MiniSymp2011 Bradley

•Descargar como PPTX, PDF•

1 recomendación•5,029 vistas

1) Historically, chemistry relied on a few "trusted sources" for property data like melting points, but technology now allows a more transparent and data-driven approach using multiple sources. 2) An analysis of melting point data for several compounds from various sources found inconsistencies, outliers, and errors that highlighted issues with solely relying on a single source. 3) Making assumptions and data sources open allows for transparency, validation of data, and faster/better scientific progress as evidenced by several examples of collaborative melting point analysis and predictive models.

Educación Tecnología

The Impact of Openness on the Quality of Chemistry Data and Implications for Organic Synthesis Drexel Chemistry Mini Symposium Jean-Claude Bradley Associate Professor of Chemistry Drexel University September 29, 2011

The Trusted Source Model Before online databases (early 90s) searching for properties like melting points using ONE “trusted source” was practical and acceptable as part of the chemistry culture. ,[object Object]

Chemical Vendor Catalogs (e.g. Sigma-Aldrich)

Peer-Reviewed JournalsSingle values don’t tend to be contradicted

Question Assumptions Using technology, we can begin to replace the “trusted source” model with one based on transparency and provenance

The Chemical Information Validation Sheet 567 curated and referenced measurements from Fall 2010 Chemical Information Retrieval course

Discovering outliers for melting points (stdev/average)

Investigating the m.p. inconsistencies of EGCG

Investigating the m.p. inconsistencies of cyclohexanone

Alfa Aesar donates melting points to the public

Open Melting Point Explorer (Andrew Lang)

Outliers MDPI dataset EPI (donated all data to public also)

Outliers for ethanol: Alfa Aesar and Oxford MSDS

Inconsistencies and SMILES problems within MDPI dataset

MDPI Dataset labeled with High Trust Level

Open Melting Point Datasets Currently 27,000 mps for 20,000 compounds

What is the melting point of 4-benzyltoluene? American Petroleum Institute5 C PHYSPROP-30 C PHYSPROP 125 C peer reviewed journal (2008)97.5 C government database-30 C government database4.58 C

The quest to resolve the melting point of 4-benzyltoluene: liquid at room temp and can be frozen <-30C (Evan Curtin)

Open Lab Notebook page measuring the melting point of 4-benzyltoluene

Motivation: Faster Science,Better Science

Ruling out all melting points above -15C?

Oops – 4-benzyltoluene freezes after 16 days at -15C!

Measuring the melting point by slowly heating from -15 C gives 5 C

There are NO FACTS, only measurements embedded within assumptions Open Notebook Science maintains the integrity of data provenance by making assumptions explicit

Open Random Forest modeling of Open Melting Point data using CDK descriptors (Andrew Lang) R2 = 0.78, TPSA and nHdon most important

Melting point predictions and measurements on iPhone/iPad (Andrew Lang and Alex Clark)

Using melting point for temperature dependent solubility prediction

Web services for summary data (Andrew Lang)

Publication of double+ validated melting point dataset to Nature Precedings and LuLu

Reaction Attempts Book: Reactants listed Alphabetically

Google Apps Scripts for conveniently exploring melting point data

Comparison of model with triple validated measurements Straight chain carboxylic acids from 1 to 10 carbons Straight chain alcohols from 1 to 10 carbons

Cyclic primary amines from 3 to 6 carbons (cyclobutylamine flagged for validation – only single source available)

Google Apps Scripts for planning reactions and creating schemes

Open Melting Points in Supplementary Data Pages of Wikipedia (Martin Walker)

Más contenido relacionado

La actualidad más candente

Jean-Claude Bradley presented at a panel on New Forms of Scholarly Communication in Science at the Special Libraries Association meeting on June 15, 2011. The talk covered the role of trust in science, with a focus on the validation of melting point data. Where the literature was unable to reconcile measurements, Open Notebook Science was used to clarify. The collection of an Open Dataset of melting point measurements for 20,000 compounds was described as well as ongoing curation efforts and corresponding web services. (collaborators Andrew Lang and Antony Williams)

Bradley SLA Talk on Open Melting Point Collections

Jean-Claude Bradley

Chemical Information Retrieval Class 1

Jean-Claude Bradley

ACRL Trust in Science Talk

Jean-Claude Bradley

A brief description of the Chemical Rediscovery Survey and Open Chemistry in ...

