Archive for category ChemSpider Chemistry

The UK National Chemical Database Service as an integration of commercial and public chemistry services to support chemists in the United Kingdom

This is a presentation I gave at the ACS National Meeting in Dallas on Wednesday 19th March 2014

The UK National Chemical Database Service – an integration of commercial and public chemistry services to support chemists in the United Kingdom

At a time when the data explosion has simply been redefined as “Big”, the hurdles associated with building a subject-specific data repository for chemistry are daunting. Combining a multitude of non-standard data formats for chemicals, related properties, reactions, spectra etc., together with the confusion of licensing and embargoing, and providing for data exchange and integration with services and platforms external to the repository, the challenge is significant. This all at a time when semantic technologies are touted as the fundamental technology to enhance integration and discoverability. Funding agencies are demanding change, especially a change towards access to open data to parallel their expectations around Open Access publishing. The Royal Society of Chemistry has been funded by the Engineering and Physical Science Research of the UK to deliver a “chemical database service” for UK scientists. This presentation will provide an overview of the challenges associated with this project and our progress in delivering a chemistry repository capable of handling the complex data types associated with chemistry. The benefits of such a repository in terms of providing data to develop prediction models to further enable scientific discovery will be discussed and the potential impact on the future of scientific publishing will also be examined.

 

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Ontology work at the Royal Society of Chemistry #ACSDallas

This is a presentation at I gave at the ACS Spring meeting in Dallas, Texas on March 17th 2014

Ontology work at the Royal Society of Chemistry

We provide an overview of the use we make of ontologies at the Royal Society of Chemistry.  Our engagement with the ontology community began in 2006 with preparations for Project Prospect, which used ChEBI and other Open Biomedical Ontologies to mark up journal articles. Subsequently Project Prospect has evolved into DERA (Digitally Enhancing the RSC Archive) and we have developed further ontologies for text markup, covering analytical methods and name reactions. Most recently we have been contributing to CHEMINF, an open-source cheminformatics ontology, as part of our work on disseminating calculated physicochemical properties of molecules via the Open PHACTS. We show how we represent these properties and how it can serve as a template for disseminating different sorts of chemical information.

 

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Big data challenges associated with building a national data repository for chemistry

I gave a presentation at the ICIC 2013 meeting in Vienna focused on the “Big data challenges associated with building a national data repository for chemistry“. The Slideshare presentation is shown below.

At a time when the data explosion has simply been redefined as “Big”, the hurdles associated with building a subject-specific data repository for chemistry are daunting. Combining a multitude of non-standard data formats for chemicals, related properties, reactions, spectra etc., together with the confusion of licensing and embargoing, and providing for data exchange and integration with services and platforms external to the repository, the challenge is significant. This all at a time when semantic technologies are touted as the fundamental technology to enhance integration and discoverability. Funding agencies are demanding change, especially a change towards access to open data to parallel their expectations around Open Access publishing. The Royal Society of Chemistry has been funded by the Engineering and Physical Science Research of the UK to deliver a “chemical database service” for UK scientists. This presentation will provide an overview of the challenges associated with this project and our progress in delivering a chemistry repository capable of handling the complex data types ssociated with chemistry. The benefits of such a repository in terms of providing data to develop prediction models to further enable scientific discovery will be discussed and the potential impact on the future of scientific publishing will also be examined.

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The importance of standards for data exchange and interchange on the Royal Society of Chemistry eScience platforms

This is my seventh and LAST talk at the ACS Meeting in Indianapolis:

The importance of standards for data exchange and interchange on the Royal Society of Chemistry eScience platforms

The Royal Society of Chemistry provides access to a number of databases hosting chemicals data, reactions, spectroscopy data and prediction services. These databases and services can be accessed via web services utilizing queries using standard data formats such as InChI and molfiles. Data can then be downloaded in standard structure and spectral formats allowing for reuse and repurposing. The ChemSpider database integrates to a number of projects external to RSC including Open PHACTS that integrates chemical and biological data. This project utilizes semantic web data standards including RDF. This presentation will provide an overview of how structure and spectral data standards have been critical in allowing us to integrate many open source tools, ease of integration to a myriad of services and underpin many of our future developments.

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Digitizing documents to provide a public spectroscopy database

This is my sixth presentation at the ACS Fall Meeting in Indianapolis:

Digitizing documents to provide a public spectroscopy database

RSC hosts a number of platforms providing free access to chemistry related data. The content includes chemical compounds and associated experimental and predicted data, chemical reactions and, increasingly, spectral data. The ChemSpider database primarily contains electronic spectral data generated at the instrument, converted into standard formats such as JCAMP, then uploaded for the community to access. As a publisher RSC holds a rich source of spectral data within our scientific publications and associated electronic supplementary information. We have undertaken a project to Digitally Enable the RSC Archive (DERA) and as part of this project are converting figures of spectral data into standard spectral data formats for storage in our ChemSpider database. This presentation will report on our progress in the project and some of the challenges we have faced to date.

