2015-05-19 Open PHACTS Drug Discovery Workflow Workshop - The API
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1. The document describes the Open PHACTS API workflow for querying biological and chemical data. 2. It provides an overview of the API including documentation, entry points, response templates, and concept types that can be queried. 3. Examples are given of API calls to retrieve information on compounds, targets, tissues, diseases, and pathways from various data sources.
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Structure identification by Mass Spectrometry Non-Targeted Analysis using the...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Identification of unknowns in mass spectrometry based non-targeted analyses (NTA) requires the integration of complementary pieces of data to arrive at a confident, consensus structure. Researchers use chemical reference databases, spectral matching, fragment prediction tools, retention time prediction tools, and a variety of other data to arrive at tentative, probable, and confirmed, if possible, identifications. With the diverse, robust data contained within the US EPA’s CompTox Chemistry Dashboard (https://comptox.epa.gov), the goal of this research is to identify and implement a harmonized identification tool and workflow using previously generated chemistry data. Data has been compiled from product use, functional use prediction models, environmental media occurrence prediction models, and PubMed references, among other sources. We will report on our development of a visualization tool whereby users can visualize the relative contribution of identification-based metrics on a list of candidate structures and observe the greatest likelihood of occurrence. These data and visualization tools support NTA identification via the Dashboard and demonstrate an open, accessible tool for all users of HRMS data. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Delivering The Benefits of Chemical-Biological Integration in Computational T...
Delivering The Benefits of Chemical-Biological Integration in Computational T...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.The EPA Online Prediction Physicochemical Prediction Platform to Support Envi...
The EPA Online Prediction Physicochemical Prediction Platform to Support Envi...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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 influence of data curation on QSAR Modeling – examining issues of qualit...
The influence of data curation on QSAR Modeling – examining issues of qualit...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The construction of QSAR models is critically dependent on the quality of available data. As part of our efforts to develop public platforms to provide access to predictive models, we have attempted to discriminate the influence of the quality versus quantity of data available to develop and validate QSAR models. We have focused our efforts on the widely used EPISuite software that was initially developed over two decades ago. Specific examples of quality issues for the EPISuite data include multiple records for the same chemical structure with different measured property values, inconsistency between the structure, chemical name and CAS registry number for single records, the inability to convert the SMILES strings into chemical structures, hypervalency in the chemical structures and the absence of stereochemistry for thousands of data records. Relative to the era of EPISuite development, modern cheminformatics tools allow for more advanced capabilities in terms of chemical structure representation and storage, as well as enabling automated data validation and standardization approaches to examine data quality. This presentation will review both our manual and automated approaches to examining key datasets related to the EPISuite training and test data. This includes approaches to validate between chemical structure representations (e.g. molfile and SMILES) and identifiers (chemical names and registry numbers), as well as approaches to standardize the data into QSAR-consumable formats for modeling. We have quantified and segregated the data into various quality categories to allow us to thoroughly investigate the resulting models that can be developed from these data slices and to examine to what extent efforts into the development of large high-quality datasets have the expected pay-off in terms of prediction performance. This abstract does not reflect U.S. EPA policy.Delivering The Benefits of Chemical-Biological Integration in Computational T...
Delivering The Benefits of Chemical-Biological Integration in Computational T...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
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. US-EPA CompTox Chemicals Dashboard as a web-based data resource to help ident...
US-EPA CompTox Chemicals Dashboard as a web-based data resource to help ident...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Non-targeted screening, targeted screening and suspect screening, as well as “Known Unknowns” and “Unknown Unknowns” are now common terms in the field of water analysis. While data processing can be highly automated, the identification of chemicals from extracted masses, formulae or fragmentation utilizes reference spectral libraries or identification and ranking of tentative candidate lists from large structure libraries. The US-EPA CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard) provides access to data for ~875,000 substances, searchable by mass and formula and then ranked using associated meta-data. Cheminformatics approaches are also utilized to provide mapped relationships between individual substances and their “MS-Ready” (desalted, non-stereospecific) forms. This presentation will review how the freely available Dashboard application can be utilized to support structure identification using mass spectrometry and our efforts to enhance the application using computational spectral fragmentation and access to predicted data such as relative retention time index values and computed collision cross section values to support ion mobility spectrometry. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.The EPA Comptox Chemistry Dashboard: A Web-Based Data Integration Hub for Tox...
