Web Crawling Chemistry
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ChemSpider is a free access online structure-based community for chemists to research data and information. The database of over 20 million chemical structures and associated data has been derived from depositions by well over a hundred contributing data sources including chemical vendors, commercial database providers, web-based scraping of data and individual scientists looking to share their information with the community. Text-mining and conversion of chemical names and identifiers to chemical structures has made an enormous contribution to the availability of diverse data on ChemSpider and includes contributions from patents, open access articles and various online resources. This presentation will provide an overview of the present state of development of this important public resource and review the processes and procedures for the harvesting, deposition and curation of large datasets derived via text-mining and conversion.Using Text-Mining and Crowdsourced Curation to Build a Structure Centric Comm...
Using Text-Mining and Crowdsourced Curation to Build a Structure Centric Comm...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
A Talk delivered at both UNC Chapel Hill and Drexel University
There is an increasing availability of free and open access resources for scientists to use on the internet. Coupled with the increasing availability of Open Source software tools we are in the middle of a revolution in data availability and tools to manipulate these data. However, freedom costs and in many cases the cost is quality. ChemSpider is a free access website for chemists built with the intention of providing a structure centric community for chemists. As an aggregator of chemistry related information from many sources, at present over 21.5 million unique chemical entities from over 150 separate data sources, ChemSpider has taken on the task of both robotically and manually curating publicly available data sources. This presentation will provide an overview of the issue of quality in many chemistry-related databases, approaches to cleaning up the data and how a curated platform can become the centralized hub for resourcing information about chemical entities. This includes experimental and predicted properties, analytical data, publications, suppliers and integrated databases. I will detail three efforts :1) the curation of chemistry on Wikipedia 2) an examination of structure integrity on the FDA Daily Med website, a web site of medication content and labeling as found in medication package inserts 3) recognizing chemical names in documents and providing a platform for structure-based searching of Open Access chemistry literature.Crowdsourcing, Collaborations And Text Mining In A World Of Open Chemistry
Crowdsourcing, Collaborations And Text Mining In A World Of Open ChemistryUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This was a presentation I gave to an audience at Nature Publishing Group in New York on May 7th 2009. It's a long presentation and over an hour in length. Not much new here relative to other presentations...just a knitting together of many of the others on here.
There is an increasing availability of free and open access resources for scientists to use on the internet. Coupled with an increasing number of Open Source software programs we are in the middle of a revolution in data availability and tools to manipulate these data. ChemSpider is a free access website built with the intention of providing a structure centric community for chemists. As an aggregator of chemistry related information from many sources, at present over 21.5 million unique chemical entities from over 190 separate data sources, ChemSpider has taken on the task of both robotically and manually integrating and curating publicly available data sources. ChemSpider has also provided an environment for users to deposit, curate and annotate chemistry-related information. This has allowed the community to enhance ChemSpider by adding analytical data, associating synthetic pathways and publications and connecting to social networking resources. I will discuss how ChemSpider is fast becoming the premier curated platform and centralized hub for resourcing information about chemical entities and how the platform provides the foundation data for services allowing the analysis of analytical data and collaborative science.ChemSpider as a Foundation for Crowdsourcing and Collaborations in Open Chemi...
ChemSpider as a Foundation for Crowdsourcing and Collaborations in Open Chemi...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
ChemSpider – The Vision and Challenges Associated with Building a Free Online...
ChemSpider – The Vision and Challenges Associated with Building a Free Online...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
ChemSpider is a free access website for chemists built with the vision of providing a structure centric community for chemists. Vision is great…execution is better. ChemSpider is now one of the internet’s primary portals for chemistry offering access to over 23 million unique chemical structures from over 200 data sources and expanding daily. Even though there are tens if not hundreds of chemical structure databases such as literature data, chemical vendor catalogs, molecular properties, environmental data, toxicity data, analytical data etc. there has been no single way to search across them. Despite the fact that there are a large number of databases containing chemical compounds and data available online their inherent quality, accuracy and completeness remains lacking in many regards. With ChemSpider we have provided a platform whereby the chemistry community could contribute to cleaning up the data, improving the quality of data online and expanding the information available to include data such as reaction syntheses, analytical data, experimental properties and linking to other valuable resources.
This presentation will provide an overview of ChemSpider and its value to chemists as a search tool, as a public repository of information and how it can become one of the primary foundations of internet-based chemistry. I will also discuss the vision for ChemSpider and some of the exciting goals we are setting for the system moving forward.Why Chemistry and the Web Will Benefit from a ChemSpider
Why Chemistry and the Web Will Benefit from a ChemSpiderUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
ChemSpider is a free access website for chemists built with the intention of providing a structure centric community for chemists. It was developed to index available sources of chemical structures and their associated data into a single searchable repository and making it available to everybody, at no charge. While there are a large number of databases containing chemical compounds and data available online their inherent quality, accuracy and completeness is severely lacking. ChemSpider has provided a platform so that the chemistry community could contribute to improving the quality of data online and expanding the information to include data such as reaction syntheses, analytical data, experimental properties and linkages to other valuable resources. It has grown into a resource containing over 21 million unique chemical structures from over 200 data sources.
This presentation will provide an overview of ChemSpider and its value to chemists as a search tool, as a public repository of information and how it can become one of the primary foundations of internet-based chemistry. I will also discuss the vision for ChemSpider and some of the lofty goals we are setting for the system moving forward.
Crawling Across the Web of Chemistry Using ChemSpider
Crawling Across the Web of Chemistry Using ChemSpider US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
I am an adjunct prof at University of North Carolina Chapel Hill so when I stopped by yesterday for a business meeting I was informed that I had been lined up to give a talk to the students at 1pm. I had 20 minutes to prepare and assembled a mish-mash of information that might be of value to Citizen Chemists, those who might want to contribute to chemistry on the internetTaming The Wild West Of Internet Based Chemistry You Can Help
Taming The Wild West Of Internet Based Chemistry You Can HelpUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Recommandé
ChemSpider is a free access online structure-based community for chemists to research data and information. The database of over 20 million chemical structures and associated data has been derived from depositions by well over a hundred contributing data sources including chemical vendors, commercial database providers, web-based scraping of data and individual scientists looking to share their information with the community. Text-mining and conversion of chemical names and identifiers to chemical structures has made an enormous contribution to the availability of diverse data on ChemSpider and includes contributions from patents, open access articles and various online resources. This presentation will provide an overview of the present state of development of this important public resource and review the processes and procedures for the harvesting, deposition and curation of large datasets derived via text-mining and conversion.Using Text-Mining and Crowdsourced Curation to Build a Structure Centric Comm...
