Author Archives: Jessica Polka

ASAPbio newsletter vol 10 – Meeting on 7/19, licensing task force

Dear subscribers,

The preprint ecosystem is growing rapidly. The CZI/bioRxiv partnership will fuel the expansion of the leading preprint server in the life sciences, and many other servers and platforms with varying degrees of disciplinary overlap exist or are planned (arXiv, PeerJ Preprints, preprints.org, OSF Preprints, ChemRxiv, SSRN, SciELO, PsyArxiv, EngArXiv, SocArXiv, Authorea, F1000Research, etc). Funding agencies are enacting policies supporting preprints, such as those developed by the Wellcome Trust and the Medical Research Council, while agencies like the NIH have gone a step further and developed guidelines for selecting a preprint server.

ASAPbio is now working to identify any gaps/opportunities in the preprint ecosystem, which will help to inform the revision of ASAPbio’s plans before the close of our RFA suspension.

Toward this end, we’re hosting a one-day meeting in Cambridge, MA on Wednesday, July 19th. The attendees—including funders, researchers, and leaders of preprint services—will discuss new developments, opportunities for collaboration, and perspectives on standards and best practices. A tentative agenda and attendee list can be found here. The meeting will be live-streamed via our YouTube channel, and we invite you to participate live by tweeting your questions and comments with #ASAPbio.

Meanwhile, we’re also working on understanding stakeholder attitudes toward preprint licensing, which is becoming an important topic as journals and funders begin to release policies in the area. We’ve established a preprint licensing task force that will study funder, journal, and researcher needs, provide informative resources, and potentially recommend licenses that benefit the public good.

Best,
Jessica Polka
Director, ASAPbio

ASAPbio launches preprint licensing task force

Every month, more and more life scientists are choosing to post a preprint. This decision can give scientists visibility in their field, establish priority of their work in progress, gain recognition by funding agencies, and elicit feedback to improve their manuscript.

But once the decision to preprint is made, authors posting to some servers are faced with another important choice: which license to pick—that is, what they will allow others to do with their work. The aggregate effect of such choices will expand or restrict the possible future benefits of preprinting.

Permissive licenses, such as CC-BY, remove barriers to the innovative reuse of content. Such reuse could include new display tools incorporating annotation (such as SciLite and SourceData), discovery tools that excerpt passages to create summaries, archives for preservation, or use of the figures in educational materials. Restrictive licenses, on the other hand, could create barriers for reuse scenarios, such as those that create modified versions of the work or that are commercially motivated. The choice of license has implications not only for potential uses, but also for the journal that ultimately publishes the papers.

The current state of preprint licensing

Some preprint servers (preprints.org and PeerJ Preprints) apply a CC-BY license by default, making all preprints full open access. Others (arXiv and bioRxiv) only require authors to grant the preprint server a license to post the article; in addition, they offer a range of creative commons licenses or the choice to retain all their rights.

Presented with choices, authors do not prefer permissive licenses at bioRxiv or arXiv. However, based on initial conversations, we find that licensing and the ramification of different licensing are issues that are very poorly understood by the scientific community.

Recently, some funders and journals have also entered the conversation. The NIH encourages the use of CC-BY licenses for preprints, while some journals have implemented policies that concern preprints posted under certain licenses, but not others.

ASAPbio’s Preprint Licensing Task Force

To stimulate informed conversation on the licensing of preprints, ASAPbio has established a Preprint Licensing Task Force.

The goals of the task force are to:

  • Understand stakeholder (author, funder, publisher, and preprint server) attitudes toward these licenses
  • Create resources to help inform stakeholder decisions
  • Potentially recommend preprint licenses that will maximize scientific progress and social benefit

The Task Force began work in late May of 2017. It is chaired by Dick Wilder, Associate General Counsel at the Bill & Melinda Gates Foundation and non-voting affiliate on the ASAPbio Board of Directors, and contains among its members researchers, lawyers, and representatives of funding agencies and journals.

