{"id":3690,"date":"2016-08-12T00:00:00","date_gmt":"2016-08-12T00:00:00","guid":{"rendered":"http:\/\/pl-asapbio.local\/cs-appendix-2\/"},"modified":"2025-03-28T21:38:29","modified_gmt":"2025-03-28T21:38:29","slug":"cs-appendix-2","status":"publish","type":"post","link":"https:\/\/asapbio.org\/cs-appendix-2\/","title":{"rendered":"Appendix 2: Current feedback on Central Service features"},"content":{"rendered":"<p><i><\/i><em><strong>Central Service model documents<\/strong><\/em><\/p>\n<ul>\n<li><a href=\"https:\/\/asapbio.org\/summary-of-a-central-preprint-service-model\">Summary: Background and a draft model<\/a><\/li>\n<li><a href=\"https:\/\/asapbio.org\/cs-appendix-1\">Appendix 1: Rationale for a <span class=\"boomerang-time-zone\">Central<\/span> Service<\/a><\/li>\n<li><a href=\"https:\/\/asapbio.org\/cs-appendix-2\">Appendix 2:&nbsp;Current feedback on <span class=\"boomerang-time-zone\">Central<\/span> Service&nbsp;features<\/a><\/li>\n<\/ul>\n<h2><span style=\"font-weight: 400;\">Current discussions with the community on proposed features of the Central Service<\/span><\/h2>\n<h3><span style=\"font-weight: 400;\">Surveys and information from scientists<\/span><\/h3>\n<p><span style=\"font-weight: 400;\">We will continue to engage the scientific community on what services they want to see in a next generation of preprints. However, based upon a survey that ASAPbio conducted in May 2016 (<\/span><a href=\"https:\/\/asapbio.org\/wp-content\/uploads\/2016\/05\/Preprint-server-preferences-survey.pdf\"><span style=\"font-weight: 400;\">Results summary (pdf)<\/span><\/a><span style=\"font-weight: 400;\"> and <\/span><a href=\"https:\/\/asapbio.org\/wp-content\/uploads\/2016\/05\/anonymized-ASAPbio-preprint-preferences-survey-WITH-CHARTS_2.xlsx\"><span style=\"font-weight: 400;\">Anonymized responses (xls)<\/span><\/a><span style=\"font-weight: 400;\">) and other resources (e.g. <\/span><a href=\"https:\/\/docs.google.com\/spreadsheets\/d\/1UoTuzVVFe5qdMGenxAAbD9xEDOrnxuqpi29tO-frMXU\/edit#gid=488933191\" target=\"_blank\" rel=\"noopener\"><span style=\"font-weight: 400;\">Preprint user stories<\/span><\/a><span style=\"font-weight: 400;\"> compiled by Jennifer Lin at Crossref and <\/span><a href=\"https:\/\/asapbio.org\/survey\"><span style=\"font-weight: 400;\">ASAPbio survey #1<\/span><\/a><span style=\"font-weight: 400;\"> (early 2016)), we believe that biologists want:<\/span><\/p>\n<ul>\n<li style=\"font-weight: 400;\"><span style=\"font-weight: 400;\">High visibility and discoverability of preprints<\/span>\n<ul>\n<li style=\"font-weight: 400;\"><span style=\"font-weight: 400;\">A single recognized website<\/span><\/li>\n<li style=\"font-weight: 400;\"><span style=\"font-weight: 400;\">Good search tool<\/span><\/li>\n<li style=\"font-weight: 400;\"><span style=\"font-weight: 400;\">Email notifications<\/span><\/li>\n<\/ul>\n<\/li>\n<li><span style=\"font-weight: 400;\">Web-readable xml format<\/span>\n<ul>\n<li><span style=\"font-weight: 400;\">Click on link to figures to display them<\/span><\/li>\n<li><span style=\"font-weight: 400;\">Ability to click on links to references<\/span><\/li>\n<li><span style=\"font-weight: 400;\">Export to more readable and compact pdfs<\/span><\/li>\n<\/ul>\n<\/li>\n<li style=\"font-weight: 400;\"><span style=\"font-weight: 400;\">A system for cross-referencing versions of the same work<\/span>\n<ul>\n<li style=\"font-weight: 400;\"><span style=\"font-weight: 400;\">Linking the final journal publication to preprint versions (and vice versa), so that the history of the work is transparent and preserved<\/span><\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<h3><span style=\"font-weight: 400;\"><img fetchpriority=\"high\" decoding=\"async\" class=\"alignnone