Using Text-Mining and Crowdsourced Curation to Build a Structure Centric Comm...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
A Talk delivered at both UNC Chapel Hill and Drexel University
There is an increasing availability of free and open access resources for scientists to use on the internet. Coupled with the increasing availability of Open Source software tools we are in the middle of a revolution in data availability and tools to manipulate these data. However, freedom costs and in many cases the cost is quality. ChemSpider is a free access website for chemists built with the intention of providing a structure centric community for chemists. As an aggregator of chemistry related information from many sources, at present over 21.5 million unique chemical entities from over 150 separate data sources, ChemSpider has taken on the task of both robotically and manually curating publicly available data sources. This presentation will provide an overview of the issue of quality in many chemistry-related databases, approaches to cleaning up the data and how a curated platform can become the centralized hub for resourcing information about chemical entities. This includes experimental and predicted properties, analytical data, publications, suppliers and integrated databases. I will detail three efforts :1) the curation of chemistry on Wikipedia 2) an examination of structure integrity on the FDA Daily Med website, a web site of medication content and labeling as found in medication package inserts 3) recognizing chemical names in documents and providing a platform for structure-based searching of Open Access chemistry literature.Crowdsourcing, Collaborations And Text Mining In A World Of Open Chemistry
Crowdsourcing, Collaborations And Text Mining In A World Of Open ChemistryUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This was a presentation I gave to an audience at Nature Publishing Group in New York on May 7th 2009. It's a long presentation and over an hour in length. Not much new here relative to other presentations...just a knitting together of many of the others on here.
There is an increasing availability of free and open access resources for scientists to use on the internet. Coupled with an increasing number of Open Source software programs we are in the middle of a revolution in data availability and tools to manipulate these data. ChemSpider is a free access website built with the intention of providing a structure centric community for chemists. As an aggregator of chemistry related information from many sources, at present over 21.5 million unique chemical entities from over 190 separate data sources, ChemSpider has taken on the task of both robotically and manually integrating and curating publicly available data sources. ChemSpider has also provided an environment for users to deposit, curate and annotate chemistry-related information. This has allowed the community to enhance ChemSpider by adding analytical data, associating synthetic pathways and publications and connecting to social networking resources. I will discuss how ChemSpider is fast becoming the premier curated platform and centralized hub for resourcing information about chemical entities and how the platform provides the foundation data for services allowing the analysis of analytical data and collaborative science.ChemSpider as a Foundation for Crowdsourcing and Collaborations in Open Chemi...
ChemSpider as a Foundation for Crowdsourcing and Collaborations in Open Chemi...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
ChemSpider – The Vision and Challenges Associated with Building a Free Online...
ChemSpider – The Vision and Challenges Associated with Building a Free Online...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
ChemSpider is a free access website for chemists built with the vision of providing a structure centric community for chemists. Vision is great…execution is better. ChemSpider is now one of the internet’s primary portals for chemistry offering access to over 23 million unique chemical structures from over 200 data sources and expanding daily. Even though there are tens if not hundreds of chemical structure databases such as literature data, chemical vendor catalogs, molecular properties, environmental data, toxicity data, analytical data etc. there has been no single way to search across them. Despite the fact that there are a large number of databases containing chemical compounds and data available online their inherent quality, accuracy and completeness remains lacking in many regards. With ChemSpider we have provided a platform whereby the chemistry community could contribute to cleaning up the data, improving the quality of data online and expanding the information available to include data such as reaction syntheses, analytical data, experimental properties and linking to other valuable resources.
This presentation will provide an overview of ChemSpider and its value to chemists as a search tool, as a public repository of information and how it can become one of the primary foundations of internet-based chemistry. I will also discuss the vision for ChemSpider and some of the exciting goals we are setting for the system moving forward.Why Chemistry and the Web Will Benefit from a ChemSpider
Why Chemistry and the Web Will Benefit from a ChemSpiderUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
ChemSpider is a free access website for chemists built with the intention of providing a structure centric community for chemists. It was developed to index available sources of chemical structures and their associated data into a single searchable repository and making it available to everybody, at no charge. While there are a large number of databases containing chemical compounds and data available online their inherent quality, accuracy and completeness is severely lacking. ChemSpider has provided a platform so that the chemistry community could contribute to improving the quality of data online and expanding the information to include data such as reaction syntheses, analytical data, experimental properties and linkages to other valuable resources. It has grown into a resource containing over 21 million unique chemical structures from over 200 data sources.
This presentation will provide an overview of ChemSpider and its value to chemists as a search tool, as a public repository of information and how it can become one of the primary foundations of internet-based chemistry. I will also discuss the vision for ChemSpider and some of the lofty goals we are setting for the system moving forward.
Crawling Across the Web of Chemistry Using ChemSpider
Crawling Across the Web of Chemistry Using ChemSpider US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
I am an adjunct prof at University of North Carolina Chapel Hill so when I stopped by yesterday for a business meeting I was informed that I had been lined up to give a talk to the students at 1pm. I had 20 minutes to prepare and assembled a mish-mash of information that might be of value to Citizen Chemists, those who might want to contribute to chemistry on the internetTaming The Wild West Of Internet Based Chemistry You Can Help
Taming The Wild West Of Internet Based Chemistry You Can HelpUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
There is an increasing availability of free and open access resources for chemists to use on the internet. Coupled with the increasing availability of Open Source software tools we are in the middle of a revolution in data availability and tools to manipulate these data. ChemSpider is a free access website for chemists built with the intention of providing a structure centric community for chemists. It was developed with the intention of aggregating and indexing available sources of chemical structures and their associated information into a single searchable repository and making it available to everybody, at no charge.
There are tens if not hundreds of chemical structure databases such as literature data, chemical vendor catalogs, molecular properties, environmental data, toxicity data, analytical data etc. and no single way to search across them. Despite the fact that there were a large number of databases containing chemical compounds and data available online their inherent quality, accuracy and completeness was lacking in many regards. The intention with ChemSpider was to provide a platform whereby the chemistry community could contribute to cleaning up the data, improving the quality of data online and expanding the information available to include data such as reaction syntheses, analytical data, experimental properties and linking to other valuable resources. It has grown into a resource containing over 21 million unique chemical structures from over 200 data sources.