If you would like to provide your perspective on preprint licensing to the Task Force, please contact Jessica Polka (jessica.polka@asapbio.org).

Requesting your feedback: how should life scientists set standards for preprints?

May 10, 2017 update: ASAPbio has announced a four-month suspension of the RFA process to reassess the preprint ecosystem and community needs. 

Preprints (scientific manuscripts that have been posted prior to completion of peer review) allow for the direct exchange of knowledge between scientists. They constitute a global public good that promotes scientific progress. However, preprint servers, which have a 25 year history in physics, are relatively new to the life sciences, and their recent appearance has raised many questions about how they should best be used. What content should constitute a preprint? What type of information (metadata) should accompany preprints? How should they be licensed? How should preprints be screened? How should preprints and journals interact in productive ways? How should servers handle ethical issues such as human subjects research? These issues are examples of many that have been raised, and more will undoubtedly arise as scholarly communication evolves in the future. Rather than “hard wiring” rules for preprints now, we need to consider a thoughtful mechanism for ensuring that preprints develop and adapt to serve the scientific community, both now and in the future.

Currently, preprints in the life sciences can be found on several different servers and platforms (bioRxiv, arXiv q-bio,  PeerJ Preprints, F1000Research, figshare, preprints.org, and more are on the way). A diversity of preprint servers offers more choices for authors, but each has its own metadata, formatting, licensing, screening, and preservation standards. Each makes decisions according to its own board or advisors. Collectively, this can make it more difficult to know which servers conform to policies and technological standards requested by funders, and which ones will be most visible to scientific peers.

Creating an aggregator for life sciences preprints

The provisionally-named Central Service is a proposed aggregation site similar to PubMed Central. It would provide convenient access to a corpus of life science preprints for both humans (via a search interface) and machines (via an API and bulk download). This will ensure consistent access to preprints for purposes of archiving, text and data mining, and development of other services. Moreover, the central service will be established with a community governance structure to make it responsive to the needs and developing standards of the community.  ASAPbio has received a grant to catalyze the development of this service, and we are also working with 11 other funders to establish funding over a 5 year period. We’ve released an RFA for service providers, and expect the technical components of the service to launch in 2018.

However, the technology of the service must be complemented by outstanding leadership and oversight by respected members of the scientific community. Each depends upon the other; the cart and horse must be hooked up together. It is critical that a mechanism for community governance begins operation prior to or at the same time as the Central Service.  

Establishing community governance

What can we learn from other organizations with similar missions of serving the scientific community? Many such organizations operate through governing bodies composed of elected or appointed members from their relevant scientific community. These governing bodies make decisions according to bylaws, which effectively serve as a written constitution for that organization. Even though the elected officials turn over, the bylaws ensure that the organization maintains its operating principles over time. Virtually all scientific societies have established bylaws and elect a governing body. Some scientific resources, such as the Protein Data Bank and the preprint server arXiv, also operate in a similar manner. However, scholarly communication in biology currently lacks community governance; decisions are largely made by individual publishers or mandates by funding agencies. While preprints are just starting to gain acceptance in biology, now is an opportune time for the creation of an independent, scientist-led governing body for preprints with transparent governance processes similar to those of scientific societies and community repositories. We hope to hold elections in July and begin operation of the governing body in September or October.

To prepare for this, ASAPbio has worked with an international task force composed of ~30 scientists from a variety of fields and career stages, as well experts in scholarly infrastructure, to draft Operating Principles and Bylaws for this governing body. Representatives from the Funders Consortium also have provided valuable edits and feedback on this document.

Now is the time for communities of life scientists to establish a governance structure for preprints, and we are asking for your input. Please provide your feedback on the draft Operating Principles and Bylaws by leaving comments and suggested edits in the Google Doc. You may also email jessica.polka@asapbio.org, but we strongly encourage you to leave comments publicly in order to stimulate a dialog among stakeholders.

