{"id":16292,"date":"2016-04-17T12:55:45","date_gmt":"2016-04-17T11:55:45","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=16292"},"modified":"2016-06-26T08:26:35","modified_gmt":"2016-06-26T07:26:35","slug":"collaborative-fair-data-sharing","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16292","title":{"rendered":"Collaborative  FAIR data sharing."},"content":{"rendered":"<div class=\"kcite-section\" kcite-section-id=\"16292\">\n<p>\n\tI want to describe a recent attempt by a group of collaborators to share the research data associated with their just published article.<span id=\"cite_ITEM-16292-0\" name=\"citation\"><a href=\"#ITEM-16292-0\">[1]<\/a><\/span>\n<\/p>\n<p>\n\t<a href=\"http:\/\/doi.org\/10.14469\/hpc\/244\" target=\"_blank\"><img decoding=\"async\" alt=\"\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/04\/277.jpg\" width=\"450\" \/><\/a>\n<\/p>\n<p>\n\tI am here introducing things in a hierarchical form <em>(i.e.<\/em> not necessarily the serial order in which actions were taken).\n<\/p>\n<ol>\n<li>\n\t\tThe data repository selected for the data sharing is described by (<a href=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=16251\" target=\"_blank\">m3data<\/a>) doi: <a href=\"http:\/\/doi.org\/10.17616\/R3K64N\" target=\"_blank\">10.17616\/R3K64N<\/a><span id=\"cite_ITEM-16292-1\" name=\"citation\"><a href=\"#ITEM-16292-1\">[2]<\/a><\/span>\n\t<\/li>\n<li>\n\t\tA collaborative <span style=\"color: #0000ff;\">project collection<\/span> was established on this repository (doi: <a href=\"http:\/\/doi.org\/10.14469\/hpc\/244\" target=\"_blank\">10.14469\/hpc\/244<\/a><span id=\"cite_ITEM-16292-2\" name=\"citation\"><a href=\"#ITEM-16292-2\">[3]<\/a><\/span>). This data collection has some of the following attributes:\n\t<\/li>\n<li>\n\t\tIts metadata is sent here: <a href=\"https:\/\/search.datacite.org\/ui?&amp;q=10.14469\/hpc\/244\" target=\"_blank\">https:\/\/search.datacite.org\/ui?&amp;q=10.14469\/hpc\/244<\/a> where it can be queried&nbsp;for other details.\n\t<\/li>\n<li>\n\t\tThe project collaborators are all identified by their ORCID, used to obtain further individual information about the researchers.&nbsp;This information is also propagated to the metadata sent to DataCite.\n\t<\/li>\n<li>\n\t\tIn the section labelled <strong>associated DOIs<\/strong> there is a link to the&nbsp;recently published peer-reviewed article, which itself cites the data <em>via<\/em>&nbsp;doi: <a href=\"http:\/\/doi.org\/10.14469\/hpc\/244\" target=\"_blank\">10.14469\/hpc\/244<\/a> and&nbsp;which thus establishes a <span style=\"color: #0000ff;\">bidirectional link<\/span> between the article and its data.\n\t<\/li>\n<li>\n\t\tAlso in the <strong>associated DOIs section <\/strong>are other DOIs (to two figures and two tables) held in a separate location. One example: doi: <a href=\"http:\/\/10.14469\/hpc\/332doi.org\/\" target=\"_blank\">10.14469\/hpc\/332<\/a><span id=\"cite_ITEM-16292-3\" name=\"citation\"><a href=\"#ITEM-16292-3\">[4]<\/a><\/span>) which illustrates the original type of data sharing <a href=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=701\" target=\"_blank\">we started about 10<\/a> years ago. This form has been variously called a &quot;WEO&quot; or Web-enhanced object (by the ACS) or interactivity boxes (RSC, etc). In such WEOs, we wrap the data into an interactive visual appearance using Jmol or JSmol software. The data itself is directly available to the reader using the Jmol export functions (right mouse click in the visual window).<\/p>\n<p>\n\t\t\t&nbsp;\n\t\t<\/p>\n<ul>\n<li>\n\t\t\t\tIn this specific example the WEO has been assigned its DOI using the repository noted above.<span id=\"cite_ITEM-16292-1\" name=\"citation\"><a href=\"#ITEM-16292-1\">[2]<\/a><\/span>&nbsp;\n\t\t\t<\/li>\n<li>\n\t\t\t\tWe have in the past also used Figshare<span id=\"cite_ITEM-16292-4\" name=\"citation\"><a href=\"#ITEM-16292-4\">[5]<\/a><\/span>) for this purpose, see <em>e.g.