News – ChemSpider Blog

Archive for the ‘News’ Category

Webinar 3: Chemistry data: Challenges and opportunities. Watch the recording

18 Nov 2023

We will explore ongoing and planned initiatives developing standards and tools, research infrastructures, and cultures to support FAIR chemistry data as well as its preparation, publication, and reuse.

Webinar 3: Challenges and opportunities

Held 7 December 2023. Recording available on-demand. Register now to watch the recording

Speakers

“How to initiate the cultural change towards digital chemistry” SLIDES
Sonja Herres-Pawlis
Chair of Bioinorganic Chemistry, RWTH Aachen

“How can we combat heterogeneous, unfair and disparate data in digital chemistry? ” SLIDES
Samantha Kanza
Senior Enterprise Fellow, University of Southampton
Pathfinder Lead, Physical Sciences Data Infrastructure (PSDI)

“How data journals can support (chemistry) data sharing and discovery” SLIDES
Guy Jones
Chief Editor of Scientific Data, Springer Nature

Sponsored by Revvity

Revvity Signals Software, formerly PerkinElmer Informatics, has over three decades of experience providing support for scientific workflows.

Our powerful informatics solutions are used in R&D across disciplines from drug discovery to materials development. Now under our Signals Research Suite, our end-to-end SaaS solution integrates workflows to accelerate innovation and help scientists collaborate. In addition, our solution powered by TIBCO® Spotfire® can transform clinical trials.

From our flagship ChemDraw® and E-Notebook applications, to our Signals Research Suite, to our TIBCO® Spotfire® partnership for data analytics, Revvity Signals offers a powerful suite of scientific solutions.

Supported by

About ChemSpider

Explore more than 128 million structures on the ChemSpider database. Including over 200 data sources, ChemSpider is a valuable source of information for chemical scientists working with data.

Freely accessible and comprehensive, this rich source of structure-based chemistry information is a fundamental resource for chemical scientists working with data everywhere.

Learn more about ChemSpider

Comments Off on Webinar 3: Chemistry data: Challenges and opportunities. Watch the recording

Webinar 2: What does the future hold? Watch the recording

17 Oct 2023

Webinar 2: What does the future hold?

Held on 17 November 2023 – recording available on-demand. Register now to watch the recording

Speakers

“Data explosion in chemistry: what are we going to do with all the data, and what will it do to us?” SLIDES
Lynn Kamerlin
Professor and Georgia Research Alliance Vasser Woolley Chair in Molecular Design, Georgia Tech

“Will an AI win a chemistry Nobel Prize and replace us?” SLIDES
Simon Coles
Professor of Structural Chemistry, University of Southampton

“Data sharing at the RSC” SLIDES
May Copsey
Executive Editor, Chemical Science, RSC
Anna Rulka
Executive Editor, Digital Discovery, RSC

Sponsored by Revvity

Revvity Signals Software, formerly PerkinElmer Informatics, has over three decades of experience providing support for scientific workflows.

Supported by

About ChemSpider

Explore more than 128 million structures on the ChemSpider database. Including over 200 data sources, ChemSpider is a valuable source of information for chemical scientists working with data.

Freely accessible and comprehensive, this rich source of structure-based chemistry information is a fundamental resource for chemical scientists working with data everywhere.

Learn more about ChemSpider

Comments Off on Webinar 2: What does the future hold? Watch the recording

Webinar 1: Where are we with digital chemistry data? Watch the recording

09 Oct 2023

These webinars will explore how digital chemistry data is enabling research – existing models, current challenges and exemplars, and what’s needed to evolve towards a better future using chemistry data.

We will focus on how data is enabling research – existing models, current challenges and exemplars, and what’s needed to evolve a better future using chemistry data.

Webinar 1: Where are we with digital chemistry data?

Watch on-demand: Regis ter now to watch the recording

Webinar recorded on 17 October 2023

Speakers

“WANTED: standard notation for reusable chemical data” SLIDES
Leah McEwen
Chemistry Librarian, Cornell University

Kevin Jablonka
Research Group Leader, University of Jena

Pierre Morieux
Chemistry Product Marketing Manager, Revvity Signals

Sponsored by Revvity

Revvity Signals Software, formerly PerkinElmer Informatics, has over three decades of experience providing support for scientific workflows.

