{"id":19483,"date":"2018-03-07T11:38:06","date_gmt":"2018-03-07T11:38:06","guid":{"rendered":"https:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=19483"},"modified":"2018-03-07T20:16:42","modified_gmt":"2018-03-07T20:16:42","slug":"how-fair-are-the-data-associated-with-the-2017-molecules-of-the-year","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=19483","title":{"rendered":"How FAIR are the data associated with the 2017 Molecules-of-the-Year?"},"content":{"rendered":"
\n

C&EN has again run a vote for the 2017 Molecules of the year<\/a>. Here I take a look not just at these molecules, but at how FAIR (Findable, Accessible, Interoperable and Reusable) the data associated with these molecules actually is.<\/p>\n

I went about finding out as follows:<\/p>\n

    \n
  1. The article DOI for all seven candidates was linked to the C&EN site.<\/li>\n
  2. From there I manually tracked down the Supporting information<\/li>\n
  3. Some of this SI gave a CCDC deposition number for crystal structure data for the molecule in question. The easiest way of going directly to the data was to use the search.datacite.org<\/a> search engine and to enter the keywords CCDC + deposition number. This gives a DOI for the data, examples of which are included in the table below.<\/li>\n
  4. In other examples, I used the CSD Conquest search program and entered the names of 2-3 of the authors of the articles. This also worked well.<\/li>\n
  5. Most of the SI files, downloaded as PDF files also had static images of NMR spectra included. This is not active data, and hence does not fulfil the F and I of FAIR, and probably the A as well. None of it is FAIR as defined by my post here<\/a> although\u00a0it is actually really easy to make it so. One of the examples had ~116 spectra so unFAIRed.<\/li>\n
  6. In another example there was also computational data, included simply as a set of XYZ coordinates and again contained in the PDF file. This too is not really FAIR, since one has to know how to extract it from this container and repurpose it. It also represents a tiny subset of the data potentially available.<\/li>\n<\/ol>\n\n\n\n\n\n\n\n\n\n\n\n
    How FAIR are the data associated with the 2017 Molecules-of-the-Year?<\/a><\/th>\n<\/tr>\n
    #<\/th>\nTitle<\/th>\nArticle DOI<\/th>\nData DOI<\/th>\n<\/tr>\n
    1<\/td>\nPersulfurated Coronene: A New Generation of \u201cSunflower\u201d<\/td>\n10.1021\/jacs.6b12630<\/a><\/td>\nData available only as PDF
    \n Hosted by Figshare<\/a>
    \n The SI also has its own DOI:
    \n     10.1021\/jacs.6b12630.s001<\/a><\/td>\n<\/tr>\n
    2<\/td>\nA Truncated Molecular Star<\/td>\n10.1021\/jacs.6b12630<\/a><\/td>\nCrystal structure data:
    \n 10.5517\/ccdc.csd.cc1nb303<\/a><\/td>\n<\/tr>\n
    3<\/td>\nSynthesis of trinorbornane<\/td>\n10.1039\/c7cc06273g<\/a><\/td>\nCrystal structure data:
    \n 10.5517\/ccdc.csd.cc1p7806<\/a><\/td>\n<\/tr>\n
    4<\/td>\nBraiding a molecular knot with eight crossings<\/td>\n10.1126\/science.aal1619<\/a><\/td>\nCrystal structure data:
    \n 10.5517\/ccdc.csd.cc1m85y0<\/a><\/td>\n<\/tr>\n
    5<\/td>\nUnique physicochemical and catalytic properties dictated by the B3<\/sub>NO2<\/sub> ring system<\/td>\n10.1038\/nchem.2708<\/a><\/td>\nCrystal structure data:
    \n 10.5517\/ccdc.csd.cc1lkff0<\/a><\/td>\n<\/tr>\n
    6<\/td>\nTotal synthesis of mycobacterial arabinogalactan containing 92 monosaccharide units<\/td>\n10.1038\/ncomms148510<\/a><\/td>\n116 NMR spectra available only as PDF. No crystal structure<\/td>\n<\/tr>\n
    7<\/td>\nNitrogen Lewis Acids<\/td>\n10.1021\/jacs.6b12360<\/a><\/td>\nNMR spectra available only as PDF.
    \n Computed coordinates available only as PDF
    \n Crystal structures data:
    \n CCDC 1457983-1457987,1458000-1458001<\/a>
    \n e.g.<\/i>     10.5517\/ccdc.csd.cc1ky4qc<\/a>
    \n     10.5517\/ccdc.csd.cc1ky4rd<\/a><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

    The FAIRness of the data for these molecules of the year is largely rescued by the crystal structure data deposited with the CCDC in their CSD database and rendered F of FAIR by the persistent identifiers such as the (parochial) deposition numbers or the more general DOI. Now if the NMR and computational data were also covered in this way, we would be making great progress. There are of course many other types of data included with these examples, and procedures for making such data also FAIR have to be worked out by the community.<\/p>\n