The EPA Comptox Chemistry Dashboard: A Web-Based Data Integration Hub for Tox...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 but recent developments have focused on the development of a new software architecture that assembles the resources into a single platform. A new web application, the CompTox Chemistry Dashboard provides access to data associated with ~720,000 chemical substances. These data include experimental and predicted physicochemical property data, bioassay screening data associated with the ToxCast program, product and functional use information and a myriad of related data of value to environmental scientists.
The dashboard provides chemical-based searching based on chemical names, synonyms and CAS Registry Numbers. Flexible search capabilities allow for chemical identification based on non-targeted analysis studies using mass spectrometry. Chemical identification using both mass and formula-based searching utilizes rank-ordering of results via functional use statistics, thereby providing a solution to help prioritize chemicals for further review when detected in environmental media.
This presentation will provide an overview of the CompTox Dashboard, its capabilities for delivering data to the environmental toxicology community and how the architecture provides a foundation for the development of additional applications to support chemical risk assessment. This abstract does not reflect U.S. EPA policy.
Adding complex expert knowledge into chemical database and transforming surfa...
Adding complex expert knowledge into chemical database and transforming surfa...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This document discusses adding complex expert knowledge about surfactants to chemical databases to aid in the identification of unknown compounds from wastewater samples. It describes how over 60% of peaks detected by high resolution mass spectrometry in wastewater samples are unknown. Literature data on surfactant properties and spectra were compiled and added to databases to support the identification of homologous series and complex mixtures present. A list of surfactants was developed and incorporated into toxicity databases to enable in silico modeling and computational mass spectrometry approaches to aid non-target screening. International collaboration is helping to establish a global exchange of suspect lists to support the identification of unknown contaminants.Integrating and curating internet based chemistry resources to serve life sci...
Integrating and curating internet based chemistry resources to serve life sci...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The internet now offers access to a myriad of online resources that can be of value to chemists working in the Life Sciences. While finding information online is, in many cases, a simple search away, the accuracy and validity of the associated data and information should be questioned. As more databases and resources are introduced online, and commonly not integrated to other resources, a scientist must perform multiple searches and then undertake the task of meshing and merging data. ChemSpider is a freely accessible online database that has taken on the challenge of meshing together distributed resources across the internet to provide a structure-based hub. It is a crowdsourcing environment hosting over 26 million unique compounds linked out to over 400 data sources. With well defined programming interfaces for integration ChemSpider has been integrated to many commercial and open software packages and is presently serving as the chemistry foundation for the IMI Open PHACTS project.
Chemical identification of unknowns in high resolution mass spectrometry usin...
Chemical identification of unknowns in high resolution mass spectrometry usin...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
Non-targeted and suspect screening studies using high resolution mass spectrometry (HRMS) have revolutionized the detection of chemicals in complex matrices. However, data processing remains challenging due to the vast number of chemicals detected in samples, software and computational requirements of data processing, and inherent uncertainty in confidently identifying chemicals from candidate lists. The US EPA has developed functionality within the CompTox Chemicals Dashboard (https://comptox.epa.gov) to address challenges related to data processing and analysis in HRMS. These tools include the generation of “MS-Ready” structures to optimize database searching, retention time prediction for candidate reduction, consensus ranking using chemical metadata, and in silico MS/MS fragmentation prediction for spectral matching. Combining these tools into a comprehensive workflow improves certainty in candidate identification. This presentation will introduce the tools and combined workflow, including visualization and access via the CompTox Chemicals Dashboard. These tools, data, and visualization approaches within an open chemistry resource provides a publicly available software tool to support structure identification and non-targeted analyses. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.IUPHAR/BPS Guide to Pharmacology
Poster presented at the Elixir All-Hands Meeting in Lisbon, June 2019. Gives a broad summary of Guide to Pharmacology activities in the last year. Emphasising new tools and our extension into malaria pharmacology.
Web-based access to experimental and predicted data for environmental fate, t...
