Serving up and consuming community content for chemists using wikis
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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.
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There is an overwhelming number of new resources for chemistry that would likely benefit both librarians and students in terms of improving access to data and information. While commercial solutions provided by an institution may be the primary resources there is now an enormous range of online tools, databases, resources, apps for mobile devices and, increasingly, wikis. This presentation will provide an overview of how wiki-based resources for scientists are developing and will introduce a number of developing wikis. These include wikis that are being used to teach chemistry to students as well as to source information about scientists, scientific databases and mobile apps.Navigating scientific resources using wiki based resources
Navigating scientific resources using wiki based resourcesUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The internet has revolutionized the manner by which we can represent ourselves online by providing us the ability to expose our data, experiences and skills online via blogs, wikis and other crowdsourcing venues. As a result it is possible to contribute to the community while developing a social profile as a scientist. While research scientists are primarily still measured by their contributions to science using the classical method of citation statistics, a number of freely available online tools are now available for scientists to develop their online profile. This is particularly important at a time when alternative measures of contributions to science are being developed – the so-called world of Alternative Metrics. The concept of “rewards and recognition” for participation will be discussed in terms of how the Royal Society of Chemistry intends to add to the alternative metrics data flow to acknowledge scientists for their contributions. This presentation will provide an overview of the myriad of tools available to you at any stage of your career and will hopefully encourage you to actively manage your profile as a scientist as the resume of the future will likely be summarized by your activities and profiles online. I will highlight how to ensure that your personal social media profiles can be made engaging to potential collaborators and employers, how social media can be utilized to engage people into events and how to drive traffic to your own sites should you choose to set them up. I will review how my own profiles cover my diverse career in chemistry from “lab-rat” to software product manager, to entrepreneur and into the publishing world and my personal efforts to try and popularize science using some of the social media tools.Online social networking for the chemical sciences
Online social networking for the chemical sciencesUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The teaching of spectroscopy can be a complex and challenging task. The Royal Society of Chemistry has been developing online resources for a number of years that provide access to analytical data as well as interactive quizzes and challenge sets. The RSC data repository houses over 250,000 spectra at this time including mass spectrometry, NMR and IR data and these are utilized to provide online games to test students capabilities, to underpin the SpectraSchool training website and to produce source data for students and teachers alike to use in their teaching and self-training efforts. This presentation will provide an overview of RSC resources that can be used to teach spectroscopy using our online data and tools.Teaching analytical spectroscopy using online spectroscopic data
Teaching analytical spectroscopy using online spectroscopic dataUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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There is an overwhelming number of new resources for chemistry that would likely benefit both librarians and students in terms of improving access to data and information. While commercial solutions provided by an institution may be the primary resources there is now an enormous range of online tools, databases, resources, apps for mobile devices and, increasingly, wikis. This presentation will provide an overview of how wiki-based resources for scientists are developing and will introduce a number of developing wikis. These include wikis that are being used to teach chemistry to students as well as to source information about scientists, scientific databases and mobile apps.Navigating scientific resources using wiki based resources
Navigating scientific resources using wiki based resourcesUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The internet has revolutionized the manner by which we can represent ourselves online by providing us the ability to expose our data, experiences and skills online via blogs, wikis and other crowdsourcing venues. As a result it is possible to contribute to the community while developing a social profile as a scientist. While research scientists are primarily still measured by their contributions to science using the classical method of citation statistics, a number of freely available online tools are now available for scientists to develop their online profile. This is particularly important at a time when alternative measures of contributions to science are being developed – the so-called world of Alternative Metrics. The concept of “rewards and recognition” for participation will be discussed in terms of how the Royal Society of Chemistry intends to add to the alternative metrics data flow to acknowledge scientists for their contributions. This presentation will provide an overview of the myriad of tools available to you at any stage of your career and will hopefully encourage you to actively manage your profile as a scientist as the resume of the future will likely be summarized by your activities and profiles online. I will highlight how to ensure that your personal social media profiles can be made engaging to potential collaborators and employers, how social media can be utilized to engage people into events and how to drive traffic to your own sites should you choose to set them up. I will review how my own profiles cover my diverse career in chemistry from “lab-rat” to software product manager, to entrepreneur and into the publishing world and my personal efforts to try and popularize science using some of the social media tools.Online social networking for the chemical sciences
Online social networking for the chemical sciencesUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The teaching of spectroscopy can be a complex and challenging task. The Royal Society of Chemistry has been developing online resources for a number of years that provide access to analytical data as well as interactive quizzes and challenge sets. The RSC data repository houses over 250,000 spectra at this time including mass spectrometry, NMR and IR data and these are utilized to provide online games to test students capabilities, to underpin the SpectraSchool training website and to produce source data for students and teachers alike to use in their teaching and self-training efforts. This presentation will provide an overview of RSC resources that can be used to teach spectroscopy using our online data and tools.Teaching analytical spectroscopy using online spectroscopic data
Teaching analytical spectroscopy using online spectroscopic dataUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The Royal Society of Chemistry provides a variety of databases and services covering multiple domains of Chemistry. That includes our electronic publishing platform, ChemSpider and its related databases, the National Chemistry Database and digital access to the RSC archive that spans over 170 years. In order to support the rising tide of semantic web technologies we are now working on exposing our data to conform with the linked data paradigm. This presentation will provide an overview of our work to introduce semantic structure to all RSC electronic resources as well as outlining ways to access this information using standard formats and various APIs.Building support for the semantic web for chemistry at the Royal Society of C...
