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Compound and spectra deposition into ChemSpider

18 Oct 2017

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. You can watch a demonstration video on YouTube.

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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New NCDS Introductory Video

16 Jul 2015

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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Chemicalize Webinar

15 Aug 2013

Thank you to Andras Stracz from ChemAxon Ltd. for presenting a webinar discussing the possibilities of Chemicalize .

Chemicalize is a public web resource developed by ChemAxon which uses name to structure parsing to identify chemical structures on webpages and other text. Chemicalize can be accessed via the Chemical Database Service

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SPRESIweb webinar

05 Aug 2013

Many thanks to Valentina Eigner-Pitto from InfoChem for an excellent webinar running through the capabilities of SPRESIweb.

SPRESIweb is a structure and reaction database for organic chemists. The user can search 5.52 million molecules and 4.26 million reactions, extracted from 675,000 references and 164,000 patents covering the years 1974 – 2011.

The next CDS summer webinar, “Overview of Chemicalize from ChemAxon” will be held on the 13th August at 4pm BST. Register here.

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ACD/Labs I-Lab Webinar and Tutorials

12 Jul 2013

Many thanks to Richard Lee of ACD/Labs for giving an informative webinar on ACD/Labs I-Lab.

Three additional ACD/Labs I-Lab tutorials covering NMR Spectra Prediction and Databases, Names from Structures and Physicochemical Property Prediction can also be found on the CDS YouTube Channel.

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Accessing the Inorganic Crystal Structure Database through the Chemical Database Service

02 Jan 2013

The Inorganic Crystal Structure Database (ICSD) will be available initially via the Chemical Database Service by providing access via the web-based interface to ICSD. This is a start point for our support of crystallographic data that will be enhanced with additional development during the lifetime of the project.

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Integrating the CDS to RSC Graphical Databases

02 Jan 2013

At release RSC will provide access to RSC Graphical Databases. There are presently three of these that will be available: Natural Product Updates, Catalysts and Catalyzed Reactions and Methods of Organic Synthesis. We will unveil access to all of these at release and will collect feedback and usage statistics from the user base of the CDS.

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Initial Overview of Integration to SPRESIWeb

30 Dec 2012

When the Chemical Database Service releases it will already be integrated to SPRESIWeb. This movie gives a very early view of the integration in place at release. The movie is available online here and shown embedded below.

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Substructure Searching of the Accelrys Available Chemicals Directory Work in Progress

30 Dec 2012

When the National Chemical Database Service is released we will already have integration in place to the Accelrys Available Chemicals Directory. We are presently doing development work to introduce substructure searching in the near future as shown in this movie. This is an example of the substructure searching in action. This capability is NOT yet released as of 12/30/2012.

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Initial Demonstrations of the Interactive Laboratory Service as part of the Chemical Database Service

28 Dec 2012

There are a number of services that will be integrated to the Chemical Database Service moving forward and on January 2nd when we release we will only have had time to integrate a small number of these….in about a month of effort with Christmas and New Year in between. It’s been a dedicated effort to get this much done in such a short time but we owe a lot to the providers of the systems and services that we will be integrating. One of these is the ACD/Labs I-Lab, the Interactive Laboratory. As they describe on their website…I-Lab is out to save time and effort and improve productivity.

“Reduce the need for labor intensive experimental testing and literature searches, by using the online ACD/I-Lab prediction engine to predict physicochemical properties, NMR spectra and chemical shifts, and ADME toxicities. I-Lab provides predictions for NMR spectra/chemical shifts/coupling constants, nomenclature and structure generation, and advanced physicochemical properties”

For academia there is MUCH to be learned using a system such as this and we look forward to hearing how our users are getting benefit from it.

At release we will also provide TRIAL access to the I-Lab ADME and Toxicity property prediction algorithms. We want to provide access to the community of users so that we can garner feedback regarding the value of such capabilities to the user community. If they are of high value we will take this into account as we work to match the available funding to delivering the optimal service to the CDS users.

For an initial view of what is possible with Ilab check out the movie here: http://www.youtube.com/watch?v=27tdROmMeVQ

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