size-full wp-image-798\" src=\"https:\/\/asapbio.org\/wp-content\/uploads\/2025\/03\/as-a-reader-2.png\" alt=\"as a reader\" width=\"1212\" height=\"699\" srcset=\"https:\/\/asapbio.org\/wp-content\/uploads\/2025\/03\/as-a-reader-2.png 1212w, https:\/\/asapbio.org\/wp-content\/uploads\/2025\/03\/as-a-reader-2-300x173.png 300w, https:\/\/asapbio.org\/wp-content\/uploads\/2025\/03\/as-a-reader-2-768x443.png 768w, https:\/\/asapbio.org\/wp-content\/uploads\/2025\/03\/as-a-reader-2-1024x591.png 1024w, https:\/\/asapbio.org\/wp-content\/uploads\/2025\/03\/as-a-reader-2.png 624w\" sizes=\"(max-width: 1212px) 100vw, 1212px\"> <img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-full wp-image-802\" src=\"https:\/\/asapbio.org\/wp-content\/uploads\/2025\/03\/servers-responsible-2.png\" alt=\"servers responsible\" width=\"855\" height=\"510\" srcset=\"https:\/\/asapbio.org\/wp-content\/uploads\/2025\/03\/servers-responsible-2.png 855w, https:\/\/asapbio.org\/wp-content\/uploads\/2025\/03\/servers-responsible-2-300x179.png 300w, https:\/\/asapbio.org\/wp-content\/uploads\/2025\/03\/servers-responsible-2-768x458.png 768w, https:\/\/asapbio.org\/wp-content\/uploads\/2025\/03\/servers-responsible-2.png 624w\" sizes=\"auto, (max-width: 855px) 100vw, 855px\"> <img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-full wp-image-803\" src=\"https:\/\/asapbio.org\/wp-content\/uploads\/2025\/03\/submission-process-2.png\" alt=\"submission process\" width=\"874\" height=\"517\" srcset=\"https:\/\/asapbio.org\/wp-content\/uploads\/2025\/03\/submission-process-2.png 874w, https:\/\/asapbio.org\/wp-content\/uploads\/2025\/03\/submission-process-2-300x177.png 300w, https:\/\/asapbio.org\/wp-content\/uploads\/2025\/03\/submission-process-2-768x454.png 768w, https:\/\/asapbio.org\/wp-content\/uploads\/2025\/03\/submission-process-2.png 624w\" sizes=\"auto, (max-width: 874px) 100vw, 874px\"><\/span><\/h3>\n<h3><span style=\"font-weight: 400;\">Input from servers, publishers, funders and data management experts<\/span><\/h3>\n<p><span style=\"font-weight: 400;\">In July-August 2016, ASAPbio conducted informal interviews with preprint servers, funders, scientists and developers. We originally presented a variety of Central Preprint Service models of increasing complexity and centralization, ranging from a PubMed-like metadata search tool (Model 1) to a PubMed Central-like database that hosts well-formed XML content (JATS) and makes it available through a web display tool and an API (Model 4). One version also included a central submission tool (Model 5).<\/span><\/p>\n<p><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-full wp-image-804\" src=\"https:\/\/asapbio.org\/wp-content\/uploads\/2025\/03\/5models-2.png\" alt=\"5models\" width=\"1074\" height=\"448\" srcset=\"https:\/\/asapbio.org\/wp-content\/uploads\/2025\/03\/5models-2.png 1074w, https:\/\/asapbio.org\/wp-content\/uploads\/2025\/03\/5models-2-300x125.png 300w, https:\/\/asapbio.org\/wp-content\/uploads\/2025\/03\/5models-2-768x320.png 768w, https:\/\/asapbio.org\/wp-content\/uploads\/2025\/03\/5models-2-1024x427.png 1024w, https:\/\/asapbio.org\/wp-content\/uploads\/2025\/03\/5models-2.png 624w\" sizes=\"auto, (max-width: 1074px) 100vw, 1074px\"><\/p>\n<p><span style=\"font-weight: 400;\">While responses to the creation of a central tool were generally very positive, opinions on the best implementation varied. Below is a summary of some of the critical feedback we received.