ChemSpider has enabled real time curation of the data, association of analytical data with chemical structures, real-time deposition of single or batch chemical structures (including with activity data) and transaction-based predictions of physicochemical data. The social community aspects of the system demonstrate the potential of this approach. Curation of the data continues daily and thousands of edits and depositions by members of the community have dramatically improved the quality of the data relative to other public resources for chemistry.
This presentation will provide an overview of the history of ChemSpider, the present capabilities of the platform and how it can become one of the primary foundations of the semantic web for chemistry. It will also discuss some of the present projects underway since the acquisition of ChemSpider by the Royal Society of Chemistry.
ChemSpider - Building a Foundation for the Semantic Web by Hosting a Crowd So...
ChemSpider - Building a Foundation for the Semantic Web by Hosting a Crowd So...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The ability to query across a chemistry publishers content using chemical structure searching can dramatically enhance discoverability. RSC has been applying a number of procedures to integrate RSC’s ChemSpider community resource with our published content and databases. These include: 1) entity extraction procedures 2) chemical name conversion procedures using software algorithms and curated dictionaries 3) semantic markup and 4) a crowdsourced curation processes. This presentation will provide an overview of the processes we have utilized in order to provide structure-based integration to RSC content. We will discuss our ongoing efforts to extend the approaches to the mining of data from the rich supplementary information sections of many RSC publications. Our intention is to provide access to synthesis procedures and analytical data and further enrich the ChemSpider database for the benefit of the chemistry community. Enhancing Discoverability Across Royal Society Of Chemistry Content By Integr...
Enhancing Discoverability Across Royal Society Of Chemistry Content By Integr...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Many of us nowadays invest significant amounts of time in sharing our activities and opinions with friends and family via social networking tools. However, despite the availability of many platforms for scientists to connect and share with their peers in the scientific community the majority do not make use of these tools, despite their promise and potential impact and influence on our future careers. We are being indexed and exposed on the internet via our publications, presentations and data. We also have many more ways to contribute to science, to annotate and curate data, to “publish” in new ways, and many of these activities are as part of a growing crowdsourcing network. This presentation will provide an overview of the various types of networking and collaborative sites available to scientists and ways to expose your scientific activities online. Many of these can ultimately contribute to the developing measures of you as a scientist as identified in the new world of alternative metrics. Participating offers a great opportunity to develop a scientific profile within the community and may ultimately be very beneficial, especially to scientists early in their career. Data integration and building a profile for yourself as an online scientist
Data integration and building a profile for yourself as an online scientistUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
These are the slides I will be giving here at the Science Commons Symposium Pacific Northwest at the Microsoft Campus here in Redmond in about 5 minutes timeRSC ChemSpider Science Commons Symposium Pacific Northwest #scspn
RSC ChemSpider Science Commons Symposium Pacific Northwest #scspnUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The structure elucidation of natural product structures from analytical data, specifically NMR and MS, remains a major challenge. With an enormous palette of NMR experiments to choose from, and supported by breakthrough technologies in hardware, the generation of high quality data to enable even the most complex of natural product structures to be determined is no longer the major hurdle. The challenge is in the analysis of the data. We are in a new era in terms of approaches to structure elucidation: one where computers, databases, and a synergy between scientists and algorithms can offer an accelerated path forward. Software tools are capable of digesting spectroscopic data to elucidate extremely complex natural products. Scientists can now elucidate chemical structures utilizing multinuclear chemical shift data, correlation data from an array of 2D NMR experiments and utilize existing data sets for the purpose of dereplication and computer-assisted structure elucidation. With the explosion of online data especially, in public databases such as PubChem and ChemSpider, many tens of millions of chemical structures are available to seed fragment databases to include in the elucidation process. This presentation will provide an overview of how cheminformatics and chemical databases have been brought together to assist in the identification of natural products. It will include an examination of the state-of-the-art developments in Computer-Assisted Structure Elucidation. Cheminformatics and the Structure Elucidation of Natural Products
Cheminformatics and the Structure Elucidation of Natural ProductsUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This presentation was given at the CLIR/DLF Postdoctoral Fellowship Summer Seminar at Bryn Mawr college in Pennsylvania on July 29th 2014. The intention was to communicate what we are doing in the fields of text and data mining in the domain of chemistry and specifically around mining the RSC archive publication and chemistry dissertations and theses. How would these experiences map over to the humanities?Data Mining Dissertations and Adventures and Experiences in the World of Chem...
Data Mining Dissertations and Adventures and Experiences in the World of Chem...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The Royal Society of Chemistry hosts a growing collection of online chemistry content. For much of our work the InChI identifier is an important component underpinning our projects. This enables 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 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 platform encompassing efforts in Open Source Drug Discovery and the support of data management for neglected diseases.How the InChI identifier is used to underpin our online chemistry databases a...
How the InChI identifier is used to underpin our online chemistry databases a...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This is the presentation I gave at OpenSciNY 2010. It was a great gathering of Librarians and people interested in Open Science. Sharing the stage with Beth Brown Jean-Claude Bradley and Heather Joseph was, as usual, a good opportunity to discuss how openness and online data sharing is changing the way we access and share data. We live in interesting and exciting times.ChemSpider - Building a Crowdsourced Chemical Database for the Chemistry Comm...
ChemSpider - Building a Crowdsourced Chemical Database for the Chemistry Comm...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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.ChemSpider – disseminating data and enabling an abundance of chemistry platforms
ChemSpider – disseminating data and enabling an abundance of chemistry platformsUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This presentation was given on October 15th 2014 at the University of Connecticut to a class hosted by Mark Peczuh. The intention was to provide an overview of data upload to ChemSpider and ChemSpider SyntheticPages as well as the new direction with the data repository.Building a data repository to manage chemistry research data
Building a data repository to manage chemistry research dataUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The increasing availability of free and open access resources for scientists on the internet presents us with a revolution in data availability. The Royal Society of Chemistry hosts ChemSpider, a free access website for chemists built with the intention of building community for chemists (http://www.chemspider.com/).
ChemSpider is an aggregator of chemistry related information, at present over 20 million unique chemical entities linked out to over 300 separate data sources, ChemSpider has taken on the task of both robotically and manually curating publicly available data sources. It is also a public deposition platform where chemists can deposit their own data including novel structures, analytical data, synthesis procedures and host data associated with the growing activities associated with Open Notebook Science.