 

 

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Accessing chemical health and safety data online using Royal Society of Chemistry resources

This is the second presentation I gave at the ACS Meeting in Indianapolis

Accessing chemical health and safety data online using Royal Society of Chemistry resources

The internet has opened up access to large amounts of chemistry related data that can be harvested and assembled into rich resources of value to chemists. The Royal Society of Chemistry’s ChemSpider database has assembled an electronic collection of over 28 million chemicals from over 400 data sources and some of the assembled data is certainly of value to those searching for chemical health and safety information. Since ChemSpider is a text and structure searchable database chemists are able to find relevant information using both of their general search approaches. This presentation will provide an overview of the types of chemical health and safety data and information made available via ChemSpider and discuss how the data are sourced, aggregated and validated. We will examine how the data can be made available via mobile devices and examine the issue of data quality and its potential impacts on such a database.

 

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Apps and approaches to mobilizing chemistry from the Royal Society of Chemistry

This is the first presentation I gave at the ACS Meeting in Indianapolis

Apps and approaches to mobilizing chemistry from the Royal Society of Chemistry

Mobilizing chemistry by delivering data and content from Royal Society of Chemistry resources has become an important component of our activities to increase accessibility. Content includes access to our publications, our magazine content and our chemistry databases. Mobile devices also allow us to deliver access to tools to support teaching, game-based learning, annotation and curation of data. This presentation will provide an overview of our varied activities in enhancing access to chemistry related data and materials. This will include providing data feeds associated with RSC graphical databases, our experiences in optical structure recognition using smartphone apps and our future vision for supporting chemistry on mobile devices.

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The future of scientific information & communication presented at the SUNY Potsdam Academic Festival

This is a LONG presentation….I talk about the “It’s All About Me” attitude that can positively feed science….we want to share OUR science, we want people to know about our opinions, our activities, our collaborators, we want to get funding, recognition and attribution. And why not…it can all be to the benefit of science.

This presentation was given at the SUNY Potsdam Academic Festival

The future of scientific information & communication

Our access to scientific information has changed in ways that were hardly imagined even by the early pioneers of the internet. The immense quantities of data and the array of tools available to search and analyze online content continues to expand while the pace of change does not appear to be slowing. While scientists now have access to the enormous capacities and capability of the internet the vast majority of scientific communication continues to be through peer-reviewed scientific journals. The measure of a scientist’s contribution is primarily represented by their publication profile and the citations to their published works and offers an incomplete view of their activities. However, we are at the beginning of a new revolution where the ability to communicate offers the opportunity to embrace new forms of publishing and where scientific participation and influence will be measured in new ways. This presentation will provide an overview of our new generation of “openness” in which open source, open standards, open access and open data are proliferating. The future of scientific information and communication will be underpinned by these efforts, influenced by increasing participation from the scientific community and facilitated collaboration and ultimately accelerate scientific progress.

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Engaging students in publishing on the internet early in their careers

Presentation given at ACS New Orleans Spring Meeting

As a result of the advent of internet technologies supporting participation on the internet via blogs, wikis and other social networking approaches, chemists now have an opportunity to contribute to the growing chemistry content on the web. As scientists an important skill to develop is the ability to succinctly report in a published format the details of scientific experimentation. The Royal Society of Chemistry provides a number of online systems to share chemistry data, the most well known of these being the ChemSpider database. In parallel the ChemSpider SyntheticPages (CSSP) platform is an online publishing platform for scientists, and especially students, to publish the details of chemical syntheses that they have performed. Using the rich capabilities of internet platforms, including the ability to display interactive spectral data and movies, CSSP is an ideal environment for students to publish their work, especially syntheses that might not support mainstream publication.

 

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ChemSpider – disseminating data and enabling an abundance of chemistry platforms

Presentation given at ACS New Orleans Spring Meeting

ChemSpider is one of the chemistry community’s primary public compound databases. Containing tens of millions of chemical compounds and its associated data ChemSpider serves data to many tens of websites and software applications at this point. This presentation will provide an overview of the expanding reach of the ChemSpider platform and the nature of solutions that it helps to enable. We will also discuss some of the future directions for the project that are envisaged and how we intend to continue expanding the impact for the platform.

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