I occasionally post about "RDM" (research data management), an activity that has recently become a formalised essential part of the research processes. I say recently formalised, since researchers have of course kept research notebooks recording their activities and their data since the dawn of science, but not always in an open and transparent manner. The desirability of doing so was revealed by the 2009 "Climategate" events. In the UK, Climategate was apparently the catalyst which persuaded the funding councils (such as the EPSRC, the Royal Society, etc) to formulate policies which required all their funded researchers to adopt the principles of RDM by May 2015 and in their future researches. An early career researcher here, anxious to conform to the funding body instructions, sent me an email a few days ago asking about one aspect of RDM which got me thinking.
Archive for the ‘Chemical IT’ Category
Data-free research data management? Not an oxymoron.
Tuesday, May 24th, 2016Tags:Academic publishing, chemical identifiers, chemical names and chemical terms, chemical tagger page, CrossRef, Data management, Data management plan, DataCite, Identifiers, ORCiD, RDM, researcher, Royal Society, Singular spectrum analysis, Technical communication, Technology/Internet
Posted in Chemical IT | No Comments »
What is the approach trajectory of enhanced (super?) nucleophiles towards a carbonyl group?
Wednesday, May 11th, 2016I have previously commented on the Bürgi–Dunitz angle, this being the preferred approach trajectory of a nucleophile towards the electrophilic carbon of a carbonyl group. Some special types of nucleophile such as hydrazines (R2N-NR2) are supposed to have enhanced reactivity[1] due to what might be described as buttressing of adjacent lone pairs. Here I focus in on how this might manifest by performing searches of the Cambridge structural database for intermolecular (non-bonded) interactions between X-Y nucleophiles (X,Y= N,O,S) and carbonyl compounds OC(NM)2.
References
- G. Klopman, K. Tsuda, J. Louis, and R. Davis, "Supernucleophiles—I", Tetrahedron, vol. 26, pp. 4549-4554, 1970. https://doi.org/10.1016/s0040-4020(01)93101-1
Tags:Bases, Bürgi–Dunitz angle, Carbonyl, Electrophile, Ester, Flippin–Lodge angle, Functional groups, hydrazine, non-metal attachments, Nucleophile, Physical organic chemistry, search query, Superbase
Posted in Chemical IT, crystal_structure_mining | 1 Comment »
Collaborative FAIR data sharing.
Sunday, April 17th, 2016I want to describe a recent attempt by a group of collaborators to share the research data associated with their just published article.[1]
References
- C. Romain, Y. Zhu, P. Dingwall, S. Paul, H.S. Rzepa, A. Buchard, and C.K. Williams, "Chemoselective Polymerizations from Mixtures of Epoxide, Lactone, Anhydride, and Carbon Dioxide", Journal of the American Chemical Society, vol. 138, pp. 4120-4131, 2016. https://doi.org/10.1021/jacs.5b13070
Tags:10.17616, Academic publishing, DataCite, energy profile diagrams, Figshare, Identifiers, Open science, ORCiD, PDF, Scholarly communication, Technical communication, Technology/Internet, Web-enhanced object
Posted in Chemical IT | No Comments »
Metametadata: data about data about (chemical) data.
Saturday, April 16th, 2016Scientists are familiar with the term data, at least in a scientific or chemical context, but appreciating metadata (meaning "after", or "beyond") is slightly more subtle, in the sense of using it to mean data about data. The challenge lies in clarifying where the boundary between data and its metadata lies and in specifying and controlling the vocabulary used for these metadata descriptions. Items in a chemical metadata dictionary might include e.g. subject classifications such as Organic Molecular Chemistry or identifiers such as InChIkey. But what could metametadata be? Here I briefly show some examples by way of illustration.
Tags:Academic publishing, automated software analysis, BASE, chemical context, Chemical Database Service, chemical metadata, chemical metadata dictionary, chemical space, City: Cambridge, Data dictionary, Data management, Identifiers, Knowledge representation, programmer, Registry of Research Data Repositories, search.datacite.org/api, SPECTRa, Technology/Internet
Posted in Chemical IT | No Comments »
Publishing embargoes.
