{"id":16628,"date":"2016-08-01T11:09:43","date_gmt":"2016-08-01T10:09:43","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=16628"},"modified":"2016-09-17T07:53:30","modified_gmt":"2016-09-17T06:53:30","slug":"managing-open-nmr-data-a-working-example-using-mpublish","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16628","title":{"rendered":"Managing (open) NMR data: a working example using Mpublish."},"content":{"rendered":"<div class=\"kcite-section\" kcite-section-id=\"16628\">\n<p>\n\tIn March, I posted from&nbsp;the ACS meeting in San Diego on the topic of <a href=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=15916\" target=\"_top\">Research data: Managing spectroscopy-NMR<\/a>, and noted a talk by MestreLab Research on&nbsp;how a tool called <strong>Mpublish<\/strong> in the forthcoming release of their NMR analysis software <strong>Mestrenova<\/strong> could help. With that release <a href=\"http:\/\/mestrelab.com\/software\/mnova\/download\/\" target=\"_top\">now out<\/a>, the opportunity arose to test the system.\n<\/p>\n<p>\n\tI will start by reminding that NMR data associated with a published article is (or should be) openly free: one should not need a subscription to the journal to access it (although one might in order to find it). Now, NMR data as it emerges from a spectrometer is highly sophisticated, comprising a collection of (sometimes) binary proprietary files containing the measured free induction decays (FID). Turning this raw data into an interpretable NMR spectrum, the visual form of the data that so appeals to human beings, is non trivial. This requires what may be highly sophisticated software and that in turn means that it may be a commercial product. Of course there are also examples of non-commercial open software packages that are best-of-breed; indeed in its early life-cycle MestreNova was known as MESTREC before becoming a commercial product. Could one achieve the benefits of both open and fully functional NMR data with no loss from the original instrument coupled&nbsp;with the ability to apply top-quality software for its analysis in an open manner? This is a demonstration of how <strong>Mpublish<\/strong> achieves this.\n<\/p>\n<ol>\n<li>\n\t\tInvoke the URL <a href=\"http:\/\/data.datacite.org\/chemical\/x-mnpub\/10.14469\/hpc\/1087\" target=\"_top\">data.datacite.org\/chemical\/x-mnpub\/10.14469\/hpc\/1087<\/a> from a browser\n\t<\/li>\n<li>\n\t\tThis action queries the metadata deposited with DataCite for the doi <a href=\"http:\/\/doi.org\/10.14469\/hpc\/1087\" target=\"_top\">10.14469\/hpc\/1087<\/a> and retrieves the first instance of any file associated with that dataset that has the format type <strong>chemical\/x-mnpub<\/strong>. You can directly view this metadata by invoking just <a href=\"http:\/\/data.datacite.org\/10.14469\/hpc\/1087\" target=\"_blank\">data.datacite.org\/10.14469\/hpc\/1087<\/a> where you can find both mnpub and mnova formats listed. A command such as <a href=\"http:\/\/data.datacite.org\/chemical\/x-mnpub\/10.14469\/hpc\/1087\" target=\"_top\">data.datacite.org\/chemical\/x-mnpub\/10.14469\/hpc\/1087<\/a> allows the file retrieval to be incorporated into automated workflows based just on the doi and the media type desired. Note my parenthetical comment above about finding data; here you only need its doi to retrieve it!\n\t<\/li>\n<li>\n\t\tThe URL above downloads a small text file with the suffix <strong>.mnpub<\/strong> which contains in essence two components:<\/p>\n<ul>\n<li>\n\t\t\t\tA URL pointing directly to&nbsp;an&nbsp;<strong>.mnova<\/strong>&nbsp;file at the repository for which the doi has been issued\n\t\t\t<\/li>\n<li>\n\t\t\t\tA signature key derived used to verify that the public key of the publisher (the data repository in this instance) was counter-signed by Mestrelab.\n\t\t\t<\/li>\n<\/ul>\n<\/li>\n<li>\n\t\tIf you now <a href=\"http:\/\/mestrelab.com\/\" target=\"_blank\">download<\/a> the application program and install it (but for the purpose of this demonstration, ignore any requests to try to license the program. Use it unlicensed) and open the .<strong>mnpub<\/strong> file using it,&nbsp;you should get the below.The application program has checked the signature key, and if valid, proceeds to download a full data file (a<strong> .mnova <\/strong>file in this case), and to analyze and display it within the program. The data is fully active; it can be manipulated and analysed. Notice in the picture below, the red arrow points to the state of the license, in this case not present.