Archive for the ‘Chemical IT’ Category

A Non-nitrogen Containing Morpholine Isostere; an application of FAIR data principles.

Sunday, August 4th, 2019

In the pipeline reports on an intriguing new ring system acting as an isostere for morpholine. I was interested in how the conformation of this ring system might be rationalised electronically and so I delved into the article.[1] Here I recount what I found.

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References

  1. H. Hobbs, G. Bravi, I. Campbell, M. Convery, H. Davies, G. Inglis, S. Pal, S. Peace, J. Redmond, and D. Summers, "Discovery of 3-Oxabicyclo[4.1.0]heptane, a Non-nitrogen Containing Morpholine Isostere, and Its Application in Novel Inhibitors of the PI3K-AKT-mTOR Pathway", Journal of Medicinal Chemistry, 2019. http://dx.doi.org/10.1021/acs.jmedchem.9b00348

Metadata. Why?

Tuesday, July 2nd, 2019

I have had some interesting discussions recently regarding metadata. What emerges is that it can be quite a broadly defined concept and it is clear that a variety of answers might be obtained when asking the simple question “what is it useful for?” Here I set out some of my answers to that question.

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A search of some major chemistry publishers for FAIR data records.

Friday, April 12th, 2019

In recent years, findable data has become ever more important (the F in FAIR). Here I test that F using the DataCite search service.

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Impossible molecules.

Monday, April 1st, 2019

Members of the chemical FAIR data community have just met in Orlando (with help from the NSF, the American National Science Foundation) to discuss how such data is progressing in chemistry. There are a lot of themes converging at the moment. Thus this article[1] extolls the virtues of having raw NMR data available in natural product research, to which we added that such raw data should also be made FAIR (Findable, Accessible, Interoperable and Reusable) by virtue of adding rich metadata and then properly registering it so that it can be searched. These themes are combined in another article which made a recent appearance.[2]

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References

  1. J.B. McAlpine, S. Chen, A. Kutateladze, J.B. MacMillan, G. Appendino, A. Barison, M.A. Beniddir, M.W. Biavatti, S. Bluml, A. Boufridi, M.S. Butler, R.J. Capon, Y.H. Choi, D. Coppage, P. Crews, M.T. Crimmins, M. Csete, P. Dewapriya, J.M. Egan, M.J. Garson, G. Genta-Jouve, W.H. Gerwick, H. Gross, M.K. Harper, P. Hermanto, J.M. Hook, L. Hunter, D. Jeannerat, N. Ji, T.A. Johnson, D.G.I. Kingston, H. Koshino, H. Lee, G. Lewin, J. Li, R.G. Linington, M. Liu, K.L. McPhail, T.F. Molinski, B.S. Moore, J. Nam, R.P. Neupane, M. Niemitz, J. Nuzillard, N.H. Oberlies, F.M.M. Ocampos, G. Pan, R.J. Quinn, D.S. Reddy, J. Renault, J. Rivera-Chávez, W. Robien, C.M. Saunders, T.J. Schmidt, C. Seger, B. Shen, C. Steinbeck, H. Stuppner, S. Sturm, O. Taglialatela-Scafati, D.J. Tantillo, R. Verpoorte, B. Wang, C.M. Williams, P.G. Williams, J. Wist, J. Yue, C. Zhang, Z. Xu, C. Simmler, D.C. Lankin, J. Bisson, and G.F. Pauli, "The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research", Natural Product Reports, vol. 36, pp. 35-107, 2019. http://dx.doi.org/10.1039/c7np00064b
  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, vol. 4, pp. 3280-3286, 2019. http://dx.doi.org/10.1021/acsomega.8b03005

Free energy relationships and their linearity: a test example.

Sunday, January 13th, 2019

Linear free energy relationships (LFER) are associated with the dawn of physical organic chemistry in the late 1930s and its objectives in understanding chemical reactivity as measured by reaction rates and equilibria.

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Re-inventing the anatomy of a research article.

Saturday, December 29th, 2018

The traditional structure of the research article has been honed and perfected for over 350 years by its custodians, the publishers of scientific journals. Nowadays, for some journals at least, it might be viewed as much as a profit centre as the perfected mechanism for scientific communication. Here I take a look at the components of such articles to try to envisage its future, with the focus on molecules and chemistry.

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Open Access journal publishing debates – the elephant in the room?

Sunday, November 4th, 2018

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 miss one important point, how to publish data.

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How FAIR are the data associated with the 2017 Molecules-of-the-Year?

Wednesday, March 7th, 2018

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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