Supported by

About ChemSpider

Explore more than 128 million structures on the ChemSpider database. Including over 200 data sources, ChemSpider is a valuable source of information for chemical scientists working with data.

Freely accessible and comprehensive, this rich source of structure-based chemistry information is a fundamental resource for chemical scientists working with data everywhere.

Learn more about ChemSpider

Comments Off on Webinar 1: Where are we with digital chemistry data? Watch the recording

ChemSpider webinars – helping you embrace digital chemistry data with expert insights

22 Sep 2023

How can you learn about chemistry data trends and best practices happening right now? Elevate your knowledge for future success with leading experts in our three-part webinar series.

The webinar series will focus on how data is enabling research – the current challenges and examples and how a better future can be created using chemistry data. It will showcase current and planned initiatives to develop standards and tools, research infrastructures, and developing cultures to support Findable Accessible Interoperable Reusable (FAIR) chemistry data preparation, publication and reuse.

Elevate your data practices

Created as a free, three-part series for chemical scientists working with data, learn more about chemistry data today, what the future holds, and the current challenges and opportunities of digital chemistry data. Make the most of this opportunity to discover insights from the experts in the field – register for all three webinars.

Webinar 3: Challenges and opportunities

7 December 2023. Register now to watch the recording

Speakers

“How to initiate the cultural change towards digital chemistry” SLIDES
Sonja Herres-Pawlis
Chair of Bioinorganic Chemistry, RWTH Aachen

“How can we combat heterogeneous, unfair and disparate data in digital chemistry?” SLIDES
Samantha Kanza
Senior Enterprise Fellow, University of Southampton
Pathfinder Lead, Physical Sciences Data Infrastructure (PSDI)

“How data journals can support (chemistry) data sharing and discovery” SLIDES
Guy Jones
Chief Editor of Scientific Data, Springer Nature

Webinar 1: Where are we with digital chemistry data?

Held on 17 October 2023 – recording available on-demand. Regis ter now to watch the recording

Speakers

“Wanted – standard notation for reusable chemistry data” SLIDES
Leah McEwen
Chemistry Librarian, Cornell University

Kevin Jablonka
Research Group Leader, University of Jena

Pierre Morieux
Chemistry Product Marketing Manager, Revvity Signals

Webinar 2: What does the future hold?

Held on 17 November 2023 – recording available on-demand. Register now to watch the recording

Speakers

“Will an AI win a chemistry Nobel Prize and replace us?” SLIDES
Simon Coles
Professor of Structural Chemistry, University of Southampton

“Data sharing at the RSC” SLIDES
May Copsey
Executive Editor, Chemical Science, RSC
Anna Rulka
Executive Editor, Digital Discovery, RSC

Sponsored by Revvity

Revvity Signals Software, formerly PerkinElmer Informatics, has over three decades of experience providing support for scientific workflows.

Supported by

About ChemSpider

Explore more than 128 million structures on the ChemSpider database. Including over 200 data sources, ChemSpider is a valuable source of information for chemical scientists working with data.

Freely accessible and comprehensive, this rich source of structure-based chemistry information is a fundamental resource for chemical scientists working with data everywhere.

Learn more about ChemSpider

Comments Off on ChemSpider webinars – helping you embrace digital chemistry data with expert insights

ChemSpider Mobile app

28 Oct 2019

ChemSpider Mobile was an app developed by Molecular Materials Informatics Inc¹ on behalf of the Royal Society of Chemistry to allow users to explore the benefits of ChemSpider on mobile devices. Since its launch we have made improvements to ChemSpider.com, including responsive design elements to allow it to work better on smart phones and tablets² and upgrades to the ChemSpider web services³ that power it. As a result of these developments we felt it was timely to review the community’s need for the app and have taken the decision to discontinue support for the services that power the app from 31^st October. We would like to thank everyone who used and provided feedback on the app to aid its development and encourage you to switch to using ChemSpider.com for future mobile use.