One point on which there has been considerable discussion and no clear consensus is the definition of the community that votes to elect Governing Body members. Should it be individuals who have submitted a preprint, those who have published a scientific paper in the past 5 years, or people holding an ORCID number (for which there are no prerequisites)? Please leave your thoughts on this important issue in the comment section below this post.

 

The commenting period will close on May 21, 2017. We look forward to hearing from you!

 

 

ASAPbio newsletter vol 9 – NIH encourages the use of preprints, Central Service update, ASAPbio on Twitter

Dear subscribers,

It’s been a big month for preprints!

NIH encourages preprints

On March 24, the world’s largest biomedical research agency released a landmark policy on preprints and other interim research products. The notice states that “The NIH encourages investigators to use interim research products, such as preprints, to speed the dissemination and enhance the rigor of their work.” It explains that “Interim research products can be cited anywhere other research products are cited,” and indicates that after May 25, 2017, “awardees can claim these products on their progress report publication list.  They can also report them on their RPPR […] and link them to their award in their My Bibliography account.”

The policy is also highly detailed, providing guidance on desirable qualities of preprint repositories and expectations for author practices (including funding and competing interests disclosures). The notice states that “the NIH strongly encourages awardees to select a Creative Commons Attribution (CC-BY) license or dedicate their work to the public domain.”

The announcement was covered in Science Magazine, The Scientist, and STAT, and more information on the NIH’s process can be found in a post on the NIH’s Open Mike blog. The new NIH policy was developed in consideration of responses submitted to last fall’s RFI, some of which (including ASAPbio’s) can be found on our website.

ASAPbio news

ASAPbio’s RFA for a Central Service (a PubMed Central-like aggregator for preprints) will close in about 3 weeks on April 30. To prepare for the evaluation process, we’ve invited external reviewers as described in the RFA. In order to ensure that a community-selected governing body can launch well ahead of the inception of the service, we are also revising a draft set of operating principles and bylaws for this board. We will be releasing this governance document for public comment in the coming weeks.

Those of you on Twitter may be familiar with the #ASAPbio hashtag, which is often populated by discussion and community news. To complement the hashtag, you can now follow @ASAPbio_ for major policy developments and updates on our work.

Thank you!
Jessica Polka
Director, ASAPbio

ASAPbio newsletter vol 8 – Scientific Society engagement, a new grant, ASAPbio retrospective

Dear subscribers,

Last month, we held a Town Hall meeting for Scientific Societies at NAS in Washington, DC. The meeting featured presentations by representatives of ASAPbio, NIH, and scientific societies who are innovating with preprints and publishing. More information and a video recording of the meeting is available online.

At the meeting, Neil Thakur of NIH shared results of the NIH’s Request For Information (RFI) on the use of preprints & interim research products in NIH grant applications and reports, which were overwhelmingly in favor of preprints. His slides are available to download here.

Also at the meeting, we announced a new $1 million grant to ASAPbio (which recently incorporated as a non-profit) that will help to catalyze the development of the Central Service. For more information about the service, please see our blog post that accompanied the release of an RFA (closing date April 30) and a list of principles and requirements established by funders.

Finally, it’s been a little over one year since our first meeting at HHMI Headquarters in Chevy Chase, MD. While we didn’t realize it at the time, that conference would turn out to be the catalyst for a year of work in promoting a culture of preprinting in biology. To celebrate, we’ve put together an interactive timeline detailing the history of ASAPbio along with major developments in preprint policy. View it here.

Stay tuned for more Central Service developments concerning community governance!

Ron Vale, Founder
Jessica Polka, Executive Director

RFA questions

When questions of general relevance about the requirements and process of the Central Service RFA are received, we will post anonymized summaries of these questions and their answers here. Please direct any additional questions to jessica.polka@asapbio.org.

Bidders’ information meetings

Audio of February 24th, 2017 bidders’ information meeting. The March 29th 9pm EDT meeting had no participants.

Q&A

Q: What will the governance model look like?

A: ASAPbio will release a draft of a proposal for the governance for public comment shortly. In brief, the current draft describes selection of a governing body by election. The slate of candidates would be selected by a membership committee of the governing body, derived from open nominations. Terms are staggered.