This presentation will examine chemistry on the internet, the dubious quality of what is available and how the ChemSpider crowdsourced curation platform is fast becoming one of the centralized hubs for resourcing information about chemical entities.
We will also review our efforts to provide free resources for synthesis procedures, spectral data and structure-based searching of the chemistry literature and how chemists can contribute directly to each of these projects.
RSC ChemSpider -- Managing and Integrating Chemistry on the Internet to Build...
RSC ChemSpider -- Managing and Integrating Chemistry on the Internet to Build...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The Royal Society of Chemistry provides open access to data associated with tens of millions of chemical compounds. The richness and complexity of the data has continued to expand dramatically and the original vision for providing an integrated hub for structure-centric data has been delivered across the world to hundreds of thousands of users. With an intention of expanding the reach to cover more diverse aspects of chemistry-related data including compounds, reactions and analytical data, to name just a few data-types, we are in the process delivering a Chemistry Data Repository. The data repository will manage the challenges of associated metadata, the various levels of required security (private, shared and public) and exposing the data as appropriate using semantic web technologies. Ultimately this platform will become the host for all chemicals, reactions and analytical data contained within RSC publications and specifically supplementary information. This presentation will report on the challenges of managing “Big Data” for chemists around the world and providing access to tools for structure dereplication, spectral database searching and the crowdsourcing of the worlds’ largest spectral database.Dealing with the complex challenge of managing diverse analytical chemistry d...
Dealing with the complex challenge of managing diverse analytical chemistry d...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Over the past five years the Royal Society of Chemistry has become world renowned for its public domain compound database that integrates chemical structures with online resources and available data. ChemSpider regularly serves over 50,000 users per day who are seeking chemistry related data. In parallel we have used ChemSpider and available software services to underpin a number of grant-based projects that we have been involved with: Open PHACTS – a semantic web project integrating chemistry and biology data, PharmaSea – seeking out new natural products from the ocean and the National Chemical Database Service for the United Kingdom. We are presently developing a new architecture that will offer broader scope in terms of the types of chemistry data that can be hosted. This presentation will provide an overview of our Cheminformatics activities at RSC, the development of a new architecture for a data repository that will underpin a global chemistry network, and the challenges ahead, as well as our activities in releasing software and data to the chemistry community. A chemistry data repository to serve them all
A chemistry data repository to serve them allUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The Royal Society of Chemistry (RSC) is one of the world’s most prominent scientific societies and STM publishers. Our contributions to the scientific community include the delivery of a myriad of resources to support the chemistry community to access chemistry-related data, information and knowledge. This includes ChemSpider, a compound centric platform linking together over 30 million chemical compounds with internet-based resources. Using this compound database and its associated chemical identifiers as a basis the RSC is utilizing text and data mining approaches to data enable our published archive of scientific publications. This presentation will provide an overview of our technical approaches to text and data enable our archive of scientific articles, how we are developing an integrated database of chemical compounds, reactions, physical and analytical data and how it will be used to facilitate scientific discovery.The application of text and data mining to enhance the RSC publication archive
The application of text and data mining to enhance the RSC publication archiveUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This is a presentation I gave at the FDA on December 1st 2009 in Wahington DC as part of a symposium involving PubChem, ChemIDPLus, PillBox, DailyMed and other related systems. The focus was, as usual, on the quality of data online and how to clean up the information and with a specific focus on the quality of data on the FDA's DailyMed and our efforts to apply semantic markup to the DailyMed articlesChemSpider and How The Wisdom Of The Crowds Can Improve The Quality Of ...
ChemSpider and How The Wisdom Of The Crowds Can Improve The Quality Of ...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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There is an increasing availability of free and open access resources for chemists to use on the internet. Coupled with the increasing availability of Open Source software tools we are in the middle of a revolution in data availability and tools to manipulate these data. ChemSpider is a free access website for chemists built with the intention of providing a structure centric community for chemists. It was developed with the intention of aggregating and indexing available sources of chemical structures and their associated information into a single searchable repository and making it available to everybody, at no charge.
There are tens if not hundreds of chemical structure databases such as literature data, chemical vendor catalogs, molecular properties, environmental data, toxicity data, analytical data etc. and no single way to search across them. Despite the fact that there were a large number of databases containing chemical compounds and data available online their inherent quality, accuracy and completeness was lacking in many regards. The intention with ChemSpider was to provide a platform whereby the chemistry community could contribute to cleaning up the data, improving the quality of data online and expanding the information available to include data such as reaction syntheses, analytical data, experimental properties and linking to other valuable resources. It has grown into a resource containing over 21 million unique chemical structures from over 200 data sources.
ChemSpider has enabled real time curation of the data, association of analytical data with chemical structures, real-time deposition of single or batch chemical structures (including with activity data) and transaction-based predictions of physicochemical data. The social community aspects of the system demonstrate the potential of this approach. Curation of the data continues daily and thousands of edits and depositions by members of the community have dramatically improved the quality of the data relative to other public resources for chemistry.
This presentation will provide an overview of the history of ChemSpider, the present capabilities of the platform and how it can become one of the primary foundations of the semantic web for chemistry. It will also discuss some of the present projects underway since the acquisition of ChemSpider by the Royal Society of Chemistry.
ChemSpider - Building a Foundation for the Semantic Web by Hosting a Crowd So...
ChemSpider - Building a Foundation for the Semantic Web by Hosting a Crowd So...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The ability to query across a chemistry publishers content using chemical structure searching can dramatically enhance discoverability. RSC has been applying a number of procedures to integrate RSC’s ChemSpider community resource with our published content and databases. These include: 1) entity extraction procedures 2) chemical name conversion procedures using software algorithms and curated dictionaries 3) semantic markup and 4) a crowdsourced curation processes. This presentation will provide an overview of the processes we have utilized in order to provide structure-based integration to RSC content. We will discuss our ongoing efforts to extend the approaches to the mining of data from the rich supplementary information sections of many RSC publications. Our intention is to provide access to synthesis procedures and analytical data and further enrich the ChemSpider database for the benefit of the chemistry community. Enhancing Discoverability Across Royal Society Of Chemistry Content By Integr...