Web-based access to experimental and predicted data for environmental fate, t...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
This document describes the CompTox Chemistry Dashboard, a publicly accessible website developed by the EPA's National Center for Computational Toxicology that provides data on over 762,000 chemicals. The dashboard contains experimental and predicted physicochemical property data, environmental fate and transport data, toxicity data, and models. It allows users to search, view detailed chemical pages, access prediction reports, perform batch searches, and will integrate additional predicted properties and data in the future. The goal is to provide a central resource for computational toxicology data to support chemical safety assessments.Structure Identification Using High Resolution Mass Spectrometry Data and the...
Structure Identification Using High Resolution Mass Spectrometry Data and the...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The iCSS CompTox 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. In order to examine its performance for structure identification, especially in terms of rank-ordering database hits, we have compared it with the ChemSpider database, a well-regarded public database that has become one of the community standards for structure identification. The study has shown that the CompTox Dashboard outperforms ChemSpider in terms of structure identification and ranking providing improved outcomes for mass spectrometry analysis of “known unknowns”. Using the US EPA’s CompTox Chemistry Dashboard for structure identification a...
Using the US EPA’s CompTox Chemistry Dashboard for structure identification a...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
High resolution mass spectrometry (HRMS) and non-targeted analysis (NTA) are advancing the identification of emerging contaminants in environmental matrices, improving the means by which exposure analyses can be conducted. However, confidence in structure identification of unknowns in NTA presents challenges to analytical chemists. Structure identification requires integration of complementary data types such as reference databases, fragmentation prediction tools, and retention time prediction models. The goal of this research is to optimize and implement structure identification functionality within the US EPA’s CompTox Chemistry Dashboard, an open chemistry resource and web application containing data for ~760,000 substances. Rank-ordering the number of sources associated with chemical records within the Dashboard (Data Source Ranking) improves the identification of unknowns by bringing the most likely candidate structures to the top of a search results list. Database searching has been further optimized with the generation of MS-Ready Structures. MS-Ready structures are de-salted, stripped of stereochemistry, and mixture separated to replicate the form of a chemical observed via HRMS. Functionality to conduct batch searching of molecular formulae and monoisotopic masses was designed and released to improve searching efforts. Finally, a scoring-based identification scheme was developed, optimized, and surfaced via the Dashboard using multiple data streams contained within the database underlying the Dashboard. The scoring-based identification scheme improved the identification of unknowns over previous efforts using data source ranking alone. Combining these steps within an open chemistry resource provides a freely available software tool for structure identification and NTA. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Accessing information for chemicals in hydraulic fracturing fluids using the ...
Accessing information for chemicals in hydraulic fracturing fluids using the ...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The document describes the EPA's CompTox Chemistry Dashboard, which provides access to data on over 760,000 chemicals. It focuses on how the Dashboard can be used to access information on chemicals used in hydraulic fracturing. Key features include searching for chemicals by name or formula, viewing associated property and hazard data, and links to other resources. The process of curating chemical lists from sources like EPA's hydraulic fracturing study involves mapping names to CAS numbers and structures through iterative checking. This allows accessing additional screening data, exposure information, and integrating identifiers to support searches.ChemInform RxnFinder
This document describes RxnFinder, a database workflow tool for organic synthesis researchers. It contains over 2 million chemical reactions and 1.7 million substances. Researchers can use it to search for synthetic routes, reaction conditions, catalysts, and more. Key features include its focus on novel methods, inclusion of failed reactions, and display of full reaction schemes with scope and limitations. The document provides examples of different types of searches researchers can perform, including transformational, substructure, and property searches. It also describes how search results in RxnFinder can link to detailed article information on Wiley Online Library.
Metabolic Set Enrichment Analysis - chemrich - 2019
ChemRICH is a method for metabolite set enrichment analysis that uses chemical similarity clustering rather than biochemical pathways. It groups metabolites into non-overlapping sets based on chemical similarity rather than pathway membership. It then uses the Kolmogorov-Smirnov test rather than the hypergeometric test to identify which sets are significantly different between study groups. This overcomes limitations of pathway-based analysis, such as metabolites not being annotated to pathways or pathways having unclear boundaries. The online ChemRICH app allows interactive analysis and downloading of results.
