{"id":3395,"date":"2020-11-02T00:00:00","date_gmt":"2020-11-02T00:00:00","guid":{"rendered":"http:\/\/pl-asapbio.local\/bims-biomed-news\/"},"modified":"2025-03-28T21:36:53","modified_gmt":"2025-03-28T21:36:53","slug":"bims-biomed-news","status":"publish","type":"post","link":"https:\/\/asapbio.org\/bims-biomed-news\/","title":{"rendered":"bims: Biomed News"},"content":{"rendered":"<h2 class=\"wp-block-heading\" id=\"block-06b98a3d-2f6e-4e6e-996d-149ea838eeb8\">Organizer<\/h2>\n<p id=\"block-8b3931da-0012-46c3-9c61-56f527dc73b2\">Directed by Gavin McStay (<a href=\"https:\/\/staffs.ac.uk\/\" target=\"_blank\" rel=\"noopener\">Staffordshire&nbsp;University<\/a>), founded by&nbsp;<a href=\"http:\/\/openlib.org\/home\/krichel\/\" target=\"_blank\" rel=\"noopener\">Thomas&nbsp;Krichel<\/a>&nbsp;(<a href=\"http:\/\/society.openlib.org\/\" target=\"_blank\" rel=\"noopener\">Open&nbsp;Library&nbsp;Society<\/a>)<\/p>\n<h4 class=\"wp-block-heading\" id=\"block-b4382d69-a007-406a-aed7-bdf3dc50cb41\">Website or social media links<\/h4>\n<p><a href=\"http:\/\/biomed.news\" target=\"_blank\" rel=\"noopener\">http:\/\/biomed.news<\/a><\/p>\n<h4 class=\"wp-block-heading\" id=\"block-f3438834-f58d-464b-a425-59d903d78b51\">Current stage of development<\/h4>\n<p id=\"block-fb08e20b-74b7-4852-84d8-4ffddae8ba27\">Ongoing<\/p>\n<h4 class=\"wp-block-heading\" id=\"block-7d3a70dc-2249-408a-a261-f7efefe57d68\">Project duration<\/h4>\n<p id=\"block-e0da5d42-18cb-471b-9f32-2850cda07ae8\">Indefinite<\/p>\n<h2 class=\"wp-block-heading\" id=\"block-644359d4-9680-44fc-9101-3b905df5e3c0\">Project aims<\/h2>\n<p>Bims is a rapid dissemination system for new papers in PubMed. Bims is powered by human selectors acting as machine teachers.How does this benefit preprints?<\/p>\n<ul class=\"wp-block-list\">\n<li>We expect that PubMed will increase its coverage of preprints. A rapid circulation system like bims will amplify the timeliness advantage of preprints.<\/li>\n<li>It is harder for preprints to reach readers as they are not classified by subject in the same way as journal articles are. Bims helps to bridge the gap.<\/li>\n<\/ul>\n<h3 class=\"wp-block-heading\" id=\"block-85685a4c-551d-475b-99a1-89a6556626fc\">Background information&nbsp;on current practices<\/h3>\n<p>1993  Thomas Krichel published the world\u2019s first online electronic economics working paper.<\/p>\n<p>1997  His continued efforts lead to the&nbsp;<a href=\"http:\/\/repec.org\/\" target=\"_blank\" rel=\"noopener\">RePEc<\/a>&nbsp;project. It enabled the survival of economics working papers.<\/p>\n<p>1998  He founded the&nbsp;<a href=\"http:\/\/nep.repec.org\/\" target=\"_blank\" rel=\"noopener\">NEP:&nbsp;New&nbsp;Economics&nbsp;Papers<\/a>&nbsp;project. It circulates the latest adivitions to RePEc\u2019s working paper stock into weekly subject-specific reports curated by selectors.<\/p>\n<p>2004  He created ernad, a special software for maintaining NEP reports.<\/p>\n<p>2013  He started to refactor ernad so it could apply to various document collections.<\/p>\n<p>2017  He persuaded Gavin McStay to direct a project to apply ernad to PubMed. Now we have \u201c<a href=\"http:\/\/biomed.news\/\" target=\"_blank\" rel=\"noopener\">bims:&nbsp;Biomed&nbsp;News<\/a>\u201d.<\/p>\n<p>2020  PubMed started to index some preprints. Bims became a rapid circulation tool for them.<\/p>\n<figure class=\"wp-block-image size-large\"><img fetchpriority=\"high\" decoding=\"async\" width=\"1024\" height=\"762\" src=\"https:\/\/asapbio.org\/wp-content\/uploads\/2025\/03\/Screen-Shot-2020-11-02-at-1.03.33-PM-2-1024x762.png\" alt=\"\" class=\"wp-image-5171\" srcset=\"https:\/\/asapbio.org\/wp-content\/uploads\/2025\/03\/Screen-Shot-2020-11-02-at-1.03.33-PM-2-1024x762.png 1024w, https:\/\/asapbio.org\/wp-content\/uploads\/2025\/03\/Screen-Shot-2020-11-02-at-1.03.33-PM-2-300x223.png 300w, https:\/\/asapbio.org\/wp-content\/uploads\/2025\/03\/Screen-Shot-2020-11-02-at-1.03.33-PM-2-768x572.png 768w, https:\/\/asapbio.org\/wp-content\/uploads\/2025\/03\/Screen-Shot-2020-11-02-at-1.03.33-PM-2.png 1378w\" sizes=\"(max-width: 1024px) 100vw, 1024px\"><\/figure>\n<p>This graph shows the evolution of the number of&nbsp;<a href=\"http:\/\/biomed.news\/reports\" target=\"_blank\" rel=\"noopener\">issues&nbsp;in&nbsp;actively&nbsp;maintained&nbsp;reports<\/a>&nbsp;over time.&nbsp;The downward shifts occur when we close a report.