    In order to construct the table above, I had to put about two hours of effort into tracking down the items (and this only because I have done this sort of search before). Perhaps next year I might persuade C&EN to include such a table in their own article!<\/p>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

    C&EN has again run a vote for the 2017 Molecules of the year. Here I take a look not just at these molecules, but at how FAIR (Findable, Accessible, Interoperable and Reusable) the data associated with these molecules actually is. I went about finding out as follows: The article DOI for all seven candidates was […]<\/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":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},"jetpack_post_was_ever_published":false},"categories":[2,1745,4],"tags":[2388,1395,2387,2390,1410,2389,327,2391,1222,2393,2392,1405],"ppma_author":[2661],"class_list":["post-19483","post","type-post","status-publish","format-standard","hentry","category-chemical-it","category-crystal_structure_mining","category-interesting-chemistry","tag-carotenoids","tag-chemistry","tag-epoxides","tag-macrocycles","tag-organic-chemistry","tag-organofluorides","tag-pdf","tag-peptides","tag-search-engine","tag-search-program","tag-search-datacite-org-search-engine","tag-technologyinternet"],"yoast_head":"\nHow FAIR are the data associated with the 2017 Molecules-of-the-Year? - 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=19483\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"How FAIR are the data associated with the 2017 Molecules-of-the-Year? - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"C&EN has again run a vote for the 2017 Molecules of the year. Here I take a look not just at these molecules, but at how FAIR (Findable, Accessible, Interoperable and Reusable) the data associated with these molecules actually is. I went about finding out as follows: The article DOI for all seven candidates was […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=19483\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2018-03-07T11:38:06+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2018-03-07T20:16:42+00:00\" \/>\n<meta name=\"author\" content=\"Henry Rzepa\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"Henry Rzepa\" \/>\n\t<meta name=\"twitter:label2\" content=\"Estimated reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"3 minutes\" \/>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"How FAIR are the data associated with the 2017 Molecules-of-the-Year? - Henry Rzepa's Blog","robots":{"index":"index","follow":"follow","max-snippet":"max-snippet:-1","max-image-preview":"max-image-preview:large","max-video-preview":"max-video-preview:-1"},"canonical":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=19483","og_locale":"en_GB","og_type":"article","og_title":"How FAIR are the data associated with the 2017 Molecules-of-the-Year? - Henry Rzepa's Blog","og_description":"C&EN has again run a vote for the 2017 Molecules of the year. Here I take a look not just at these molecules, but at how FAIR (Findable, Accessible, Interoperable and Reusable) the data associated with these molecules actually is. I went about finding out as follows: The article DOI for all seven candidates was […]","og_url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=19483","og_site_name":"Henry Rzepa's Blog","article_published_time":"2018-03-07T11:38:06+00:00","article_modified_time":"2018-03-07T20:16:42+00:00","author":"Henry Rzepa","twitter_card":"summary_large_image","twitter_misc":{"Written by":"Henry Rzepa","Estimated reading time":"3 minutes"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"Article","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=19483#article","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=19483"},"author":{"name":"Henry Rzepa","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"headline":"How FAIR are the data associated with the 2017 Molecules-of-the-Year?","datePublished":"2018-03-07T11:38:06+00:00","dateModified":"2018-03-07T20:16:42+00:00","mainEntityOfPage":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=19483"},"wordCount":593,"commentCount":0,"keywords":["Carotenoids","Chemistry","Epoxides","Macrocycles","Organic chemistry","Organofluorides","PDF","Peptides","search engine","search program","search.datacite.org search engine","Technology\/Internet"],"articleSection":["Chemical IT","crystal_structure_mining","Interesting chemistry"],"inLanguage":"en-GB","potentialAction":[{"@type":"CommentAction","name":"Comment","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=19483#respond"]}]},{"@type":"WebPage","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=19483","url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=19483","name":"How FAIR are the data associated with the 2017 Molecules-of-the-Year? - Henry Rzepa's Blog","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#website"},"datePublished":"2018-03-07T11:38:06+00:00","dateModified":"2018-03-07T20:16:42+00:00","author":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"breadcrumb":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=19483#breadcrumb"},"inLanguage":"en-GB","potentialAction":[{"@type":"ReadAction","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=19483"]}]},{"@type":"BreadcrumbList","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=19483#breadcrumb","itemListElement":[{"@type":"ListItem","position":1,"name":"Home","item":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog"},{"@type":"ListItem","position":2,"name":"How FAIR are the data associated with the 2017 Molecules-of-the-Year?"