{"id":19892,"date":"2018-08-07T17:54:12","date_gmt":"2018-08-07T16:54:12","guid":{"rendered":"https:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=19892"},"modified":"2025-05-08T08:08:10","modified_gmt":"2025-05-08T07:08:10","slug":"harnessing-fair-data-a-suggested-useful-persistent-identifier-pid-for-quantum-chemical-calculations","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=19892","title":{"rendered":"Harnessing FAIR data: A suggested useful persistent identifier (PID) for quantum chemical calculations."},"content":{"rendered":"
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Harnessing FAIR data<\/a> is an event being held in London on September 3rd; no doubt all the speakers will espouse its virtues and speculate about how to realize its potential.\u2665<\/sup><\/span> Admirable aspirations indeed. Capturing hearts and minds also needs lots of real life applications! Whilst assembling a forthcoming post<\/a> on this blog, I realized I might have one nice application which also pushes the envelope a bit further, in a manner that I describe below.<\/p>\n

The post I refer to above is about using quantum chemical calculations to chart possible mechanistic pathways for the reaction between a carboxylic acid and an amine to form an amide. The FAIR data for the entire project is collected<\/span> at DOI:\u00a010.14469\/hpc\/4598<\/a>. Part of what makes it FAIR is the metadata not only collected about this data but also formally registered with the DataCite agency. Registration in turn enables Finding<\/span>; it is this aspect I want to demonstrate here.<\/p>\n

The metadata<\/a> for the above DOI includes information such as;<\/p>\n

    \n
  1. The ORCID persistent identifier (PID) for the creator of the data (in this instance myself)<\/li>\n
  2. Date stamps for the original creation date and subsequent modifications.<\/li>\n
  3. A rights declaration, in this case the CC0 license which describes how the data can be re-used.<\/li>\n
  4. Related identifiers, in this case describing members of this collection<\/span>.<\/li>\n<\/ol>\n

    The data itself is held in the members of the collection, each of which is described by a more specific set of metadata<\/a> in addition to the more general types in the above list (e.g.\u00a010.14469\/hpc\/4606<\/a>).<\/p>\n

      \n
    1. One important additional metadata descriptor is the ORE<\/strong> locator (Object Re-use and Exchange, itself almost a synonym for FAIR). This allows a machine to deduce a direct path to the data file itself, and hence to retrieve it automatically if desired. It is important to note that the DOI itself (i.e.\u00a010.14469\/hpc\/4606<\/a>) points only to the “landing page” for the dataset, and does not necessarily describe the direct path to any specific file in the dataset. The ORE path can be used with e.g.<\/em> software such as JSmol to directly load a molecule based only on its DOI. You can see an example of this here<\/a>.<\/li>\n
    2. Each molecule-based dataset contains additional specific metadata relating to the molecule itself. For example this is how the InChiKey, an identifier specific to that molecule, is expressed in metadata;
      \n<subject subjectScheme=\"inchikey\" schemeURI=\"http:\/\/www.inchi-trust.org\/\">PVXKWVPAMVWJSQ-UHFFFAOYSA-N<\/subject><\/tt>
      \nThe advantage of expressing the metadata in this way is that a general search of the type:
      \n      https:\/\/commons.datacite.org\/doi.org?query=subjexts.subjectScheme:inchikey+AND+subjects.subject:CZABGBRSHXZJCF-UHFFFAOYSA-N<\/a><\/tt>
      \ncan be used to track down any molecule with metadata corresponding to the above InChIkey.<\/li>\n
    3. Here is more metadata, introduced in this blog. It relates to the (computed) value of the Gibbs energy (the energy unit is in Hartree\u2020<\/sup>), as returned by the Gaussian program;
      \n<subject subjectScheme=\"Gibbs_Energy\" schemeURI=\"https:\/\/goldbook.iupac.org\/html\/G\/G02629.html\" valueURI=\"http:\/\/gaussian.com\/thermo\/\">-649.732417<\/subject><\/tt>
      \nI here argue that it represents a unique identifier for a molecule calculation using the quantum mechanical procedures implemented in e.g.<\/i> Gaussian. This identifier is different from the InChIkey, in that it can be truncated to provide different levels of information.<\/p>\n