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Category Archives: ChemConnector

Accessing Royal Society of Chemistry resources and making chemistry mobile

This is a presentation I gave at the ACS Dallas meeting on March 19th 2014

Accessing Royal Society of Chemistry resources and making chemistry mobile

The ongoing drive towards mobile devices is now simply one of generic ubiquity. It is less an issue of whether a scientist has a mobile device but rather what brand, what generation and what apps do they have installed. Chemistry has fast been moving to mobile devices for a number of years now and today is it possible to draw chemical compounds, perform searches of databases both on device and in the cloud. Modeling of data using server based platforms is increasing in scope and capabilities. The Royal Society of Chemistry was early in recognizing the potential power of mobile platforms in terms to allowing scientists to access data and the benefits of such devices to allowing students access to data and content. This presentation will provide an overview of our efforts to date in supporting chemistry technologies on mobile devices and our recent developments in this domain.

 

 

Data enhancing the Royal Society of Chemistry publication archive

This is a presentation I gave at the ACS Dallas meeting on March 19th 2014

Data enhancing the Royal Society of Chemistry publication archive

The Royal Society of Chemistry has an archive of hundreds of thousands of published articles containing various types of chemistry related data – compounds, reactions, property data, spectral data etc. RSC has a vision of extracting as much of these data as possible and providing access via ChemSpider and its related projects. To this end we have applied a combination of text-mining extraction, image conversion and chemical validation and standardization approaches. The outcome of this project will result in new chemistry related data being added to our chemical and reaction databases and in the ability to more tightly couple web-based versions of the articles with these extracted data. The ability to search across the archive will be enhanced as a result. This presentation will report on our progress in this data extraction project and discuss how we will ultimately use similar approaches in our publishing pipeline to enhance article markup for new publications.

 

 

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.

 

 

Royal Society of Chemistry Activities to Develop a Data Repository for Chemistry-Specific Data

This is a presentation I have at the ACS Meeting in Dallas, Texas on March 17th 2014

Royal Society of Chemistry Activities to Develop a Data Repository for Chemistry-Specific Data 

In recent years the Royal Society of Chemistry has become known for our development of freely accessible data platforms including ChemSpider, ChemSpider Reactions and our new chemistry data repository. In order to support drug discovery RSC participates in a number of projects including the Open PHACTS semantic web project, the PharmaSea natural products discovery project and the Open Source Drug Discovery project in collaboration with a team in India. Our most recent developments include extending our efforts to support neglected diseases by the provision of high quality datasets resulting from our curation efforts to support modeling, the delivery of enhanced application programming interfaces to allow open source drug discovery teams to both source and deposit data from our chemistry databases and the provision of a micropublishing platform to report on various aspects of work supporting neglected disease drug discovery. This presentation will review our existing efforts and our plans for extended development.

 

The Social Profile of a Chemist Online

This is my fifth talk at the ACS Indianapolis Conference:

The Social Profile of a Chemist Online – The Potential Profits of Participation

Unless a scientist is limited by their employer from exposing their scientific activities through publications and presentations, their future impact, whether expected to be at a bench, in front of an instrument or surrounded by robotics, will largely be represented online through their published works, their citation profile and other forms of recognition of their work by their peers. Search engines are already harvesting information about a scientist and aggregating into profiles such as those offered by Google Scholar Citations and Microsoft Academic Search. Rather than be limited to the online representation provided by such services students are encouraged to participate in the creation of their online profile and architect the representation of themselves online to as large a degree as possible to represent themselves to future employers and collaborators. This presentation will give an overview of potential approaches to participating in development of their online persona.

 

 

Practical semantics in the pharmaceutical industry – the Open PHACTS project

This is ,y fourth talk at the ACS Indianapolis Conference:

Practical semantics in the pharmaceutical industry – the Open PHACTS project

The information revolution has transformed many business sectors over the last decade and the pharmaceutical industry is no exception. Developments in scientific and information technologies have unleashed an avalanche of content on research scientists who are struggling to access and filter this in an efficient manner. Furthermore, this domain has traditionally suffered from a lack of standards in how entities, processes and experimental results are described, leading to difficulties in determining whether results from two different sources can be reliably compared. The need to transform the way the life-science industry uses information has led to new thinking about how companies should work beyond their firewalls. In this talk we will provide an overview of the traditional approaches major pharmaceutical companies have taken to knowledge management and describe the business reasons why pre-competitive, cross-industry and public-private partnerships have gained much traction in recent years. We will consider the scientific challenges concerning the integration of biomedical knowledge, highlighting the complexities in representing everyday scientific objects in computerised form. This leads us to discuss how the semantic web might lead us to a long-overdue solution. The talk will be illustrated by focusing on the EU-Open PHACTS initiative (openphacts.org), established to provide a unique public-private infrastructure for pharmaceutical discovery. The aims of this work will be described and how technologies such as just-in-time identity resolution, nanopublication and interactive visualisations are helping to build a powerful software platform designed to appeal to directly to scientific users across the public and private sectors.

 

 

Personal experiences in participating in the expanding social networks for science

This is the third presentation I gave at the ACS Meeting in Indianapolis:

Personal experiences in participating in the expanding social networks for science

The number of social networking sites available to scientists continues to grow. We are being indexed and exposed on the internet via our publications, presentations and data. We have many ways to contribute, annotate and curate, many of them as part of a growing crowdsourcing network. As one of the founders of the online ChemSpider database I was drawn into the world of social networking to participate in the discussions that were underway regarding our developing resource. As a result of my experiences in blogging, and as a result of developing collaborations and engagement with a large community of scientists, I have become very immersed in the expanding social networks for science. This presentation will provide an overview of the various types of networking and collaborative sites available to scientists and ways that I expose my scientific activities online. Many of these activities will ultimately contribute to the developing measures of me as a scientist as identified in the new world of alternative metrics.

 

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.

 

Serving up and consuming community content for chemists using wikis #ACSPhilly

Unfortunately I had to leave the ACS Meeting in Philadelphia but my colleague David Sharpe will be giving this presentation for me. I have made available a copy of the presentation on Slideshare here but also uploaded a narrated version onto YouTube.

“Wikipedia has become the world’s most famous encyclopedia using as it’s platform the MediaWiki open source software. The software is supported not only by the MediaWiki foundation but by a community of developers who build widgets and add-ons to extend the capabilities. This presentation will review how MediaWiki has been used as a container for a number of resources of value to chemists, specifically SciMobileApps, SciDBs and ScientistsDB holding content regarding mobile scientific apps, scientific databases and scientists. We will also review how chemistry content within Wikipedia has been used to enhance the content underlying the RSC ChemSpider database and how the platform supports an educational environment for chemistry students.

 

Mining public domain data as a basis for drug repurposing #ACSPhilly

Second talk delivered today at ACS Philadelphia…

Mining public domain data as a basis for drug repurposing

Online databases containing high throughput screening and other property data continue to proliferate in number. Many pharmaceutical chemists will have used databases such as PubChem, ChemSpider, DrugBank, BindingDB and many others. This work will report on the potential value of these databases for providing data to be used to repurpose drugs using cheminformatics-based approaches (e.g. docking, ligand-based machine learning methods). This work will also discuss the potentially related applications of the Open PHACTS project, a European Union Innovative Medicines Initiative project, that is utilizing semantic web based approaches to integrate large scale chemical and biological data in new ways. We will report on how compound and data quality should be taken into account when utilizing data from online databases and how their careful curation can provide high quality data that can be used to underpin the delivery of molecular models that can in turn identify new uses for old drugs.

 

 
 
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