<\/span><\/p>\n<ul>\n<li style=\"font-weight: 400;\"><b>Models 1 &amp; 2 provide little benefit over the current state of affairs. <\/b><span style=\"font-weight: 400;\">These models generated less interest among funding agencies.There are already multiple ways to search preprints (<\/span><a href=\"http:\/\/www.hsls.pitt.edu\/resources\/preprint\" target=\"_blank\" rel=\"noopener\"><span style=\"font-weight: 400;\">search.bioPreprint<\/span><\/a><span style=\"font-weight: 400;\">, <\/span><a href=\"http:\/\/www.prepubmed.org\/\" target=\"_blank\" rel=\"noopener\"><span style=\"font-weight: 400;\">PrePubMed<\/span><\/a><span style=\"font-weight: 400;\">, <\/span><a href=\"https:\/\/scholar.google.com\/\" target=\"_blank\" rel=\"noopener\"><span style=\"font-weight: 400;\">Google Scholar<\/span><\/a><span style=\"font-weight: 400;\">) and existing preprint servers already preserve their own content. <\/span><\/li>\n<li style=\"font-weight: 400;\"><b>Models without an open API and common licensing will stifle innovation.<\/b><span style=\"font-weight: 400;\"> Without free access to content, 3rd parties will have difficulty in implementing new services (such as peer review, data mining, or aggregation)<\/span><\/li>\n<li style=\"font-weight: 400;\"><b>Providing central submission and full-text display would be undesirable for some existing servers. <\/b><span style=\"font-weight: 400;\">These tools would directly compete with existing servers for traffic and recognition in the community. Also, display in multiple locations could disrupt download\/view metrics and commenting systems. However, some funders felt that the CS should have the ability for full display as well as drive traffic to server sites. Some funders have expressed an interest in allowing submission directly to the CS (Model 5), but most favor a practical solution that embraces the needs of the ecosystem.<\/span><\/li>\n<li style=\"font-weight: 400;\"><b>Many of the original models are complicated<\/b><span style=\"font-weight: 400;\"> and development of any system with many moving parts will take a long time. Therefore, \u201cperfection must not be the enemy of the good.\u201d There will be a need to generate a CS that will work \u201cout of the box\u201d and improve on it over time. The CS needs to take into account realistic development of technologies.<\/span><\/li>\n<li style=\"font-weight: 400;\"><b>Technological limitations make the use of JATS impractical.<\/b><span style=\"font-weight: 400;\"> No good unsupervised .doc -&gt; JATS converters currently exist. Thus, the conversion process requires human intervention. <\/span><\/li>\n<li style=\"font-weight: 400;\"><b>Document conversion is costly<\/b><span style=\"font-weight: 400;\">. Server-side conversion to a structured format (such as JATS) is expensive (on the order of ~$20+); therefore, it doesn\u2019t make sense for preprint servers to provide this, especially when preprints generate no revenue. <\/span><span style=\"font-weight: 400;\">The CS should be close to cost-neutral to servers and other publishing entities<\/span><span style=\"font-weight: 400;\">.<\/span><\/li>\n<li style=\"font-weight: 400;\"><b>Licensing has generated a diversity of opinion.<\/b><span style=\"font-weight: 400;\"> Some parties favor author or publisher choice in licensing, arguing that scientists will have concerns of the re-use of their material. Our own surveys and interactions with scientists suggest that most do not understand licensing options and their associated benefits\/disadvantages. Most funders favor a uniform licensing policy for the material in the CS in order to allow re-use in innovative ways and avoid complicated restrictions for data mining. The license most favored at the moment is CC-BY, although this may require research and engagement with the scientific community.<\/span><\/li>\n<li style=\"font-weight: 400;\"><b>Servers, Platforms, Publishers consulted were generally interested in working with the CS.