Building support for the semantic web for chemistry at the Royal Society of C...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
It is never too early, or too late in your scientific career to start to build a profile as a scientist. The web has revolutionized the manner by which we can represent ourselves online by providing us the ability to expose our data, experiences and skills online via blogs, wikis and other crowdsourcing venues. As a result it is possible to contribute to the community while developing a social profile as a scientist. While research scientists are primarily still measured by their contributions to science using the classical method of citation statistics a number of freely available online tools are now available for scientists to actively manage and develop their online profile. This is particularly important at a time when alternative measures of contributions to science are being developed – the so-called world of AltMetrics. This presentation will provide an overview of the myriad of tools available to you at any stage of your career. The workshop will take you outside of the world of Twitter and Facebook into the social networking tools for scientists. The workshop can be as interactive as you wish it to be so bring along your computer and hopefully during the presentation and discussions you are actively visiting, registering and seeing the value of the various sites in terms of enhancing your online profile. The resume of the future will likely be a summary of your activities online.How to build an online profile as a scientist
How to build an online profile as a scientistUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The internet continues to offer increased access to chemistry data that may be of value to scientists interested in populating systems containing reference toxicology data as well as to provide data for the development of predictive models. This presentation will give an overview of some of the various sources of data available via the internet, provide an overview of some of the challenges associated with gathering high-quality data and discuss methods by which to mesh together disparate data sources.Sourcing high quality online data resources for computational toxicology
Sourcing high quality online data resources for computational toxicologyUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Access to scientific information has changed in a manner that was likely never even imagined by the early pioneers of the internet. The quantities of data, the array of tools available to search and analyze, the devices and the shift in community participation continues to expand while the pace of change does not appear to be slowing. RSC hosts a number of chemistry data resources for the community including ChemSpider, one of the community’s primary online public compound databases. Containing tens of millions of chemical compounds and its associated data ChemSpider serves data tens of thousands of chemists every day and it serves as the foundation for many important international projects to integrate chemistry and biology data, facilitate drug discovery efforts and help to identify new chemicals from under the ocean. This presentation will provide an overview of the expanding reach of this cheminformatics platform and the nature of the solutions that it helps to enable including structure validation and text mining and semantic markup. ChemSpider is limited in scope as a chemical compound database and we are presently architecting the RSC Data Repository, a platform that will enable us to extend our reach to include chemical reactions, analytical data, and diverse data depositions from chemists across various domains. We will also discuss the possibilities it offers in terms of supporting data modeling and sharing. The future of scientific information and communication will be underpinned by these efforts, influenced by increasing participation from the scientific community.Current initiatives in developing research data repositories at the Royal Soc...
Current initiatives in developing research data repositories at the Royal Soc...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The traditional perception of the publishing process has been that it culminates in a print article. The Royal Society of Chemistry (RSC) has for many years been acutely aware that there is a wealth of information contained in scientific communications that we publish and that its true value can only be unlocked by enabling the discovery of the data within them. This is challenging due to the variety of ways that scientists provide data, textually, graphically, and increasingly in supplementary information. This talk will outline how the RSC has applied innovative approaches, developed both internally and externally, to identifying important chemical data within the literature and provides tools to anyone using chemical data to analyse and improve its quality. Examples will include: Project Prospect, the Experimental Data Checker, our CIF data importer, ChemSpider and our structure validation and standardization service.
This presentation was given by David Sharpe at the ACS Fall Meeting 2012 in PhiladelphiaApproaches for extraction and digital chromatography of chemical data
Approaches for extraction and digital chromatography of chemical dataUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Jean-Claude Bradley had an incredible passion for providing open science tools and data to the community. He had boundless energy, no shortage of ideas and ran so many projects in parallel that it was often difficult to keep up. But at RSC we tried. We provided access to our data, our application programming interfaces and lots of our out-of-hours time to help turn his vision into reality. As a result we helped in the delivery of the SpectralGame to help people learn about NMR and we supported the integration of our services into GoogleDocs underpinning the management and curation of physicochemical property data. We tweaked a number of our services based on JC’s input and as a result we have ended up with a suite of capabilities that serve many of our existing efforts to integrate to electronic lab notebooks and support the ongoing shift towards Open Chemistry. JC was very much ahead of his time….and we were glad to have supported his work. This presentation will give a snapshot of some of the work we did to support his vision. Providing support for JC Bradleys vision of open science using RSC cheminform...
