{"id":21928,"date":"2020-02-14T06:58:09","date_gmt":"2020-02-14T06:58:09","guid":{"rendered":"https:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=21928"},"modified":"2020-02-14T17:06:20","modified_gmt":"2020-02-14T17:06:20","slug":"encouraging-submission-of-fair-data-at-the-journal-of-organic-chemistry-and-organic-letters","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=21928","title":{"rendered":"Encouraging Submission of FAIR Data at the Journal of Organic Chemistry and Organic Letters"},"content":{"rendered":"
\n

In a welcome move, one of the American chemical society journals has published an encouragement to submit what is called FAIR data to the journal.[1]<\/a><\/span>. A reminder that FAIR data is data that can be Found (F), Accessed (A), Interoperated(I) and Re-used( R). I thought I might try to explore this new tool here.<\/p>\n

You start at the ACS Research Data Center<\/a>\u00a0 with the tag line Submit your NMR Data.<\/b> By this they mean the primary or “raw” NMR data as it emerges from a spectrometer. At this point I would note that primary data is not necessarily FAIR data yet. It is however a great deal more easily inter-operated and re-used than say the more conventional form of such data, which is a visual spectrum stored as a PDF file. If you did want to re-analyse the data, the primary data is the place to start, not the PDF spectrum!<\/p>\n

The tool next asks to to drop your FID file into the upload area. Depending on the spectrometer type, this can take the form of a ZIP archive of various instrument files (typical of Bruker spectrometers) or just a single file (JDF, typical of Jeol spectrometers). The next request is for some “metadata” such as Title, Funder and Author(s), with an additional request to provide an ORCID for the latter. All these are easily provided. It was the next step where my exploration on this occasion had to stop, since the next button takes you to the Manuscript submission page, which can only be followed if you have a manuscript to complete!\u00a0<\/p>\n

What would I expect to happen next? Well, this metadata has to be augmented with molecule metadata, such as for example an InChI of the molecule. This is what would turn our primary data in fully FAIR data. To complete the process, the data and its now completed metadata descriptors would need to be Registered<\/strong>, in order to facilitate its discovery and hence enable the F of FAIR. This is normally completed with the DataCite registration agency, and in exchange you get a DOI corresponding to the registered metadata and you can then infer a link of the type https:\/\/data.datacite.org\/application\/vnd.datacite.datacite+xml\/…your-allocated…DOI<\/a> which allows you to inspect the metadata and search for it (see eg DOI:\u00a010.14469\/hpc\/5920<\/a>\u00a0for examples of such searches).\u00a0Currently I do not know if this happens with this ACS tool. I would certainly like to inspect the collected metadata before I could comment on whether the title of this post is accurate, ie the encouragement of FAIR data. It would also be interesting to see what (if any) procedures are used to generate an InChI for the molecule and its NMR data, and exactly how that is also included in the metadata.<\/p>\n

I would also note one other crucial aspect of this process, how to enable the A<\/strong> of FAIR. Primary or raw NMR data is entirely opaque (the files themselves are often binary encoded files) and you do need a tool to transform this data into visual or spectral form. So you will need to acquire such a tool, most often in the form of software such as MestreNova or Topspin. This can be a complex process, and may well involve paying the vendors money. In this context, I would note the Mpublish tool,[2]<\/a><\/span> which allows a single-free-to-use license to be generated which allows e.g. MestreNova to be freely used for that dataset only. Some form of suitable A<\/strong>ccess to a FAIR dataset is an essential (if often unmentioned) component of the process.<\/p>\n

At this stage therefore, there are quite a few questions about this new ACS system which I cannot provide answers to. On these answers will depend whether the process can be truly described as the submission of FAIR data<\/strong>. If anyone reading this manages to complete the process above, do please describe the subsequent experiences. I fancy there will have to be a future follow up to this post! Meanwhile, if you do have a manuscript you are ready to submit, give it a go and perchance report your experiences here!<\/p>\n

References<\/h2>\n
  1. A.M. Hunter, E.M. Carreira, and S.J. Miller, \"Encouraging Submission of FAIR Data at <i>The Journal of Organic Chemistry<\/i> and <i>Organic Letters<\/i>\", Organic Letters<\/i>, vol. 22, pp. 1231-1232, 2020. https:\/\/doi.org\/10.1021\/acs.orglett.0c00383<\/a>\n\n<\/li>\n
  2. A. Barba, S. Dominguez, C. Cobas, D.P. Martinsen, C. Romain, H.S. Rzepa, and F. Seoane, \"Workflows Allowing Creation of Journal Article Supporting Information and Findable, Accessible, Interoperable, and Reusable (FAIR)-Enabled Publication of Spectroscopic Data\", ACS Omega<\/i>, vol. 4, pp. 3280-3286, 2019. https:\/\/doi.org\/10.1021\/acsomega.8b03005<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

    In a welcome move, one of the American chemical society journals has published an encouragement to submit what is called FAIR data to the journal.. A reminder that FAIR data is data that can be Found (F), Accessed (A), Interoperated(I) and Re-used( R). I thought I might try to explore this new tool here. 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Originally entangled into scientific articles in the form of tables of numbers or diagrams, it was (partially) disentangled into supporting information when journals became electronic in the late 1990s. The next phase was the introduction of\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":17951,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17951","url_meta":{"origin":21928,"position":1},"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 "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":20601,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=20601","url_meta":{"origin":21928,"position":2},"title":"Impossible molecules.","author":"Henry Rzepa","date":"April 1, 2019","format":false,"excerpt":"Members of the chemical FAIR data community have just met in Orlando (with help from the NSF, the American National Science Foundation)\u00a0to discuss how such data is progressing in chemistry. There are a lot of themes converging at the moment. Thus this article extolls the virtues of having raw NMR\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":20342,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=20342","url_meta":{"origin":21928,"position":3},"title":"Open Access journal publishing debates – the elephant in the room?","author":"Henry Rzepa","date":"November 4, 2018","format":false,"excerpt":"For perhaps ten years now, the future of scientific publishing has been hotly debated. The traditional models are often thought to be badly broken, although convergence to a consensus of what a better model should be is not apparently close. But to my mind, much of this debate seems to\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":26086,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=26086","url_meta":{"origin":21928,"position":4},"title":"“For chemists, the AI revolution has yet to happen”.","author":"Henry Rzepa","date":"May 25, 2023","format":false,"excerpt":"This editorial from Nature is a timely reminder of the importance of data. But also, not just any data, but \"accurate and accessible training data\". Accessible of course is one of the attributes of FAIR (Findable, Accessible, Interoperable and Re-usable). The editorial also states \"data need to be recorded in\u2026","rel":"","context":"Similar post","block_context":{"text":"Similar post","link":""},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":19483,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=19483","url_meta":{"origin":21928,"position":5},"title":"How FAIR are the data associated with the 2017 Molecules-of-the-Year?","author":"Henry Rzepa","date":"March 7, 2018","format":false,"excerpt":"C&EN has again run a vote for the 2017 Molecules of the year. Here I take a look not just at these molecules, but at how FAIR (Findable, Accessible, Interoperable and Reusable) the data associated with these molecules actually is. 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