Archive for the ‘Chemical IT’ Category
Saturday, February 3rd, 2018
The topic of open citations was presented at the PIDapalooza conference and represents a third component in the increasing corpus of open scientific information.
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Tags:Academic publishing, Applied linguistics, article processing charge, British National Corpus, chemical stories, cited author, Corpus linguistics, David Shotton, Entertainment/Culture, Linguistics, Open access, Quotation, RDF, social media, Texas A&M–Corpus Christi Islanders women's basketball
Posted in Chemical IT | 2 Comments »
Tuesday, January 23rd, 2018
Another occasional conference report (day 1). So why is one about “persistent identifiers” important, and particularly to the chemistry domain?
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Tags:Academic publishing, Andy Mabbett, Digital Object Identifier, Identifiers, Imperial College, Index, Information science, Johanna McEntyre, Knowledge, Mark Hahnel, ORCiD, Persistent identifier, Publishing, Quotation, researcher, Scholarly communication, SciCrunch, search engines, Technical communication, Technology/Internet, Tom Gillespie
Posted in Chemical IT | 1 Comment »
Thursday, December 7th, 2017
FAIR data is increasingly accepted as a description of what research data should aspire to; Findable, Accessible, Inter-operable and Re-usable, with Context added by rich metadata (and also that it should be Open). But there are two sides to data, one of which is the raw data emerging from say an instrument or software simulations and the other in which some kind of model is applied to produce semi- or even fully processed/interpreted data. Here I illustrate a new example of how both kinds of data can be made to co-exist.
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Tags:computing, Context, data, Data management, Information, Knowledge, Raw data, software simulations, Technology/Internet
Posted in Chemical IT, crystal_structure_mining | No Comments »
Tuesday, November 14th, 2017
PIDapalooza is a new forum concerned with discussing all things persistent, hence PID. You might wonder what possible interest a chemist might have in such an apparently arcane subject, but think of it in terms of how to find the proverbial needle in a haystack in a time when needles might look all very similar. Even needles need descriptions, they are not all alike and PIDs are a way of providing high quality information (metadata) about a digital object.
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Tags:chemist, computing, Information, Information science, Knowledge representation, librarian, Needle, PID
Posted in Chemical IT | No Comments »
Sunday, November 12th, 2017
A few years back, I took a look at the valence-shell electron pair repulsion approach to the geometry of chlorine trifluoride, ClF3 using so-called ELF basins to locate centroids for both the covalent F-Cl bond electrons and the chlorine lone-pair electrons. Whereas the original VSEPR theory talks about five “electron pairs” totalling an octet-busting ten electrons surrounding chlorine, the electron density-based ELF approach located only ~6.8e surrounding the central chlorine and no “octet-busting”. The remaining electrons occupied fluorine lone pairs rather than the shared Cl-F regions. Here I take a look at ClMe3, as induced by the analysis of SeMe6.
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Tags:Chemical bond, chemical bonding, Chemistry, Chlorine, Covalent bond, Lone pair, Oxidizing agents, Quantum chemistry, Stereochemistry, Valence, VSEPR theory
Posted in Chemical IT, Hypervalency | 5 Comments »
Thursday, October 5th, 2017
We have heard a lot about OA or Open Access (of journal articles) in the last five years, often in association with the APC (Article Processing Charge) model of funding such OA availability. Rather less discussed is how the model of the peer review of these articles might also evolve into an Open environment. Here I muse about two experiences I had recently.
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Tags:Academic publishing, article processing charge, author, Company: Facebook, Company: Publons, Company: Twitter, editor, Electronic publishing, Entertainment/Culture, Hybrid open access journal, Internet giants, OA, Open access, Organic Syntheses, Public sphere, Publishing, Scholarly communication, search engines, Social Media & Networking, Technology/Internet
Posted in Chemical IT, General | 5 Comments »
Friday, July 21st, 2017
There is much focus at the moment on how to ensure experimental replicability in e.g. the molecular sciences. An important aspect of that is having access to FAIR data; data which is findable, accessible, inter-operable and re-usable. One of the “gold standards” in chemistry is the data associated with crystal structures. Here I take an inside peek into the standard file-type for carrying crystal structure data, the CIF file (the Crystallographic Information File).
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Posted in Chemical IT | 7 Comments »
Thursday, June 8th, 2017
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
- H.S. Rzepa, A. Mclean, and M.J. Harvey, "InChI As a Research Data Management Tool", Chemistry International, vol. 38, 2016. https://doi.org/10.1515/ci-2016-3-408
Tags:chemical content, chemical/x- media type, chemical/x-gaussian, Company: DataCite, Company: Google, digital repository search, domain-specific chemical content, media type, media:chemical/x-mnpub, media:chemical\/x\-gaussian*, Question, search definition, search engines, search string, search syntax, subject search
Posted in Chemical IT | 1 Comment »
Friday, June 2nd, 2017
In 2016, the world heard that gravitational waves had been detected and now a third instance is reported.‡ Given that the data associated with these detections are perhaps amongst the most important instances in recent times, I thought I might take a peek at how it was managed.
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Tags:Astronomy, Binary stars, Black holes, famous chemical controversy, General relativity, Gravitational wave, Gravity, Physics, search procedures, Technology/Internet, Wave
Posted in Chemical IT | 1 Comment »
Thursday, June 1st, 2017
Conformational polymorphism occurs when a compound crystallises in two polymorphs differing only in the relative orientations of flexible groups (e.g. Ritonavir).[1] At the Beilstein conference, Ian Bruno mentioned another type; tautomeric polymorphism, where a compound can crystallise in two forms differing in the position of acidic protons. Here I explore three such examples.
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References
- G.J.O. Beran, I.J. Sugden, C. Greenwell, D.H. Bowskill, C.C. Pantelides, and C.S. Adjiman, "How many more polymorphs of ROY remain undiscovered", Chemical Science, vol. 13, pp. 1288-1297, 2022. https://doi.org/10.1039/d1sc06074k
Tags:Chemistry, chloroform solutions, Conformational isomerism, Crystal, crystallography, gas phase, Ian Bruno, Isomerism, Polymorphism, Ritonavir, S-centre, Tautomer
Posted in Chemical IT, crystal_structure_mining | No Comments »