Central Service – ASAPbio https://asapbio.org Fri, 28 Mar 2025 21:38:22 +0000 en-US hourly 1 https://wordpress.org/?v=6.9 https://asapbio.org/wp-content/uploads/2025/02/cropped-ASAPbio-favicon-32x32.png Central Service – ASAPbio https://asapbio.org 32 32 New directions for ASAPbio: outcomes of the July 19 workshop https://asapbio.org/july-outcomes/ https://asapbio.org/july-outcomes/#respond Wed, 02 Aug 2017 00:00:00 +0000 http://pl-asapbio.local/july-outcomes/ On July 19, preprint service providers, funders, and researchers gathered in Cambridge, MA and via videoconference for a live-streamed ASAPbio workshop about the evolving preprint ecosystem (see video recording and collaborative notes). The goal of the meeting was to assess outstanding needs in light of recent developments, including CZI’s partnership with bioRxiv. At the meeting, representatives from a number of preprint servers shared an update on their planned developments, and much of the agenda was devoted to discussing how communities of stakeholders can work together to promote constructive developments, both technological (manuscript conversion and screening tools and formats) and social (best practices and increased awareness in diverse communities).

Terminating the Central Service RFA

In learning more about CZI/bioRxiv’s plans, ASAPbio—in collaboration with representatives from the Consortium of Funders supporting Preprints in the Life Sciences—have decided to terminate the request for applications for the Central Service and the development of bylaws and election of a governance body for a Central Service. Many of the goals of the RFA (making preprints easier to find, accessible by machines, and capable of scaling to accommodate a significant fraction of the literature in the life sciences) will be accomplished by the CZI partnership and other developments in this rapidly evolving ecosystem. While we are not pursuing the CS/governing body at this time, we will continue to monitor the preprint space and may potentially revisit infrastructure developments if there is a strong need.

We thank all of the respondents who developed outstanding applications, two of which have been shared publicly, a group of ~30 individuals who provided considerable work and advice toward the development of the governance principles and bylaws, and all members of the larger community who have provided feedback and advice to us.

What’s next for ASAPbio? Preprint standards, awareness, and new directions

At our July 19 workshop, a general consensus was reached around the need for standards and best practices for preprints. This need was articulated most strongly by funding agencies who would like to be able to direct their grantees in selecting an appropriate repository for sharing their results. Currently, there are no broadly agreed-upon best practices or mechanisms by which to evaluate preprint servers in areas such as metadata, preservation, access, screening/manuscript removal, and manuscript scope/completeness. The funders have encouraged ASAPbio to create such standards in consultation with the scientific community, funders, and preprint servers. This effort will allow funding agencies to more readily adopt and use preprints, and it will also increase the reliability of preprints as a form of scientific communication. ASAPbio is committed to transparency and community engagement in all of our work, and we look forward to hearing your feedback as this process moves forward over the next several months.

Furthermore, the meeting identified a strong need for increased awareness of preprints among many communities of researchers. ASAPbio will continue to partner with our ambassadors and others to promote discussions about preprints.

ASAPbio stands for Accelerating Science And Publication in biology. We are working toward the ultimate goal of improving the entire process of communicating research. In addition to preprints, other elements of the publishing system require the attention and involvement of the scientific community. We are currently exploring these directions and will share news about upcoming plans in the near future.

 

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New developments and plans for the Central Service RFA and Governing Body https://asapbio.org/plans-for-cs/ https://asapbio.org/plans-for-cs/#respond Wed, 10 May 2017 00:00:00 +0000 http://pl-asapbio.local/plans-for-cs/ Funding agencies are crucial to the development of the preprint movement. The adoption of preprints by the life sciences community has been accelerated by grant-making policies that recognize these manuscripts as a valid form of scholarly communication. Investments in preprint infrastructure, services, and technologies are thus necessary to build capacity for growth.