Enhancing Discoverability Across Royal Society Of Chemistry Content By Integr...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Many of us nowadays invest significant amounts of time in sharing our activities and opinions with friends and family via social networking tools. However, despite the availability of many platforms for scientists to connect and share with their peers in the scientific community the majority do not make use of these tools, despite their promise and potential impact and influence on our future careers. We are being indexed and exposed on the internet via our publications, presentations and data. We also have many more ways to contribute to science, to annotate and curate data, to “publish” in new ways, and many of these activities are as part of a growing crowdsourcing network. This presentation will provide an overview of the various types of networking and collaborative sites available to scientists and ways to expose your scientific activities online. Many of these can ultimately contribute to the developing measures of you as a scientist as identified in the new world of alternative metrics. Participating offers a great opportunity to develop a scientific profile within the community and may ultimately be very beneficial, especially to scientists early in their career. Data integration and building a profile for yourself as an online scientist
Data integration and building a profile for yourself as an online scientistUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
These are the slides I will be giving here at the Science Commons Symposium Pacific Northwest at the Microsoft Campus here in Redmond in about 5 minutes timeRSC ChemSpider Science Commons Symposium Pacific Northwest #scspn
RSC ChemSpider Science Commons Symposium Pacific Northwest #scspnUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The structure elucidation of natural product structures from analytical data, specifically NMR and MS, remains a major challenge. With an enormous palette of NMR experiments to choose from, and supported by breakthrough technologies in hardware, the generation of high quality data to enable even the most complex of natural product structures to be determined is no longer the major hurdle. The challenge is in the analysis of the data. We are in a new era in terms of approaches to structure elucidation: one where computers, databases, and a synergy between scientists and algorithms can offer an accelerated path forward. Software tools are capable of digesting spectroscopic data to elucidate extremely complex natural products. Scientists can now elucidate chemical structures utilizing multinuclear chemical shift data, correlation data from an array of 2D NMR experiments and utilize existing data sets for the purpose of dereplication and computer-assisted structure elucidation. With the explosion of online data especially, in public databases such as PubChem and ChemSpider, many tens of millions of chemical structures are available to seed fragment databases to include in the elucidation process. This presentation will provide an overview of how cheminformatics and chemical databases have been brought together to assist in the identification of natural products. It will include an examination of the state-of-the-art developments in Computer-Assisted Structure Elucidation. Cheminformatics and the Structure Elucidation of Natural Products
Cheminformatics and the Structure Elucidation of Natural ProductsUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This presentation was given at the CLIR/DLF Postdoctoral Fellowship Summer Seminar at Bryn Mawr college in Pennsylvania on July 29th 2014. The intention was to communicate what we are doing in the fields of text and data mining in the domain of chemistry and specifically around mining the RSC archive publication and chemistry dissertations and theses. How would these experiences map over to the humanities?Data Mining Dissertations and Adventures and Experiences in the World of Chem...
Data Mining Dissertations and Adventures and Experiences in the World of Chem...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The Royal Society of Chemistry hosts a growing collection of online chemistry content. For much of our work the InChI identifier is an important component underpinning our projects. This enables 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 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 platform encompassing efforts in Open Source Drug Discovery and the support of data management for neglected diseases.How the InChI identifier is used to underpin our online chemistry databases a...
How the InChI identifier is used to underpin our online chemistry databases a...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This is the presentation I gave at OpenSciNY 2010. It was a great gathering of Librarians and people interested in Open Science. Sharing the stage with Beth Brown Jean-Claude Bradley and Heather Joseph was, as usual, a good opportunity to discuss how openness and online data sharing is changing the way we access and share data. We live in interesting and exciting times.ChemSpider - Building a Crowdsourced Chemical Database for the Chemistry Comm...
ChemSpider - Building a Crowdsourced Chemical Database for the Chemistry Comm...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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.ChemSpider – disseminating data and enabling an abundance of chemistry platforms
ChemSpider – disseminating data and enabling an abundance of chemistry platformsUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This presentation was given on October 15th 2014 at the University of Connecticut to a class hosted by Mark Peczuh. The intention was to provide an overview of data upload to ChemSpider and ChemSpider SyntheticPages as well as the new direction with the data repository.Building a data repository to manage chemistry research data
Building a data repository to manage chemistry research dataUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The increasing availability of free and open access resources for scientists on the internet presents us with a revolution in data availability. The Royal Society of Chemistry hosts ChemSpider, a free access website for chemists built with the intention of building community for chemists (http://www.chemspider.com/).
ChemSpider is an aggregator of chemistry related information, at present over 20 million unique chemical entities linked out to over 300 separate data sources, ChemSpider has taken on the task of both robotically and manually curating publicly available data sources. It is also a public deposition platform where chemists can deposit their own data including novel structures, analytical data, synthesis procedures and host data associated with the growing activities associated with Open Notebook Science.
This presentation will examine chemistry on the internet, the dubious quality of what is available and how the ChemSpider crowdsourced curation platform is fast becoming one of the centralized hubs for resourcing information about chemical entities.
We will also review our efforts to provide free resources for synthesis procedures, spectral data and structure-based searching of the chemistry literature and how chemists can contribute directly to each of these projects.
RSC ChemSpider -- Managing and Integrating Chemistry on the Internet to Build...
RSC ChemSpider -- Managing and Integrating Chemistry on the Internet to Build...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The Royal Society of Chemistry provides open access to data associated with tens of millions of chemical compounds. The richness and complexity of the data has continued to expand dramatically and the original vision for providing an integrated hub for structure-centric data has been delivered across the world to hundreds of thousands of users. With an intention of expanding the reach to cover more diverse aspects of chemistry-related data including compounds, reactions and analytical data, to name just a few data-types, we are in the process delivering a Chemistry Data Repository. The data repository will manage the challenges of associated metadata, the various levels of required security (private, shared and public) and exposing the data as appropriate using semantic web technologies. Ultimately this platform will become the host for all chemicals, reactions and analytical data contained within RSC publications and specifically supplementary information. This presentation will report on the challenges of managing “Big Data” for chemists around the world and providing access to tools for structure dereplication, spectral database searching and the crowdsourcing of the worlds’ largest spectral database.Dealing with the complex challenge of managing diverse analytical chemistry d...