Wednesday, April 13th, 2016Publishing embargoes seem a relatively new phenomenon, probably starting in areas of science when the data produced for a scientific article was considered more valuable than the narrative of that article. However, the concept of the embargo seems to be spreading to cover other aspects of publishing, and I came across one recently which appears to take such embargoes into new and uncharted territory.
Tags:Academic publishing, Embargo, Open access, Publishing, Royal Society of Chemistry, Technology/Internet, Uncharted, Uncharted Territory
Posted in Chemical IT | No Comments »
Celebrating Paul Schleyer: searching for hidden treasures in the structures of metallocene complexes.
Saturday, April 2nd, 2016A celebration of the life and work of the great chemist Paul von R. Schleyer was held this week in Erlangen, Germany. There were many fantastic talks given by some great chemists describing fascinating chemistry. Here I highlight the presentation given by Andy Streitwieser on the topic of organolithium chemistry, also a great interest of Schleyer's over the years. I single this talk out since I hope it illustrates why people still get together in person to talk about science.
Tags:Centroid, chemical effect, chemical insights, chemical interpretation, City: Erlangen, Country: Germany, Degree of a continuous mapping, Ferrocene, Hydrogen bond, individual search definition, metal, overall search collection, Streitwieser, terminal H-positions, Torsion, X-ray
Posted in Chemical IT, crystal_structure_mining, Interesting chemistry | 6 Comments »
Does combining molecules with augmented reality have a future?
Monday, March 28th, 2016Augmented reality, a superset if you like of virtual reality (VR), has really been hitting the headlines recently. Like 3D TV, its been a long time coming! Since ~1994 or earlier, there have been explorations of how molecular models can be transferred from actual reality to virtual reality using conventional computers (as opposed to highly specialised ones). It was around then that a combination of software (Rasmol) and hardware (Silicon Graphics, and then soon after standard personal computers with standard graphics cards) became capable of such manipulations. VRML (virtual reality modelling language) also proved something of a false start‡ So have things changed?
Tags:Augmented reality, chemical article, Company: Microsoft, Company: Silicon Graph, for 3D printing, Google Cardboard, jmol, RasMol, User interface techniques, Virtual reality, VRML
Posted in Chemical IT, General | No Comments »
Research data: Managing spectroscopy-NMR.
Wednesday, March 16th, 2016At the ACS conference, I have attended many talks these last four days, but one made some “connections” which intrigued me. I tell its story (or a part of it) here.
Tags:Archive formats, chemical structure, ELN, Nuclear magnetic resonance, PDF, research data management, spectroscopy, suitable processing software, XML, Zip
Posted in Chemical IT | 1 Comment »
Global initiatives in research data management and discovery: searching metadata.
Monday, March 7th, 2016The upcoming ACS national meeting in San Diego has a CINF (chemical information division) session entitled "Global initiatives in research data management and discovery". I have highlighted here just one slide from my contribution to this session, which addresses the discovery aspect of the session.
Tags:Academic publishing, chemical, chemical information division, Chemical nomenclature, chemical structures, Chemical substance, chemical/x-wavefunction, Cheminformatics, City: San Diego, content media, data repository search, format type chemical/x-* , Identifiers, Imperial College, Imperial College London, International Chemical Identifier, JSON, media types, multipurpose internet media extensions, ORCiD, PDF, potential such systems, research data management, Search queries, Technical communication, Technology/Internet
Posted in Chemical IT | 2 Comments »
LEARN Workshop: Embedding Research Data as part of the research cycle
Monday, February 1st, 2016I attended the first (of a proposed five) workshops organised by LEARN (an EU-funded project that aims to ...Raise awareness in research data management (RDM) issues & research policy) on Friday. Here I give some quick bullet points relating to things that caught my attention and or interest. The program (and Twitter feed) can be found at https://learnrdm.wordpress.com where other's comments can also be seen.
Tags:Academic publishing, European Union, first Open Scientist, first secretary, Free culture movement, Henry Oldenburg, Jean Claude Bradley, Open access, Open data, Open science, RDM, Research, researcher, Royal Society, Science, Scientific method, Scientific misconduct, scientist, Technology/Internet
Posted in Chemical IT | 1 Comment »