1. http://molmatinf.com/

2. http://blogs.rsc.org/chemspider/2015/05/21/introduction-to-the-new-chemspider-website/

3. https://developer.rsc.org/

Comments Off on ChemSpider Mobile app

Chemical Validation and Standardization Platform (CVSP)

30 Nov 2018

The Chemical Validation and Standardization Platform (CVSP)¹ was developed during the Open PHACTS IMI project² to process chemical structure files through tested validation and standardization protocols. The aim was to provide the community with rigorous analysis of their chemical structure files to ensure that data released into the public domain via online databases was pre-validated. The online CVSP site provided a useful means to test the rulesets and allow users to validate their structure files, but the standalone website was taken offline in November 2018. As a legacy, the codebase and ruleset has been evolved and applied to the ChemSpider deposition system at deposit.chemspider.com³ and the community discussions around appropriate standardisation of chemical structure files continue. The original code is also available from GitHub.⁴

The Chemical Validation and Standardization Platform (CVSP): large-scale automated validation of chemical structure datasets, J. Cheminf., 2015, 7:30, https://doi.org/10.1186/s13321-015-0072-8
https://www.openphacts.org
https://deposit.chemspider.com/
https://github.com/openphacts/ops-crs/tree/master/CVSP

Comments Off on Chemical Validation and Standardization Platform (CVSP)

Royal Society of Chemistry Renews Partnership with ACD/Labs to Continue Providing Industry-Leading Data to Worldwide Research Community

30 Jul 2018

ACD/Labs algorithms will continue to equip ChemSpider with physicochemical property values and chemical nomenclature following ten year milestone.

Toronto, CANADA (July 26, 2018)—ACD/Labs, an informatics company that develops and commercializes solutions in support of R&D, today announced the continued collaboration with ChemSpider, a leading chemical database owned by the Royal Society of Chemistry, to continue furnishing predicted physicochemical properties and chemical nomenclature to the ever-expanding platform. For over ten years, scientists have accessed this publically-available free resource to gather information on chemical compounds in preparation of research or experimentation.

As the industry standard for physicochemical prediction software, ACD/Labs was chosen to generate property information including logP, logD (at various pHs), Lipinski rule-of-5 values, and boiling point, and to provide Name-to-structure (and vice-versa) capabilities. The renewal of the partnership further reflects the success of the platform and its continued importance as one of the most robust online chemical structure databases for the scientific community. As the platform advances, ChemSpider will continue to use ACD/Labs algorithms to provide quality insights to researchers.

“We set out with the mission of empowering researchers with a comprehensive view of chemical data to inform R&D initiatives,” said Richard Kidd, Publisher, Royal Society of Chemistry. “By working with ACD/Labs and utilizing its property information, we’ve been able to meet our users’ need for knowledge, which is reflected in our rapid growth since the Royal Society of Chemistry acquired ChemSpider ten years ago. To-date, property information populated by ACD/Labs’ algorithms has been among the most accessed on ChemSpider, and remains a key driver in our service.”

While ChemSpider has doubled the size of its database, it has remained committed to maintaining high quality data from selective sources. As the platform continues to grow, ChemSpider will use ACD/Percepta prediction algorithms and ACD/Name tools in a batch-wise fashion to populate the database and enhance publicly available chemical intelligence.

“Enabling the dissemination of chemical knowledge and providing solutions to accelerate R&D are among our top priorities at ACD/Labs,” said Gabriela Cimpan, Senior Director Sales, Europe, ACD/Labs. “ChemSpider is empowering knowledge throughout the chemical community and we feel privileged to be able to support learning worldwide.”

For more information on ACD/Percepta, visit https://www.acdlabs.com/percepta

For more information on ACD/Labs Chemical Nomenclature tools, visit https://www.acdlabs.com/name

For more information on ChemSpider, visit http://www.chemspider.com

About Advanced Chemistry Development, Inc.

ACD/Labs is a leading provider of scientific informatics technologies to R&D organizations that rely on analytical data and molecular information for decision-making, problem-solving, and product lifecycle control. Our software automates and accelerates molecular characterization, product development, and knowledge management. We integrate with existing informatics systems and undertake custom projects including enterprise-level automation.