The latest strong support for preprints comes from the Chan Zuckerberg Initiative (CZI), which recently announced financial support for bioRxiv, the leading preprint server in the life sciences, along with resources to develop new open source software, including tools for manuscript conversion to XML. ASAPbio applauds the decision by CZI to provide funding for bioRxiv and further technological development, both of which will very positively advance the growth and readability of preprints.

ASAPbio also has advocated for funder investment in these areas. Together with a group of funders, ASAPbio developed plans for a Central Service, an aggregation site of preprint content meeting certain standards, new search tools, and software for XML document conversion. Seven applications were received on the April 30 RFA deadline. In parallel, ASAPbio also commissioned a 30 person task force to develop bylaws for a community-elected Governing Body, which have been released for public comment.

In light of the CZI/bioRxiv partnership that was announced on April 26, ASAPbio and the Funders Consortium have jointly decided to suspend the RFA and Governing Body for a four month period in order to reassess the needs of the scientific community. Since some objectives of the RFA are now being pursued by CZI/bioRxiv, we do not wish to duplicate or compete with their efforts. The need, role and mandate of any Governing Body may also require re-evaluation. During this four month period, we will gather more information from CZI/bioRxiv and engage the broad community of scientists, funders, scientific societies, and publishers to learn more about their opinions and needs. This represents an exciting opportunity to further advance scholarly communication by building upon the CZI/bioRxiv initiative and thus better serve the scientific community. Consistent with our mission, we will aim to bring together various stakeholders for conversations, identify and debate opportunities, and encourage input from open discussions with the community. We will release more information in the next few weeks regarding this planning process. Feel free to contact us with your input, suggestions or questions now or in the future.  

We appreciate the support and patience of everyone who has provided feedback on the Central Service governance and RFA process thus far, including the funders who have articulated principles for supporting preprint infrastructure, the RFA respondents who have written thoughtful and in many cases highly collaborative applications, attendees of our technical workshop and other meetings, members of our governance task force, our external reviewers, and many other individuals who have shared their feedback on our draft proposals for infrastructure and governance. We will continue to engage the broader community as we work to advance and accelerate scientific communication.

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Requesting your feedback: how should life scientists set standards for preprints? https://asapbio.org/gov/ https://asapbio.org/gov/#comments Fri, 21 Apr 2017 00:00:00 +0000 http://pl-asapbio.local/gov/ 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.

[aio_button align=”none” animation=”none” color=”red” size=”small” icon=”none” text=”View Operating Principles and Bylaws now” relationship=”dofollow” url=”https://docs.google.com/document/d/1KPrfFu7ftGOwejbOd7iuGae0tH2Cr7gSypM0-S1Y4zo/edit?usp=sharing”]

 

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

[ssbp]

 

 

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ASAPbio awarded $1 million from Helmsley Charitable Trust for next-generation life sciences preprint infrastructure https://asapbio.org/feb23/ https://asapbio.org/feb23/#respond Thu, 23 Feb 2017 00:00:00 +0000 http://pl-asapbio.local/feb23/ 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.

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The Benefits of a “Central Service” for Biology Preprints https://asapbio.org/benefits-of-a-cs/ https://asapbio.org/benefits-of-a-cs/#comments Mon, 13 Feb 2017 00:00:00 +0000 http://pl-asapbio.local/benefits-of-a-cs/ 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.

Preprints in the life sciences come from multiple sources, making them difficult to discover

Preprints in physics have coalesced into one location – arXiv.org. The critical mass and “one stop shopping” offered by a single distribution site has been critical for arXiv’s success. The relatively few preprints in biology are distributed on several servers (bioRxiv, Peer J, F1000, qbio section of arXiv), with bioRxiv receiving the most submissions. In addition, more parties are considering developing preprint services including prominent journal publishers such as PLOS. Thus, preprint entities in biology are more likely to expand rather than collapse into one source. The expansion of entry points could dramatically increase preprint numbers and offer unique features for authors. However, fragmentation of preprint sources makes the knowledge harder to find and potentially creates more ambiguity of preprint quality, reuse and preservation. Collecting preprints from multiple intake sources into a unified database (the Central Service) would provide a single repository for searching and mining preprints.

