Tag Archives: open access

Storify of Chris Kelty talk for #ProvostForum on Open Access, Piracy, and the Scholarly Publishing Market

Improving Ability to Identify Possible Conflicts of Interest of Scholars 1: Adding a Disclosure Field to ORCID

Real and perceived conflicts of interest are a critically important topic in scholarly activities that I believe has not received enough attention from the scientific community.  Right now, disclosures of possible conflicts of interest are handled incredibly very unevenly and poorly by academia and industry and government.  Even when people do the right thing and make detailed disclosures, such information is hard to find and ephemeral.  There are many things that the community could do to improve the ability to find such information.

One simple step that I believe could be useful would be to link disclosures to universal scholar ID systems.  Although there are multiple UID systems for scholars, right now the UID of choice appears to be ORCID. ORCID currently allows scholars to compile information about their education, employment, funding and scholarly works.

I therefore propose that ORCID add a new category: DISCLOSURES.  What would be included here? Well, I don’t know exactly but would include things like board membership, stock in companies, funding not listed elsewhere, any other significant relationship with a group, and more.  Sure this could get messy.  But I think we need to do more to make it easier to share and find information that could be a actual or potential conflict of interest.
Something like this:
If anyone knows of other tools for doing this I would love to hear about them.

Talk for UC Davis Pre-Health Meeting (#UCDPHSA): Opening up to Diversity

Sunday I gave a talk at the “12th National UC Davis Pre-Health Student Alliance Pre-Medical and Pre-Health Professions Conference“.  I normally try to not give talks on weekends (to spend time with my family) but I made an exception here since this meeting has a strong commitment to issues relating to diversity in health and STEM fields.  This mission statement for the meeting reads:

The UC Davis Pre-Health Student Alliance’s objective is to introduce and support academic, admission, and preparatory opportunities for all students interested in health professions with a focus on those underrepresented in healthcare (with regard to gender, economic, social, educational, linguistic, cultural, racial, and ethnic background). We target universities, community colleges and high schools throughout the United States. The UC Davis Pre-Health Student Alliance aims to impact health education, increase diversity amongst the healthcare workforce, and inspire future leaders of healthcare through hosting the largest national pre-health professions conference.

It was that mission statement that got me to ditch my wife and kids Sunday AM (and also much of Saturday PM for a dinner and to work on my talk).  I went to a dinner Saturday for some of the speakers with the new Dean of the UC Davis School of Medicine Julie Freischlag.  The dinner had about 20 or so people and I met some quite interesting folks there working on various aspects of human and animal health.

And then Sunday AM I got up early, decided to use slides (was not sure) and finished off the slide set I had worked on the night before.  I decided that, in the spirit of the meeting, I would talk about two main things – diversity and access.  And I planned to tell three stories about my work in this area.  I wove in some personal stories since, at the dinner the night before Barbara Ross-Lee (who I sat next to) helped remind me of the importance of making talks personal.  So in the end I talked about myself, diabetes, diversity of microbes, antibiotics, diversity in STEM, and open science.  I came up with a title I was OK with: Opening up to Diversity.

My talk went well, I think.  I am pretty sure it was vbideotaped but not sure where that recording will end up. I did however post my slides to slideshare.  See below:

Opening up to Diversity talk by @phylogenomics at #UCDPHSA from Jonathan Eisen

And I also recorded the talk using Camtasia (basically, it allows recording of the screen, the video camera on my computer, and the audio).  I posted the recording (without the video feed which shows mostly my neck) to Youtube.  See below:

UPDATE 10/16 –

I have scanned in my notes that I made in planning this talk.  Figured, why not post them.

Update: 12/10/2014 – just discovered a video of the talk was posted to Youtube 

NIH Announces Revised Genome Data Release Policies

Just got notified of this by the UC Davis Med. School grants administration: NOT-OD-14-124: NIH Genomic Data Sharing Policy.  Lots of interesting things in here including a summary of the comments that they received on the draft policy.

I have copied some of the more interesting and relevant bits below:

  • Sharing research data supports the NIH mission and is essential to facilitate the translation of research results into knowledge, products, and procedures that improve human health.  NIH has longstanding policies to make a broad range of research data, in addition to genomic data, publicly available in a timely manner from the research activities that it funds. 
  • The public comments have been posted on the NIH GDS website. http://gds.nih.gov/pdf/GDS_Policy_Public_Comments.PDF
  • The statement of scope remains intentionally general enough to accommodate the evolving nature of genomic technologies and the broad range of research that generates genomic data.
  • Several comments were submitted by representatives or members of tribal organizations about data access.  Tribal groups expressed concerns about the ability of DACs to represent tribal preferences in the review of requests for tribal data.
  • The GDS Policy expects that basic sequence and certain related data made available through NIH-designated data repositories and all conclusions derived from them will be freely available.  It discourages patenting of “upstream” discoveries, which are considered pre-competitive, while it encourages the patenting of “downstream” applications appropriate for intellectual property.  
  • NIH expects investigators and their institutions to provide basic plans for following this Policy in the “Genomic Data Sharing Plan” located in the Resource Sharing Plan section of funding applications and proposals.  Any resources that may be needed to support a proposed genomic data sharing plan (e.g., preparation of data for submission) should be included in the project’s budget. 
  • Large-scale non-human genomic data, including data from microbes, microbiomes, and model organisms, as well as relevant associated data (e.g., phenotype and exposure data), are to be shared in a timely manner. 

The Conversation on China’s embracing #openaccess for Science but not the Humanities

Well, this is very interesting and exactly the type of topic that fits in well with our ICIS project:

Humanities left behind as China embraces open access science.

The article reports on how China as a whole is pushing open access in the sciences but how the humanities in China are pretty much the opposite. The writer Michael Hockx suggests that a big revolution could happen if China embraced green open access in the humanities. Really interesting points here.