Dealing with the complex challenge of managing diverse analytical chemistry d...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Over the past five years the Royal Society of Chemistry has become world renowned for its public domain compound database that integrates chemical structures with online resources and available data. ChemSpider regularly serves over 50,000 users per day who are seeking chemistry related data. In parallel we have used ChemSpider and available software services to underpin a number of grant-based projects that we have been involved with: Open PHACTS – a semantic web project integrating chemistry and biology data, PharmaSea – seeking out new natural products from the ocean and the National Chemical Database Service for the United Kingdom. We are presently developing a new architecture that will offer broader scope in terms of the types of chemistry data that can be hosted. This presentation will provide an overview of our Cheminformatics activities at RSC, the development of a new architecture for a data repository that will underpin a global chemistry network, and the challenges ahead, as well as our activities in releasing software and data to the chemistry community. A chemistry data repository to serve them all
A chemistry data repository to serve them allUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The Royal Society of Chemistry (RSC) is one of the world’s most prominent scientific societies and STM publishers. Our contributions to the scientific community include the delivery of a myriad of resources to support the chemistry community to access chemistry-related data, information and knowledge. This includes ChemSpider, a compound centric platform linking together over 30 million chemical compounds with internet-based resources. Using this compound database and its associated chemical identifiers as a basis the RSC is utilizing text and data mining approaches to data enable our published archive of scientific publications. This presentation will provide an overview of our technical approaches to text and data enable our archive of scientific articles, how we are developing an integrated database of chemical compounds, reactions, physical and analytical data and how it will be used to facilitate scientific discovery.The application of text and data mining to enhance the RSC publication archive
The application of text and data mining to enhance the RSC publication archiveUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Tendances (20)
ChemSpider - Building a Foundation for the Semantic Web by Hosting a Crowd So...
ChemSpider - Building a Foundation for the Semantic Web by Hosting a Crowd So...
Enhancing Discoverability Across Royal Society Of Chemistry Content By Integr...
Enhancing Discoverability Across Royal Society Of Chemistry Content By Integr...
Data integration and building a profile for yourself as an online scientist
Data integration and building a profile for yourself as an online scientist
RSC ChemSpider Science Commons Symposium Pacific Northwest #scspn
RSC ChemSpider Science Commons Symposium Pacific Northwest #scspn
Cheminformatics and the Structure Elucidation of Natural Products
Cheminformatics and the Structure Elucidation of Natural Products
Data Mining Dissertations and Adventures and Experiences in the World of Chem...
Data Mining Dissertations and Adventures and Experiences in the World of Chem...
Chemical intelligence that makes hidden knowledge effortlessly reachable
Chemical intelligence that makes hidden knowledge effortlessly reachable
How the InChI identifier is used to underpin our online chemistry databases a...
How the InChI identifier is used to underpin our online chemistry databases a...
ChemSpider - Building a Crowdsourced Chemical Database for the Chemistry Comm...
ChemSpider - Building a Crowdsourced Chemical Database for the Chemistry Comm...
ChemSpider – disseminating data and enabling an abundance of chemistry platforms
ChemSpider – disseminating data and enabling an abundance of chemistry platforms
Building a data repository to manage chemistry research data
Building a data repository to manage chemistry research data
RSC ChemSpider -- Managing and Integrating Chemistry on the Internet to Build...
RSC ChemSpider -- Managing and Integrating Chemistry on the Internet to Build...
Dealing with the complex challenge of managing diverse analytical chemistry d...
Dealing with the complex challenge of managing diverse analytical chemistry d...
2013 CrossRef Annual Meeting Flash Update ORCID, Ed Pentz.
2013 CrossRef Annual Meeting Flash Update ORCID, Ed Pentz.
The application of text and data mining to enhance the RSC publication archive
The application of text and data mining to enhance the RSC publication archive
Introduction to CrossCheck, Webinar Presentation, 2009, Kirsty Meddings
Introduction to CrossCheck, Webinar Presentation, 2009, Kirsty Meddings
Similaire à Web Crawling Chemistry
This is a presentation I gave at the FDA on December 1st 2009 in Wahington DC as part of a symposium involving PubChem, ChemIDPLus, PillBox, DailyMed and other related systems. The focus was, as usual, on the quality of data online and how to clean up the information and with a specific focus on the quality of data on the FDA's DailyMed and our efforts to apply semantic markup to the DailyMed articlesChemSpider and How The Wisdom Of The Crowds Can Improve The Quality Of ...
ChemSpider and How The Wisdom Of The Crowds Can Improve The Quality Of ...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This is a presentation I gave to a group of students at Drexel University via webex and skype. This is the Powerpoint presentation component but it was intersected with a live demo of multiple online databases. The movie of the presentation is online at SciVee here: http://www.scivee.tv/node/14770Citizen Scientists and Their Contributions to Internet Based Chemistry
Citizen Scientists and Their Contributions to Internet Based ChemistryUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This is a presentation given at the Triangle Chromatography Discussion Group with a focus on Mass Spectrometry and associated web services and what is possible for chromatographersHow an Online Resource for Chemistry Can Change Our World
How an Online Resource for Chemistry Can Change Our WorldUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
There is an increasing availability of free and open access resources for scientists to use on the internet. Coupled with the increasing availability of Open Source software tools we are in the middle of a revolution in data availability and tools to manipulate these data. ChemSpider is a free access website for chemists built with the intention of providing a structure centric community for chemists. As an aggregator of chemistry related information from many sources, at present over 21.5 million unique chemical entities from over 200 separate data sources, ChemSpider has taken on the task of both robotically and manually curating publicly available data sources. This presentation will provide an overview of the ChemSpider platform and how it is fast becoming the centralized hub for resourcing information about chemical entities. Navigating the Complex Web of Chemistry Using ChemSpider
Navigating the Complex Web of Chemistry Using ChemSpiderUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
With an intention to provide a free internet resource of chemistry related data for the community, ChemSpider provides an online database of chemical compounds, reaction syntheses and related data. Members of the community can contribute to the database via the deposition of chemical structures, synthesis procedures and analytical data. Data are also aggregated from many other depositors, at present over 400 data sources. The aggregation of data associated with over 25 million chemical compounds does not come without data quality issues. By engaging the community to curate the data the quality continues to improve on a daily basis. The presentation will provide an overview of our ongoing efforts to expand and curate the database. Using a combination of game-based and recognition systems as well as our dependence on societal giveaway by the community ChemSpider continues its path to become a high quality resource and foundation for the semantic web for chemistry.How Community Crowdsourcing and Social Networking is Helping to Build a Quali...
