{"id":26202,"date":"2023-07-12T11:37:17","date_gmt":"2023-07-12T10:37:17","guid":{"rendered":"https:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=26202"},"modified":"2023-07-13T12:25:54","modified_gmt":"2023-07-13T11:25:54","slug":"physical-sample-identifiers-the-future","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=26202","title":{"rendered":"Physical Sample identifiers – the future?"},"content":{"rendered":"
\n

I have variously talked about persistent identifiers<\/a> on this blog. These largely take the form of DOIs (Digital object identifiers), and here they relate to either journal articles or datasets associated with either the article or the blog post or both. Other disciplines, particularly the earth sciences, have long used persistent identifiers (PIDs) to identify physical objects rather than digital ones. One of my ambitions is to assign such identifiers to a small but highly historical collection of physical objects in my possession, as described at this post<\/a>. As a prelude to this project, here I describe some ways of searching for physical objects that have been assigned a PID. Thanks Rorie for providing these!\u00a0<\/p>\n

    \n
  1. Here is a general search for physical objects with associated metadata describing them as registered with DataCite. https:\/\/commons.datacite.org\/doi.org?query=types.resourceTypeGeneral:PhysicalObject<\/a> (11,269,090 items)<\/li>\n
  2. The search can be slightly constrained to find only identifiers that originate from the earlier IGSN ID (International generic sample number) see here for details<\/a> and https:\/\/www.igsn.org\/about\/<\/a> for the organisation set up) using the syntax query=client.client_type:igsnCatalog types.resourceTypeGeneral:PhysicalObject<\/a> (9,642,030 items)<\/li>\n<\/ol>\n

    The exciting prospect is that in due time, such searches could be constrained by adding specifically chemical properties, most obviously eg an InChI identifier. At the moment, it is unlikely any existing samples have even been registered with such a term.<\/p>\n

      \n
    1. Thus combining two queries would give the following:
      \n      query=client.client_type:igsnCatalog types.resourceTypeGeneral:PhysicalObject+AND+subjects.subjectScheme:inchikey+AND+subjects.subject:*<\/a><\/small><\/li>\n
    2. Removing the PhysicalObject constrain gives a different response:
      \n      query=(subjects.subjectScheme:inchikey+AND+subjects.subject:*+OR+subjects.subjectScheme:inchi+AND+subjects.subject:*)<\/a><\/small><\/li>\n<\/ol>\n

      \u00a0When this becomes possible, (see project above!), it would enable for example journal articles (or the FAIR data associated with them) to reference information about a physical sample associated with eg the preparation of a molecule new to science.<\/p>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

      I have variously talked about persistent identifiers on this blog. These largely take the form of DOIs (Digital object identifiers), and here they relate to either journal articles or datasets associated with either the article or the blog post or both. Other disciplines, particularly the earth sciences, have long used persistent identifiers (PIDs) to identify […]<\/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":[],"tags":[],"ppma_author":[2661],"class_list":["post-26202","post","type-post","status-publish","format-standard","hentry"],"yoast_head":"\nPhysical Sample identifiers - 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=26202\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Physical Sample identifiers - the future? - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"I have variously talked about persistent identifiers on this blog. These largely take the form of DOIs (Digital object identifiers), and here they relate to either journal articles or datasets associated with either the article or the blog post or both. 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A conference like no other!","author":"Henry Rzepa","date":"January 23, 2018","format":false,"excerpt":"Another occasional conference report (day 1). So why is one about \"persistent identifiers\" important, and particularly to the chemistry domain? The PID most familiar to most chemists is the DOI (digital object identifier). 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There are many ways of helping people make these connections - attending a conference or seminar, searching journals for published articles and nowadays also searching for data are just a few examples. For about\u2026","rel":"","context":"In "WATOC reports"","block_context":{"text":"WATOC reports","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2238"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":20669,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=20669","url_meta":{"origin":26202,"position":2},"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. 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I say recently formalised, since researchers have of course kept\u00a0research notebooks recording their activities and their data since the dawn of science, but not\u00a0always in an open and transparent\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":16251,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16251","url_meta":{"origin":26202,"position":5},"title":"Metametadata: data about data about (chemical) data.","author":"Henry Rzepa","date":"April 16, 2016","format":false,"excerpt":"Scientists are familiar with the term data, at least in a scientific or chemical context, but appreciating metadata (meaning \"after\", or \"beyond\") is slightly more subtle, in the sense of using it to mean data about data. The challenge lies in clarifying where the boundary between data and its metadata\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":[]}],"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\/26202","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=26202"}],"version-history":[{"count":10,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/26202\/revisions"}],"predecessor-version":[{"id":26213,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/26202\/revisions\/26213"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=26202"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=26202"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=26202"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=26202"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}