Update on Curtobacterium and Other Musings

In my first year in the Eisen lab, I was lucky to be able to participate on the Undergraduate Genome Sequencing Project in which I published the draft genome of Curtobacterium flaccumfaciens, the first of it’s genus. An important aspect of this project was blogging about what we were doing: All the successes, the failures, and everything in between, something that I was terrible at evidenced by my one maybe two blog posts. However, the longer I have been in this lab, I find the significance of social media in science, both to myself and the world, grows.

After almost a year since the paper was published, the Eisen lab received an email inquiring about my blog post on Curtobacterium and the difficulties we had with getting enough active DNA and continuing with sequencing. They wanted to know if we were having trouble with DNA extractions on the bacteria, especially since they were interested in sequencing other species of Curtobacterium and were worried if the genus was finicky. We had later found that the viability of our ligase decreased with each successive freeze-thaw causing the huge issue in DNA library prep and were able to inform them that extracting DNA and sequencing Curtobacterium should be a relatively painless process.

There were two things that stuck me as interesting when David, my supervisor on the project, informed me about the email exchange. First, that it was awesome that a blog post that I, an insignificant undergraduate, wrote was seen by other researchers and contained information (as small as it was) that could help them in their research. Second, and more abstract, that science has increasingly become more of a collaborative effort. When I originally thought about sharing in science, the infamous Koch-Pasteur rivalry quickly came to mind. Information simply wasn’t shared as readily at that time. I like to think idealistically that the idea of hoarding information to get ahead of contemporaries has become less common and science will become even more collaborative than it is now. Or the idea of charging to view more than just the Abstract will cease to exist and the number of open-access articles will continue to grow because at the root of researchers (at least originally) is the pursuit of knowledge and dissemination of information. Just some musings I had and who am I to talk? I haven’t even graduated undergrad yet and haven’t joined the race to find the richly rewarding cure to cancer.

Interested in #OpenAccess publishing?: definitely take a look at this working paper from CREATe

Well, this is certainly the most comprehensive treatise I have ever seen on Open Access publishing: Open Access Publishing: A Literature Review | CREATe.  It was written by “Giancarlo Frosio under the supervision of Estelle Derclaye (2014)” and

comes from the Centre for Copyright and New Business Models in the Creative Economy (CREATe).  It is VERY comprehensive and has discussion, review, and comments on just about every issue associated with Open Access publishing that one could think of. I do not know if there is any particular “angle” to the writings here.  What I looked at (not all of the document) seemed to be a relatively objective assessment of various OA issues.  Anyway, it is definitely worth a look for anyone interested in scholarly publishing or Open Access publishing or related issues.

Wanted – low cost system for publishing an #OpenAccess journal

Well, I figure, if I am going to write blog posts about academic publishing, why not post them here, rather than at my “normal” blog.  One area of great interest to many in academic publishing is in how one can publish a new journal at low cost  – and yet have the journal be Open Access.  Although there is a lot of chatter about this topic, I figured I would use social media to get some additional ideas in this area.  So I posted a request to Twitter yesterday about this and have gotten a decent diversity of responses.  I have created a Storify summary of these responses. Any other ideas or suggestions would be welcome.

Email from #UCDavis on UC #OpenAccess Policy

Just got this email

Just got this email

On behalf of Provost Hexter and Academic Chair Nachtergaele, please find the attached letter regarding the UC Open Access policy. For your convenience and reference, the text of the letter is pasted below.




Dear Colleagues:

We are pleased to inform you that on July 24, 2013, the Academic Council voted to adopt an Open Access Policy for scholarly articles published by Senate faculty across the University of California system. An article deposit system to support the policy was released, on a pilot basis, at UCLA, UC Irvine and UC San Francisco on November 1, 2013, and will be officially rolled out at the other campuses on November 1, 2014, pending the outcome of the pilot.

The Open Access Policy allows faculty members to maintain legal control over their research articles while making their work much more widely available to the public. The policy does not require faculty to publish in open access journals, or to pay fees or charges to publish; instead it commits faculty to making a version of each article available publicly in an open access repository.

Faculty can take advantage of this right by using UC’s eScholarship digital repository via http://www.escholarship.org/ (or any other open access repository) to make a version of any article publicly and freely available worldwide. While it is expected that faculty at UCLA, UC Irvine and UCSF will make their articles freely available (via eScholarship or another OA Repository) effective immediately, faculty at the other 7 UC campuses are also free to begin depositing their articles now if they wish. Faculty authors may opt out of the policy for any given article, may delay the date of appearance of the article (“embargo” it), and may choose the terms of use that will be applied to each article (for example, whether it is for commercial or non-commercial reuse).

This policy has been under review by the Senate divisions and committees for two years and its implementation is a move of major significance. Policies like this one have been adopted by more than 175 universities but none as large, influential or productive as the University of California. The move signals to publishers that UC faculty want to see open access implemented on their own terms.

The California Digital Library and the campus libraries have developed a streamlined eScholarship deposit system and tools for obtaining waivers and embargoes to assist faculty in complying with the policy. The CDL has also contacted over 600 publishers to alert them to the policy and encourage their cooperation with its terms. Faculty on all campuses may receive questions about compliance from publishers and can consult the resources listed below (including an FAQ) for assistance.

Learn more about your rights and responsibilities under this policy at the UC Open Access Policy website.


Watch a 90-second video about the policy – and pass it on!


Discover how easy it is to deposit your articles in eScholarship.


Find out who to contact at your campus library for assistance.



Ralph J. Hexter

Provost and Executive Vice Chancellor

Bruno Nachtergaele

Chair, Davis Division of the Academic Senate

Open Access Policy 11.26.13.pdf