{"id":2962,"date":"2010-12-07T14:12:11","date_gmt":"2010-12-07T13:12:11","guid":{"rendered":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2962"},"modified":"2013-07-19T17:18:49","modified_gmt":"2013-07-19T16:18:49","slug":"data-round-tripping-wherein-the-future","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2962","title":{"rendered":"Data-round-tripping: wherein the future?"},"content":{"rendered":"
\n

Moving (chemical) data around in a manner which allows its (automated) use in whichever context it finds itself must be a holy grail for all scientists and chemists. I posted earlier<\/a> on the fragile nature of molecular diagrams making the journey between the editing program used to create them (say ChemDraw) and the Word processor used to place them into a context (say Microsoft office), via<\/em> an intermediate storage area known as the clipboard<\/em>. The round trip between the Macintosh (OS X) versions of these programs had been broken a little while, but it is now fixed! A small victory. This blog reports what happened when such a\u00a0Mac-created Word document is sent to someone using Microsoft Windows as an OS (or vice versa<\/em>).<\/p>\n

As you might have guessed, the molecular diagram arrives largely dead, and not re-usable. Opening the .docx<\/strong> archive (it is nothing more than a zip file) reveals only a JPEG file residing inside. Nothing that can be chemically repurposed. If the reverse process is undertaken, of creating a chemdraw diagram, and pasting it into Word on Windows, one finds in the .docx two components; a bit-mapped image linked to an active object containing the data. Only the first of these is recognised if the file makes its way to a Macintosh; i.e.<\/em> the same story, the data is again lost. So the bottom line is that Mac users and Windows users cannot<\/em><\/strong>, after all, exchange repurposable molecular diagrams using Word documents using this combination of programs. This is not good<\/strong>.<\/p>\n

But let me remind what happened around 1993. The word processor was joined by a program called the Web browser. In 1996, the underlying content carrier, HTML, became XHTML (an instance of XML). Right from day 1 almost, such XHTML could, and frequently was repurposed. A memorable example is that search engines could use it to index the Web. The XHTML easily survived trips to and from clipboards. In 1996, CML<\/a> joined HTML as a way of carrying chemical information capable of round-tripping without loss (if need be). There are other chemical XML languages in use nowadays, including CDXML used by the ChemDraw program. Word itself now uses XML (the x<\/strong> in .docx). So, after 14 years, why am I still describing the difficulties above? I am frankly at a loss to explain why there is still a need to write this post.<\/p>\n

All is not entirely lost. The\u00a0CML4Word<\/a> approach is designed to enable (chemical) data round tripping from the outset. Although I do not yet know if the CML created and stored in the Word document using this mechanism is recognised anywhere outside of Word 2007 on Windows? \u00a0If anyone can let me know of examples where such a CML-enabled Word document can be used in other environments, I would be very grateful (but not on \u00a0OS X, as I know already).<\/p>\n

And as I might have mentioned in the previous post on this topic, things may not however be getting better in that other carrier of information and data, the mobile phone\/iPad, as exemplified by operating systems such as iOS or Android. Watch this space, as they say.<\/p>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

Moving (chemical) data around in a manner which allows its (automated) use in whichever context it finds itself must be a holy grail for all scientists and chemists. I posted earlier on the fragile nature of molecular diagrams making the journey between the editing program used to create them (say ChemDraw) and the Word processor […]<\/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":false,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2}},"categories":[2],"tags":[344,336,27,341,2647,340,78,328,337,329,430,228,343,1108,338,342,339,323,124],"ppma_author":[2661],"class_list":["post-2962","post","type-post","status-publish","format-standard","hentry","category-chemical-it","tag-android","tag-cellular-telephone","tag-chemical","tag-chemical-information","tag-chemical-it","tag-content-carrier","tag-html","tag-ipad","tag-jpeg","tag-mac-os-x","tag-macintosh","tag-microsoft","tag-microsoft-windows","tag-opendata","tag-operating-systems","tag-search-engines","tag-web-browser","tag-word-processor","tag-xml"],"yoast_head":"\nData-round-tripping: wherein the future? - 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=2962\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Data-round-tripping: wherein the future? - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"Moving (chemical) data around in a manner which allows its (automated) use in whichever context it finds itself must be a holy grail for all scientists and chemists. 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We could acquire a computer which could be used to draw chemical structures in one application, and via a mysterious and mostly invisible entity called the clipboard, paste it into a word processor (it was\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":11735,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=11735","url_meta":{"origin":2962,"position":1},"title":"Chemistry data round-tripping. Has there been ANY progress?","author":"Henry Rzepa","date":"December 2, 2013","format":false,"excerpt":"This is one of those topics that seems to crop up every three years or so. Since then, new versions of operating systems, new versions of programs, mobile devices and perhaps some progress?\u00a0 Right, I will briefly recapitulate. Chemical structure diagrams are special; they contain chemical semantics (what an atom\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":5011,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5011","url_meta":{"origin":2962,"position":2},"title":"Steve Jobs and chemistry: a personal recollection.","author":"Henry Rzepa","date":"October 9, 2011","format":false,"excerpt":"Steve Jobs death on October 5th 2011 was followed by a remarkable number of tributes and reflections on the impact the company he founded has had on the world. Many of these tributes summarise the effect as a visionary disruption. Here I describe from my own perspective some of the\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.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/10\/jobs1.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":26754,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=26754","url_meta":{"origin":2962,"position":3},"title":"The Macintosh computer at 40.","author":"Henry Rzepa","date":"January 25, 2024","format":false,"excerpt":"On 24th January 1984, the Macintosh computer was released, as all the media are informing us. Apparently, some are still working. I thought I would give my own personal recollections of that period. In fact, the Mac reached UK stores via a dealership only in 1985. What brought it to\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\/01\/IMG_0315-150x150.jpeg?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2024\/01\/IMG_0315-150x150.jpeg?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2024\/01\/IMG_0315-150x150.jpeg?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2024\/01\/IMG_0315-150x150.jpeg?resize=700%2C400&ssl=1 2x, https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2024\/01\/IMG_0315-150x150.jpeg?resize=1050%2C600&ssl=1 3x"},"classes":[]},{"id":15907,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=15907","url_meta":{"origin":2962,"position":4},"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":4578,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=4578","url_meta":{"origin":2962,"position":5},"title":"Computers 1967-2011: a personal perspective. 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