Preprints represent a potential rich source of data but are difficult to read by humans and machines

The scientific knowledge base is growing at a staggering rate, making it increasingly difficult for scientists to find information that might be relevant for their work. Currently, preprints take the form of an author-submitted PDF, which can be cumbersome to read on the web and is difficult for machines to search for content. To circumvent these limitations, the CS will develop a conversion tool that will receive manuscripts in word processing formats currently used by life scientists and convert them into XML-based formats that are easier for humans and and computers to read. This advance will make it easier for scientists to find the content that they need.

Preprints should be a starting point for innovation

The corpus of preprints should be made available for creative use, discovery and innovation. The CS will provide interfaces for programmatic access (via open APIs) so that third parties have access to all content and can build innovative tools for scientists. Such tools could include better search algorithms, tools that aggregate knowledge and customize it for individual use, links to data or reagents, or annotation. The CS will provide a platform for the emergence of new innovations that can help scientists, which in turn would help to drive the adoption of preprint communication.

The future development of preprints should be overseen by scientists

Preprints are emerging as a new method of communication in the life sciences, and questions related to standards, licensing, and best practices of use will continuously arise. These issues should be addressed by an international, scientist-led governance body that acts in the best interests of the research community and the public. The creation of the CS will be accompanied by the simultaneous creation of a Governance Body whose function is to oversee the work of the CS and define standards for work that should be included in the CS. Without a CS, oversight and mandating standard practices of many preprint sources will be difficult, as is the case in the present journal system.

Funding agencies, universities, scientific societies want clarity on a “respected preprint source”

To be useful for scientists for career advancement, preprints should be citable in grants and promotion packages. However, funding agencies, universities and scientific societies have expressed concern about the quality of preprints, especially if they come from multiple sources. Material in the CS will adhere to common standards for ethics, metadata, and scholarly preservation. This will simplify the “definition of a preprint” for funding agencies, universities, and scientific societies.

Preprints need to be stored in perpetuity

For preprints to serve a major role in scholarly communication, they need to be stably preserved. However, because currently most preprint servers are run without profit as a service to the community, their indefinite continuation cannot be assumed. The Central Service will maintain stable backups of all content to ensure that the knowledge contained in preprints is always available.

Preprint software development should be open source and provide community resources

Preprints embody the philosophy of open communication and knowledge sharing. The infrastructure for preprints should reflect these values. The creation of a CS with an open source mandate will ensure that developed software and APIs will be shared with the goal of lowering barriers for innovation in scholarly communication.

Explanation of parties contributing to the Central Service for Preprints

The Central Service: Is a provisional name for the database of preprints that will provide 1) intake from multiple sources according to standards (format, content, and licensing) and ethical guidelines established by the governing body, 2) document conversion through open source software, 3) data storage, 4) search tools and limited display for scientists, and 5) an open API to make its content available to third-party innovators.

The Central Service Provider(s): Is/are the entities that receive grants or contracts from ASAPbio to provide the implementation of the central service.

ASAPbio: Is a non-profit corporation whose mission is to advocate for the productive use of preprints in biology and to administer grants/contracts for the operation of the CS. ASAPbio will collect funds from the funders’ consortium and distribute them to CS providers. It will act as a secretariat to the governing body and organize their meetings and reports. ASAPbio.org will serve as information portal to the scientific community.

The Governing Body (GB): Is an independent, international body supported by funds and administrative services provided by ASAPbio but with its own bylaws. It will set standards for intake and operations of the CS, evaluate the CS, and prepare reports for the funders.

Funders: We anticipate that an international consortium of funders will provide support for the CS, with commitments to be established later in 2017.

 

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Principles for establishing a Central Service for Preprints: a statement from a consortium of funders https://asapbio.org/principles/ https://asapbio.org/principles/#respond Mon, 13 Feb 2017 00:00:00 +0000 http://pl-asapbio.local/principles/ 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.)

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Preprints: a definition

Complete and public drafts of scientific documents, yet to be certified by peer review.

