Scientists 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.
Posts Tagged ‘Technology/Internet’
Metametadata: data about data about (chemical) data.
Saturday, April 16th, 2016Tags:Academic publishing, automated software analysis, BASE, chemical context, Chemical Database Service, Chemical IT, 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
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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, Chemical IT, Embargo, Open access, Publishing, Royal Society of Chemistry, Technology/Internet, Uncharted, Uncharted Territory
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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 IT, 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
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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, Chemical IT, 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
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A visualization of the anomeric effect from crystal structures.
Thursday, August 27th, 2015The anomeric effect is best known in sugars, occuring in sub-structures such as RO-C-OR. Its origins relate to how the lone pairs on each oxygen atom align with the adjacent C-O bonds. When the alignment is 180°, one oxygen lone pair can donate into the C-O σ* empty orbital and a stabilisation occurs. Here I explore whether crystal structures reflect this effect.
Tags:Alkane stereochemistry, Anomeric effect, Carbohydrate chemistry, Carbohydrates, Carbon–oxygen bond, Chemical bond, Chemical IT, Ether, Lone pair, Physical organic chemistry, Quantum chemistry, Stereochemistry, Technology/Internet
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Single Figure (nano)publications, reddit AMAs and other new approaches to research reporting
Wednesday, August 5th, 2015I recently received two emails each with a subject line new approaches to research reporting. The traditional 350 year-old model of the (scientific) journal is undergoing upheavals at the moment with the introduction of APCs (article processing charges), a refereeing crisis and much more. Some argue that brand new thinking is now required. Here are two such innovations (and I leave you to judge whether that last word should have an appended ?).
Tags:10.15200, 143871.12809, Academia, Academic publishing, advocate, Chemical IT, Citation, data mining, Digital Object Identifier, Do, General, Knowledge, knowledge mining, Microattribution, Mobley, original researcher, Peer review, Publishing, scholarly publishing tools, Technology/Internet, the New Reddit Journal, Yogi Berra
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The 2015 Bradley-Mason prize for open chemistry.
Friday, June 26th, 2015Open principles in the sciences in general and chemistry in particular are increasingly nowadays preached from funding councils down, but it can be more of a challenge to find innovative practitioners. Part of the problem perhaps is that many of the current reward systems for scientists do not always help promote openness. Jean-Claude Bradley was a young scientist who was passionately committed to practising open chemistry, even though when he started he could not have anticipated any honours for doing so. A year ago a one day meeting at Cambridge was held to celebrate his achievements, followed up with a special issue of the Journal of Cheminformatics. Peter Murray-Rust and I both contributed and following the meeting we decided to help promote Open Chemistry via an annual award to be called the Bradley-Mason prize. This would celebrate both “JC” himself and Nick Mason, who also made outstanding contributions to the cause whilst studying at Imperial College. The prize was initially to be given to an undergraduate student at Imperial, but was also extended to postgraduate students who have promoted and showcased open chemistry in their PhD researches.
Tags:Cambridge, chemical data, Chemical IT, Chemistry Central, Collective intelligence, Crowdsourcing, Doctor of Philosophy, Education, European Union, France, GITHUB INC., Imperial College, Jean Claude Bradley, lab on a chip, Lyon, Nick Mason, Nonprofit technology, Open content, Peter Murray-Rust, reward systems, Technology/Internet, Tom Arrow, Tom Phillips, Wikimedia Foundation, wikipedia, World Wide Web, young scientist
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Personal web pages on digital repositories.
Saturday, June 20th, 2015The university sector in the UK has quality inspections of its research outputs conducted every seven years, going by the name of REF or Research Excellence Framework. The next one is due around 2020, and already preparations are under way! Here I describe how I have interpreted one of its strictures; that all UK funded research outputs (i.e. research publications in international journals) must be made available in open unrestricted form within three months of the article being accepted for publication, or they will not be eligible for consideration in 2020.
Tags:Academia, Academic publishing, Archival science, author, Chemical IT, Data management, Digital library, EPrints, Institutional repository, Knowledge, Knowledge representation, Library science, metadata, Open access, PDF, personal web page, Preprint, Publishing, Repository, researcher, ROMEO GREEN, Science, Technology/Internet, United Kingdom, web server
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Discovering chemical concepts from crystal structure statistics: The Jahn-Teller effect
Saturday, May 30th, 2015I am on a mission to persuade my colleagues that the statistical analysis of crystal structures is a useful teaching tool. One colleague asked for a demonstration and suggested exploring the classical Jahn-Teller effect (thanks Milo!). This is a geometrical distortion associated with certain molecular electronic configurations, of which the best example is illustrated by octahedral copper complexes which have a d9 electronic configuration. The eg level shown below is occupied by three electrons and which can therefore distort in one of two ways to eliminate the eg degeneracy by placing the odd electron into either a x2-y2 or a z2 orbital. Here I explore how this effect can be teased out of crystal structures.
Tags:basic search, Chemical bond, chemical bonding, Chemical IT, Chemistry, classical Jahn-Teller, clear Jahn-Teller, Coordination chemistry, Coordination complex, Copper(II) nitrate, dynamic Jahn-Teller, Edward Teller, Inorganic chemistry, Jahn-Teller, Jahn–Teller effect, Metal ions in aqueous solution, search criteria, Technology/Internet, Transition metals
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