{"id":83,"date":"2009-04-03T13:18:13","date_gmt":"2009-04-03T12:18:13","guid":{"rendered":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=83"},"modified":"2013-07-19T17:21:20","modified_gmt":"2013-07-19T16:21:20","slug":"on-the-importance-of-digital-repositories-in-chemistry","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=83","title":{"rendered":"On the importance of  Digital repositories in Chemistry"},"content":{"rendered":"<div class=\"kcite-section\" kcite-section-id=\"83\">\n<p>The preceeding blog entries contain stories about chemical behaviour. If you have clicked on the diagrams, you may even have gotten a Jmol view of the relevant molecules popping up. But if you are truly curious, you may even have the urge to acquire the relevant 3D information about the molecule, and play with it yourself. Even after 15 years of the \u00a0(chemical) Web, this can be distressingly difficult to achieve (or can it be that it is only myself who wishes to view molecules in their \u00a0<i>native<\/i> mode?). \u00a0Thus the standard mechanism is to seek out on journal pages that disarming little entry entitled \u00a0<b>supporting information<\/b> and to hope that you might find something useful embedded there. \u00a0Embedded is the correct description, since the information is often found within the confines of an Acrobat file, and has to be extracted from there. \u00a0Indeed, that is what \u00a0I had to resort to in order to write one of the blog entries below. I ground my teeth whilst doing so.\u00a0<br \/> <img loading=\"lazy\" decoding=\"async\" class=\"aligncenter size-full wp-image-93\" title=\"blog11\" onclick=\"jmolInitialize('..\/Jmol\/');jmolSetAppletColor('yellow');jmolApplet([450,450],'load wp-content\/uploads\/2009\/04\/42-557.xyz; frame 1; zoom 100;vectors  on;vectors 4;vectors scale 5.0; color vectors orange;vibration 6;connect (atomno=2) (atomno=1) partial;connect (atomno=6) (atomno=1) aromatic;connect (atomno=3) (atomno=2) aromatic;connect (atomno=5) (atomno=4) aromatic;connect (atomno=3) (atomno=4) aromatic;connect (atomno=6) (atomno=5) partial;');\" alt=\"blog11\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2009\/04\/blog11.jpg\" width=\"304\" height=\"287\" \/><br \/> So is there a better way? We think so! The \u00a0<strong>digital repository<\/strong>. If you click on <a href=\"http:\/\/hdl.handle.net\/10042\/to-2117\" target=\"new\">this<\/a> you should see the entry directly. What can you do there? Well, if you have suitable programs, you can download eg a <em>Checkpoint<\/em> file of the calculation that created the molecule model and re-activate it there. Or you can download just the <strong>CML<\/strong> file for viewing in any CML-compliant program (such as e.g. Jmol). Or you can check up on the <b>InCHi<\/b> string or the <b>InChI Key<\/b> of the molecule.<\/p>\n<p>What about the specific entry above? Well, it corresponds to the calculation for the \u03c04 + \u03c02 cycloaddition described in the blog entry below. You can now verify for yourself the assertions made in that entry, ie that the rotation mode is disrotatory, or that the bond is forming antarafacially. You do not need to take my word for it! If the Digital repository is too much trouble for you, click on the graphic instead to get a similar result.<\/p>\n<p>We now regularly put such links into journal articles, in the form of <em>Web-enhanced<\/em> tables and figures, so that it is literally just one click away from such an article to having a vibrant molecule dancing in front of you. All (chemistry) journals should do this. If they do not yet, then contact their editor in chief when you next submit an article and ask them why not!<\/p>\n<p>See also the blog by <a href=\"http:\/\/wwmm.ch.cam.ac.uk\/blogs\/murrayrust\/\" rel=\"friend colleague\">Peter Murray-Rust.<\/a><\/p>\n<!-- kcite active, but no citations found -->\n<\/div> <!-- kcite-section 83 -->","protected":false},"excerpt":{"rendered":"<p>The preceeding blog entries contain stories about chemical behaviour. If you have clicked on the diagrams, you may even have gotten a Jmol view of the relevant molecules popping up. But if you are truly curious, you may even have the urge to acquire the relevant 3D information about the molecule, and play with it [&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":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":false,"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":[29,904,27,26,2647,30,1108,31,28],"ppma_author":[2661],"class_list":["post-83","post","type-post","status-publish","format-standard","hentry","category-chemical-it","tag-acrobat","tag-checkpoint","tag-chemical","tag-chemical-behaviour","tag-chemical-it","tag-editor-in-chief","tag-opendata","tag-peter-murray-rust","tag-web-enhanced-tables"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.6 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>On the importance of Digital repositories in Chemistry - 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=83\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"On