Category Archives: News

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

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 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.

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

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.

 

 

Principles for establishing a Central Service for Preprints: a statement from a consortium of funders

At the ASAPbio Funders’ Workshop, representatives from a number of funding agencies asked ASAPbio to “develop a proposal describing the governance, infrastructure and standards desired for a preprint service that represents the views of the broadest number of stakeholders.” Following iterative discussions about the technical and organizational aspects of such a project, ASAPbio is now positioned to issue an RFA for the development of a “Central Service” for preprints. To guide this effort, a group of funders have independently formulated the following principles that will shape the Central Service.

The funders are interested in getting additional funding bodies and research performing organizations to endorse these Principles. If you represent such an agency and are interested in signing on to these principles (or would like to discuss this matter), please contact Robert Kiley, Development Lead, Open Research at the Wellcome Trust (r.kiley@wellcome.ac.uk.)

Continue reading

Societies clarify positions on preprints in grants

Following increased interest in may scientific societies’ positions on the use of preprints in NIH grant applications, several societies have released statements providing their perspectives.

ASCB

The ASCB leadership, after careful consideration, believes preprints should be able to be included in grant applications and referenced in NIH progress reports, with the proper references so they are not confused with peer reviewed published papers. In short, the pace of science is too fast and the process of publication too slow to ignore preprints.

American Society for Microbiology (ASM)

ASM also supports the proposal that NIH allow preprints to be included in grant applications and progress reports, provided they are listed separately from peer-reviewed journal publications, given that they serve different purposes and hold different status.

Genetics Society of America (GSA)

American Society for Biochemistry and Molecular Biology (ASBMB)

While the ASBMB doesn’t oppose preprints being included in grant applications, some members do have concerns about how preprints will be used and whether they will increase the burden on grant reviewers.

ASAPbio response to FASEB’s statement on the NIH RFI on preprints

1/19/2017 update: We will close the signature drive at 9pm EST on Sunday, 1/22/2017.

Summary

The NIH released a RFI (request for information) on “including preprints and interim research products in the NIH applications and reports.”  ASAPbio, and many individual scientists, responded with arguments in favor of providing scientists with the option, not requirement, of citing preprints in NIH applications/reports as public evidence of their most recent work and productivity. FASEB, a scientific society claiming to be the voice of 125,000 scientists, issued a strong negative response to allowing preprints to be used in NIH grant review.  We, junior and senior scientists of the ASAPbio Board of Directors feel that there are many deeply problematic issues with FASEB’s arguments including 1) an unfamiliarity with preprints and even an articulation of incorrect information, 2) a lack of transparency of how they derived their decision, and 3) a view that there is “no need to read” original scientific papers, which we feel is not the type of culture that the funding agencies should foster in order to promote excellence in grant review. Because FASEB claims to speak for many societies and many scientists, their letter (signed only by the FASEB President) could be given disproportionate weight by the NIH (for a past historical example, see this article).  ASAPbio therefore has written this detailed response to FASEB (see below). We are also collecting signatures of scientists who support the option to cite preprints in NIH grant applications and reports here until 9pm EST on 1/22/2017.

Continue reading

Update on development of a Central Service Request for Applications (RFA)

At the ASAPbio Funders’ Workshop in May of 2016, representatives of funding agencies requested that ASAPbio “develop a proposal describing the governance, infrastructure and standards desired for a preprint service that represents the views of the broadest number of stakeholders.” Toward this end, we proposed a model for a “Central Service” (CS) that would aggregate content from multiple preprint servers, facilitating human and machine access to preprints via a search tool and an API.

Three separate processes are now ongoing to define this service:

Continue reading

ASAPbio’s response to the NIH RFI on preprints

Note: the RFI is now closed. The NIH has announced a policy that encourages the use of preprints.

The NIH has recently released a request for information (RFI) on the use of preprints and other interim research products. We encourage all interested parties to respond to the RFI using the submission website by the deadline of December 9th 2016 (extended from November 29th).

ASAPbio’s draft response is posted below. Even if you completely agree with our draft, we encourage you to submit your own responses as well. A large number of responses will be critical in conveying a strong message of community interest in preprints and other interim research products to the NIH. Responses from individual scientists at all career stages are encouraged. You do not have to respond to all questions, and the responses can be short. If you would like to share comments or your own response to the RFI, please use the comment section below the post.
Continue reading