Compound and spectra deposition into ChemSpider

Our data deposition service is now live, representing part of our commitment in hosting the EPSRC National Chemical Database Service. Details are given below – we will add to this post to build up an FAQ.

What it is

The data deposition service allows researchers to upload research data in the form of chemical structures and associated experimental spectra, link them to relevant publications, and receive DOIs for these depositions to cite them elsewhere. While the community’s preferred use cases are yet to be determined, the initial focus is on raw spectral data to provide greater value to researchers and readers than traditional electronic supplementary information files.

How to access it and what it does

It’s available through the ChemSpider link on the NCDS site, which now gives the option to either search ChemSpider or deposit data (https://deposit.chemspider.com)

The workflow for a user is to:

  • Login with an ORCID to validate their identity
  • Submit a mol file, which is checked by our Chemical Validation and Standardisation Platform (CVSP) flagging any errors or warnings
  • Upload spectral data (raw data is preferred, with the ideal format being a zip folder containing all of the original files from the instrument), and any associated publication DOIs
  • Click through to approve publication under a CC0 licence
  • Publish to ChemSpider, generating a landing page containing the structure, submitter details and links to spectra and related publications
  • Metadata is deposited with DataCite to register DOIs for the compound and any spectra, and includes related publication DOIs

Integration with ChemSpider

Any structure that is not already found in ChemSpider will be deposited when it is added to the repository. There is potential to strengthen these links with ChemSpider in the future, by exposing data from the repository directly on ChemSpider records or by expanding the new deposition route for other uses.

What’s next

We know there are a lot of features that could be added, but we are keen to get this initial version out and then build on it via user feedback. We see the ability to deposit research data more directly into ChemSpider as an important building block for the future.

Who to contact

Please contact cds@rsc.org if you have any questions or feedback.

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Remote desktop updated with recent Cambridge Structural Database data release

The February 2017 Cambridge Structural Database (CSD) data update is now available through the remote desktop. This release added 18,092 new entries to the database and updated CSD software to the latest versions.

(This update was delayed by other maintenance work on the remote desktop. Normally updates are applied as soon as they are released by CCDC.)

The CSD remote desktop offer users of the Chemical Database Service the ability to log in remotely from any computer and use the majority of the software and features found in a local CSD installation. For more information, visit http://cds.rsc.org/about.asp and choose Cambridge Structural Database (CSD).

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Help us demonstrate the scientific impact of the National Chemical Database Service

We’re gathering evidence of the National Chemical Database Service’s scientific impact to ensure UK academia’s continued access to these important resources – and we need your help.

The National Chemical Database Service is supported by the Engineering and Physical Sciences Research Council on the basis that it meets a community need: access to specialist databases that enable research in chemistry and related fields. As part of EPSRC’s routine review of mid-range facility provision, we are preparing an application (called a Statement of Need) to justify continued support of the NCDS after 2017. While we will collate the application on behalf of our Advisory Board, it represents the views and needs of the UK scientific community, so your input is vital to its success. You can help us ensure that all of UK academia retains access to the NCDS resources in the following ways:

What is a Statement of Need?

A Statement of Need details the scientific community’s need for a particular facility, service or piece of equipment, and gives evidence demonstrating how that facility enables high-quality science and offers value for money. For the NCDS, this means that we need to show examples of how access to NCDS resources underpins high-quality research in the UK.

Each Statement of Need is reviewed by experts in the field, and then prioritised by an EPSRC panel based on the reviewers’ comments. This prioritisation determines which facilities will be funded.

The purpose of the Statement of Need process is to determine whether or not to continue funding the NCDS, not to decide if the Royal Society of Chemistry should continue to host it. If funding is continued, a tender process in 2018 will determine which organisation will run the service in the future.

What is a mid-range facility?