Q: Would metadata only aggregation (vs full text aggregation) fulfill the needs of the CS?

A: Our ambition is to facilitate easy and reliable machine access to preprints. Therefore, convenient access to full text is essential, but we do not wish to be overly prescriptive about the approach.

Q: Will the RFA result in the selection of a single bid?

A: Possibly, but not necessarily. As described in the RFA, ASAPbio reserves the right to explore whether multiple organizations, which may not have co-submitted a bid, could work together to develop a more compelling final proposal for presentation to the funders’ consortium.

Q: Are for-profit entities candidates for the CS?

A: Yes. All candidates, regardless of tax status, should be willing to adhere to principles such as openness and community governance as laid out in the RFA.

Q: My organization has developed software that is not open source. Can we use this to develop the CS?

A: All components required to run CS must be broadly available for other parties to use. If you have an existing proprietary closed-source code base upon which new code would depend, this code must be released under an OSI-approved license as well.

Q: Can indirect costs be listed in the budget?

A: Because we do not know the agencies and mechanisms that may fund the CS, we do not know if indirect costs can be provided. Please do not include indirect costs in the budget, but rather list all the costs of delivering the service (rent, utilities, administrative personnel, etc) prorated according to the fraction of your activities occupied by the CS.

Q: Can the service include disciplines other than life science?

A: Given the requirement for independent governance, the ASAPbio effort should focus on the life sciences, at least initially. We could explore ways to expand this to other disciplines over time if desirable to other scientific communities. That said, there is nothing to prevent the inclusion of other domains in the service if supported by other funding.

Q: Can the service provide commenting?

A: Section 2B.2C of the RFA reads: “Respondents are also invited to highlight other functionality they would suggest the site should support, although all features and functionality of the CS will require Governance Body approval.”

Continue reading

ASAPbio awarded $1 million from Helmsley Charitable Trust for next-generation life sciences preprint infrastructure

Date: Thursday, February 23, 2017
Contact: Jessica Polka | Director, ASAPbio | jessica.polka@asapbio.org

ASAPbio, a biologist-driven project to promote the productive use of preprints in the life sciences, has received a $1 million, 18-month grant from The Leona M. and Harry B. Helmsley Charitable Trust to develop a new service to aggregate life sciences preprints and promote their visibility and innovative reuse

Preprints are complete scientific documents posted online and made freely available to the global scientific community. They are frequently the same version of a paper that is submitted to a journal for peer review. Preprints are widely used in physics, mathematics, and computer science, but are still a new (albeit rapidly-growing) communication system in the life sciences. Mainstream adoption of preprints is challenged by the current difficulties of finding these documents, which are hosted on several unconnected servers; the lack of community governance over the standards that define a preprint; and technological barriers to accessing content for reuse.

The Helmsley award provides funds for ASAPbio to address these problems by constructing a community-governed service that will aggregate, preserve, and deliver life sciences preprints to human and machine readers. It will also develop open-source tools for manuscript screening and conversion to formats such as XML. The guiding principles of this service have been defined by a consortium of funders including the Helmsley Charitable Trust. ASAPbio has issued an RFA to identify potential technical suppliers for the service.

“The grant from the Helmsley Charitable Trust is a giant step forward for the life science community to translate ideas for next-generation preprint services into a reality. This coming summer, we anticipate that other funders will follow the lead of Helmsley and provide further multi-year support for building the technologies for a powerful preprint knowledge repository that facilitates scientific progress through open sharing of data,” says Ron Vale, Founder of ASAPbio. “The support of major funding agencies and the development of new tools for discovering recent scientific findings should encourage life scientists to share their scientific manuscripts in the form of preprints.”

ASAPbio’s work focuses on convening stakeholders for discussions about the role of preprints in the life sciences (namely, an initial conference at HHMI in February of 2016 (see report in Science) and follow-up workshops for funders, technical experts, and scientific societies). Via these meetings, online discussions, and a network of local representatives, ASAPbio seeks to promote the cultural change necessary to complement new developments in technology and policy, from funders, universities, and journals.