Preamble

At the ASAPbio1 Funders Workshop (held on the 24th May 2016) broad agreement was reached on the value of a Central Service (CS) for preprints. Although the detail of the proposed CS was not fully determined, there was support for the view that a future CS would aggregate content from multiple sources2 and provide new ways for researchers and machines to search, access and reuse this content. The CS would also have an archival function, ensuring long term, stable access to preprints. To help realise these different functions – archival, access, re-use etc – there is assumption the CS would also convert all ingested preprints to a standard file format.

The Funders listed below believe that sharing of preprints provides researchers with a faster way to disseminate their work, establish priority of their discoveries, acknowledge funders’ contributions to research advancement, and obtain feedback. They also offer a more current understanding of an investigator’s work.

We also believe the development of the CS will provide the research community with a crucial resource that will ensure that preprints , regardless of origin and format, can be discovered, accessed and used.

As a consequence of these factors the Funders are highly supportive of the work ASAPbio has been doing to encourage preprint sharing in the life and biomedical sciences and, more recently, their work to start to define the key elements of the proposed CS.

While the Funders (listed at the end of this document) are not committing themselves to fund a CS, we strongly encourage ASAPbio to develop a proposal describing the governance, infrastructure and standards desired for a CS that represents the views and needs of the research community, which includes both researchers and funders. The proposal should include a budget, goals, milestones, implementation timeline and sustainability plan after 5 years of funding to bring an appropriate community-defined preprint CS into a stable, long-term service.

To help frame the proposal – and understand the intent of the Funders with regard to establishing a CS – the Funders have drawn up this document which articulates a number of principles and, in some cases, requirements, which will need to be adhered to as a condition of any future funding.

Developing a Central Service for Preprints: overarching principles

Principle 1: The Central Service must have an independent governance structure

1.1 Governance: overview

We support the notion that the CS should be governed by an independent governance body that is international in scope and led by highly respected members of the research community, and includes other relevant experts including organizations that serve the research community; policy and legal experts; and technical experts. For the purpose of this document we will assume that ASAPbio is the entity which is responsible for managing the CS. As a consequence, we also assume that the primary decision making body will be an ASAPbio Board of Directors.

This body will be responsible for defining the details of the service – what is an acceptable repository from which content can be aggregated and what types of preprints are within scope – and determining a longer term sustainability model for the CS. We also assume that this body will be responsible for managing and running a procurement process to identify a supplier (or a consortium of suppliers) to deliver this CS.

At this stage it is unclear whether ASAPbio will be the entity which will actually contract/grant fund the supplier(s) of the CS – or whether this is managed by funders of the CS, either collectively or through a designated lead funder. In the event that funding for the CS is managed directly by those funders supporting the cost of the CS, then the ASAPbio Board will be expected to advise the funders on which supplier (or consortium of suppliers) should be funded to deliver the CS.

To help ensure that the services continue to meet the needs of the research community, we envisage that the ASAPbio Board of Directors will be supported by a Scientific Advisory Board (SAB) appointed by, and reporting to, the ASAPbio Board of Directors.

Funder requirement:

The CS must have an independent governance structure.

1.2 Governance: Funder role

The Funders do not envisage having any formal role on the ASAPbio Board of Directors or the SAB; indeed it is critical that the major decision making bodies should be independent of the Funders.

Working on the assumption that a consortium of funders will fund the CS, a mechanism will be needed to ensure that the service being developed is in line with the requirements of the research community.

One mechanism to explore might involve the ASAPbio Board of Directors providing an annual report to the Funders of the CS – outlining what they have done over the past 12 months and what developments are planned for the next 12 months. This report would be developed with input from the Scientific Advisory Board. Funders would use the report as a mechanism for determining whether to release the next 12 months of funding.

Principle 2: The Central Service should seek to secure widespread community support

2.1 Community support

It is essential that ASAPbio engages broadly with the research community to ensure that the CS enjoys as much community support as possible. The Funders will expect ASAPbio and the SAB to continue to engage with the research community to seek their input on the future direction of the CS and to promote its use.