The IUPHAR/MMV Guide to Malaria Pharmacology
This document summarizes the creation of the IUPHAR/MMV Guide to Malaria Pharmacology (GtoMPdb) database by the authors. It captures antimalarial compounds, targets, and their relationships by curating data from publications. The database has adapted the Guide to Pharmacology data model and has begun capturing data on 28 antimalarial ligands. Future plans include expanding the curation, developing an online portal, and submitting data to PubChem to link compounds to publications and make the data more accessible.
New developments in delivering public access to data from the National Center...
New developments in delivering public access to data from the National Center...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The National Center for Computational Toxicology at the EPA has developed the CompTox Chemistry Dashboard to provide public access to toxicity and chemical property data. The dashboard integrates data from high-throughput screening, predicted properties, chemical hazard assessments, literature searches, and exposure information for over 760,000 chemicals. It allows users to search for chemicals individually or in batches, access detailed chemical pages, view predicted and experimental properties, and download open data. The dashboard is meant to be an integration hub that makes NCCT's data and models more accessible and reusable to other scientists.sot2016_mn-am_abstract_2476_cosmosDataSharePoint
- COSMOS DB v2.0 is a publicly available, international database maintained through the COSMOS DataShare Point initiative to house qualified human health toxicity data.
- It contains over 80,000 chemical records and 12,000 toxicity studies across 27 endpoints for safe evaluation of chemicals without animal testing.
- Direct collaboration allows data exchange between international organizations for regulatory use.
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Structure identification by Mass Spectrometry Non-Targeted Analysis using the...
Structure identification by Mass Spectrometry Non-Targeted Analysis using the...
Delivering The Benefits of Chemical-Biological Integration in Computational T...
Delivering The Benefits of Chemical-Biological Integration in Computational T...
The EPA Online Prediction Physicochemical Prediction Platform to Support Envi...
The EPA Online Prediction Physicochemical Prediction Platform to Support Envi...
The influence of data curation on QSAR Modeling – examining issues of qualit...
The influence of data curation on QSAR Modeling – examining issues of qualit...
Delivering The Benefits of Chemical-Biological Integration in Computational T...
Delivering The Benefits of Chemical-Biological Integration in Computational T...
US-EPA CompTox Chemicals Dashboard as a web-based data resource to help ident...
US-EPA CompTox Chemicals Dashboard as a web-based data resource to help ident...
The EPA Comptox Chemistry Dashboard: A Web-Based Data Integration Hub for Tox...
The EPA Comptox Chemistry Dashboard: A Web-Based Data Integration Hub for Tox...
Adding complex expert knowledge into chemical database and transforming surfa...
Adding complex expert knowledge into chemical database and transforming surfa...
Integrating and curating internet based chemistry resources to serve life sci...
Integrating and curating internet based chemistry resources to serve life sci...
Chemical identification of unknowns in high resolution mass spectrometry usin...
Chemical identification of unknowns in high resolution mass spectrometry usin...
Web-based access to experimental and predicted data for environmental fate, t...
Web-based access to experimental and predicted data for environmental fate, t...
Structure Identification Using High Resolution Mass Spectrometry Data and the...
Structure Identification Using High Resolution Mass Spectrometry Data and the...
Using the US EPA’s CompTox Chemistry Dashboard for structure identification a...
Using the US EPA’s CompTox Chemistry Dashboard for structure identification a...
Accessing information for chemicals in hydraulic fracturing fluids using the ...
Accessing information for chemicals in hydraulic fracturing fluids using the ...
Metabolic Set Enrichment Analysis - chemrich - 2019
Metabolic Set Enrichment Analysis - chemrich - 2019
New developments in delivering public access to data from the National Center...
New developments in delivering public access to data from the National Center...
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2011-10-11 Open PHACTS at BioIT World Europe
The document discusses the Innovative Medicines Initiative's Open PHACTS project, which aims to develop robust standards and apply them in a semantic integration platform ("Open Pharmacological Space") to integrate drug discovery data from various public and private sources. The project brings together partners from industry, academia, and non-profits to build an open infrastructure for linking drug discovery knowledge and supporting ongoing research. It outlines the technical approach, priorities, and initial progress on developing exemplar applications and a prototype "lash up" system.
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A summary of the first 6 months of the Open PHACTS IMI project, presented by Richard Kidd to the Healthcare Innovation Seminar 2011.