ASAPbio is additionally supported by the Alfred P. Sloan Foundation, the Gordon and Betty Moore Foundation, the Laura and John Arnold Foundation, and the Simons Foundation. ASAPbio is incorporated as a nonprofit California corporation.

ASAPbio newsletter vol 7 – Funders sign onto principles for preprint development, RFA released, scientific society town hall

Dear subscribers,

Since the summer of 2016, ASAPbio has been iterating on a proposal for a “Central Service” for life sciences preprints, a database that would aggregate preprints from multiple sources and make them easier to access by humans and machines. We explain the benefits of such a service in a recent blog post.

Yesterday, 11 funders endorsed a set of principles for establishing a Central Service for preprints, and ASAPbio released an RFA to invite potential suppliers to apply to provide it. These developments were covered in articles in Nature, Science, and The Scientist, and more information can be found on the Wellcome Trust, MRC, and NIH websites. We welcome any thoughts or reactions through comments on the web or by email to jessica.polka (at) asapbio.org.

We’re also continuing our engagement with scientific societies. On February 23, we will hold a Scientific Society Preprint Town Hall meeting at NAS in Washington, DC to discuss how preprints can benefit scientific societies in the future. The meeting will feature perspectives from scientists, funders, and societies that are innovating with preprints. Please encourage your scientific societies to attend! More information is available by emailing jessica.polka (at) asapbio.org.

In other exciting news, the list of funding agencies supporting the use of preprints as evidence of productivity is growing: since December, HFSP, Wellcome Trust, MRC, and HHMI have announced new policies on allowing these products to be listed in grants and reports. We’ll continue to monitor these and other developments to policies at funding agencies, journals and institutions.

The Benefits of a “Central Service” for Biology Preprints

Preprints are complete and public manuscripts with associated data shared before undergoing peer review. Physicists, mathematicians, and computer scientists post 100,000 preprints per year to arXiv, a scientist-governed preprint server that has been in operation for over a quarter of a century. Preprints in the life sciences are in a more embryonic stage, with less than 10,000 posted manuscripts per year. However, several meetings hosted by ASAPbio have ended with the conclusion that preprints, in conjunction with journals, hold great potential for enhancing scholarly communication in biology.

Recently, eleven major international funding agencies (Wellcome Trust, National Institutes of Health, Medical Research Council (UK), Helmsley Trust, Howard Hughes Medical Institute (HHMI), European Research Council, Simons Foundation, Canadian Institutes for Health Research, Alfred P. Sloan Foundation, Department of Biotechnology (Government of India), Laura and John Arnold Foundation) have released a statement calling for further technology development and the creation of a central resource for preprints, which is being provisionally called the Central Service (CS). The CS will be a database that aggregates preprints from multiple sources, making them easier to read by humans and machines. These features will enable scientists to find new knowledge that can accelerate their research. The CS will be overseen by a scientist-led governing body, which will ensure its mission in serving the scientific community and the public good.

ASAPbio (a scientist-driven organization to promote the productive use of preprints in biology) has released a Request for Applications (RFA) for the development of this service, which is open to all. After independent reviewers select the preferred applicants(s), and pending commitment of funders, the CS is expected to launch in 2018. Here we discuss why the Central Service is needed and its potential for advancing knowledge dissemination in the life sciences. Continue reading

RFA

May 10, 2017 update: ASAPbio has announced a four-month suspension of the RFA process to reassess the preprint ecosystem and community needs.

ASAPbio is releasing a Request for Applications for the development of a Central Service (provisional name) for preprints in the life sciences issued by ASAPbio. This Request is open to all prospective bidders, and we encourage responses from interested parties able to deliver the services described below. For a concise description of the goals of this project, please see our blog post entitled The Benefits of a “Central Service” for Biology Preprints. Proposals are due on April 30, 2017.