<\/b><span style=\"font-weight: 400;\"> However, alignment and preference for models varied between model 2 and model 4. &nbsp;<\/span><\/li>\n<li style=\"font-weight: 400;\"><b>A major topic in which opinion varies is \u2018display\u2019.<\/b><span style=\"font-weight: 400;\"> Some funders and publishers the CS should have capability of displaying its archived content. &nbsp;Others feel that the CS should not display content to readers (other than abstracts) and that display should reside with servers and publishers.<\/span><\/li>\n<li style=\"font-weight: 400;\"><b>Use existing technologies whenever possible. <\/b><span style=\"font-weight: 400;\">Don\u2019t reinvent the wheel, and carefully evaluate existing software\/infrastructure. <\/span><\/li>\n<li style=\"font-weight: 400;\"><b>Balances immediate concerns against opportunities for future development.<\/b><span style=\"font-weight: 400;\"> Expressed by many, this sentiment emphasizes the need for a governance body that can continuously weigh these issues over time and make adjustments. In addition, inter-operability between preprints systems in biology, physics and other disciplines may need to be considered in the future.<\/span><\/li>\n<\/ul>\n<p><span style=\"font-weight: 400;\">We have drafted a provisional model of the Central Service (<\/span><a href=\"https:\/\/asapbio.org\/summary-of-a-central-preprint-service-model\"><span style=\"font-weight: 400;\">Summary<\/span><\/a><span style=\"font-weight: 400;\">) that takes into account the various input received above. The model emphasizes the development of document conversion services and the provision of web-ready full-text outputs to the input server. Providing full-text display via intake server\/publishers will deliver to scientists many of the benefits they want while providing intake servers with incentives to participate in the program. <\/span><\/p>\n<h2><span style=\"font-weight: 400;\">Possible benefits of the proposed service<\/span><\/h2>\n<p><span style=\"font-weight: 400;\">To scientists<\/span><\/p>\n<ul>\n<li style=\"font-weight: 400;\"><span style=\"font-weight: 400;\">Preservation<\/span><\/li>\n<li style=\"font-weight: 400;\"><span style=\"font-weight: 400;\">Ease of use and readability (through web display at intake server)<\/span><\/li>\n<li style=\"font-weight: 400;\"><span style=\"font-weight: 400;\">Adherence to standards of author identity and ethical guidelines for research and disclosure<\/span><\/li>\n<li style=\"font-weight: 400;\"><span style=\"font-weight: 400;\">Potential for innovative reuse (with appropriate attribution)<\/span><\/li>\n<\/ul>\n<p><span style=\"font-weight: 400;\">To intake servers\/platforms<\/span><\/p>\n<ul>\n<li style=\"font-weight: 400;\"><span style=\"font-weight: 400;\">No-cost document conversion into web-readable format<\/span><\/li>\n<li style=\"font-weight: 400;\"><span style=\"font-weight: 400;\">No-cost preservation<\/span><\/li>\n<li style=\"font-weight: 400;\"><span style=\"font-weight: 400;\">Improved exposure through a search portal that links exclusively to the intake server for display<\/span><\/li>\n<li style=\"font-weight: 400;\"><span style=\"font-weight: 400;\">\u201cAccreditation\u201d of servers or individual preprints through central screening process<\/span><\/li>\n<\/ul>\n<p><span style=\"font-weight: 400;\">To funders<\/span><\/p>\n<ul>\n<li style=\"font-weight: 400;\"><span style=\"font-weight: 400;\">Uniform standards of quality<\/span><\/li>\n<li style=\"font-weight: 400;\"><span style=\"font-weight: 400;\">Access to entire corpus via API<\/span><\/li>\n<li style=\"font-weight: 400;\"><span style=\"font-weight: 400;\">Ability to search\/filter by funding source<\/span><\/li>\n<\/ul>\n<h2><span style=\"font-weight: 400;\">Desired technical features for discussion<\/span><\/h2>\n<p><span style=\"font-weight: 400;\">We welcome comments on the list of desired features below, which could become an agenda for discussion at the Technical Workshop (August 30, 2016).