Providing support for JC Bradleys vision of open science using RSC cheminform...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
High quality chemical databases are struggling with protecting their data from the flow of wild machine-generated chemistry and lower-quality data. The period of primarily human curation prior to deposition in a database is gone and quality-conscious databases need to heavily rely on automated validation checks. An automated chemical validation system is being developed by the cheminformatics team at the Royal Society of Chemistry to be the “quality gatekeeper” of databases at the point of deposition. ChemSpider is leading a community-wide standardization approach starting with our support of the Open PHACTS semantic web project, an Innovative Medicines Initiative. The Chemical Validation and Standardization Platform (CVSP) is being designed as an open, flexible chemical validation and standardization platform that validates and standardizes chemical records. This presentation will review the existing beta version of the system and work in progress.The RSC chemical validation and standardization platform, a potential path to...
The RSC chemical validation and standardization platform, a potential path to...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This is the session that Sean Ekins (@collabchem) and I will lead at ScienceOnline2013 (#scio13)
This session will discuss what open science means and how we can encourage it, if indeed we need to.
Questions:
- How do we define openness – Open Access, Open Data, Open Science?
- Are there obvious benefits to openness in science?
- If yes, what are the blocks towards openness? Tools, Systems, IP concerns, organizational support.
- Do scientists have to be fully open or is partial or part time open?
- What are incentives to move scientists towards openness
- Do journals, patents, IP all prevent openness?
- Do open journals promote open science or not?
- What projects can we launch at SciO13 and monitor/measure for impact of Open Science
- Which prominent open scientist can we invite to scio13?Leading scientists towards openness
Leading scientists towards opennessUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
ChemSpider is an online database of almost 25 million chemical compounds linked out to over 400 different internet resources. Together with its partner site, ChemSpider SyntheticPages, a crowdsourced database of reaction syntheses, these two resources provide an environment where chemists can deposit, share, source and use the data as the basis of lesson plans, games and developing deeper understanding in chemistry. This presentation will provide an overview of how ChemSpider is fast becoming the central online portal for sourcing chemistry data, how the ability for students to engage in the hosting of their own data and the curation and annotation of already existing data can engage students in a social networking environment. These efforts can become the basis of training students in spectroscopy, online data validation and the provision of supporting information for their own experiments.RSC ChemSpider as an environment for teaching and sharing chemistry
RSC ChemSpider as an environment for teaching and sharing chemistryUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This presentation is an overview of some of the projects we are involved with at RSC eScience. The presentation was given at the FDA Meeting regarding the “Development of a Freely Distributable Data System for the Registration of SubstancesChemical Database Projects Delivered by RSC eScience
Chemical Database Projects Delivered by RSC eScienceUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The Royal Society of Chemistry hosts one of the largest online chemistry databases containing almost 30 million unique chemical structures. The database, ChemSpider, provides the underpinning for a series of eScience projects allowing for the integration of chemical compounds with our archive of scientific publications, the delivery of a reaction database containing millions of reactions as well as a chemical validation and standardization platform developed to help improve the quality of structural representations on the internet. The InChI has been a fundamental part of each of our projects and has been pivotal in our support of international projects such as the Open PHACTS semantic web project integrating chemistry and biology data and the PharmaSea project focused on identifying novel chemical components from the ocean with the intention of identifying new antibiotics. This presentation will provide an overview of the importance of InChI in the development of many of our eScience platforms and how we have used it specifically in the ChemSpider project to provide integration across hundreds of websites and chemistry databases across the web. We will discuss how we are now expanding our efforts to develop a Global Chemistry Network encompassing efforts in Open Source Drug Discovery and the support of data management for neglected diseases.The importance of the InChI identifier as a foundation technology for eScienc...
The importance of the InChI identifier as a foundation technology for eScienc...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The production of valid and appropriate chemical structure representations which are appropriate for deposition into chemical structure databases and for inclusion into scientific publications requires adoption of a set of pre-processing filters and standardization procedures. As part of our ongoing effort to improve the quality of data for deposition into the RSC ChemSpider database, to provide a manner by which to validate and prepare data for publication and to provide a valuable service to the chemistry community, we have delivered the ChemValidator online service. This website provides access to an intuitive user interface for the upload of chemical compounds in various formats, pre-processing and standardization relative to a defined set of standards and validation checking of the chemicals according to a number of rules including hypervalency, absence of stereochemistry and charge balance. This presentation will report on the development of ChemValidator.
This presentation was given by David Sharpe at the ACS Fall Meeting in 2012ChemValidator – an online service for validating and standardizing chemical s...