Principle 3: Content in the Central Service should be open and meet scholarly standards

3.1 Preprints should be made maximally useful through permissive licensing

We believe that to maximise the benefits which arise through the sharing of preprints, content made available through the CS should be licensed in ways which facilitates re-use, text and data mining and the development of services which allows others to innovate on this content. As funders we strongly believe that this can best be facilitated by ensuring that the content made available through the CS is licensed using the Creative Commons Attribution licence, CC-BY.

However, we also recognise that if we limit the CS to only aggregate CC-BY content, this may adversely impact the uptake of preprints and the CS’s intent to be the premier discovery system for preprints.

In the longer term the Funders would like to get a position whereby the CS only aggregates CC-BY licensed content. We will work with the CS, and the community more broadly, through ASAPbio, to determine the most effective policy levers to bring this about.

Funder requirements:

All preprints made available through the CS must include a licence statement, which makes it clear how that content can be used.

All aggregated content must be included in the full text corpus for search (e.g. showing snippets like Google books) and be made available for text and data mining and other computational uses (via the CS API).

Content providers – including existing preprint servers, publishers and users who post directly to the CS (if that is deemed to be a useful service) – who want their content to be discoverable through the CS – must agree to these conditions.

3.2 Preprint – the underlying data

As Funders we recognise the importance of making the underlying data – referenced in a preprint – available for others. Sharing data reduces waste, supports reproducibility and helps accelerate discovery and its application for health benefit.

Consequently, we strongly encourage both existing and emerging preprint servers to develop their services such that, going forward, all preprints (which are aggregated by the CS) include a data availability statement. We also encourage researchers to make the underlying data available under a CC-BY or the Creative Commons Public Domain Dedication waiver (CC Zero), at the time of formal (peer reviewed) publication, provided that this is consistent with any commercial, legal and ethical obligations.

In terms of data availability we strongly encourage researchers to deposit data in recognised repositories. Where these do not exist, we encourage researchers to make their data available via more generic repositories, such as Dryad, Figshare and Zenodo.

3.3 Preprint – scholarly standards

As funders we feel that it is important that the CS must uphold scholarly standards of publication. Preprints ingested into the CS must adhere to standard scholarly publication practices such as authorship, regulation and ethical, legal and societal standards. They must also provide appropriate funding acknowledgements. In addition, the CS workflow must support mechanisms (e.g. screening of content) to ensure that these standards are maintained.

Funder requirement:

The ASAPbio Board must develop a clear set of guidelines to ensure that content aggregated into the CS upholds scholarly standards of publication.

Principle 4: Where possible, the CS should make use of and build on existing infrastructure, services and good practice

4.1 Build on existing infrastructure and services

A number of relevant services, tools, and applications already exist which potentially could be used to support the development of the CS. Where appropriate, we encourage ASAPbio to issue a proposal that fosters relations with these providers of services, tools, and/or applications, so as to maximise support and collaboration from existing “preprint communities”.

In terms of best practice, we would expect the CS to make use of proven technology (one example might be the use of JATS XML for document conversion) but at the same time keep an open mind to experiment as new opportunities emerge.

Principle 5: Any new code to build the Central Service should be open and interoperable

5.1 Central Service: software

As Funders we wish to create a vibrant preprint ecosystem to help advance the use of scientific publications. We believe that we will best achieve this by adopting an open source licensing model.

Funder requirement:

Any software which is used or developed to support the CS should be made available under open licenses, such as those developed by MIT or BSD. If, downstream, a supplier responding to any Request for Information (RFI) or tender request is not able to comply with this approach they will need to explain why, and what public benefits will be realised by adopting a less open licensing regime.

5.2 Central Service software should support and foster interoperability

As Funders we believe that the CS will only be successful – that is making a critical mass of preprints available in ways which allows others to build and innovate on this content – if any system that is developed is built with interoperability as a key guiding principle.