Jean-Claude Bradley

Science Online 2011 ONS session

Jean-Claude Bradley

White House Open Notebook Science Poster

Jean-Claude Bradley

Jean-Claude Bradley presents at the University of Delaware Tuesday Tech Talks on February 12, 2013. The aim is to make a compelling case that openness is valuable to the educational process and augmenting scientific knowledge. Specific examples in chemistry relating to solubility, melting point and recrystallization will be detailed, as well as the technical solutions that have proved most useful.

The Value of Openness in Research and Teaching

Jean-Claude Bradley

Jean-Claude Bradley presents on October 9, 2009 at the Northeastern Regional Meeting of the American Chemical Society in Hartford. This talk, entitled "Leveraging Transparency and Crowdsourcing in Chemistry Using Open Notebook Science", was part of a symposium on Publishing and Promoting Chemistry in the Internet Age. It consists of an overview of Open Notebook Science with some new content on solubility prediction algorithms written by Andrew Lang and a few example of students taking a Chemical Information Retrieval class at Drexel University using research logs on a wiki to flesh out their projects.

Leveraging Transparency and Crowdsourcing in Chemistry Using Open Notebook Sc...

Jean-Claude Bradley

Presentation delivered by Colin Batchelor from the RSC eScience team at ACS New Orleans Spring Meeting April 2013. There are dozens of public compound databases now available online, some of these providing access to tens of millions of chemical compounds. However, very little effort has been put into the delivery of databases of chemical reactions with the majority of large resources being commercial in nature. In our five years of delivering chemical based data resources to the chemistry community one of the primary requests has been that chemists want to know how to synthesize many of the chemicals they are researching. This presentation will provide an overview of our concerted efforts to enhance access to freely available chemistry data and will discuss the ChemSpider Reactions as an integrating hub of content including data extracted from US patents, from RSC Journals and databases and from our micro-publishing platform ChemSpider Synthetic Pages (CSSP).

ChemSpider reactions – delivering a free community resource of chemical synth...

US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure

Increasingly online databases are being used for the purpose of structure identification. In many cases an unknown to an investigator is known in the chemical literature or online database and these “known unknowns” are commonly available in these aggregated internet resources. The identification of these types of compounds in commercial, environmental, forensic, and natural product samples can be identified by searching against these large aggregated databases querying by either elemental composition or monoisotopic mass. We will report on the search approaches that we offer on aggregated compound databases hosted by the Royal Society of Chemistry and how these resources can be used for the purpose of structure identification.

Using online chemistry databases to facilitate structure identification in ma...

US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure

Information and data on chemicals is used by scientists to evaluate potential health and ecological risks due to environmental exposures. EPA’s CompTox Chemicals Dashboard (https://comptox.epa.gov) helps evaluate the safety of chemicals by providing public access to a variety of information on over 760,000 chemicals. Within the Dashboard, users can access chemical structures, chemistry information, toxicity data, hazard data, exposure information, and additional links to relevant websites and applications. These data are compiled from sources including EPA’s computational toxicology research databases, from public domain databases and with collaborators across the world. Chemical lists have been added that provide access to various classes of chemicals and project-based datasets are under constant development. Specific functionality has been delivered within the Dashboard to support mass spectrometry including “MS-ready forms” of chemical substances that would be detectable by mass spectrometry. Workflows have been developed to assist in candidate identification and have now been proven with multiple published studies. An integration path between the dashboard and MetFrag has also been established to provide users the significant benefits resulting from the marriage between the two applications. The datasets underpinning the dashboard are freely available (https://comptox.epa.gov/dashboard/downloads) for integration into third party databases. This presentation will provide an overview of the available data types and functionality of the dashboard prior to examining how it is developing to support mass spectrometry based analyses within the agency and for the community in general. This will include a review of our research efforts to enhance the dashboard using in silico MS/MS fragmentation prediction for spectral matching. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.