ChemValidator – an online service for validating and standardizing chemical s...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Mobile hardware and software technology continues to evolve very rapidly and presents drug discovery scientists with new platforms for accessing data and performing data analysis. Smartphones and tablet computers can now be used to perform many of the operations previously addressed by laptops or desktop computers. Although the smaller screen sizes and requirements for touch screen manipulation can present user interface design challenges, especially with chemistry related applications, these limitations are driving innovative solutions. We will present an introduction to some of the mobile apps we have been involved with most closely. One example is the Green Solvents app which utilizes data created by the ACS Green Chemistry Institute Pharmaceutical roundtable. We will also describe a wiki to capture information about scientific mobile apps (www.scimobileapps.com) and provide our perspective on what mobile platforms may provide the drug discovery scientist in the future as this disruptive technology takes off. Mobile apps for drug discovery
Mobile apps for drug discoveryUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The collaborative project PharmaSea brings European researchers to some of the deepest, coldest and hottest places on the planet. Scientists from the UK, Belgium, Norway, Spain, Ireland, Germany, Italy, Switzerland and Denmark are working together to collect and screen samples of mud and sediment from huge, previously untapped, oceanic trenches. The large-scale, four-year project is backed by almost 10 million euros of funding and brings together 24 partners from 13 countries from industry, academia and non-profit organisations. The PharmaSea project focuses on biodiscovery research and the development and commercialisation of new bioactive compounds from marine organisms, including deep-sea sponges and bacteria, to evaluate their potential as novel drug leads or ingredients for nutrition or cosmetic applications. The Royal Society of Chemistry is responsible for developing a number of capabilities to support the Pharmasea project including a chemical registration system for new compounds, dereplication technologies to assist in the identification of new compounds and search techniques for mass spectrometrists within the project. This presentation will provide an overview of the project and our progress to contributing chemical information technologies to support the effort.Applying Royal Society of Chemistry cheminformatics skills to support the Pha...
Applying Royal Society of Chemistry cheminformatics skills to support the Pha...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This is a short presentation given to chemistry students at Drexel University as a remote presentation. This was for the class of Jean-Claude Bradley.ChemSpider and Traveling the Internet via Chemical Structures Cheminformatics...
ChemSpider and Traveling the Internet via Chemical Structures Cheminformatics...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
There is an expanding interest in repurposing and repositioning of drugs as well as how in silico methods can assist these endeavors. Recent repurposing project tendering calls by the National Center for Advancing Translational Sciences (US) and the Medical Research Council (UK) have included compound information and pharmacological data. However none of the internal company development code names were assigned to chemical structures in the official documentation. This not only abrogates in silico analysis to support repurposing but consequently necessitates data gathering and curation to assign structures. We describe here the methods results and challenges associated with this, including the fact that ~40-50% of the code names remain completely blinded. In addition we describe the in silico predictions that are enabled once the structures are accessible. Consequently we suggest approaches to encourage earlier release of name to structure mappings into the public domain.Challenges and recommendations for obtaining chemical structures of industry
Challenges and recommendations for obtaining chemical structures of industryUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Today ChemSpider (www.chemspider.com) is one of the community’s primary online resources for chemists. Now hosting over 28 million unique chemical compounds linked to over 400 data sources, ChemSpider offers its users a structure centric platform facilitating access to publications and patents, experimental and predicted property data, spectral data and many other forms of data and information that can benefit a chemist. ChemSpider is a crowdsourcing platform allowing the community to contribute data directly to the database by allowing the deposition and sharing of structure data, properties, spectra and reaction syntheses. The crowdsourcing also allows for the annotation and curation of existing data thereby allowing the community to assist in the much-needed curation and validation of chemistry data on the internet. This work is imperative in order to provide the chemistry underpinnings to semantic web projects such as Open PHACTS (www.openphacts.org) of which Merck is sure to benefit when it is released to the community. This presentation will provide an overview of the ChemSpider platform and will also examine the challenges of dealing with heterogeneous data quality when attempting to provide a rich resource of data for the community. If you use the internet to research chemistry based data this presentation will be an essential guide to how to source high quality data.Chemistry Online and The vision and challenges associated with building the c...
Chemistry Online and The vision and challenges associated with building the c...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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. ChemSpider is one of the chemistry community’s primary online public compound databases. Containing tens of millions of chemical compounds and its associated data ChemSpider serves data tens of thousands of chemists every day and it serves as the foundation for many important international projects to integrate chemistry and biology data, facilitate drug discovery efforts and help to identify new chemicals from under the ocean. This presentation will provide an overview of the expanding reach of the ChemSpider platform and the nature of the solutions that it helps to enable. We will also discuss the possibilities it offers in the domain of crowdsourcing and open data sharing. 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.The expansive reach of ChemSpider as a resource for the chemistry community
The expansive reach of ChemSpider as a resource for the chemistry communityUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Many students spend enormous amounts of their time engaged with their computers, accepting of course that mobile devices are simply computers of a different form factor. Engaged with the social networks, utilizing computer platforms to source and share content of various forms, their contributions of “data” into what is the cloud, and in many cases a void, is enormous. What community and career benefit might result from those students spending some of their time contributing chemistry related data to the world? What challenges lie in the way of their participation and how might participating have a positive, or negative impact on their future career. The Royal Society of Chemistry hosts a number of chemistry data platforms to which students can actively contribute and for which their participation can be measured. Moreover the RSC’s micropublishing platform allows chemists to learn how to write up their scientific work, obtain review from their peers and chemistry professors in a non-threatening environment and produce an online published work in less than day that is both citable and available as a shared resource for the community. This presentation will demonstrate how to participate and encourage engagement from students early in their education. There are no longer any technology barriers to the sharing of the majority of chemistry related data.
Encouraging undergraduate students to participate as authors of scientific pu...