the importance of Digital repositories in Chemistry - Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"og:description\" content=\"The preceeding blog entries contain stories about chemical behaviour. If you have clicked on the diagrams, you may even have gotten a Jmol view of the relevant molecules popping up. But if you are truly curious, you may even have the urge to acquire the relevant 3D information about the molecule, and play with it [&hellip;]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=83\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"article:published_time\" content=\"2009-04-03T12:18:13+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2013-07-19T16:21:20+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2009\/04\/blog11.jpg\" \/>\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=\"2 minutes\" \/>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"On the importance of Digital repositories in Chemistry - Henry Rzepa&#039;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=83","og_locale":"en_GB","og_type":"article","og_title":"On the importance of Digital repositories in Chemistry - Henry Rzepa&#039;s Blog","og_description":"The preceeding blog entries contain stories about chemical behaviour. 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Pnictogen chains and 16 coordinate Cs.","author":"Henry Rzepa","date":"December 19, 2016","format":false,"excerpt":"I am completing my survey of the vote for molecule of the year candidates, which this year seems focused on chemical records of one type or another. The first article reports striving towards creating a molecule covering a complete column of the period table. In this case, group 7, containing\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":17376,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17376","url_meta":{"origin":83,"position":2},"title":"Revisiting (and maintaining) a twenty year old web page. Mauveine: The First Industrial Organic Fine-Chemical.","author":"Henry Rzepa","date":"February 2, 2017","format":false,"excerpt":"Almost exactly 20 years ago, I started what can be regarded as the precursor to this blog. As part of a celebration of this anniversary, I revisited the page to see whether any of it had withstood the test of time. Here I recount what I discovered. The site itself\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":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/02\/038-1024x419.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":3723,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=3723","url_meta":{"origin":83,"position":3},"title":"Chemicalizing a blog.","author":"Henry Rzepa","date":"March 30, 2011","format":false,"excerpt":"I am at the ACS meeting, attending a session on chemistry and the Internet. This post was inspired by Chemicalize, a service offered by ChemAxon, which scans a post like this one, and identifies molecules named. I had previously used generic post taggers, which frankly did not work well in\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":4525,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=4525","url_meta":{"origin":83,"position":4},"title":"Scalemic molecules: a cheminformatics challenge!","author":"Henry Rzepa","date":"July 6, 2011","format":false,"excerpt":"A scalemic molecule is the term used by Eliel to describe any non-racemic chiral compound. Synthetic chemists imply it when they describe a synthetic product with an observable enantiomeric excess or ee (which can range from close to 0% to almost 100%). There are two cheminformatics questions of interest to\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":1930,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=1930","url_meta":{"origin":83,"position":5},"title":"WebCite and Jmol","author":"Henry Rzepa","date":"April 18, 2010","format":false,"excerpt":"Since I have gotten into the habit of quoting some of my posts in other contexts, I have started to also archive them using WebCite. One can quote the resulting archive as: Rzepa, Henry. Quintuple bonds. \u00a02010-04-18. URL:http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=1722. Accessed: 2010-04-18.\u00a0(Archived by WebCite\u00ae at http:\/\/www.webcitation.org\/5p5BtuzSH) There is one issue though. \u00a0Many\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":[]}],"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\/83","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=83"}],"version-history":[{"count":1,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/83\/revisions"}],"predecessor-version":[{"id":10935,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/83\/revisions\/10935"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=83"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=83"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=83"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=83"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}