CompTox Chemicals Dashboard: Data and tools to support chemical and environme...

US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure

The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program integrates advances in biology, chemistry, and computer science to help prioritize chemicals for further research based on potential human health risks. This work involves computational and data driven approaches that integrate chemistry, exposure and biological data. As an outcome of these efforts the National Center for Computational Toxicology (NCCT) has measured, assembled and delivered an enormous quantity and diversity of data for the environmental sciences including high-throughput in vitro screening data, in vivo and functional use data, exposure models and chemical databases with associated properties. A series of software applications and databases have been produced over the past decade to deliver these data. Recent work has focused on the development of a new architecture that assembles the resources into a single platform. With a focus on delivering access to Open Data streams, web service integration accessibility and a user-friendly web application the CompTox Chemicals Dashboard provides access to data associated with ~720,000 chemical substances. These data include research data in the form of bioassay screening data associated with the ToxCast program, experimental and predicted physicochemical properties, product and functional use information and related data of value to environmental scientists. This presentation will provide an overview of the CompTox Chemicals Dashboard and its value to the community as an informational hub. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.

EPA CompTox chemicals dashboard: An online resource for environmental chemists

US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure

Researchers at the EPA’s National Center for Computational Toxicology integrate advances in biology, chemistry, and computer science to examine the toxicity of chemicals and help prioritize chemicals for further research based on potential human health risks. The intention of this research program is to quickly evaluate thousands of chemicals for potential risk but with much reduced cost relative to historical approaches. This work involves computational and data driven approaches including high-throughput screening, modeling, text-mining and the integration of chemistry, exposure and biological data. We have developed a number of databases and applications that are delivering on the vision of developing a deeper understanding of chemicals and their effects on exposure and biological processes that are supporting a large community of scientists in their research efforts. This presentation will provide an overview of our work to bring together diverse large scale data from the chemical and biological domains, our approaches to integrate and disseminate these data, and the delivery of models supporting computational toxicology. This abstract does not reflect U.S. EPA policy.

Delivering The Benefits of Chemical-Biological Integration in Computational T...

US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure

Cloud computing offers significant advantages for the hosting of RSC chemistry databases in terms of reliability, performance and access to large scale computational power. The ChemSpider database contains almost 30 million unique chemical compounds and access to compute power to regenerate properties and add new properties is essential for efficient delivery on a manageable timescale. The use of cloud-based facilities reduces the needs for internal infrastructure and enhances performance generally at the cost of significant recoding of the platforms. This presentation will review our move of our ChemSpider related projects to the cloud, the associated challenges and both the obvious and unforeseen benefits. We will also discuss our use of parallelization technologies for mass calculation using Hadoop.

The application of cloud computing to royal society of chemistry data platforms

Valery Tkachenko

As part of our efforts to develop a public platform to provide access to predictive models we have attempted to disentangle the influence of the quality versus quantity of data available to develop and validate QSAR models. Using a thorough manual review of the data underlying the well-known EPI Suite software, we developed automated processes for the validation of the data using a KNIME workflow. This includes: approaches to validate different chemical structure representations (e.g. molfile and SMILES), identifiers (chemical names and registry numbers), and methods to standardize the data into QSAR-consumable formats for modeling. Our efforts to quantify and segregate data into various quality categories has allowed us to thoroughly investigate the resulting models developed from these data slices, as well as allowing us to examine whether or not efforts into the development of large high-quality datasets has the expected pay-off in terms of prediction performance. Machine-learning approaches have been applied to create a series of models that have been used to generate predicted physicochemical and environmental parameters for over 700,000 chemicals. These data are available online via the EPA’s iCSS Chemistry Dashboard. This abstract does not reflect U.S. EPA policy.

The EPA Online Prediction Physicochemical Prediction Platform to Support Envi...