2013 Open PHACTS Exemplars Poster
This document introduces several exemplar applications that were developed to showcase the capabilities of the Open PHACTS platform API. The exemplars include ChemBio Navigator, which allows browsing chemical and biological data for drug discovery applications; Polypharmacology Browser tools like GARField and PharmaTrek that enable exploration of compound-target interactions; and the Target Dossier, which compiles target-related information for decision support in target selection and validation. These exemplars demonstrate how diverse data integrated through the Open PHACTS platform can address relevant problems in drug development and biomedical research.
2013-12-04 Experimental data guided docking allows to elucidate the molecular...
Presentation given by Gerhard Ecker (University of Vienna) to Pharma IndoChina VIII, in Ho Chi Minh City, Vietnam
Open PHACTS MIOSS may 2016
Open PHACTS provides a single access point for integrating multiple biomedical data resources. It has transitioned from an EU project to the Open PHACTS Foundation to sustain the platform long-term. Challenges included addressing licensing issues across different data sources and enabling maximum dissemination. Usage has grown to over 500 million queries. The Foundation is pursuing collaboration, grants, and industry partnerships to support ongoing development and new projects. It welcomes contributions to improve services and develop new data and workflows.
BDE-SC6 Hangout - “Insight into Virtual Currency Ecosystems”
Third SC6 webinar was held on 16 February 2017. It was organised by the Consortium of Social Science Data Archives (CESSDA) from Norway and the Semantic Web Company (SWC) from Austria. Theme of the webinar was “Insight into Virtual Currency Ecosystems” presented by Dr. Bernhard Haslhofer, Data Scientist at the Austrian Institute of Technology.
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2013-12-04 Experimental data guided docking allows to elucidate the molecular...
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BDE-SC6 Hangout - “Insight into Virtual Currency Ecosystems”
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Similar to 2015-05-19 Open PHACTS Drug Discovery Workflow Workshop - The API
2011-11-28 Open PHACTS at RSC CICAG
Presented by Richard Kidd at "The Future Information Needs of Pharmaceutical & Medicinal Chemistry", Monday 28 November 2011 at The Linnean Society, Burlington Square, London run by the RSC CICAG group.
Mashing Up Drug Discovery
This document discusses how APIs are enabling new ways of accessing and mashing up drug discovery data from various sources. It provides examples of existing bio/chem/med APIs and case studies of companies that are using APIs in novel ways for tasks like patent chemistry searching and therapeutic intelligence analysis. The document advocates for making APIs more accessible to allow broader exploration of data that can uncover new use cases and insights, while also noting challenges around usability, data discovery, and security.
Online Resources to Support Open Drug Discovery Systems
Online Resources to Support Open Drug Discovery SystemsUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The document discusses online resources that can support open drug discovery systems. It outlines how pharmaceutical companies spend billions annually on R&D and how public domain data from sources like literature, patents and databases could provide high value. However, such data is difficult to integrate and navigate due to a lack of standards and interoperability between sources. The Open PHACTS project aims to address this by developing standards to semantically integrate drug discovery data from public and private sources.Open PHACTS (Sept 2013) EBI Industry Programme
This is a talk i'm giving for the EBI's industry programme on 18th Sept. The slides are mostly what you may have seen before with a few new ones thrown in to not make it too boring! With grateful acknowledgment of all the folks in Open PHACTS who make this stuff happen.
Opening up pharmacological space, the OPEN PHACTs api
The document provides an overview of the Open PHACTS project, which aims to create an open pharmacological space (OPS) through semantic integration of public drug discovery resources. It discusses the challenges of accessing and integrating scientific data across organizational boundaries. Open PHACTS builds a service layer and applications to allow standardized access and analysis of data from various public sources. It is a collaborative project involving academic and industry partners seeking to make pre-competitive drug discovery data more accessible and useful through semantic integration and common standards.
Pistoia Alliance European Conference 2015 - Nick Lynch / Open PHACTS Foundation
Slides from a presentation given at the Pistoia Alliance European Conference 2015, in Zurich, Switzerland.