<br \/>\n\t\t<img decoding=\"async\" alt=\"mn\" class=\"aligncenter size-full wp-image-16634\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/08\/mn.jpg\" width=\"440\" srcset=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/08\/mn.jpg 893w, https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/08\/mn-300x191.jpg 300w, https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/08\/mn-768x490.jpg 768w\" sizes=\"(max-width: 893px) 100vw, 893px\" \/>\n\t<\/li>\n<li>\n\t\tIt is also possible to apply this procedure to the raw data as it emerges from the (Bruker) spectrometer, and compressed into a .zip archive. The MestreNova software will automatically process the contents by applying various default parameters, although the result may not correspond exactly to that present in <em>e.g. <\/em>the equivalent .mnova file (which may have had specific parameters applied).\n\t<\/li>\n<\/ol>\n<p>\n\tIt is my&nbsp;hope that anyone who records NMR data and processes it using software such as&nbsp;MestreNova&nbsp;will now consider using the mechanism above to accompany their submitted articles, rather than just automatically pasting a static image of the spectrum into a&nbsp;PDF file as &quot;supporting information&quot;.&nbsp;This is part of what&nbsp;is meant by&nbsp;&quot;managed research data&quot; (RDM).\n<\/p>\n<p>\n\tOne cannot help but note that many types of scientific instrument nowadays come with bespoke software for analysing the data they produce. Very often this software is unavailable to anyone who has not purchased the instrument itself. To make the data available to others, the processed data and its visual interpretation often have to be reduced, with much consequent&nbsp;information loss, to a lowest common denominator&nbsp;format such as Acrobat\/PDF. Here we see a mechanism for avoiding any such information loss whilst enabling, for that dataset only, the full potential for (re)analysing the data. It will be interesting to see if other examples of this model or its equivalent emerge in the near future.\n<\/p>\n<div class=\"citizen-ex__pane\" style=\"\">\n\t&nbsp;\n<\/div>\n<div class=\"citizen-ex__pane\" style=\"\">\n\t&nbsp;\n<\/div>\n<div class=\"citizen-ex__pane\" style=\"\">\n\t&nbsp;\n<\/div>\n<!-- kcite active, but no citations found -->\n<\/div> <!-- kcite-section 16628 -->","protected":false},"excerpt":{"rendered":"<p>In March, I posted from&nbsp;the ACS meeting in San Diego on the topic of Research data: Managing spectroscopy-NMR, and noted a talk by MestreLab Research on&nbsp;how a tool called Mpublish in the forthcoming release of their NMR analysis software Mestrenova could help. With that release now out, the opportunity arose to test the system. I [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":true,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"activitypub_content_warning":"","activitypub_content_visibility":"","activitypub_max_image_attachments":5,"activitypub_interaction_policy_quote":"anyone","activitypub_status":"","footnotes":"","jetpack_publicize_message":"","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":true,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2},"jetpack_post_was_ever_published":false},"categories":[2],"tags":[29,1880,27,1395,1689,1883,1882,1879,1881,1705,1878,1877,327,1884,1473,1645,33,1405],"ppma_author":[2661],"class_list":["post-16628","post","type-post","status-publish","format-standard","hentry","category-chemical-it","tag-acrobat","tag-analysis-software","tag-chemical","tag-chemistry","tag-city-san-diego","tag-format-type-chemicalx-mnpub","tag-media-type","tag-mestrenova","tag-non-commercial-open-software-packages","tag-nuclear-magnetic-resonance","tag-nuclear-magnetic-resonance-spectra-database","tag-nuclear-magnetic-resonance-spectroscopy","tag-pdf","tag-public-key","tag-science","tag-scientific-method","tag-spectroscopy","tag-technologyinternet"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.6 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Managing (open) NMR data: a working example using Mpublish. - Henry Rzepa&#039;s Blog<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16628\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Managing (open) NMR data: a working example using Mpublish. - Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"og:description\" content=\"In March, I posted from&nbsp;the ACS meeting in San Diego on the topic of Research data: Managing spectroscopy-NMR, and noted a talk by MestreLab Research on&nbsp;how a tool called Mpublish in the forthcoming release of their NMR analysis software Mestrenova could help. With that release now out, the opportunity arose to test the system. 