<\/span><\/p>\n<p><b>Input (collected from the author)<\/b><\/p>\n<ul>\n<li style=\"font-weight: 400;\"><span style=\"font-weight: 400;\">Original manuscript file (.doc so that reference metadata can be extracted)<\/span><\/li>\n<li style=\"font-weight: 400;\"><span style=\"font-weight: 400;\">Supplementary files<\/span><\/li>\n<li style=\"font-weight: 400;\"><span style=\"font-weight: 400;\">ORCID<\/span><\/li>\n<li style=\"font-weight: 400;\"><span style=\"font-weight: 400;\">License (note- the Governance Body task force will also address this issue)<\/span><\/li>\n<li style=\"font-weight: 400;\"><span style=\"font-weight: 400;\">User authentication<\/span><\/li>\n<li style=\"font-weight: 400;\"><span style=\"font-weight: 400;\">Metadata (if extracted from .doc, get the user to check)<\/span><\/li>\n<li style=\"font-weight: 400;\"><span style=\"font-weight: 400;\">Grant support<\/span><\/li>\n<li style=\"font-weight: 400;\"><span style=\"font-weight: 400;\">Ethical statements (note- a separate task will also address this issue)<\/span>\n<ul>\n<li style=\"font-weight: 400;\"><span style=\"font-weight: 400;\">Self-ID COI<\/span><\/li>\n<li style=\"font-weight: 400;\"><span style=\"font-weight: 400;\">All authors agree on submission<\/span><\/li>\n<li style=\"font-weight: 400;\"><span style=\"font-weight: 400;\">Methods needed to reproduce this work are contained within the work<\/span><\/li>\n<li style=\"font-weight: 400;\"><span style=\"font-weight: 400;\">The work has been conducted in agreement with human &amp; animal research guidelines<\/span><\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<p><b>Document conversion<\/b><\/p>\n<ul>\n<li style=\"font-weight: 400;\"><span style=\"font-weight: 400;\">Extraction of text from source file<\/span><\/li>\n<li style=\"font-weight: 400;\"><span style=\"font-weight: 400;\">Extraction of metadata (such as title, authors, affiliations, keywords, and abstract)<\/span><\/li>\n<li style=\"font-weight: 400;\"><span style=\"font-weight: 400;\">Extraction of references<\/span><\/li>\n<li style=\"font-weight: 400;\"><span style=\"font-weight: 400;\">Insertion of figures, or recognition of existing in-line figures<\/span><\/li>\n<\/ul>\n<p><b>Screening and moderation<\/b><\/p>\n<ul>\n<li style=\"font-weight: 400;\"><span style=\"font-weight: 400;\">Automated plagiarism detection<\/span><\/li>\n<li style=\"font-weight: 400;\"><span style=\"font-weight: 400;\">Automated detection of non-scientific content (via arXiv-like algorithm)<\/span><\/li>\n<li style=\"font-weight: 400;\"><span style=\"font-weight: 400;\">Interface for human-supervised screening\/curation\/moderation<\/span><\/li>\n<\/ul>\n<p><b>Versions and identifiers<\/b><\/p>\n<ul>\n<li style=\"font-weight: 400;\"><span style=\"font-weight: 400;\">Unique, persistent ID for each version<\/span><\/li>\n<li style=\"font-weight: 400;\"><span style=\"font-weight: 400;\">All versions linked to one another (and to published journal article)<\/span><\/li>\n<li style=\"font-weight: 400;\"><span style=\"font-weight: 400;\">Linked to datasets<\/span><\/li>\n<li style=\"font-weight: 400;\"><span style=\"font-weight: 400;\">Tombstone pages for retracted content<\/span><\/li>\n<\/ul>\n<p><b>Archiving<\/b><\/p>\n<ul>\n<li style=\"font-weight: 400;\"><span style=\"font-weight: 400;\">Stable archiving of source file (.doc) and also derivatives<\/span><\/li>\n<li style=\"font-weight: 400;\"><span style=\"font-weight: 400;\">Permission to display content if intake server reaches end of life<\/span><\/li>\n<\/ul>\n<p><b>API<\/b><\/p>\n<ul>\n<li