The title here is taken from a presentation made by Ian Bruno from CCDC at the recent conference on Open Science. It also addresses the theme here of the issues that might arise in assigning identifiers for any given molecule.
Archive for the ‘Chemical IT’ Category
Challenges in reliably representing the chemistry of crystal structures.
Monday, May 29th, 2017Tags:author, Bruno, chemical identifier, Digital Object Identifier, Ian Bruno, Identifier, InChI algorithm
Posted in Chemical IT | 2 Comments »
Curating a nine year old journal FAIR data table.
Monday, May 29th, 2017As the Internet and its Web-components age, so early pages start to decay as technology moves on. A few posts ago, I talked about the maintenance of a relatively simple page first hosted some 21 years ago. In my notes on the curation, I wrote the phrase “Less successful was the attempt to include buttons which could be used to annotate the structures with highlights. These buttons no longer work and will have to be entirely replaced in the future at some stage.” Well, that time has now come, for a rather more crucial page associated with a journal article published more recently in 2009.[1]
References
- H.S. Rzepa, "Wormholes in chemical space connecting torus knot and torus link π-electron density topologies", Phys. Chem. Chem. Phys., vol. 11, pp. 1340-1345, 2009. https://doi.org/10.1039/b810301a
Tags:Applet, compression algorithm, computing, Cross-platform software, HTML, HTML element, Internet Journal, Java, Java applet, Java platform, jmol, Markup languages, Open formats, publishers site, publishers systems, technology moves, Technology/Internet, the Internet Journal, Web browser, web technologies, Web-components age, XML, XSLT
Posted in Chemical IT | 8 Comments »
Conference report: an example of collaborative open science (reaction IRCs).
Thursday, May 25th, 2017It is a sign of the times that one travels to a conference well-connected. By which I mean email is on a constant drip-feed, with venue organisers ensuring each delegate receives their WiFi password even before their room key. So whilst I was at a conference espousing the benefits of open science, a nice example of open collaboration was initiated as a result of a received email.‡
Tags:animation, chemical reactions, City: Cupertino, Company: Cupertino Elec, Company: Firefox Communic, Computer Hardware - NEC, computing, detective, Digital media, Drip, Electronic documents, Electronic publishing, Email, HTML, Imperial College, Linux, operating system, Password, Person Location, Steven Kirk, Technology/Internet, XML
Posted in Chemical IT | No Comments »
Conference report: OPEN SCIENCE AND THE CHEMISTRY LAB OF THE FUTURE
Tuesday, May 23rd, 2017This is taking place in the idyllic surroundings of the Niederwald forest, Rüdesheim, Germany. Here I highlight only aspects of the first three talks.
Tags:article processing charges, Bad Kreuznach, chemical shift, chemical terms, City: Rüdesheim, Country: Germany, Hesse, Hesse-Nassau, Ian Bruno, Jeremy Frey, Klaus Tochtermann, Leah McEwen, Martin Hicks, metadata tools, Niederwald, Niederwalddenkmal, Quotation, Rüdesheim, Rüdesheim am Rhein, Rüdesheim an der Nahe, Rheingau-Taunus-Kreis, Rhine, Richard Kidd, spectroscopy, States of Germany, Stuart Chalk, Technology/Internet
Posted in Chemical IT | 1 Comment »
The challenges in curating research data: one case study.
Friday, April 28th, 2017Research data (and its management) is rapidly emerging as a focal point for the development of research dissemination practices. An important aspect of ensuring that such data remains fit for purpose is identifying what curation activities need to be associated with it. Here I revisit one particular case study associated with the molecular structure of a product identified from a photolysis reaction[1] and the curation of the crystallographic data associated with this study.
References
- Y. Legrand, A. van der Lee, and M. Barboiu, "Single-Crystal X-ray Structure of 1,3-Dimethylcyclobutadiene by Confinement in a Crystalline Matrix", Science, vol. 329, pp. 299-302, 2010. https://doi.org/10.1126/science.1188002
Tags:assigned chemical name, author, chemical name, chemical name synonym, chemical names, chemical structures, editor, indicated chemical name synonym, Knowledge, radiation, Research, Scientific method, Technology/Internet, X-ray
Posted in Chemical IT, crystal_structure_mining | 5 Comments »
Supporting information: chemical graveyard or invaluable resource for chemical structures.
Friday, March 31st, 2017Nowadays, 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]
References
- 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. https://doi.org/10.1021/jacs.6b13229
- 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, 2016. https://doi.org/10.1038/sdata.2016.18
Tags:Carbon, chemical databases, chemical graveyard, chemical spectra, Chemistry, digital signature, Nature, Organic, Organic chemistry, Organic compound, Organic food, search engines, Technology/Internet
Posted in Chemical IT | 3 Comments »
The provenance of scientific data – establishing an audit trail.
Thursday, March 30th, 2017In an era when alternative facts and fake news afflict us, the provenance of scientific data becomes ever more important. Especially if that data is available as open access and exploitable by others for both valid scientific reasons but potentially also by those with other motives. Here I consider the audit trail that might serve to establish data provenance in one typical situation in chemistry, the acquisition of NMR instrumental data.
Tags:Acquisition, Archival science, author, collection software, Company: NMR, data, Data management, data processing software, Evidence law, instrument data collection software, local authentication systems, Mestrenova, MestreNova system, Nuclear magnetic resonance, principal investigator, Provenance, Scientific method, service manager, spectrometer software, supervisor, Technology/Internet, Terminology
Posted in Chemical IT | 2 Comments »
A nice example of open data (in London).
Sunday, March 5th, 2017Living in London, travelling using public transport is often the best way to get around. Before setting out on a journey one checks the status of the network. Doing so today I came across this page: our open data from Transport for London.
Tags:API, chemical databases, City: London, Company: TfL, Government, Greater London, Local government in London, London, Passenger Transportation Ground & Sea - NEC, PDF, Public transport, Route planning software, search engine, Sustainable transport, Technology/Internet, Transport, Transport for London, travel apps, travel data, XML
Posted in Chemical IT | No Comments »
Open science and the chemistry lab of the future.
Thursday, February 9th, 2017The title refers to an upcoming symposium on the topic on 22-24 May, 2017. I quote here some of the issues tabled for discussion:
Tags:Contact Details, Social Media & Networking, Symposium, Technology/Internet, Will technology
Posted in Chemical IT, General | 1 Comment »
Revisiting (and maintaining) a twenty year old web page. Mauveine: The First Industrial Organic Fine-Chemical.
Thursday, February 2nd, 2017Almost exactly 20 years ago, I started what can be regarded as the precursor to this blog. As part of a celebration of this anniversary,[1] I revisited the page to see whether any of it had withstood the test of time. Here I recount what I discovered.
References
- P.W. May, S.A. Cotton, K. Harrison, and H.S. Rzepa, "The ‘Molecule of the Month’ Website—An Extraordinary Chemistry Educational Resource Online for over 20 Years", Molecules, vol. 22, pp. 549, 2017. https://doi.org/10.3390/molecules22040549
Tags:10.5517, Advertising & Marketing - NEC, chemical context, chemical markup language, City: London, Commercial REITs - NEC, Company: Chime, Company: Eastman Kodak, Company: First Industrial, digital cameras, Digital Object Identifier, food additives, HTML, Imperial College, industrial strength HTML editor, Java, JavaScript, manufacturing factory, mauveine using molecular modelling software, Person Attributes, Photographic Equipment, Technology/Internet, validation tool, Web, web archaeology, web server, XML, year old Web pages
Posted in Chemical IT, Historical | 1 Comment »