Encouraging undergraduate students to participate as authors of scientific pu...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The increasing prevalence of mobile devices offers the opportunity to provide chemistry students with easy access to a multitude of resources. As a publisher the RSC provides a myriad of content to chemists including an online database of over 26 million chemical compounds, tools for learning spectroscopy and access to scientific literature and other educational materials. This presentation will provide an overview of our efforts to make RSC content more mobile, and therefore increasingly available to chemists. In particular it will discuss our efforts to provide access to chemistry related data of high value to students in the laboratory. It will include an overview of spectroscopy tools for the review and analysis of various forms of spectroscopy data Putting chemistry into the hands of students – chemistry made mobile using re...
Putting chemistry into the hands of students – chemistry made mobile using re...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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The Royal Society of Chemistry provides a variety of databases and services covering multiple domains of Chemistry. That includes our electronic publishing platform, ChemSpider and its related databases, the National Chemistry Database and digital access to the RSC archive that spans over 170 years. In order to support the rising tide of semantic web technologies we are now working on exposing our data to conform with the linked data paradigm. This presentation will provide an overview of our work to introduce semantic structure to all RSC electronic resources as well as outlining ways to access this information using standard formats and various APIs.Building support for the semantic web for chemistry at the Royal Society of C...
Building support for the semantic web for chemistry at the Royal Society of C...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
It is never too early, or too late in your scientific career to start to build a profile as a scientist. The web has revolutionized the manner by which we can represent ourselves online by providing us the ability to expose our data, experiences and skills online via blogs, wikis and other crowdsourcing venues. As a result it is possible to contribute to the community while developing a social profile as a scientist. While research scientists are primarily still measured by their contributions to science using the classical method of citation statistics a number of freely available online tools are now available for scientists to actively manage and develop their online profile. This is particularly important at a time when alternative measures of contributions to science are being developed – the so-called world of AltMetrics. This presentation will provide an overview of the myriad of tools available to you at any stage of your career. The workshop will take you outside of the world of Twitter and Facebook into the social networking tools for scientists. The workshop can be as interactive as you wish it to be so bring along your computer and hopefully during the presentation and discussions you are actively visiting, registering and seeing the value of the various sites in terms of enhancing your online profile. The resume of the future will likely be a summary of your activities online.How to build an online profile as a scientist
How to build an online profile as a scientistUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The internet continues to offer increased access to chemistry data that may be of value to scientists interested in populating systems containing reference toxicology data as well as to provide data for the development of predictive models. This presentation will give an overview of some of the various sources of data available via the internet, provide an overview of some of the challenges associated with gathering high-quality data and discuss methods by which to mesh together disparate data sources.Sourcing high quality online data resources for computational toxicology
Sourcing high quality online data resources for computational toxicologyUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Access to scientific information has changed in a manner that was likely never even imagined by the early pioneers of the internet. The quantities of data, the array of tools available to search and analyze, the devices and the shift in community participation continues to expand while the pace of change does not appear to be slowing. RSC hosts a number of chemistry data resources for the community including ChemSpider, one of the community’s primary online public compound databases. Containing tens of millions of chemical compounds and its associated data ChemSpider serves data tens of thousands of chemists every day and it serves as the foundation for many important international projects to integrate chemistry and biology data, facilitate drug discovery efforts and help to identify new chemicals from under the ocean. This presentation will provide an overview of the expanding reach of this cheminformatics platform and the nature of the solutions that it helps to enable including structure validation and text mining and semantic markup. ChemSpider is limited in scope as a chemical compound database and we are presently architecting the RSC Data Repository, a platform that will enable us to extend our reach to include chemical reactions, analytical data, and diverse data depositions from chemists across various domains. We will also discuss the possibilities it offers in terms of supporting data modeling and sharing. The future of scientific information and communication will be underpinned by these efforts, influenced by increasing participation from the scientific community.Current initiatives in developing research data repositories at the Royal Soc...
Current initiatives in developing research data repositories at the Royal Soc...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The traditional perception of the publishing process has been that it culminates in a print article. The Royal Society of Chemistry (RSC) has for many years been acutely aware that there is a wealth of information contained in scientific communications that we publish and that its true value can only be unlocked by enabling the discovery of the data within them. This is challenging due to the variety of ways that scientists provide data, textually, graphically, and increasingly in supplementary information. This talk will outline how the RSC has applied innovative approaches, developed both internally and externally, to identifying important chemical data within the literature and provides tools to anyone using chemical data to analyse and improve its quality. Examples will include: Project Prospect, the Experimental Data Checker, our CIF data importer, ChemSpider and our structure validation and standardization service.
This presentation was given by David Sharpe at the ACS Fall Meeting 2012 in PhiladelphiaApproaches for extraction and digital chromatography of chemical data
Approaches for extraction and digital chromatography of chemical dataUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Jean-Claude Bradley had an incredible passion for providing open science tools and data to the community. He had boundless energy, no shortage of ideas and ran so many projects in parallel that it was often difficult to keep up. But at RSC we tried. We provided access to our data, our application programming interfaces and lots of our out-of-hours time to help turn his vision into reality. As a result we helped in the delivery of the SpectralGame to help people learn about NMR and we supported the integration of our services into GoogleDocs underpinning the management and curation of physicochemical property data. We tweaked a number of our services based on JC’s input and as a result we have ended up with a suite of capabilities that serve many of our existing efforts to integrate to electronic lab notebooks and support the ongoing shift towards Open Chemistry. JC was very much ahead of his time….and we were glad to have supported his work. This presentation will give a snapshot of some of the work we did to support his vision. Providing support for JC Bradleys vision of open science using RSC cheminform...