US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure

Tlad 2015 presentation amin+charles-final

Amin Chowdhury

The iCSS Chemistry Dashboard is a publicly accessible dashboard provided by the National Center for Computation Toxicology at the US-EPA. It serves a number of purposes, including providing a chemistry database underpinning many of our public-facing projects (e.g. ToxCast and ExpoCast). The available data and searches provide a valuable path to structure identification using mass spectrometry as the source data. With an underlying database of over 720,000 chemicals, the dashboard has already been used to assist in identifying chemicals present in house dust. However, it can also be applied to many other purposes, e.g., the identification of agrochemicals in waste streams. This presentation will provide a review of the EPA’s platform and underlying algorithms used for the purpose of compound identification using high-resolution mass spectrometry data. We will also discuss progress towards a high-throughput non-targeted analysis platform for use by the mass spectrometry community. This abstract does not reflect U.S. EPA policy.

Structure Identification Using High Resolution Mass Spectrometry Data and the...

US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure

The cheminformatics group at the Royal Society of Chemistry has supported a number of national and international grants for the last 5 years with the deployment of Cheminformatics tools and platforms. Among them is the Open PHACTS project which is intended to help reducing the barriers to drug discovery in industry, academia and for small businesses by providing the Open PHACTS Discovery Platform. The PharmaSea project targets the identification of leads for new antibiotics in deep sea trenches. The National Chemistry Database Service and Data Repository is a collaborative platform for handling research data. Our contribution to all of these projects has been the development of a number of open source cheminformatics library and user interface components that can be freely used in 3rd party websites and applications. In this presentation we will cover our approach to the development as well as give particular examples of applications built using our toolkits. These software components will likely be very important in the future deployment of Open Notebook Science platforms to help deliver on the vision of Jean-Claude Bradley.

Royal Society of Chemistry open source cheminformatics platforms and libraries

Valery Tkachenko

Researchers at EPA’s National Center for Computational Toxicology integrate advances in biology, chemistry, and computer science to examine the toxicity of chemicals and help prioritize chemicals for further research based on potential human health risks. The goal of this research program is to quickly evaluate thousands of chemicals, but at a much reduced cost and shorter time frame relative to traditional approaches. The data generated by the Center includes characterization of thousands of chemicals across hundreds of high-throughput screening assays, consumer use and production information, pharmacokinetic properties, literature data, physical-chemical properties as well as the predictive computational modeling of toxicity and exposure. We have developed a number of databases and applications to deliver the data to the public, academic community, industry stakeholders, and regulators. This presentation will provide an overview of our work to develop an architecture that integrates diverse large-scale data from the chemical and biological domains, our approaches to disseminate these data, and the delivery of models supporting predictive computational toxicology. In particular, this presentation will review our new publicly-accessible CompTox Dashboard as the first application built on our newly developed architecture. This abstract does not reflect U.S. EPA policy.

Delivering The Benefits of Chemical-Biological Integration in Computational T...

US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure

In the domain of chemistry one of the greatest benefits to publishing research is that data can be shared. Unfortunately, the vast majority of chemical structure data associated with scientific publications remain locked up in document form, primarily in PDF files or trapped on webpages. Despite the explosive growth of online chemical databases and the overall maturity of cheminformatics platforms, many barriers stifle the exchange of chemical structures via publications. These challenges include incomplete support by accepted standards (especially InChI) for advanced stereochemistry, organometallic compounds and generic “Markush” representations, the difference between human-readable and computer-readable forms of data, and challenges with the computer representation of chemical structures. To address these obstacles to chemical structure sharing, US EPA National Center for Computational Toxicology scientists are using a combination of cheminformatics applications and online repositories to distribute chemical structure data associated with their publications. This presentation will describe how EPA-NCCT chemical structure data that is amenable to indexing and distribution are shared and highlight the benefit of open data sharing for modeling, data integration, and increasing research impact. This abstract does not reflect U.S. EPA policy.

Sharing chemical structures with peer reviewed publications

US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure

La actualidad más candente (20)