{"id":15916,"date":"2016-03-16T20:41:06","date_gmt":"2016-03-16T20:41:06","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=15916"},"modified":"2016-04-05T08:43:24","modified_gmt":"2016-04-05T07:43:24","slug":"research-data-managing-spectroscopy-nmr","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=15916","title":{"rendered":"Research data: Managing spectroscopy-NMR."},"content":{"rendered":"
\n

At the ACS conference, I have attended many talks these last four days, but one made some “connections” which intrigued me. I tell its story (or a part of it) here.<\/p>\n

But to start, try the following experiment.<\/p>\n

    \n
  1. Find a Word document of .docx type on your hard drive<\/li>\n
  2. Remove the .docx suffix and replace it with a .zip suffix.<\/li>\n
  3. Expand as if it is an archive (it is!).<\/li>\n
  4. A folder is created and this itself contains four further folders. These all contain XML files, and in the sub-folder actually called word you will find something called document.xml<\/strong> That file contains the visible content of the document; all the others are support documents, including styles etc.<\/li>\n<\/ol>\n

    The reason this is important was made clear in Santi Dominguez’ talk. Most of it was concerned with introducing Mbook, an ELN (electronic laboratory notebook) but the relevance to the above comes from his introduction of Mpublish<\/strong>, a forthcoming product targeting the area of research data management. What is the connection? Well, NMR spectrometers produce raw outputs as collections of files, much in the manner of the exploded word document above. Some files contain the raw FID, others contain the acquisition parameters, etc. These files are then turned into the traditional spectra by suitable processing software such as Mestrenova (part of the same ecosystem as Mpublish). Most users of such programs then squirt the spectra into a PDF file and it is this last document that is preserved as “research data” – almost invariably this is the version sent off to journals as the supporting information or SI for the article. SI is called information for a good reason; in such a container it is very often not easily usable data, and functions just visually.<\/p>\n

    So what is<\/strong> the problem? Well, the conversion of the NMR fileset (and quite possibly many other forms of spectroscopy) into a PDF file is a lossy process. It cannot be reversed; information has been lost. And only really a human who can easily retrieve and interpret such a visual presentation.<\/p>\n

    Santi described how Mpublish can assemble all the files associated with the instrumental outputs, optionally add chemical structure and other information, collect suitable metadata describing the contents and create a .zip archive. As we saw with Word however, the suffix does not even need to be .zip. It was suggested that it be this information-complete archive that should really be used as SI to accompany an article in which NMR data is invoked to support the narrative. In the reverse process, anyone downloading this zip archive could themselves potentially acquire full access, without information loss, to the original NMR data. There is a little further magic that needs to be included to make the process work which I do not include here. When Mpublish becomes available to play with, I will complete that story here.<\/p>\n

    It is good to report that software is starting to appear which enhances the management and reporting of research data as part of the publication process. The “rules” and “best practice” of this game are still being written however. In this regard, I feel that it is the researchers themselves that must play a vital role in defining the rules. Let us not cede that role just to publishers.<\/p>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

    At the ACS conference, I have attended many talks these last four days, but one made some “connections” which intrigued me. 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 the .docx suffix and replace […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_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}},"categories":[2],"tags":[1704,1709,1707,1705,327,1699,33,1708,124,1706],"ppma_author":[2661],"class_list":["post-15916","post","type-post","status-publish","format-standard","hentry","category-chemical-it","tag-archive-formats","tag-chemical-structure","tag-eln","tag-nuclear-magnetic-resonance","tag-pdf","tag-research-data-management","tag-spectroscopy","tag-suitable-processing-software","tag-xml","tag-zip"],"yoast_head":"\nResearch data: Managing spectroscopy-NMR. - Henry Rzepa'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=15916\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Research data: Managing spectroscopy-NMR. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"At the ACS conference, I have attended many talks these last four days, but one made some “connections” which intrigued me. 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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 "Interesting chemistry"","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\/15916","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=15916"}],"version-history":[{"count":7,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/15916\/revisions"}],"predecessor-version":[{"id":15923,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/15916\/revisions\/15923"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=15916"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=15916"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=15916"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=15916"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}