00am-10:30am in 2802 Med Sci II.

You can get more information about this training and register here.

Cytoscape Training: Plug-Ins

Cytoscape can facilitate filtering, clustering and searching of your interactions. Many additional features are available through its extensive list of plug-ins. We will explore several of these plug-ins including: Michigan Molecular Interactions (a molecular interactions tool), Metscape (a metabolite exploration tool), MCODE (cluster finding tool), and BINGO (Gene Ontology tool).

This training will be held on Monday, February 11, 9:00am-11:00am in 2802 Med Sci II.

You can get more information about this training and register here.

Science, Scientists and Twitter

My Twitter account as data visualization
Michael Sean Gallagher: My Twitter Account as Data Visualization

Most of you have probably already heard about Aaron Swartz’s death last week, and the response from the science community focusing on supporting and promoting Aaron’s vision for open access through the hashtag #PDFtribute occurring most prominently through Twitter. You can see an overview on the ETechLib blog.

#PDFTribute — The First (And Hopefully Last) Open Access “Martyr”: http://etechlib.wordpress.com/2013/01/14/pdftribute-the-first-and-hopefully-last-open-access-martyr/

Through the passion and urgency being brought to the conversations around these events, there are many conversations emerging around related issues, from how to make a PDF, tools for sharing files with the public, tools for discovering or negotiating intellectual property rights with publishers, and even how to use Twitter appropriately for science communication and productivity. One of the posts gathering attention today through the #PDFtribute stream is “10 ways scientists can benefit from Twitter” on one of the AAAS blogs.

Summer Allen. 10 ways scientists can benefit from Twitter. Qualia. January 15, 2013. http://membercentral.aaas.org/blogs/qualia/10-ways-scientists-can-benefit-twitter

Summer highlights ways in which Twitter is useful as a productivity tool for scientists: from troubleshooting to career strategies; tracking conversations around events whether you attend in person or not; data collection; research subject recruitment; tracking emerging topics and discoveries in your research topic as well as in science and technology in general; and sharing your findings and publications to both professional and public audiences. You can see more in the original blogpost, along with tips for best practices.