Providing support for JC Bradleys vision of open science using RSC cheminform...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
High quality chemical databases are struggling with protecting their data from the flow of wild machine-generated chemistry and lower-quality data. The period of primarily human curation prior to deposition in a database is gone and quality-conscious databases need to heavily rely on automated validation checks. An automated chemical validation system is being developed by the cheminformatics team at the Royal Society of Chemistry to be the “quality gatekeeper” of databases at the point of deposition. ChemSpider is leading a community-wide standardization approach starting with our support of the Open PHACTS semantic web project, an Innovative Medicines Initiative. The Chemical Validation and Standardization Platform (CVSP) is being designed as an open, flexible chemical validation and standardization platform that validates and standardizes chemical records. This presentation will review the existing beta version of the system and work in progress.The RSC chemical validation and standardization platform, a potential path to...
The RSC chemical validation and standardization platform, a potential path to...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This is the session that Sean Ekins (@collabchem) and I will lead at ScienceOnline2013 (#scio13)
This session will discuss what open science means and how we can encourage it, if indeed we need to.
Questions:
- How do we define openness – Open Access, Open Data, Open Science?
- Are there obvious benefits to openness in science?
- If yes, what are the blocks towards openness? Tools, Systems, IP concerns, organizational support.
- Do scientists have to be fully open or is partial or part time open?
- What are incentives to move scientists towards openness
- Do journals, patents, IP all prevent openness?
- Do open journals promote open science or not?
- What projects can we launch at SciO13 and monitor/measure for impact of Open Science
- Which prominent open scientist can we invite to scio13?Leading scientists towards openness
Leading scientists towards opennessUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
ChemSpider is an online database of almost 25 million chemical compounds linked out to over 400 different internet resources. Together with its partner site, ChemSpider SyntheticPages, a crowdsourced database of reaction syntheses, these two resources provide an environment where chemists can deposit, share, source and use the data as the basis of lesson plans, games and developing deeper understanding in chemistry. This presentation will provide an overview of how ChemSpider is fast becoming the central online portal for sourcing chemistry data, how the ability for students to engage in the hosting of their own data and the curation and annotation of already existing data can engage students in a social networking environment. These efforts can become the basis of training students in spectroscopy, online data validation and the provision of supporting information for their own experiments.RSC ChemSpider as an environment for teaching and sharing chemistry
RSC ChemSpider as an environment for teaching and sharing chemistryUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This presentation is an overview of some of the projects we are involved with at RSC eScience. The presentation was given at the FDA Meeting regarding the “Development of a Freely Distributable Data System for the Registration of SubstancesChemical Database Projects Delivered by RSC eScience
Chemical Database Projects Delivered by RSC eScienceUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The Royal Society of Chemistry hosts one of the largest online chemistry databases containing almost 30 million unique chemical structures. The database, ChemSpider, provides the underpinning for a series of eScience projects allowing for the integration of chemical compounds with our archive of scientific publications, the delivery of a reaction database containing millions of reactions as well as a chemical validation and standardization platform developed to help improve the quality of structural representations on the internet. The InChI has been a fundamental part of each of our projects and has been pivotal in our support of international projects such as the Open PHACTS semantic web project integrating chemistry and biology data and the PharmaSea project focused on identifying novel chemical components from the ocean with the intention of identifying new antibiotics. This presentation will provide an overview of the importance of InChI in the development of many of our eScience platforms and how we have used it specifically in the ChemSpider project to provide integration across hundreds of websites and chemistry databases across the web. We will discuss how we are now expanding our efforts to develop a Global Chemistry Network encompassing efforts in Open Source Drug Discovery and the support of data management for neglected diseases.The importance of the InChI identifier as a foundation technology for eScienc...
The importance of the InChI identifier as a foundation technology for eScienc...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The production of valid and appropriate chemical structure representations which are appropriate for deposition into chemical structure databases and for inclusion into scientific publications requires adoption of a set of pre-processing filters and standardization procedures. As part of our ongoing effort to improve the quality of data for deposition into the RSC ChemSpider database, to provide a manner by which to validate and prepare data for publication and to provide a valuable service to the chemistry community, we have delivered the ChemValidator online service. This website provides access to an intuitive user interface for the upload of chemical compounds in various formats, pre-processing and standardization relative to a defined set of standards and validation checking of the chemicals according to a number of rules including hypervalency, absence of stereochemistry and charge balance. This presentation will report on the development of ChemValidator.
This presentation was given by David Sharpe at the ACS Fall Meeting in 2012ChemValidator – an online service for validating and standardizing chemical s...