How Community Crowdsourcing and Social Networking is Helping to Build a Quali...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The internet has revolutionized the sharing of data and information and in the domain of chemistry there are many resources available to help with our research. In recent years various online resources have been introduced that allow users to access information, properties and data associated with chemical entities. At a time when CAS has declared that they now have over 50 million unique chemical entities in the registry the number of chemical structures distributed across the internet also measures in the tens of millions. There are many tens of databases on the internet hosting chemical structures associated with data focused on the specific nature of the collection – metabolic pathways, spectral data collections, chemical vendor collections, biological assay data and crystal structures are examples. Unfortunately there has been no single way to search across all of these resources. ChemSpider has taken on the task of integrating the multiple online resources of information into a single database using the chemical structure as the primary key and retaining the link out and attribution to the original datasource. In this manner ChemSpider intends to become a structure-centric hub for the chemistry community. This talk will provide an overview of the ChemSpider platform, how it is being used as a crowdsourcing platform for community-based curation of the data and the future vision of ChemSpider as one of the pillars of the semantic web of chemistry.Navigating the Complex Web of Chemistry Using ChemSpider
Navigating the Complex Web of Chemistry Using ChemSpiderUS 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...
Building an integrated system for chemistry markup and online publishing inte...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Scientists commonly find themselves in a state of overwhelm in regards to the availability of information accessible to them. The distribution of resources now includes the entire space of the worldwide web, access to primary databases such as CAS and, commonly, a plethora of internally developed systems. While the web has provided improved access to chemistry-related information there has not been an online central resource allowing integrated chemical structure-searching of chemistry databases, chemistry articles, patents and web pages such as blogs and wikis. ChemSpider has built a structure centric community for chemists by providing free access to an online database and collaboration tool for chemists. The online database offers an environment for curating the data on ChemSpider as well as the deposition of chemical structures, analytical data and associated information and provides a significant knowledge base and resource for chemists working in different domains. An overview of present and future capabilities is given.Chemspider Presentation at the ACS Meeting in New orleans
Chemspider Presentation at the ACS Meeting in New orleansUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The Royal Society of Chemistry (RSC) is a major participant in providing access to chemistry related data via the web. As an internationally renowned society for the chemical sciences, a scientific publisher and the host of the ChemSpider database for the community, RSC continues to make dramatic strides in providing online access to data. ChemSpider provides access to over 30 million chemicals sourced from over 500 data suppliers and linked out to related information on the web. The platform is a crowdsourcing environment whereby members of the community can participate in validating and expanding the content of the database. With a set of application programming interfaces ChemSpider is used by various organizations and projects to serve up data for various purposes. These include structure identification for mass spectrometry instrument vendors, RSC databases such as the Marinlit natural products database and a European grant-based project from the Innovative Medicines Initiative fund. This presentation will provide an overview of various cheminformatics activities and projects that RSC is involved with to serve the medicinal chemistry community. This will include the Open PHACTS semantic web project, the PharmaSea project to identify new pharmaceutical leads from the ocean and the UK National Compound Collection to identify new lead compounds contained within PhD theses.Serving the medicinal chemistry community with Royal Society of Chemistry che...
Serving the medicinal chemistry community with Royal Society of Chemistry che...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The Internet is the world’s publicly accessible container for a myriad of resources containing chemistry related data. Whether it be collections of millions of chemical compounds with their associated properties, interactive displays for analytical data, access to publications and patents or tapping into the increasing availability of online computational engines, the web has became the primary enabling technology to source information and data. Scientists collectively applaud and utilize the availability of such resources and an increasing proportion of the community are willing to support these resources by contributing both their data and skills to help curate and validate information on the web. This “crowdsourcing” has started to contribute large amounts of data to the commons and serves has a valuable platform for reference and, potentially, discovery.
ChemSpider is one of the chemistry community’s primary online resources and allows scientists to search across 25 million unique chemical compounds linked out to over 400 original data sources and has become a central hub for searching for chemistry-related data. The platform however offers much more to the community and has become a central repository for analytical data, specifically spectra, is a host for community-authored chemical syntheses and facilitates data curation and annotation by any of its users. This presentation will provide an overview of the ChemSpider platform in terms of available data and its efforts to act as a public repository and clearing ground for data curation. We will discuss how such a platform, when coupled with game-based approaches, facilitates both teaching and data validation and will discuss whether public domain resources such as ChemSpider will ultimately become authorities for chemistry.
ChemSpider hosting linking and curating chemistry data for the community
ChemSpider hosting linking and curating chemistry data for the communityUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The internet has provided access to unprecedented quantities of data. In the domain of chemistry specifically over the past decade the web has become populated with tens of millions of chemical structures and related properties of assays together with tens of thousands of spectra and syntheses. The data have, to a large extent, remained disparate and disconnected. In recent years with the wave of Web 2.0 participation any chemist can contribute to both the sharing and validation of chemistry-related data whether it be via Wikipedia, the online encyclopedia, or one of the multiple public compound databases. The presentation will offer a perspective of what is available today, our experiences of building a public compound database to link together the internet and a suggested path forward for enabling even greater integration and connectivity for chemistry data for the masses to both use and participate in developing. How the web has weaved a web of interlinked chemistry data final
How the web has weaved a web of interlinked chemistry data finalUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This is a presentation given to the Royal Society General Assembly in Birmingham on November 20th 2009. This covers the present status and future vision for ChemSpiderConnecting Chemists to the Internet Through ChemSpider
Connecting Chemists to the Internet Through ChemSpiderUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This is a presentation I gave at the Nature Publishing group offices in London UK. It covers general information about ChemSPider and our efforts with ChemMantis.A Presentation at Nature Publishing Group Crowdsourcing, Collaborations and T...
A Presentation at Nature Publishing Group Crowdsourcing, Collaborations and T...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The presentation of ChemSpider was to a groub of science librarians, specifically chemistry librarians, and was meant to provide an overview of the platform and answer the question posed: What is the difference between ChemSpider, CAS Scifinder and Reaxys. ChemSpider Presentation At University Of Toronto
ChemSpider Presentation At University Of TorontoUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
An overview of what we do to curate and annotate small molecules and how it's the basis of Chemmantis. A presentation given to the PDB team at Rutgers UniversityChecking, Curating And Qualifying Chemistry
Checking, Curating And Qualifying ChemistryUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This is a general presentation about our efforts to build an internet based community for chemists using ChemSpider. A general overview of data quality online, crowdsourced deposition and curation and our progress to deliver a solution to the community for resourcing data.RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For ChemistsUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
ChemSpider was developed with the intention of aggregating and indexing available sources of chemical structures and their associated information into a single searchable repository and making it available to everybody, at no charge. There are many tens of chemical structure databases such as literature data, chemical vendor catalogs, molecular properties, environmental data, toxicity data, analytical data etc. and no single way to search across them. Despite the diversity of databases available online their inherent quality, accuracy and completeness is lacking in many regards. ChemSpider was established to provide a platform whereby the chemistry community could contribute to cleaning up the data, improving the quality of data online and expanding the information available to include data such as reaction syntheses, analytical data and experimental properties. ChemSpider has now grown into a database of over 20 million chemical substances integrated with over 300 disparate data sources, many of these directly supporting the Life Sciences. This presentation will provide an overview of our efforts to improve the quality of data online, to provide a foundation for the semantic web for chemistry and to provide access to a set online tools and services to support access to these data. I will also discuss how ChemSpider is being used to enhance Semantic Publishing in Chemistry at RSC.