ACD/Labs solutions are used globally in a variety of industries including pharma/biotech, chemicals, consumer goods, agrochemicals, petrochemicals, and academic/government institutions. We provide worldwide sales and support, and more than 20 years of experience and success helping organizations accelerate R&D and leverage corporate intelligence. For more information, please visit www.acdlabs.com. Follow us on Twitter @ACDLabs.

About the Royal Society of Chemistry

The Royal Society of Chemistry is the world’s leading chemistry community, advancing excellence in the chemical sciences. With over 50,000 members and a knowledge business that spans the globe, we are the UK’s professional body for chemical scientists; a not-for-profit organisation with 175 years of history and an international vision for the future. We promote, support and celebrate chemistry. We work to shape the future of the chemical sciences – for the benefit of science and humanity.

Comments Off on Royal Society of Chemistry Renews Partnership with ACD/Labs to Continue Providing Industry-Leading Data to Worldwide Research Community

Adding RSC CIFS to ChemSpider

09 Dec 2013

Written by Aileen Day.

We are pleased to announce that we have just imported 1047 CIFs to ChemSpider of crystal structures that were previously reported in RSC papers (and are available as ESI for those) to ChemSpider for the relevant compounds, and linked those back to the original articles and to the CCDC’s webCSD, e.g. example compound with RSC article CIF (see the CIF infobox). Since each CIF that is uploaded into ChemSpider must be associated with a ChemSpider compound, the difficult part of this task was working out a 2D molecular structure (in .mol file format) for each 3D crystal structure (in .cif file format) – which is particularly difficult because CIFs only contain information about each atomic position and not how the atoms are bonded to each other in the crystal or whether they are charged or not.
Ultimately we would like this CIF to mol conversion (and the whole upload) to be performed programmatically without human intervention. However, there is no reliable way to do that currently – although programs such as OpenBabel can be used to extract mols from each CIF, the reliability of this conversion isn’t 100%.
So as one of our student intern projects at the University of Southampton this summer (in parallel with another student intern project at Southampton University to share thesis data in ChemSpider) we used OpenBabel (version 2.3.2, run from the command line with the options -i cif inputfilename.txt -o mol -m –unique -d –AddPolarH) to extract mols for all the CIFs in the RSC archive (over 43,000 files as of June 2013) and enlisted Julija Kezina (shown below) to review the results of these conversions to ensure that only good structure and CIF pairs would be deposited to ChemSpider, and to better understand the problems in the conversion process with a view to fixing them. One problem that became immediately apparent was that because the 2D structure obtained was just a projection of the 3D structure along the a cell axis, which is not always the orientation which shows the molecule most clearly, even if they did have the write chemical connections between the atoms, so all mol structures were run through OpenEye’s cleaning algorithm before being reviewed.

Julija Kezina – Southampton University intern who examined CIF to Mol conversion

Julija compared each structure in the output mol files with those in the original CIF files to judge whether the conversion was accurate or not. In addition, as an extra check, all of the output mol structures were submitted to ChemSpider validation and standardisation platform to filter out molecules with structural problems (e.g. stereochemistry, valence or congestion issues).
Overall, approximately 30% of the CIF to mol conversions that Julija checked were good, with the right connectivity of atoms and ions (although approximately 30% of these needed the atomic positions to be repositioned to clean or tidy up the structure, either manually or using ChemDraw’s cleaning functionality). The 1047 of these mols which contain only a single molecule (without solvent molecules or cocrystals etc.) are those which have been deposited into ChemSpider with their corresponding CIFs.
The journals which had the highest successful conversion percentage were Molecular BioSystems (57%), MedChemComm (51%), Organic and Biomolecular Chemistry (44%) and Green Chemistry (44%) – the journals which in general are about small organic molecules.
Julija was working in the National Crystallography Service’s office at the University of Southampton, under the co-supervision of Professor Simon Coles, and we are grateful to them for their help and advice about the finer points of the CIF file format.