ChemValidator – an online service for validating and standardizing chemical s...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Mobile hardware and software technology continues to evolve very rapidly and presents drug discovery scientists with new platforms for accessing data and performing data analysis. Smartphones and tablet computers can now be used to perform many of the operations previously addressed by laptops or desktop computers. Although the smaller screen sizes and requirements for touch screen manipulation can present user interface design challenges, especially with chemistry related applications, these limitations are driving innovative solutions. We will present an introduction to some of the mobile apps we have been involved with most closely. One example is the Green Solvents app which utilizes data created by the ACS Green Chemistry Institute Pharmaceutical roundtable. We will also describe a wiki to capture information about scientific mobile apps (www.scimobileapps.com) and provide our perspective on what mobile platforms may provide the drug discovery scientist in the future as this disruptive technology takes off. Mobile apps for drug discovery
Mobile apps for drug discoveryUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The collaborative project PharmaSea brings European researchers to some of the deepest, coldest and hottest places on the planet. Scientists from the UK, Belgium, Norway, Spain, Ireland, Germany, Italy, Switzerland and Denmark are working together to collect and screen samples of mud and sediment from huge, previously untapped, oceanic trenches. The large-scale, four-year project is backed by almost 10 million euros of funding and brings together 24 partners from 13 countries from industry, academia and non-profit organisations. The PharmaSea project focuses on biodiscovery research and the development and commercialisation of new bioactive compounds from marine organisms, including deep-sea sponges and bacteria, to evaluate their potential as novel drug leads or ingredients for nutrition or cosmetic applications. The Royal Society of Chemistry is responsible for developing a number of capabilities to support the Pharmasea project including a chemical registration system for new compounds, dereplication technologies to assist in the identification of new compounds and search techniques for mass spectrometrists within the project. This presentation will provide an overview of the project and our progress to contributing chemical information technologies to support the effort.Applying Royal Society of Chemistry cheminformatics skills to support the Pha...
Applying Royal Society of Chemistry cheminformatics skills to support the Pha...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This is a short presentation given to chemistry students at Drexel University as a remote presentation. This was for the class of Jean-Claude Bradley.ChemSpider and Traveling the Internet via Chemical Structures Cheminformatics...
ChemSpider and Traveling the Internet via Chemical Structures Cheminformatics...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
There is an expanding interest in repurposing and repositioning of drugs as well as how in silico methods can assist these endeavors. Recent repurposing project tendering calls by the National Center for Advancing Translational Sciences (US) and the Medical Research Council (UK) have included compound information and pharmacological data. However none of the internal company development code names were assigned to chemical structures in the official documentation. This not only abrogates in silico analysis to support repurposing but consequently necessitates data gathering and curation to assign structures. We describe here the methods results and challenges associated with this, including the fact that ~40-50% of the code names remain completely blinded. In addition we describe the in silico predictions that are enabled once the structures are accessible. Consequently we suggest approaches to encourage earlier release of name to structure mappings into the public domain.Challenges and recommendations for obtaining chemical structures of industry
Challenges and recommendations for obtaining chemical structures of industryUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Today ChemSpider (www.chemspider.com) is one of the community’s primary online resources for chemists. Now hosting over 28 million unique chemical compounds linked to over 400 data sources, ChemSpider offers its users a structure centric platform facilitating access to publications and patents, experimental and predicted property data, spectral data and many other forms of data and information that can benefit a chemist. ChemSpider is a crowdsourcing platform allowing the community to contribute data directly to the database by allowing the deposition and sharing of structure data, properties, spectra and reaction syntheses. The crowdsourcing also allows for the annotation and curation of existing data thereby allowing the community to assist in the much-needed curation and validation of chemistry data on the internet. This work is imperative in order to provide the chemistry underpinnings to semantic web projects such as Open PHACTS (www.openphacts.org) of which Merck is sure to benefit when it is released to the community. This presentation will provide an overview of the ChemSpider platform and will also examine the challenges of dealing with heterogeneous data quality when attempting to provide a rich resource of data for the community. If you use the internet to research chemistry based data this presentation will be an essential guide to how to source high quality data.Chemistry Online and The vision and challenges associated with building the c...
Chemistry Online and The vision and challenges associated with building the c...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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. ChemSpider is one of the chemistry community’s primary online public compound databases. Containing tens of millions of chemical compounds and its associated data ChemSpider serves data tens of thousands of chemists every day and it serves as the foundation for many important international projects to integrate chemistry and biology data, facilitate drug discovery efforts and help to identify new chemicals from under the ocean. This presentation will provide an overview of the expanding reach of the ChemSpider platform and the nature of the solutions that it helps to enable. We will also discuss the possibilities it offers in the domain of crowdsourcing and open data sharing. 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.The expansive reach of ChemSpider as a resource for the chemistry community
The expansive reach of ChemSpider as a resource for the chemistry communityUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Many students spend enormous amounts of their time engaged with their computers, accepting of course that mobile devices are simply computers of a different form factor. Engaged with the social networks, utilizing computer platforms to source and share content of various forms, their contributions of “data” into what is the cloud, and in many cases a void, is enormous. What community and career benefit might result from those students spending some of their time contributing chemistry related data to the world? What challenges lie in the way of their participation and how might participating have a positive, or negative impact on their future career. The Royal Society of Chemistry hosts a number of chemistry data platforms to which students can actively contribute and for which their participation can be measured. Moreover the RSC’s micropublishing platform allows chemists to learn how to write up their scientific work, obtain review from their peers and chemistry professors in a non-threatening environment and produce an online published work in less than day that is both citable and available as a shared resource for the community. This presentation will demonstrate how to participate and encourage engagement from students early in their education. There are no longer any technology barriers to the sharing of the majority of chemistry related data.