ChemSpider – A Community Platform for Chemistry and Resources Supporting the ...
ChemSpider – A Community Platform for Chemistry and Resources Supporting the ...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
RSC|ChemSpider is one of the world’s largest online resources for chemistry related data and services. Developed with the intention of delivering access to structure-based chemistry data via the internet the ChemSpider platform hosts over 26 million unique chemical compounds aggregated from over 400 data sources and provides an environment for the community to both annotate and curate these existing data as well as deposit new data to the system. The search system delivers flexible querying capabilities together with links to external sites for publication and patent data. ChemSpider has spawned a number of projects include ChemSpider SyntheticPages for hosting openly peer-reviewed chemical synthesis articles. This presentation will review the present capabilities of the ChemSpider system providing direct examples of how to use the system to source high quality data of value to pharmaceutical companies. We will discuss some of the challenges associated with validating data quality, examine how ChemSpider is a part of the semantic web for chemistry and investigate approaches to using ChemSpider integrated to analytical instrumentation.Improving online chemistry one structure at a time
Improving online chemistry one structure at a timeUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Similaire à Web Crawling Chemistry (20)
ChemSpider and How The Wisdom Of The Crowds Can Improve The Quality Of ...
ChemSpider and How The Wisdom Of The Crowds Can Improve The Quality Of ...
Citizen Scientists and Their Contributions to Internet Based Chemistry
Citizen Scientists and Their Contributions to Internet Based Chemistry
How an Online Resource for Chemistry Can Change Our World
How an Online Resource for Chemistry Can Change Our World
Navigating the Complex Web of Chemistry Using ChemSpider
Navigating the Complex Web of Chemistry Using ChemSpider
How Community Crowdsourcing and Social Networking is Helping to Build a Quali...
How Community Crowdsourcing and Social Networking is Helping to Build a Quali...
Navigating the Complex Web of Chemistry Using ChemSpider
Navigating the Complex Web of Chemistry Using ChemSpider
Building an integrated system for chemistry markup and online publishing inte...
Building an integrated system for chemistry markup and online publishing inte...
Chemspider Presentation at the ACS Meeting in New orleans
Chemspider Presentation at the ACS Meeting in New orleans
Serving the medicinal chemistry community with Royal Society of Chemistry che...
Serving the medicinal chemistry community with Royal Society of Chemistry che...
Chemspider hosting linking and curating chemistry data for the community
Chemspider hosting linking and curating chemistry data for the community
ChemSpider hosting linking and curating chemistry data for the community
ChemSpider hosting linking and curating chemistry data for the community
How the web has weaved a web of interlinked chemistry data final
How the web has weaved a web of interlinked chemistry data final
Connecting Chemists to the Internet Through ChemSpider
Connecting Chemists to the Internet Through ChemSpider
A Presentation at Nature Publishing Group Crowdsourcing, Collaborations and T...
A Presentation at Nature Publishing Group Crowdsourcing, Collaborations and T...
RSC ChemSpider – Building An Internet Based Community For Chemists
RSC ChemSpider – Building An Internet Based Community For Chemists
ChemSpider – A Community Platform for Chemistry and Resources Supporting the ...
ChemSpider – A Community Platform for Chemistry and Resources Supporting the ...
Improving online chemistry one structure at a time
Improving online chemistry one structure at a time
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Bajaj Allianz Life Insurance Company - Insurer Innovation Award 2024
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Web Crawling Chemistry
- 1. Weaving a New Web for Chemistry Antony Williams
- 3. Searching from the Structure Balloon
- 7. Tell me about Aspirin
- 8. Tell me about Aspirin
- 9. Link outs
- 10. Links out to KEGG Kyoto Encyclopedia of Genes and Genomes
- 11. Tell me about Aspirin
- 12. Tell me About Aspirin
- 13. Tell me about Aspirin
- 14. Tell me about Aspirin
- 15. Tell me about Aspirin
- 17. Open Access Literature Search
- 18. Search PubMed – ChemSpider
- 20. Other Searches
- 21. Complex Search
- 24. Quality is a Major Issue- Search Butanol
- 25. Wikipedia – Crowdsourcing Chemistry
- 28. Differences between ChemSpider/Wikipedia No Analytical Data Active editors – about 50 (?) Active depositors/curators – 30 No Prediction of properties ???? 5000 people/day; 1100 registered Detailed compound monographs Compound monographs linked Text Complex queries – Properties, Text, structure/substructure, OA publishers, Data Sources, … ~5000 organics, 2000 others >21 million unique structures Wikipedia ChemSpider
- 29. Differences between Wikipedia/ChemSpider Growing reputation as focused on quality Worldwide reputation as quality source Chemistry is the focus of ‘Spider Chemistry is a subset of the ‘Pedia Mixed “licensing” GFL licensing for everything Growing team of WP:Chem advocates, curators and admins Strong team of WP:Chem advocates, curators and admins “ Out of a basement” on three servers and 5 volunteers Established infrastructure and Wikipedia Foundation Team Primarily Microsoft .NET technologies with OS components Supported by tried and tested Media-Wiki platform. ChemSpider Wikipedia
- 31. Multi-level Curation and Approval
- 35. Adding to the Database - Structure
- 36. Adding New Text Data Add Publication Add Identifier Add URL
- 37. Adding Supplementary Info to a Structure
- 48. NLM/DTD markup
- 51. Document markup
- 52. Searching from the Structure Balloon
- 54. Online Markup
- 55. Automated markup
- 56. Name to Structure Conversion
- 58. Cryptomisrine
- 60. Supports Word .DOC, HTML, RTF