Unsuccessful CIF to mol conversions

Running and evaluating OpenBabel on such a large and varied set of structures has given us a useful opportunity to identify and categorise the most common problems encountered. Here we share these and give examples that would enable the identification of some easy fixes in the pipeline that might benefit the whole community and be used as test cases when doing so. We will report these bugs to the OpenBabel forum and because OpenBabel is open source, hope to resolve at least some of these issues in the future through collaboration with its other developers.

The following OpenBabel bugs look like they might be most straightforward to fix:

Details	Example
Category: BAD_NITRO Frequency: 233 Description: there are different ways of representing nitro groups in structure drawers – OpenBabel currently does so by producing a mol with a pentavalent nitrogen. In ChemSpider we we choose to avoid this in favour of a format with a charge-separated nitro. Solution: Allow OpenBabel to have a different output option for nitro groups to output them as shown in corrected mol file.	CIF: CCDC 194360 ChemSpider: 10001804
Category: BAD_MULT Frequency: 434 Description: Duplicate (exactly identical, including stereochemistry) molecules are present in the resulting mol file despite running OpenBabel with the –unique option (which should filter out duplicate molecules based on their inchis) Solution: Fix OpenBabel when run with the –unique option so that it works.	CIF: CCDC 229590 ChemSpider: 3915
Category: BAD_MISSINGPARTOFMOLECULE Frequency: 724 Description: Part of the molecule is missing Cause: OpenBabel doesn’t understand crystal symmetry – only the atoms in the CIF that are explicitly listed with positions are included in the resulting mol file, and those that are inferred by symmetry are not. Solution: Make OpenBabel generate the full molecule from the symmetry in the CIF file, or recommend that a script/program that can process a CIF to generate another CIF with all atoms is run before OpenBabel.	CIF: CCDC 185091 ChemSpider: 11917
Category: BAD_PARTIALOCCUPANCY Frequency: 432 Description: partial occupancy of multiple sites for a particular atom in the CIF file Cause: In CIF files sometimes positions of multiple sites are specified with occupancy less than one – OpenBabel doesn’t recognise this and assumes that the occupancy of all sites is one effectively, so that there are duplicates of some atoms or fragments in the mol file. Solution: Where the _atom_site_occupancy is less than one, group together atoms into those which are alternatives of each other (by type, proximity, and those which add up to a total occupancy of 1) and choose only one of them to include in the final mol file (that with the highest site occupancy, or if two have equal occupancies of e.g. 0.5 then pick one at random). Note that there needs to be consistency, so that if for example a C is discarded, then all of the adjoining H’s with partial occupancy are also discarded but those bonded to the C that is included are included (as in the attached example).	CIF: CCDC 854369 ChemSpider: 68005704

Many of the problems were caused by idiosynchronies or errors in the input CIFs, but these on the whole weren’t handled well by OpenBabel (e.g. by writing an error message and terminating the program) but rather, in the majority of cases went into an infinite loop and the program hung. Because of this, and because the OpenBabel conversions were part of a longer script, all OpenBabel jobs had to be run with an arbitary timeout so that if still running after this timeout they were killed, which may have discarded some valid but long-running OpenBabel jobs. We will investigate whether there is a validation program that can be automatically performed on CIFs to filter out ones with these problems (similar to the CCDC’s EnCIFer but which can be run programmatically), but it would be relatively straightforward to make OpenBabel more reliable by being able to exit nicely when it encounters these problems so that pre-validation wasn’t necessary. These problems are listed in the table below:

Details	Example
Category: CIF_NOCOORDINATES Frequency: 378 Description: cif doesn’t contain any coordinates Cause: Some CIFs contain e.g. powder diffraction refinement data and don’t contain coordinates. Solution: OpenBabel already issues an error: “CIF Error: no atom found ! (in data block:XXX)” – simply abort the program if this is found (rather than trying to continue).
Category: CIF_MISSINGLOOP Frequency: 85 Description: cif misses a “loop_” line Solution: Do an initial check that there is at least one loop_ line in the expected place before attempting to do the conversion.	CIF: CCDC 753484
Category: CIF_COMMENTEDFIELD Frequency: 36 Description: if there is a CIF field name in a commented section of the CIF, OpenBabel doesn’t ignore it and goes into an infinte loop Solution: It would be trivial to make sure that OpenBabel ignores CIF field names which are commented out (between a pair of semicolons).	CIF: CCDC 840581

The following OpenBabel bugs were the most frequent in occurence, but will be difficult to fix. They arise from the problem that the CIF format does not record charges on atoms/ions or the types of bong between them so OpenBabel needs to work them out which is hard to do correctly.