Specifically, we believe that the CS will need to interoperate with other systems – ingest servers, screening services, metadata and utilization statistics, etc – and that a system that does not support open APIs is unlikely to succeed. And, though the CS should be limited in scope to preprints in the life and biological sciences, we should be mindful that as research becomes more interdisciplinary it may be desirable to bring in preprints from other disciplines to create an “all scholarship preprint service”, or, at the very least, allow others to use the software developed by the CS to establish their own services.

Principle 6: Access to the Central Service must be free at the point of use

6.1 Free, unfettered access

To foster uptake of preprints amongst the life sciences research community we believe that access to the CS must be free at the point of use for both suppliers and consumers of content.

Funder requirement:

Access to the CS must be free at the point of use for both suppliers and consumers of content.

Principle 7: the Central Service must be easy to use

7.1 Easy and rewarding to use

For the CS to be successful it must be easy for researchers, developers, publishers etc. to use and engage with. By way of example, it must be possible for the CS to aggregate content directly – either from existing preprint servers or from publishers who wish to make submitted manuscripts available to the CS. If it deemed important for the CS to offer a “direct deposit mechanism” (so researchers can post directly to the CS) then this must also be easy to use.

Equally, the CS should provide a rich search and discovery experience so that researchers can identify, access and, where available, download content that is most relevant. Finally, it should offer usage/impact metrics and facilitate incentives that reward researchers for posting preprints and other service activity (commenting, data sharing, screening, etc.).

Beyond these core features, we encourage ASAPbio to work with the community to help better understand how researchers might want to use the CS and what services need to be developed to support these needs. We believe this represents an unprecedented opportunity to further scholarly communication in the life and biomedical sciences.

7.2 Easy for developers and other applications to use

In addition to researchers, we believe that key users of the CS will be other developers and applications who wish to build rich, value-added services on top of the CS. To enable this, the CS would need to develop a suite of open APIs to support these capabilities.

Funder requirement:

The CS must provide open APIs to allow others to build new services based on the content it has aggregated.

Principle 8: The Central Service must have a sustainable model

8.1 Sustainability

The proposal to develop the CS should include a credible plan to develop and sustain an appropriate community-defined CS for preprints.

Funder requirement:

A credible sustainability plan is required, to demonstrate how the CS will support itself in the long term.

8.2 Cost effective and flexible approach

The research community, including funders, are already spending significant sums of money on scholarly communication (mainly in the form of subscriptions and open access costs). Given this, the CS proposal would represent another cost for Funders, at least in the short term. Consequently, it is essential that the approach taken be cost effective and flexible (so that it can adapt to changes in the ecosystem and stakeholder needs) and that any aspect of the CS that is not adding value is eliminated.

Funders supporting these principles

Funder name Funder representative
Wellcome Trust Robert Kiley
National Institutes of Health Patricia Flatley Brennan
Medical Research Council (UK) Tony Peatfield
Helmsley Trust Megan Deichler
Howard Hughes Medical Institute (HHMI) Judith Glaven
European Research Council Dagmar Meyer
Simons Foundation John Spiro
Canadian Institutes for Health Research Matthew Garsia
Alfred P. Sloan Foundation Josh Greenberg
Department of Biotechnology, Government of India K. VijayRaghavan
Laura and John Arnold Foundation Mike Stebbins


This document was prepared by Robert Kiley, Wellcome and Philip Bourne, NIH (Associate Director of NIH for Data Science, 3.14-1.17), with additional input and comment from Stuart Buck (Arnold Foundation), Lorraine Egan (Damon Runyon Cancer Research Foundation) Sindy Escobar-Alvarez (Doris Duke Charitable Foundation), Michele Garfinkel (EMBO), Josh Greenberg (Sloan Foundation), Maria Leptin (EMBO), Tony Peatfield (Medical Research Council) John Spiro (Simons Foundation), and Neil Thakur (NIH).

Footnotes

  1.  ASAPbio is a scientist-driven initiative to promote the productive use of preprints in the life sciences
  2. This would include existing preprint services, such as bioRxiv and Peerj Preprints, and future services, perhaps those established by publishers or other discipline-based services (e.g. ChemRxiv).
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