{"id":22043,"date":"2020-04-07T11:04:44","date_gmt":"2020-04-07T10:04:44","guid":{"rendered":"https:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=22043"},"modified":"2020-04-07T18:19:56","modified_gmt":"2020-04-07T17:19:56","slug":"new-generations-of-globally-aggregating-search-engines-for-chemical-data","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=22043","title":{"rendered":"New generations of globally aggregating search engines &#8211; for (chemical) data."},"content":{"rendered":"<div class=\"kcite-section\" kcite-section-id=\"22043\">\n<p>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)\u00a0<a href=\"https:\/\/scifinder.cas.org\/\">SciFinder (Scholar)<\/a>\u00a0and <a href=\"https:\/\/www.reaxys.com\/\">Reaxys<\/a>\u00a0or those that arrived in the 1990s in the online era<sup>\u2021<\/sup> such as the non-commercial <a href=\"https:\/\/pubchem.ncbi.nlm.nih.gov\">Pubchem<\/a> or <a href=\"https:\/\/www.chemspider.com\">ChemSpider<\/a> (there are more). But you may not be as familiar with the latest generation of global search engines and here I will focus on three relatively new ones that specialise specifically in tracking down data rather than just publications.<\/p>\n<p>I will illustrate first using a <i>regular<\/i> or <i>non-advanced<\/i> search. The keyword will be <strong>obtusallene<\/strong>, which is selected largely because it is a relatively unique string which is likely to result in fewer false positives. It is a family of marine alkaloids containing, unusually, bromine and \/or chlorine<span id=\"cite_ITEM-22043-0\" name=\"citation\"><a href=\"#ITEM-22043-0\">[1]<\/a><\/span> and the citation here is to a journal article describing some of its chemistry. But what if you want to find data associated with such molecules?<\/p>\n<ol>\n<li><strong>DataCite<\/strong> (the name gives a clue) specialises in finding data. It was launched ten years ago and has been rapidly expanding its index since. A regular search can be formulated using the string\n<ul>\n<li><a href=\"https:\/\/search.datacite.org\/works?query=obtusallene\">https:\/\/search.datacite.org\/works?query=obtusallene<\/a> (25 hits).<\/li>\n<li>What might be considered an advanced query is to constrain the search, here to the occurance of the phrase in specifically the <strong>title<\/strong> field of the information descriptor of the item (also called the metadata for the item):<br \/>\n<a href=\"https:\/\/search.datacite.org\/works?query=titles.title:*Obtusallene*\">https:\/\/search.datacite.org\/works?query=titles.title:*Obtusallene*<\/a> (24 hits)<\/li>\n<li>A variation on this would be to specify the <strong>description field<\/strong>:\u00a0<a href=\"https:\/\/search.datacite.org\/works?query=descriptions.description:*Obtusallene*\"> https:\/\/search.datacite.org\/works?query=descriptions.description:*Obtusallene*<\/a> (3 hits)<\/li>\n<li>And these can be combined: <a href=\"https:\/\/search.datacite.org\/works?query=descriptions.description:*Obtusallene*+OR+titles.title:*Obtusallene*\">https:\/\/search.datacite.org\/works?query=descriptions.description:*Obtusallene*+OR+titles.title:*Obtusallene*<\/a>\u00a0(25 hits)<\/li>\n<\/ul>\n<p>As these three advanced queries imply, there are many more ways of constraining the search, which I will describe at a later time.<\/li>\n<li>A more recent introduction is <strong>DataSetSearch<\/strong> from Google.\n<ul>\n<li><a href=\"https:\/\/datasetsearch.research.google.com\/search?query=obtusallene\">https:\/\/datasetsearch.research.google.com\/search?query=obtusallene<\/a> (20 hits). Google cites as its sources DataCite itself and the specific repository Figshare (for this search query).\u00a0<\/li>\n<li>Which leaves a slight mystery. Whilst there is considerable overlap between the DataCite and Google searches, the latter should clearly be potentially a superset of the former, but in fact it is slightly less comprehensive (by at least 5 hits). <a href=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2020\/04\/google.jpg\"><img loading=\"lazy\" decoding=\"async\" class=\"aligncenter size-large wp-image-22051\" src=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2020\/04\/google-1024x1004.jpg\" alt=\"\" width=\"450\" height=\"441\" srcset=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2020\/04\/google-1024x1004.jpg 1024w, https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2020\/04\/google-300x294.jpg 300w, https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2020\/04\/google-768x753.jpg 768w, https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2020\/04\/google-1536x1505.jpg 1536w, https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2020\/04\/google.jpg 1706w\" sizes=\"auto, (max-width: 450px) 100vw, 450px\" \/><\/a><\/li>\n<\/ul>\n<\/li>\n<li>My third new engine is <strong><a href=\"https:\/\/explore.openaire.eu\/search\/find\">OpenAIRE<\/a><\/strong> (a European project supporting Open Science). It is also the search engine provided by Zenodo.\n<ul>\n<li><a href=\"https:\/\/explore.openaire.eu\/search\/find?keyword=obtusallene\">https:\/\/explore.openaire.eu\/search\/find?keyword=obtusallene <\/a> (20 hits on research data, 6 hits on publications, 5 hits on &#8220;other research products&#8221; and zero hits on &#8220;software&#8221;).<\/li>\n<li>Which introduces not just data but other concepts associated with &#8220;research objects&#8221;, clearly more useful than data alone. One of these may well shortly be <a href=\"https:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=21960\">Instruments<\/a> (as eg used to acquire data) and another is<em> e.g.