Details	Example
Category: BAD_CHARGEMISSING Frequency: 830 Description: One or more ions in the molecule have the wrong charge on them in the resulting mol file	CIF: CCDC 879075 ChemSpider: 68005707
Category: BAD_WRONGCOORDINATION Frequency: 747 Description: One or more atoms or ions in the molecule have the wrong coordination – problem observed in metal ions, S, P, Se and B	CIF: CCDC 218529 ChemSpider: 26579734
Category: BAD_BONDMISSING Frequency: 587 Description: One or more of the bonds in the molecule are of the wrong order e.g. a single bond instead of a double bond.	CIF: CCDC 926530 ChemSpider: 34226187
Category: BAD_WRONGBOND Frequency: 452 Description: Wrong sequence of single/double bonds.	CIF: CCDC 203663 ChemSpider: 238575
Category: BAD_NOCOORDL Frequency: 52 Description: no coordination to a ligand.	CIF: CCDC 218360 ChemSpider: 68005705
Category: BAD_MISSINGH Frequency: 18 Description: missing hydrogen.	CIF: CCDC 220380 ChemSpider: 21188989

There were also some problem mol files produced which either won’t be able to be fixed by OpenBabel (since they resulted from either errors or limitations of the input CIF files which cannot be fixed retrospectively) or are too difficult to fix and/or too infrequently occuring to be worth the effort:

- There were 237 cases where there were solvent molecules in the CIF (many of which have missing hydrogens, partial occupancy of the molecule or part of the molecule etc.) which give rise to spurious oxygens, fragments of molecules and radicals in the resulting mol file (see CIF: CCDC 213787 and ChemSpider record: 68005706). 148 of these cases are just water solvent molecules either with missing or detached hydrogen atoms. The poor definition of the solvent molecules is a limitation of CIF files from diffraction so it is not possible for OpenBabel to better define them in the output mol that is derived from them. However, running OpenBabel with the -r option to remove all but the largest contiguous fragment was quite successful to remove these problem solvent molecules so no further action is required to deal with this problem and this option will be used by us in the future.
- There were 81 cases where there was at least one missing hydrogen in the original CIF (or in 3 cases, all hydrogens missing) – see CCDC 259871.
- Some CIFs contain crystal structures which correspond to continuous networks rather than small molecules (e.g. polymers, MOFs, zeolites, POMs) which cannot meaningfully be captured in mol format – see CCDC 206593.
- There were a few (24) cases where the stereochemistry in the mol file obtained is incorrectly defined. However, because on the stereochemistry was well interpreted by OpenBabel and these cases were relatively few, it probably isn’t worth disturbing the apple cart to investigate these further – see CCDC 238611 and ChemSpider 9419187.

Comments Off on Adding RSC CIFS to ChemSpider

Southampton University internships to transfer thesis data into LabTrove and ChemSpider

25 Sep 2013

Written by Aileen Day.

This summer there have been a number of students from the University of Southampton doing internships on joint projects between the university and the Royal Society of Chemistry and ChemSpider. Three of these students have been sifting through theses from past members of Richard Whitby’s research group in order to extract the compound, spectra and reaction data in it (and linked lab note books, and archive spectra files) and share these in LabTrove, ChemSpider, and CSSP. The students – Alex Hartke, Yet Wai Lee and Josh Whittam (all 2nd year undergraduates) – are shown below together with the boxes of thesis data, lab notebooks and spectra print outs that they digitised.

Southampton University interns

Between them they digitised 7 theses, by A.Henderson, L. Sayer, D. Owen, D.Macfarlane, F. Giustiniano, G. Saluste, J. Stec, which resulted in 1035 LabTrove pages being published to the Whitby Group’s LabTrove blog.

The theses were a rich source of compound information – including compound structures, names, properties and spectra, all of which were also deposited into ChemSpider resulting in 208 new compound pages, and about 600 spectra.

