Update on CDS January 27th 2013

In the past week we have rolled out a couple of updates to the CDS. Of course this happens in the background with as minimum downtime as possible. These updates deliver as follows:

* ACD/Labs Ilab platform: Removal of license, Fixed bug with molfile reader, Replace drawing editor with Javascript version rather than Java

* Accelrys Available Chemicals Directory integration: Bug fixes and tweaks to the name/structure widget

We are presently focusing our efforts on the following activities:

* Moving ahead with the integration of the DETHERM database

* Identifying other online resources that the community might want to see integrated (feel free to leave your suggestions in the comments section below)

* Processing a very large deposition of Mass Spectrometry data that we can serve up as an integrated resource

* We are in discussions to integrate the WebCSD into the chemical database service

* We are also discussing with a number of other database/service suppliers in order to facilitate access to additional capabilities

* We are presently reviewing new Javascript widgets that will allow for the display of assigned NMR, IR and Mass spectral data that will be integrated into the CDS in the coming weeks

We also had our first meeting with a small panel of CDS users and advisors and will be considering and implementing as appropriate some of their feedback. This will be reported in more detail in a separate post.

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ICSD CIF Download Issue Resolved

We recently reported that we had an issue with the download of CIF files from our ICSD integration to the Chemical Database Service. This has now been resolved thanks to the team hosting the ICSD service. If you observe any more issues with any of the services please report them to us at cds@rsc.org. Despite our best efforts to test every piece of functionality under every browser configuration and operating system etc it is the feedback from the users that is most useful at pointing us to issues of relevance to you. Next up for us to resolve is the issues we are seeing with Ilab, though at present they are quite minor.

In the background at present we are in discussions regarding the new services that we hope to integrate in the near future. We will keep you updated.

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Bugs noted in the first week of release of the CDS

Last week we unveiled the initial incarnation of the Chemical Database Service and dealt with some of the earliest feedback and issues from the users. It was of course the first week back after the holidays and many people have not yet returned from vacation so the real tests will likely come in the following week.

At present here are the notable issues.

1) For those of you who use the ICSD you will likely observe that if you try to download CIF files that the system reports an error regarding maximum number of downloads exceeded. This is a significant issue and we have been discussing this with the ICSD help desk since last week and are hoping for a solution shortly. ICSD is hosted in the cloud and not at our site so we are working through the solution together.

2) For those of you using ACD/Ilab. There are two issues noted to date: A number of the properties are lacking a decimal point where there should be one and the upload of ChemDraw CDX files to predict properties appears to fail because of file interpretation issues. Both of these issues have been reported to ACD/Labs and they are presently working on producing an update to the working system

We have had feedback that there is frustration that IP address authentication is failing for some of our users but it turns out that in many cases these users are working at home over the holidays and their home IP addresses are not in the authentication list. IP authentication is for the institutions, not the individuals.

We apologize for the inconvenience that any of these issues may be causing and are working on them to resolve with the appropriate groups.

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The National Chemical Database Service goes Live

Today, January 2nd, the National Chemical Database Service went live. What we deliver will, we hope, be a good first step to the development of the new Chemical Database Service that the Royal Society of Chemistry will be hosting for the next five years. This first release will provide access to a series of databases and services commonly utilized by the UK academic community. A number of these have been accessible previously through earlier variants of the CDS but new resources are already available through the new release and this will be expanded moving forward. What we deliver today will have been assembled in just a few short weeks with the holiday season in the middle as a potential disruptor. Next up is the inclusion of other database resources that we were not able to squeeze in at the end of the year.

From this point forward we get to architect the system we intend to deliver to the community for the next five years. For clarity we should declare that the CDS that we are rolling out is not simply a matter of continuing the previous incarnation. What we will deliver will start with providing access to a series of commercial databases and services but will include development of a repository capability allowing chemists to host their data, under embargo if necessary. It will allow sharing of data between individuals, groups and institutions. It will embrace the data policies of EPSRC as a funding body and evolve as they and community practice change with time. We are at a time when the expectations regarding accessibility to data are changing and we will support the needs alongside the community. We can imagine that new data may become the basis of structure-activity relationship building, that new algorithms can be derived and existing algorithms be tweaked, all to deliver more tools, capabilities and value. We envisage a time when the investments made in the generation and analysis of chemistry data across the United Kingdom can benefit not only the UK but the entire scientific domain of chemistry, giving even greater recognition to the contributions of British Chemists.

What the CDS service will look like in five years is tough to define in detail. Technologies, expectations and levels of community engagement will surely change. In any case we believe we will break new ground to ultimately provide a revolutionary chemical database service to enable and support chemists in the UK. We expect a long and exciting journey and encourage your feedback, participation and engagement, not only as users but as contributors!

For now please find below a general introduction to the new service and some of our hopes for the future.

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Accessing the Inorganic Crystal Structure Database through the Chemical Database Service

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

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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Service launch

We aim to go live with the first set of CDS database services mid-morning on Wednesday 2nd January – just need to check first thing that everything works as it should. I’ll update here and @cds_rsc when it’s up and working.

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Initial Overview of Integration to SPRESIWeb

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

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

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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