The NCDS is an EPSRC mid-range facility; EPSRC funds these services to academia at a national level because it’s more cost-effective and efficient than individual institutions paying for the same service. Most mid-range facilities provide access to expensive equipment and specialised expertise that would be difficult for any one institution to support. Rather than being based around a particular scientific technique, the NCDS is a virtual facility, providing access to a number of key chemical data resources for all UK academics. In addition to the cost savings achieved by negotiating database subscriptions at a national level, the mid-range facility model allows us to provide centralised user support and training.

Our Advisory Board

Peter Scott Advisory Board Chair, Professor of Chemistry, University of Warwick
Isaac Abrahams Senior Lecturer and Consultant to the X-Ray Diffraction Facility, Queen Mary University of London
Morgan Alexander Professor of Biomedical Surfaces, University of Nottingham
Simon Coles Professor of Structural Chemistry, University of Southampton and Director, UK National Crystallography Service
Linda Humphreys Science Faculty Librarian, University of Bath
Niall Mac Dowell Senior Lecturer of Energy and Environmental Technology and Policy, Imperial College London
Richard Whitby Professor of Organic Chemistry, University of Southampton
Joseph Wright Lecturer in Energy Materials, University of East Anglia
Talit Ghaffar Physical Sciences Manager, EPSRC

 

Complete our questionnaire or contribute some details about you use of the NCDS.

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Learn to use ACD/I-Lab chemistry tools

The National Chemical Database Service recently held two webinars about the functionality of ACD/I-Lab, one of the resources available free to all UK academics via the NCDS.

These videos are now available to watch on our YouTube channel:

Webinar 1: NMR Predictions and drawing tools

Webinar 2: PhysChem, ADME and Tox prediction, and Name generation

Thanks to Dimitris Argyropoulos for hosting these and explaining the capabilities of ACD/I-Lab.

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The new DETHERM is here

We’ve just updated the NCDS to the all-new DETHERM website – try it out now

With 8.9 million data sets relating to 44,200 pure compounds and 139,400 mixtures, DETHERM is an invaluable resource for researchers in chemistry and related fields. This update features a much-improved search system and user interface, making it easier for you to search the DETHERM database of thermophysical properties.

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Improvements to Available Chemicals Directory interface

The Available Chemicals Directory has pricing and supplier information for 3.2 million unique chemicals from over 800 suppliers. We’ve made several improvements to our search interface to help you get the most out of this resource:

Search the Available Chemicals Directory via the NCDS

Substructure search makes finding the chemicals you need simple – and don’t forget that you can add explicit hydrogens to your search query to specify unsubstituted carbon centres.

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New NCDS Introductory Video

We’ve put together a new video to introduce the National Chemical Database Service – take a look and let us know what you think!

NCDS Introduction

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NCDS now trialling ADME-Tox predictive features

The ADME-Tox predictive features of ACD/I-Lab are now available through the National Chemical Database Service on a trial basis. These features include industry-leading algorithms for predicting ADME properties such as bioavailability and absorption, as well as toxicity properties such as LD50. A full list of predictive modules available through ACD/I-Lab can be found on ACD/Labs’ website.

Access to ACD/I-Lab is provided free to all UK academics by the NCDS.

This trial will run until the end of July 2015, after which we will use the results of the trial to determine whether ADME-Tox features should be be permanently included as an NCDS resource. If NCDS access to these features is useful for your research, please let us know your thoughts to help us understand the value of this resource to the UK academic community.

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Shibboleth access to NCDS resources now available

Web browser-based National Chemical Database Service resources at http://cds.rsc.org can now be accessed off-campus by logging in using Shibboleth. When accessing NCDS resources off-campus, click “Authenticate with Shibboleth” and then either log in using an Athens Login or choose your academic institution from the UK Federation list.

We hope that Shibboleth access will provide a convenient way for you to access National Chemical Database Service resources from any location.

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Access to ARChem is withdrawn

The access to ARChem via the Chemical Database Service will be withdrawn from 15th July 2014.  The developers, SimBioSys, wish to redevelop the product following their acquisition by Wiley, so it will not therefore be available via the CDS after this date. Existing signed-up users have been informed directly.

Find other online scientific resources and databases on the Chemical Database Service homepage.

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