For this project the students manually deposited the compound information into LabTrove and then deposited the compounds and spectra to ChemSpider. However, we are currently developing a range of ChemSpider jquery widgets which can be integrated into web-based ELNs such as LabTrove which will make it easier to enter compound information from ChemSpider into experiments, and also to publish compound and reaction data from the ELNs to ChemSpider, CSSP and ChemSpider Reactions. This will follow on from the initial proof of concept to retreive ChemSpider information and enter it into LabTrove pages.

With this long-term aim in view, the LabTrove pages that the interns stored the compound and reaction data were structured using LabTrove templates, and this structuring will make it easier for publishing widgets to understand the data and process it the correct way. In this way, the project was partly a test to ensure that the templates were suitable for storing compound data in LabTrove. As well as the ChemSpider compound and associated data template (with corresponding help page, templates were also written to store reaction data in a formatted way, since the theses were primarily focused on the synthesis of compounds. At their simplest, basic reaction data can be stored in LabTrove using the ChemSpider Reactions template (and corresponding help page, and eventually posts written in this format will be easily publishable to ChemSpider Reactions. More detailed reaction data can be stored using the ChemSpider SyntheticPages style reaction template (and corresponding help page. The initial aim was to deposit all of this reaction data into ChemSpider SyntheticPages but it became clear that it was difficult for anyone other than the researcher who conducted the reaction, or their superviser to supply the necessary level of detail for CSSP submissions, and in particular couldn’t easily be reached by retrospectively abstracting theses. As a result, only a handful of reactions were submitted to CSSP, and the majority (over 500) were stored in LabTrove for future submission to ChemSpider Reactions.

If reactions can be published easily from ELNs to ChemSpider Reactions and that is easily queryable by other researchers and their applications when performing new reactions this will be a major step towards the aims of the Dial-a-molecule (an EPSRC Grand Challenge network). An important part of the reaction data which needs to be captured is the stoichiometry table of substances used and produced in a reaction. However, these stoichiometry tables are too complicated to incorporate into a LabTrove template, so the LabTrove reaction templates will be used in conjunction with a new ChemSpider jquery widget which is currently in the process of being integrated with LabTrove (more details to follow on this blog shortly!) which will construct them. The widget performs ChemSpider lookups to retrieve compound information, and will calculate equivalents, thereby saving the researcher time when working out the amounts of reactants needed or yields of products obtained. An example of a reaction post which was initially created using the ChemSpider Reactions template and then supplemented by adding a stoichiometry table to it using the ChemSpider Edit Stoichiometry Table widget is shown here.

If you are a LabTrove user and wish to use the ChemSpider templates, their source is available via their links above, and instructions for using templates in Labtrove are documented here.

Comments Off on Southampton University internships to transfer thesis data into LabTrove and ChemSpider

Archive for the ‘News’ Category

Webinar 3: Challenges and opportunities

Held 7 December 2023. Recording available on-demand. Register now to watch the recording

Speakers

Sponsored by Revvity

Supported by

About ChemSpider

Webinar 2: What does the future hold?

Held on 17 November 2023 – recording available on-demand. Register now to watch the recording

Speakers

Sponsored by Revvity

Supported by

About ChemSpider

Webinar 1: Where are we with digital chemistry data?

Watch on-demand: Register now to watch the recording

Speakers

Sponsored by Revvity

Supported by

About ChemSpider

Elevate your data practices

Webinar 3: Challenges and opportunities

7 December 2023. Register now to watch the recording

Speakers

Webinar 1: Where are we with digital chemistry data?

Held on 17 October 2023 – recording available on-demand. Register now to watch the recording

Speakers

Webinar 2: What does the future hold?

Held on 17 November 2023 – recording available on-demand. Register now to watch the recording

Speakers

Sponsored by Revvity

Supported by

About ChemSpider

About Advanced Chemistry Development, Inc.

About the Royal Society of Chemistry

Unsuccessful CIF to mol conversions

Meta

Watch on-demand: Regis ter now to watch the recording

Held on 17 October 2023 – recording available on-demand. Regis ter now to watch the recording