Archive for the ‘Chemical IT’ Category

The “Accessible” in FAIR (data).

Thursday, April 18th, 2019
No Gravatar

In a previous post, I looked at the Findability of FAIR data in common chemistry journals. Here I move on to the next letter, the A = Accessible.

(more…)

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

Friday, April 12th, 2019
No Gravatar

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

(more…)

Questions about the (metadata) components of a scientific article.

Monday, April 8th, 2019
No Gravatar

The conventional procedures for reporting analysis or new results in science is to compose an “article”, augment that perhaps with “supporting information” or “SI”, submit to a journal which undertakes peer review, with revision as necessary for acceptance and finally publication. If errors in the original are later identified, a separate corrigendum can be submitted to the same journal, although this is relatively rare. Any new information which appears post-publication is then considered for a new article, and the cycle continues. Here I consider the possibilities for variations in this sequence of events.

(more…)

Impossible molecules.

Monday, April 1st, 2019
No Gravatar

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]

(more…)

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
No Gravatar

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.

(more…)

Re-inventing the anatomy of a research article.

Saturday, December 29th, 2018
No Gravatar

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.

(more…)

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

Sunday, November 4th, 2018
No Gravatar

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.

(more…)

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

Wednesday, March 7th, 2018
No Gravatar

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.

(more…)

First, Open Access, then Open (and FAIR) Data, now Open Citations.

Saturday, February 3rd, 2018
No Gravatar

The topic of open citations was presented at the PIDapalooza conference and represents a third component in the increasing corpus of open scientific information.

(more…)

PIDapalooza 2018. A conference like no other!

Tuesday, January 23rd, 2018
No Gravatar

Another occasional conference report (day 1). So why is one about “persistent identifiers” important, and particularly to the chemistry domain?

(more…)