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I tell its story (or a part of it) here. But to start, try the following experiment. Find a Word document of .docx type on your hard drive Remove\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":17939,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17939","url_meta":{"origin":16628,"position":1},"title":"MOLinsight: A web portal for the processing of molecular structures by blind students.","author":"Henry Rzepa","date":"March 31, 2017","format":false,"excerpt":"Occasionally one comes across a web site that manages to combine being\u00a0unusual, interesting and also useful. Thus\u00a0www.molinsight.net\u00a0is I think a unique chemistry resource for blind and visually impaired students. If you think perhaps that it might be a little too specialised to be useful for you, go visit it first.\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":17089,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17089","url_meta":{"origin":16628,"position":2},"title":"Hydrogen bonding to chloroform.","author":"Henry Rzepa","date":"November 14, 2016","format":false,"excerpt":"Chloroform, often in the deuterated form CDCl3, is a very common solvent for NMR and other types of spectroscopy. Quantum mechanics\u00a0is increasingly used to calculate such spectra to aid assignment and the solvent is here normally simulated as a continuum rather than by explicit inclusion of one or more chloroform\u2026","rel":"","context":"In &quot;crystal_structure_mining&quot;","block_context":{"text":"crystal_structure_mining","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1745"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":17885,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17885","url_meta":{"origin":16628,"position":3},"title":"The provenance of scientific data &#8211; establishing an audit trail.","author":"Henry Rzepa","date":"March 30, 2017","format":false,"excerpt":"In an era when alternative facts and fake news afflict us, the provenance of scientific data becomes ever more important. Especially if that data is available as open access and exploitable by others for both valid scientific reasons but\u00a0potentially also by those with other\u00a0motives. Here I consider the audit trail\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":22059,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=22059","url_meta":{"origin":16628,"position":4},"title":"A cascading tutorial in finding rich NMR data using the Datacite datasearch engine.","author":"Henry Rzepa","date":"April 11, 2020","format":false,"excerpt":"In the previous post, I introduced three of a new generation of search engines specialising in the discovery of data. Data has some special features which make its properties slightly different from the conceptual (or natural language) searches we are used to performing for general information and so a search\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":21928,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=21928","url_meta":{"origin":16628,"position":5},"title":"Encouraging Submission of FAIR Data at the Journal of Organic Chemistry and Organic Letters","author":"Henry Rzepa","date":"February 14, 2020","format":false,"excerpt":"In a welcome move, one of the American chemical society journals has published an encouragement to submit what is called FAIR data to the journal.. A reminder that FAIR data is data that can be Found (F), Accessed (A), Interoperated(I) and Re-used( R). I thought I might try to explore\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":[]}],"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\/16628","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=16628"}],"version-history":[{"count":16,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/16628\/revisions"}],"predecessor-version":[{"id":16645,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/16628\/revisions\/16645"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=16628"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=16628"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=16628"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=16628"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}