<\/p>\n<h3 class=\"wp-block-heading\" id=\"block-78c31020-7243-4e17-a2e2-75675e9a4e79\">Overview of the challenge to overcome<\/h3>\n<p id=\"block-0787d489-08fe-4642-bd1b-46b97c75c8b7\">As evident from the graph, keeping users is easy. Marketing bims to new users is hard.<\/p>\n<ol class=\"wp-block-list\">\n<li>Nothing even remotely like it existed before.<\/li>\n<li>It flies in the face of conventional wisdom.<\/li>\n<li>We can\u2019t instantaneously demonstrate how it would work for a new user.<\/li>\n<li>We lack prestigious backers.<\/li>\n<\/ol>\n<h3 class=\"wp-block-heading\" id=\"block-93b7594e-3075-4968-ae1e-b1535bcdf8ff\">The ideal outcome or output of the project<\/h3>\n<ul class=\"wp-block-list\">\n<li>In about 20 years many biomedical researchers will maintain a bims report. It will be part and parcel of being research active.<\/li>\n<li>Bims is a pioneering example of an expertise sharing system. The aggregate of all reports can give a hint about the quality of papers. It would be something like a crowd-sourced evaluation.<\/li>\n<\/ul>\n<h3 class=\"wp-block-heading\" id=\"block-d7bbb775-e8ba-41af-9383-61d879d1f1bb\">Description of the intervention<\/h3>\n<p>We continue to recruit new users. Unless we get sponsorship for a server, we can\u2019t move to new ventures.<\/p>\n<h3 class=\"wp-block-heading\" id=\"block-6f8b7046-907b-40d6-b2b6-22d6debbd992\">Plan for monitoring project outcome<\/h3>\n<p>Project outcomes are publicly available. We monitor reports manually at this time. As bims grows, Machine-aided monitoring will be an interesting challenge.<\/p>\n<h3 class=\"wp-block-heading\" id=\"block-bb6f3c9d-a249-4702-a9b7-ed8405babba5\">What\u2019s needed for success<\/h3>\n<h4 class=\"wp-block-heading\" id=\"block-fddaa243-3c1f-44ad-8414-c0c061c9f58d\">Additional technology development<\/h4>\n<ul class=\"wp-block-list\">\n<li>build report home pages and rankings;<\/li>\n<li>improve presentation of PubMed records;<\/li>\n<li>bring machine learning to first issues;<\/li>\n<li>improve the machine learning;<\/li>\n<li>disseminate report issues by email lists;<\/li>\n<li>build a system inviting authors of papers selected for a report to join a mailing list for that report;<\/li>\n<li>start duplicate detection.<\/li>\n<\/ul>\n<h4 class=\"wp-block-heading\" id=\"block-fc161ad9-27ae-452b-ae95-497cd83e8b98\">Feedback, beta testing, collaboration, endorsement<\/h4>\n<ul class=\"wp-block-list\">\n<li>We disseminate our data in bulk. We we want it to be reused. The&nbsp;<a href=\"https:\/\/www.mito2i.ca\/mitochondrial-abstract-resource\" target=\"_blank\" rel=\"noopener\">mitochondrial&nbsp;abstract&nbsp;resource<\/a>&nbsp;is a start.<\/li>\n<li>We could use a preprints dataset. But needs to interoperate with PubMed. We need to highlight to bimsers any published paper that appeared as a preprint before in the report.<\/li>\n<\/ul>\n<h4 class=\"wp-block-heading\" id=\"block-7dd06873-0e67-45a4-9d1c-176c5b3f8871\">Funding<\/h4>\n<p>We urgently need funding for a server. Funding for software development would accelerate our progress.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Organizer Directed by Gavin McStay (Staffordshire&nbsp;University), founded by&nbsp;Thomas&nbsp;Krichel&nbsp;(Open&nbsp;Library&nbsp;Society) Website or social media links http:\/\/biomed.news Current stage of development Ongoing Project duration Indefinite Project aims Bims is a rapid dissemination system [&hellip;]<\/p>\n","protected":false},"author":2,"featured_media":2082,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[48],"tags":[],"class_list":["post-3395","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-preprint-sprint-proposals"],"acf":[],"_links":{"self":[{"href":"https:\/\/asapbio.org\/wp-json\/wp\/v2\/posts\/3395","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=3395"}],"version-history":[{"count":1,"href":"https:\/\/asapbio.org\/wp-json\/wp\/v2\/posts\/3395\/revisions"}],"predecessor-version":[{"id":3396,"href":"https:\/\/asapbio.org\/wp-json\/wp\/v2\/posts\/3395\/revisions\/3396"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/asapbio.org\/wp-json\/wp\/v2\/media\/2082"}],"wp:attachment":[{"href":"https:\/\/asapbio.org\/wp-json\/wp\/v2\/media?parent=3395"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/asapbio.org\/wp-json\/wp\/v2\/categories?post=3395"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/asapbio.org\/wp-json\/wp\/v2\/tags?post=3395"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}