<\/em> <a href=\"https:\/\/wl.figshare.com\/articles\/1181739\/embed?show_title=1\" target=\"figshare\">10.6084\/m9.figshare.1181739<\/a><sup>&Dagger;<\/sup>\n\t\t\t<\/li>\n<li>\n\t\t\t\tThe WEO itself can itself reference a more complete set of&nbsp;data used to create the visual appearance, for example<i> <\/i>data that allows&nbsp;the wavefunction of the molecule to be computed, &nbsp;doi: <a href=\"http:\/\/doi.org\/10.6084\/m9.figshare.2581987.v1\" target=\"_blank\">10.6084\/m9.figshare.2581987.v1<\/a><span id=\"cite_ITEM-16292-5\" name=\"citation\"><a href=\"#ITEM-16292-5\">[6]<\/a><\/span> In this instance this is held on the Figshare<span id=\"cite_ITEM-16292-4\" name=\"citation\"><a href=\"#ITEM-16292-4\">[5]<\/a><\/span> repository.\n\t\t\t<\/li>\n<\/ul>\n<\/li>\n<li>\n\t\tThe collection has another section labelled <strong>Members.<\/strong> These are individual datasets associated with the collection and held on the SAME repository as the collection itself. In this case, there are five such members, two of which are listed&nbsp;below:<\/p>\n<p>\n\t\t\t&nbsp;\n\t\t<\/p>\n<ol>\n<li>\n\t\t\t\t<a href=\"https:\/\/doi.org\/10.14469\/hpc\/281\">10.14469\/hpc\/281<\/a><span id=\"cite_ITEM-16292-6\" name=\"citation\"><a href=\"#ITEM-16292-6\">[7]<\/a><\/span> contains a variety of other data such as outputs from an IRC (intrinsic reaction coordinate), energy profile diagrams and ZIP archives of other calculations.\n\t\t\t<\/li>\n<li>\n\t\t\t\t<a href=\"http:\/\/doi.org\/10.14469\/hpc\/272\" target=\"_blank\">10.14469\/hpc\/272<\/a><span id=\"cite_ITEM-16292-7\" name=\"citation\"><a href=\"#ITEM-16292-7\">[8]<\/a><\/span> itself contains five members, one of which is <em>e.g.<\/em><\/p>\n<p>\n\t\t\t\t\t&nbsp;\n\t\t\t\t<\/p>\n<ul>\n<li>\n\t\t\t\t\t\t<a href=\"http:\/\/doi.org\/10.14469\/hpc\/267\" target=\"_blank\">10.14469\/hpc\/267<\/a><span id=\"cite_ITEM-16292-8\" name=\"citation\"><a href=\"#ITEM-16292-8\">[9]<\/a><\/span> which contains a ZIP archive with NMR data (<a href=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=15916\" target=\"_blank\">see here<\/a> for how this might be packaged in the future) and a file for a GPC (chromatography) instrument.\n\t\t\t\t\t<\/li>\n<li>\n\t\t\t\t\t\tThis last item also contains a new section labelled <strong>Metadata<\/strong>, which includes <em>e.g.&nbsp;<\/em>the InChI key and InChI string for the molecule whose properties are reported.\n\t\t\t\t\t<\/li>\n<\/ul>\n<\/li>\n<\/ol>\n<\/li>\n<\/ol>\n<p>\n\tIf this mode of presenting data seems a little more complex than a single monolithic PDF file, its because its designed for:\n<\/p>\n<ol>\n<li>\n\t\tcollaboration between scientists, potentially at different locations and institutions.\n\t<\/li>\n<li>\n\t\tattribution of provenance\/credit for the individual items (via ORCID).\n\t<\/li>\n<li>\n\t\tseparate date stamping by the various contributors.\n\t<\/li>\n<li>\n\t\tproviding bi-directional links between data and publications.\n\t<\/li>\n<li>\n\t\tholding what we call <strong>FAIR<\/strong> (findable, accessible, interoperable and reusable) data, rather than just data encapsulated in a PDF file.\n\t<\/li>\n<li>\n\t\tCollecting, storing and sending metadata for aggregation in a formal way, <em>i.e.<\/em> to DataCite using a formal schema to render the metadata properly searchable.\n\t<\/li>\n<\/ol>\n<p>\n\tThus <a href=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=15552#comment-184713:\/\/doi.org\/10.14469\/hpc\/244\" target=\"_blank\">10.14469\/hpc\/244<\/a> represents our most complex attempt yet&nbsp;at such collaborative FAIR data sharing with multiple contributors. The tools for packaging many of the datasets are still quite limited (see again <a href=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=15916\" target=\"_blank\">here<\/a>) and the design is still being optimised (call it &alpha;). When the repository<span id=\"cite_ITEM-16292-1\" name=\"citation\"><a href=\"#ITEM-16292-1\">[2]<\/a><\/span> has been more extensively tested, we intend to make it available as open source for others to experiment with. And of course, when this happens the source code&nbsp;too will have its own DOI!