}]},{"@type":"WebSite","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#website","url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/","name":"Henry Rzepa's Blog","description":"Chemistry with a twist","potentialAction":[{"@type":"SearchAction","target":{"@type":"EntryPoint","urlTemplate":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?s={search_term_string}"},"query-input":{"@type":"PropertyValueSpecification","valueRequired":true,"valueName":"search_term_string"}}],"inLanguage":"en-GB"},{"@type":"Person","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281","name":"Henry Rzepa","image":{"@type":"ImageObject","inLanguage":"en-GB","@id":"https:\/\/secure.gravatar.com\/avatar\/897b6740f7f599bca7942cdf7d7914af5988937ae0e3869ab09aebb87f26a731?s=96&d=blank&r=g370be3a7397865e4fd161aefeb0a5a85","url":"https:\/\/secure.gravatar.com\/avatar\/897b6740f7f599bca7942cdf7d7914af5988937ae0e3869ab09aebb87f26a731?s=96&d=blank&r=g","contentUrl":"https:\/\/secure.gravatar.com\/avatar\/897b6740f7f599bca7942cdf7d7914af5988937ae0e3869ab09aebb87f26a731?s=96&d=blank&r=g","caption":"Henry Rzepa"},"description":"Henry Rzepa is Emeritus Professor of Computational Chemistry at Imperial College London.","sameAs":["https:\/\/orcid.org\/0000-0002-8635-8390"],"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?author=1"}]}},"jetpack_publicize_connections":[],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"jetpack_shortlink":"https:\/\/wp.me\/pDef7-54f","jetpack-related-posts":[{"id":22043,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=22043","url_meta":{"origin":19483,"position":0},"title":"New generations of globally aggregating search engines – for (chemical) data.","author":"Henry Rzepa","date":"April 7, 2020","format":false,"excerpt":"Chemists have long been familiar with search engines that aspire to index a large proportion of the chemical literature. Think for example the old-generation (and commercial)\u00a0SciFinder (Scholar)\u00a0and Reaxys\u00a0or those that arrived in the 1990s in the online era\u2021 such as the non-commercial Pubchem or ChemSpider (there are more). But you\u2026","rel":"","context":"In "Chemical IT"","block_context":{"text":"Chemical IT","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2020\/04\/google-1024x1004.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":13826,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13826","url_meta":{"origin":19483,"position":1},"title":"Goldilocks Data.","author":"Henry Rzepa","date":"April 8, 2015","format":false,"excerpt":"Last August, I wrote about data galore, the archival\u00a0of data for 133,885 (134 kilo) molecules into a repository, together with an associated data descriptor published in the new journal Scientific Data. Since six months is a long time in the rapidly evolving field of RDM, or research data management, I\u2026","rel":"","context":"In "Chemical IT"","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":15907,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=15907","url_meta":{"origin":19483,"position":2},"title":"Global initiatives in research data management and discovery: searching metadata.","author":"Henry Rzepa","date":"March 7, 2016","format":false,"excerpt":"The upcoming ACS national meeting in San Diego has a CINF\u00a0(chemical information division) session entitled \"Global initiatives in research data management and discovery\". I have highlighted here just one slide from my contribution to this session, which addresses the discovery aspect of the session. Data, if you think about it,\u2026","rel":"","context":"In "Chemical IT"","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":18344,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18344","url_meta":{"origin":19483,"position":3},"title":"How to search data repositories for FAIR chemical content and data: SubjectScheme","author":"Henry Rzepa","date":"June 8, 2017","format":false,"excerpt":"As data repositories start to flourish, it is reasonable to ask questions such as what sort of chemistry can be found there and how can I find it? Here I give an updated worked example of a digital repository search for chemical content and also pose an important issue for\u2026","rel":"","context":"In "Chemical IT"","block_context":{"text":"Chemical IT","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/06\/171-1024x196.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":20669,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=20669","url_meta":{"origin":19483,"position":4},"title":"A search of some major chemistry publishers for FAIR data records.","author":"Henry Rzepa","date":"April 12, 2019","format":false,"excerpt":"In recent years, findable data has become ever more important (the F in FAIR). Here I test that F using the DataCite search service. Firstly an introduction to this service. This is a metadata database about datasets and other research objects. One of the properties is\u00a0relatedIdentifier which records other identifiers\u2026","rel":"","context":"In "Chemical IT"","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":18897,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18897","url_meta":{"origin":19483,"position":5},"title":"Dispersion-induced triplet aromatisation?","author":"Henry Rzepa","date":"January 3, 2019","format":false,"excerpt":"There is emerging interest in cyclic conjugated molecules that happen to have triplet spin states and which might be expected to follow a 4n rule for aromaticity. The simplest such system would be the triplet state of cyclobutadiene, for which a non or anti-aromatic singlet state is always found to\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":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2019\/01\/CBD-1024x717.jpg?resize=350%2C200&ssl=1","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\/19483","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=19483"}],"version-history":[{"count":13,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/19483\/revisions"}],"predecessor-version":[{"id":19496,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/19483\/revisions\/19496"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=19483"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=19483"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=19483"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=19483"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}