Encouraging undergraduate students to participate as authors of scientific pu...
Encouraging undergraduate students to participate as authors of scientific pu...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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The importance of the InChI identifier as a foundation technology for eScienc...
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ChemValidator – an online service for validating and standardizing chemical s...
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Applying Royal Society of Chemistry cheminformatics skills to support the Pha...
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ChemSpider and Traveling the Internet via Chemical Structures Cheminformatics...
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Challenges and recommendations for obtaining chemical structures of industry
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ChemSpider compound database as one of the pillars of a semantic web for …
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Chemistry Online and The vision and challenges associated with building the c...
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The expansive reach of ChemSpider as a resource for the chemistry community
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Encouraging undergraduate students to participate as authors of scientific pu...
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Putting chemistry into the hands of students – chemistry made mobile using re...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
At this time, and in a culture where online access is now an imperative, Wikipedia has become the definitive encyclopedia. In terms of its support for chemistry it is rich in many encyclopedic pages including named reactions, chemical and drug pages, articles about chemists, and many other forms of chemistry related information. Wikipedia is hosted on Mediawiki, an open source platform that can be utilized by anybody as the basis of their own hosted content collection. Mediawiki has been used as a collaborative environment by a number of chemists to create As a general contribution to the community Mediawiki has been used to create a number of resources that have become very popular with the chemistry community. These include VIPEr to support inorganic chemistry, ChemWiki as an online textbook and other educational resources and a Chemical Information Wikibook. Mediawiki has also been used by the author to host open source collections of data including scientists, scientific databases and mobile apps for science: the ScientistsDB, SciDBs and SciMobileApps wikis. This presentation will provide an overview of some of the chemistry resources that presently exist and celebrate the major contributions that Wikipedia and Mediawiki have made to the collaborative dissemination of chemistry. Value of the mediawiki platform for providing content to the chemistry community
Value of the mediawiki platform for providing content to the chemistry communityUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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Utilizing ChemSpider As A Platform For Education And Exposure Of Student Data...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The extraction of chemical entities from documents such as patents and publications has been pursued for a number of years. We wish to report on ChemMantis, an integrated system for chemistry-based entity extraction and document mark-up enabling access to the rich resource of online chemistry know as ChemSpider. We will discuss the development of the platform from its inception as a series of dictionaries to the integration of an entity extraction algorithm and its expansion to a public deposition and publishing platform for chemistry. Chemistry articles can now be deposited, marked-up and exposed to the public within a few minutes in many cases making it an ideal platform for communicating research and providing integrated access to data sources including PubChem, ChEBI, Wikipedia and Entrez.Building an integrated system for chemistry markup and online publishing inte...
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Serving up and consuming community content for chemists using wikis
- 1. Serving up and consuming community content for chemists using wikis David Sharpe, Antony Williams, Alexey Pshenichnov, Valery Tkachenko, Aileen Day and Sean Ekins ACS Philadelphia August 2012
- 2. Wikis
- 3. Collaborative Knowledge Management for Chemists – Wikipedia, Built by a Network
- 4. Collaborative Authoring for Drug Discovery Pfizerpedia
- 6. WikiProteins
- 7. So many Scientific Wikis…
- 11. And of different “flavors” Not all MediaWiki!
- 12. Wikis are “collaborative environments” …for anything!
- 13. RSC eLearning The Initial Vision of RSC eLearning From last two years of secondary school to end of undergraduate Integrated to a small slice of ChemSpider Introduction of more educational “games”: Chemistry quizzes – e.g reactions Hosting training/educational resources Integrate to existing RSC websites An environment of participation. It’s a WIKI!
- 16. ChemSpider is too much… Simplified interface …..to this From this…..
- 17. Substance Pages
- 18. Substance Pages
- 19. Quizzes
- 20. Fill in the Blank
- 24. Submit Structures as Answers!
- 25. Participation!!!
- 26. Lab Experiments
- 28. Tutorials
- 29. A Growing Wiki Resource
- 30. Acknowledgments RSC|Learn Chemistry team RSC|ChemSpider team – especially Aileen Day as technical lead on Learn Chemistry. Alexey Pshenichnov for SpectraSchool. Learn Chemistry Wiki: Martin Walker, Potsdam U. iChemLabs (ChemDoodle Components) GGA Software Services LLC: Ketcher
- 31. Thank you Email: williamsa@rsc.org Blog: www.chemconnector.com SLIDES: www.slideshare.net/AntonyWilliams
Notas del editor
- However, current ChemSpider user interface is not student friendly. IT contains too much information which is irrelevant to school students. Martin’s first project is developing a simpler ‘student interface’ for less experienced users. Called a substance page, being developed in our wiki environment, contains only physical data and spectra plus some information imported from wikipedia. Also has the lewis version of the structure, important because students are not introduced to skeletal forms until the later stages of A-level