\n<\/p>\n<hr \/>\n<p>\n\t<sup>&Dagger;<\/sup>A refactoring of the Figshare site in December 2015 meant that the DOI no longer points directly to the WEO, and you have to follow a manually inserted link on that page to see it.<\/p>\n<h2>References<\/h2>\n    <ol class=\"kcite-bibliography csl-bib-body\"><li id=\"ITEM-16292-0\">C. Romain, Y. Zhu, P. Dingwall, S. Paul, H.S. Rzepa, A. Buchard, and C.K. Williams, \"Chemoselective Polymerizations from Mixtures of Epoxide, Lactone, Anhydride, and Carbon Dioxide\", <i>Journal of the American Chemical Society<\/i>, vol. 138, pp. 4120-4131, 2016. <a href=\"https:\/\/doi.org\/10.1021\/jacs.5b13070\">https:\/\/doi.org\/10.1021\/jacs.5b13070<\/a>\n\n<\/li>\n<li id=\"ITEM-16292-1\">Re3data.Org., \"Imperial College Research Computing Service Data Repository\", 2016. <a href=\"https:\/\/doi.org\/10.17616\/r3k64n\">https:\/\/doi.org\/10.17616\/r3k64n<\/a>\n\n<\/li>\n<li id=\"ITEM-16292-2\">C. ROMAIN, \"Chemo-Selective Polymerizations Using Mixtures of Epoxide, Lactone, Anhydride and CO2\", 2016. <a href=\"https:\/\/doi.org\/10.14469\/hpc\/244\">https:\/\/doi.org\/10.14469\/hpc\/244<\/a>\n\n<\/li>\n<li id=\"ITEM-16292-3\">H. Rzepa, \"Table S8: Comparison of two different basis sets for selected intermediates for CHO\/PA ROCOP.\", 2016. <a href=\"https:\/\/doi.org\/10.14469\/hpc\/332\">https:\/\/doi.org\/10.14469\/hpc\/332<\/a>\n\n<\/li>\n<li id=\"ITEM-16292-4\">Re3data.Org., \"figshare\", 2012. <a href=\"https:\/\/doi.org\/10.17616\/r3pk5r\">https:\/\/doi.org\/10.17616\/r3pk5r<\/a>\n\n<\/li>\n<li id=\"ITEM-16292-5\">P. Dingwall, \"Gaussian Job Archive for C6H10O\", 2016. <a href=\"https:\/\/doi.org\/10.6084\/m9.figshare.2581987.v1\">https:\/\/doi.org\/10.6084\/m9.figshare.2581987.v1<\/a>\n\n<\/li>\n<li id=\"ITEM-16292-6\">C. ROMAIN, \"Figure 9, Figure S18, Figure S19: ROCOP of PA\/CHO + IRC\", 2016. <a href=\"https:\/\/doi.org\/10.14469\/hpc\/281\">https:\/\/doi.org\/10.14469\/hpc\/281<\/a>\n\n<\/li>\n<li id=\"ITEM-16292-7\">C. ROMAIN, \"Table 1 : Polymerizations Using Lactone, Epoxide, and CO2\", 2016. <a href=\"https:\/\/doi.org\/10.14469\/hpc\/272\">https:\/\/doi.org\/10.14469\/hpc\/272<\/a>\n\n<\/li>\n<li id=\"ITEM-16292-8\">C. ROMAIN, \"Table 1, entry 1 : Polymerizations Using Lactone, Epoxide, and CO2\", 2016. <a href=\"https:\/\/doi.org\/10.14469\/hpc\/267\">https:\/\/doi.org\/10.14469\/hpc\/267<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> <!-- kcite-section 16292 -->","protected":false},"excerpt":{"rendered":"<p>I want to describe a recent attempt by a group of collaborators to share the research data associated with their just published article. I am here introducing things in a hierarchical form (i.e. not necessarily the serial order in which actions were taken). 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I am here introducing things in a hierarchical form (i.e. not necessarily the serial order in which actions were taken). 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The challenge lies in clarifying where the boundary between data and its metadata\u2026","rel":"","context":"In &quot;Chemical IT&quot;","block_context":{"text":"Chemical IT","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":26941,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=26941","url_meta":{"origin":16292,"position":1},"title":"Internet Archeology:  reviving a 2001 article published in the Internet Journal of Chemistry.","author":"Henry Rzepa","date":"March 21, 2024","format":false,"excerpt":"In the mid to late 1990s as the Web developed, it was becoming more obvious that one area it would revolutionise was of scholarly journal publishing. Since the days of the very first scientific journals in the 1650s, the medium had been firmly rooted in paper. Even printed colour only\u2026","rel":"","context":"Similar post","block_context":{"text":"Similar post","link":""},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2024\/03\/Screenshot-297-1024x698.