Posts Tagged ‘search engines’

How to search data repositories for FAIR chemical content and data: SubjectScheme

Thursday, June 8th, 2017
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As data repositories start to flourish, it is reasonable to ask questions such as what sort of chemistry can be found there and how can I find it? Here I give an updated[1] worked example of a digital repository search for chemical content and also pose an important issue for the chemistry domain.

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References

  1. H.S. Rzepa, A. Mclean, and M.J. Harvey, "InChI As a Research Data Management Tool", Chemistry International, vol. 38, 2016. http://dx.doi.org/10.1515/ci-2016-3-408

Supporting information: chemical graveyard or invaluable resource for chemical structures.

Friday, March 31st, 2017
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Nowadays, data supporting most 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[1] has an SI which is paginated at 907; almost a mini-database in its own right! Here I ponder whether such dissemination of data is FAIR (Findable, accessible, interoperable and re-usable).[2]

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References

  1. J.M. Lopchuk, K. Fjelbye, Y. Kawamata, L.R. Malins, C. Pan, R. Gianatassio, J. Wang, L. Prieto, J. Bradow, T.A. Brandt, M.R. Collins, J. Elleraas, J. Ewanicki, W. Farrell, O.O. Fadeyi, G.M. Gallego, J.J. Mousseau, R. Oliver, N.W. Sach, J.K. Smith, J.E. Spangler, H. Zhu, J. Zhu, and P.S. Baran, "Strain-Release Heteroatom Functionalization: Development, Scope, and Stereospecificity", Journal of the American Chemical Society, vol. 139, pp. 3209-3226, 2017. http://dx.doi.org/10.1021/jacs.6b13229
  2. M.D. Wilkinson, M. Dumontier, I.J. Aalbersberg, G. Appleton, M. Axton, A. Baak, N. Blomberg, J. Boiten, L.B. da Silva Santos, P.E. Bourne, J. Bouwman, A.J. Brookes, T. Clark, M. Crosas, I. Dillo, O. Dumon, S. Edmunds, C.T. Evelo, R. Finkers, A. Gonzalez-Beltran, A.J. Gray, P. Groth, C. Goble, J.S. Grethe, J. Heringa, P.A. ’t Hoen, R. Hooft, T. Kuhn, R. Kok, J. Kok, S.J. Lusher, M.E. Martone, A. Mons, A.L. Packer, B. Persson, P. Rocca-Serra, M. Roos, R. van Schaik, S. Sansone, E. Schultes, T. Sengstag, T. Slater, G. Strawn, M.A. Swertz, M. Thompson, J. van der Lei, E. van Mulligen, J. Velterop, A. Waagmeester, P. Wittenburg, K. Wolstencroft, J. Zhao, and B. Mons, "The FAIR Guiding Principles for scientific data management and stewardship", Scientific Data, vol. 3, pp. 160018, 2016. http://dx.doi.org/10.1038/sdata.2016.18

500 chemical twists: a (chalk and cheese) comparison of the impacts of blog posts and journal articles.

Friday, June 3rd, 2016
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The title might give it away; this is my 500th blog post, the first having come some eight years ago. Very little online activity nowadays is excluded from measurement and so it is no surprise that this blog and another of my "other" scholarly endeavours, viz publishing in traditional journals, attract such "metrics" or statistics. The h-index is a well-known but somewhat controversial measure of the impact of journal articles; here I thought I might instead take a look at three less familiar ones – one relating to blogging, one specific to journal publishing and one to research data.

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Data-round-tripping: wherein the future?

Tuesday, December 7th, 2010
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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 used to place them into a context (say Microsoft office), via an intermediate storage area known as the clipboard. 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 Mac-created Word document is sent to someone using Microsoft Windows as an OS (or vice versa).

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