<\/em> the software used to analyze the data. <a href=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2020\/04\/openaire.jpg\"><img loading=\"lazy\" decoding=\"async\" class=\"aligncenter size-large wp-image-22050\" src=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2020\/04\/openaire-1024x692.jpg\" alt=\"\" width=\"450\" height=\"304\" srcset=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2020\/04\/openaire-1024x692.jpg 1024w, https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2020\/04\/openaire-300x203.jpg 300w, https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2020\/04\/openaire-768x519.jpg 768w, https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2020\/04\/openaire-1536x1038.jpg 1536w, https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2020\/04\/openaire-2048x1384.jpg 2048w\" sizes=\"auto, (max-width: 450px) 100vw, 450px\" \/><\/a><\/li>\n<\/ul>\n<\/li>\n<\/ol>\n<p>I think these new-generation search engines specialising in data have lots of exciting potential. They are still maturing and I hope we will see some interesting new capabilities emerge which we have not had before.<\/p>\n<hr \/>\n<p><sup>\u2021<\/sup>All are on-line nowadays, but engines such as SciFinder had two previous existences, from about 1980 as CAS online using merely a terminal interface, and prior to that as printed copies to be searched manually.<\/p>\n<h2>References<\/h2>\n    <ol class=\"kcite-bibliography csl-bib-body\"><li id=\"ITEM-22043-0\">J. Clarke, K.J. Bonney, M. Yaqoob, S. Solanki, H.S. Rzepa, A.J.P. White, D.S. Millan, and D.C. Braddock, \"Epimeric Face-Selective Oxidations and Diastereodivergent Transannular Oxonium Ion Formation Fragmentations: Computational Modeling and Total Syntheses of 12-Epoxyobtusallene IV, 12-Epoxyobtusallene II, Obtusallene X, Marilzabicycloallene C, and Marilzabicycloallene D\", <i>The Journal of Organic Chemistry<\/i>, vol. 81, pp. 9539-9552, 2016. <a href=\"https:\/\/doi.org\/10.1021\/acs.joc.6b02008\">https:\/\/doi.org\/10.1021\/acs.joc.6b02008<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> <!-- kcite-section 22043 -->","protected":false},"excerpt":{"rendered":"<p>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 may not be as familiar [&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":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":[],"ppma_author":[2661],"class_list":["post-22043","post","type-post","status-publish","format-standard","hentry","category-chemical-it"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.6 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>New generations of globally aggregating search engines - for (chemical) data. - 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=22043\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"New generations of globally aggregating search engines - for (chemical) data. - Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"og:description\" content=\"Chemists have long been familiar with search engines that aspire to index a large proportion of the chemical literature. 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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 &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\/06\/171-1024x196.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":12526,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=12526","url_meta":{"origin":22043,"position":1},"title":"A newcomer in the game of how we find and use data.","author":"Henry Rzepa","date":"May 17, 2014","format":false,"excerpt":"I remember a time when tracking down a particular property of a specified molecule was an all day effort, spent in the central library (or further afield). Then came the likes of STN Online (~1980) and later Beilstein. But only if your institution had a subscription. Let me then cut\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":2962,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2962","url_meta":{"origin":22043,"position":2},"title":"Data-round-tripping: wherein the future?","author":"Henry Rzepa","date":"December 7, 2010","format":false,"excerpt":"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\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":17951,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17951","url_meta":{"origin":22043,"position":3},"title":"Supporting information: chemical graveyard or invaluable resource for chemical structures.","author":"Henry Rzepa","date":"March 31, 2017","format":false,"excerpt":"Nowadays, data supporting\u00a0most publications relating to the synthesis of organic compounds is more likely than not to be found in associated \"supporting information\" rather than the (often page limited) article itself. For example, this article has an SI which is paginated at 907; almost a mini-database in its own right!\u2020\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":15907,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=15907","url_meta":{"origin":22043,"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 &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":26419,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=26419","url_meta":{"origin":22043,"position":5},"title":"Improving the Science blog &#8211; The Rogue Scholar service.","author":"Henry Rzepa","date":"September 12, 2023","format":false,"excerpt":"Some 13 years ago, I speculated about the longevity of the type of science communication then (and still now) represented by Blogs. I noted one new project called ArchivePress that was looking into providing solutions equivalent to what scientific journals have done for some 350 years of science communication. The\u2026","rel":"","context":"With 3 comments","block_context":{"text":"With 3 comments","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=26419#comments"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2023\/09\/Screenshot-79-300x175.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\/22043","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=22043"}],"version-history":[{"count":10,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/22043\/revisions"}],"predecessor-version":[{"id":22056,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/22043\/revisions\/22056"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=22043"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=22043"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=22043"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=22043"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}