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":19180,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=19180","url_meta":{"origin":16292,"position":2},"title":"FAIR data \u21cc Raw data.","author":"Henry Rzepa","date":"December 7, 2017","format":false,"excerpt":"FAIR data is increasingly accepted as a description of what research data should aspire to; Findable, Accessible, Inter-operable and Re-usable, with Context added by rich metadata (and also that it should be Open). But there are two sides to data, one of which is the raw data emerging from say\u2026","rel":"","context":"In &quot;Chemical IT&quot;","block_context":{"text":"Chemical IT","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":15313,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=15313","url_meta":{"origin":16292,"position":3},"title":"Some examples of open access publications citing managed research data (RDM).","author":"Henry Rzepa","date":"January 5, 2016","format":false,"excerpt":"In May 2015, the EPSRC funding council in the UK required researchers to publish the outcomes of the funded work to include an OA (open access) version of the narrative and to cite the managed research data used to support the research with\u00a0a DOI (digital object identifier). I was discussing\u2026","rel":"","context":"In &quot;Chemical IT&quot;","block_context":{"text":"Chemical IT","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":27090,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=27090","url_meta":{"origin":16292,"position":4},"title":"Data Discoverability as a feature of Journal Articles.","author":"Henry Rzepa","date":"June 11, 2024","format":false,"excerpt":"I can remember a time when journal articles carried selected data within their body as e.g. Tables, Figures or Experimental procedures, with the rest consigned to a box of paper deposited (for UK journals) at the British library. Then came ESI or electronic supporting information. Most recently, many journals are\u2026","rel":"","context":"In &quot;Interesting chemistry&quot;","block_context":{"text":"Interesting chemistry","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=4"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":16902,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16902","url_meta":{"origin":16292,"position":5},"title":"\u03c3 or \u03c0 nucleophilic reactivity of imines? A mechanistic twist emerges.","author":"Henry Rzepa","date":"September 28, 2016","format":false,"excerpt":"The story so far. Imines react with a peracid to form either a nitrone (\u03c3-nucleophile) or an oxaziridine (\u03c0-nucleophile). The balance between the two is on an experimental\u00a0knife-edge, being strongly influenced by substituents on the imine. Modelling these reactions using the \"normal\" mechanism for peracid oxidation did not reproduce this\u2026","rel":"","context":"In &quot;reaction mechanism&quot;","block_context":{"text":"reaction mechanism","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1086"},"img":{"alt_text":"6ts-irc1","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/09\/6TS-IRC1.gif?resize=350%2C200","width":350,"height":200},"classes":[]}],"jetpack_likes_enabled":false,"authors":[{"term_id":2661,"user_id":1,"is_guest":0,"slug":"admin","display_name":"Henry Rzepa","avatar_url":"https:\/\/secure.gravatar.com\/avatar\/897b6740f7f599bca7942cdf7d7914af5988937ae0e3869ab09aebb87f26a731?s=96&d=blank&r=g","0":null,"1":"","2":"","3":"","4":"","5":"","6":"","7":"","8":""}],"_links":{"self":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/16292","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=16292"}],"version-history":[{"count":15,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/16292\/revisions"}],"predecessor-version":[{"id":16593,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/16292\/revisions\/16593"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=16292"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=16292"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=16292"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=16292"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}