style=\"font-weight: 400;\"><span style=\"font-weight: 400;\">Bulk download of all content (.doc) and also derivatives<\/span><\/li>\n<li style=\"font-weight: 400;\"><span style=\"font-weight: 400;\">Filtering by metadata<\/span><\/li>\n<\/ul>\n<p><b>Discovery tool<\/b><\/p>\n<ul>\n<li style=\"font-weight: 400;\"><span style=\"font-weight: 400;\">Full-text indexing of all content in the central database<\/span><\/li>\n<li style=\"font-weight: 400;\"><span style=\"font-weight: 400;\">Advanced search (boolean operators, search fields such as author, keyword, funding support)<\/span><\/li>\n<li style=\"font-weight: 400;\"><span style=\"font-weight: 400;\">Alerts (RSS\/email)<\/span><\/li>\n<li style=\"font-weight: 400;\"><span style=\"font-weight: 400;\">Display of abstracts, etc, but exclusive link to intake server for full-text display<\/span><\/li>\n<\/ul>\n<h2><span style=\"font-weight: 400;\">Proposal development process<\/span><\/h2>\n<p><span style=\"font-weight: 400;\">The output of the Technical Workshop will be an announced in a Request For Information (RFI), in response to which any interested party can provide information on the development and approximate costs of developing a CS. The responses to the RFI will be shared by ASAPbio with major international funding agencies for potential consortium support. Pending their collective interest in financially supporting a plan for a CS and refining its method of operation and governance, a formal RFA may follow the RFI to which interested parties could apply for funding.<\/span><\/p>\n<p><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-full wp-image-801\" src=\"https:\/\/asapbio.org\/wp-content\/uploads\/2025\/03\/decision-process-2.jpg\" alt=\"decision process\" width=\"867\" height=\"774\" srcset=\"https:\/\/asapbio.org\/wp-content\/uploads\/2025\/03\/decision-process-2.jpg 867w, https:\/\/asapbio.org\/wp-content\/uploads\/2025\/03\/decision-process-2-300x268.jpg 300w, https:\/\/asapbio.org\/wp-content\/uploads\/2025\/03\/decision-process-2-768x686.jpg 768w, https:\/\/asapbio.org\/wp-content\/uploads\/2025\/03\/decision-process-2.jpg 624w\" sizes=\"auto, (max-width: 867px) 100vw, 867px\"><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Central Service model documents Summary: Background and a draft model Appendix 1: Rationale for a Central Service Appendix 2:&nbsp;Current feedback on Central Service&nbsp;features Current discussions with the community on proposed [&hellip;]<\/p>\n","protected":false},"author":2,"featured_media":2574,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[51],"tags":[],"class_list":["post-3690","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-central-service"],"acf":[],"_links":{"self":[{"href":"https:\/\/asapbio.org\/wp-json\/wp\/v2\/posts\/3690","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/asapbio.org\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/asapbio.org\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/asapbio.org\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/asapbio.org\/wp-json\/wp\/v2\/comments?post=3690"}],"version-history":[{"count":1,"href":"https:\/\/asapbio.org\/wp-json\/wp\/v2\/posts\/3690\/revisions"}],"predecessor-version":[{"id":3691,"href":"https:\/\/asapbio.org\/wp-json\/wp\/v2\/posts\/3690\/revisions\/3691"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/asapbio.org\/wp-json\/wp\/v2\/media\/2574"}],"wp:attachment":[{"href":"https:\/\/asapbio.org\/wp-json\/wp\/v2\/media?parent=3690"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/asapbio.org\/wp-json\/wp\/v2\/categories?post=3690"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/asapbio.org\/wp-json\/wp\/v2\/tags?post=3690"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}