Implementing chemistry platform for OpenPHACTS
The Open PHACTS project delivers an online platform integrating a wide variety of data from across chemistry and the life sciences and an ecosystem of tools and services to query this data in support of pharmacological research, turning the semantic web from a research project into something that can be used by practising medicinal chemists in both academia and industry. In the summer of 2015 it was the first winner of the European Linked Data Award. At the Royal Society of Chemistry we have provided the chemical underpinnings to this system and in this talk we review its development over the past five years. We cover both our early work on semantic modelling of chemistry data for the Open PHACTS triplestore and more recent work building an all-purpose data platform, for which the Open PHACTS data has been an important test case, what has worked well, what's missing and where this is is likely to go in future.
Enabling HTS Hit follow up via Chemo informatics, File Enrichment, and Outsou...
Enabling HTS Hit follow up via Chemo informatics, File Enrichment, and Outsourcing The history of parallel chemistry for lead discovery at Pfizer Sandwich from begining to outsourcing
Practical semantics in the pharmaceutical industry - the Open PHACTS project
Practical semantics in the pharmaceutical industry - the Open PHACTS projectUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The information revolution has transformed many business sectors over the last decade and the pharmaceutical industry is no exception. Developments in scientific and information technologies have unleashed an avalanche of content on research scientists who are struggling to access and filter this in an efficient manner. Furthermore, this domain has traditionally suffered from a lack of standards in how entities, processes and experimental results are described, leading to difficulties in determining whether results from two different sources can be reliably compared. The need to transform the way the life-science industry uses information has led to new thinking about how companies should work beyond their firewalls. In this talk we will provide an overview of the traditional approaches major pharmaceutical companies have taken to knowledge management and describe the business reasons why pre-competitive, cross-industry and public-private partnerships have gained much traction in recent years. We will consider the scientific challenges concerning the integration of biomedical knowledge, highlighting the complexities in representing everyday scientific objects in computerised form. This leads us to discuss how the semantic web might lead us to a long-overdue solution. The talk will be illustrated by focusing on the EU-Open PHACTS initiative (openphacts.org), established to provide a unique public-private infrastructure for pharmaceutical discovery. The aims of this work will be described and how technologies such as just-in-time identity resolution, nanopublication and interactive visualisations are helping to build a powerful software platform designed to appeal to directly to scientific users across the public and private sectors.2015-02-10 The Open PHACTS Discovery Platform: Semantic Data Integration for ...
The Open PHACTS Discovery Platform integrates multiple biomedical data resources into a single open access point using semantic web technology. It is guided by business questions from pharmaceutical companies to integrate data from sources like ChEMBL, DrugBank, UniProt, and more. The platform is run as a public-private partnership through 2021 to support drug discovery.
Open Phenotypic Drug Discovery Resource poster
Open Phenotypic Drug Discovery Resource poster, presented at Open PHACTS Conference "Linking Life Science Data", Feb 18-19, 2016, University of Vienna
EUGM15 - George Papadatos, Mark Davies, Nathan Dedman (EMBL-EBI): SureChEMBL:...
SureChEMBL is a new resource provided by the European Bioinformatics Institute (EMBL-EBI) that annotates, extracts and indexes chemistry from full text patent documents by means of continuous, automated text and image mining. SureChEMBL is perhaps the only open, freely available, live patent chemistry resource available, in a field that has been traditionally commercial.
Since its launch last September, the SureChEMBL interface provides sophisticated keyword and chemistry-based querying and exporting functionality against a corpus of more than 16 million compounds extracted from 13 million patent documents. Both the interface and the underlying data pipeline leverage extensively ChemAxon technologies for name to structure conversion, as well as compound standardisation, registration and searching.
In addition to providing an overview of the system, recent developments and improvements will be described. These include the introduction of various data interexchange and exporting options, such as flat files and a data feed client. Furthermore, our future plans for the SureChEMBL system will be outlined. To date, such plans include complementing the chemical annotations with biological ones, covering genes, proteins, diseases and indications. Furthermore, we are planning to further enrich the chemical annotations with a relevance score, indicating their importance in the patent document.
EDF2014: Paul Groth, Department of Computer Science & The Network Institute, ...
Invited Talk by Paul Groth, Department of Computer Science & The Network Institute, VU University Amsterdam, Netherlands at the European Data Forum 2014, 20 March 2014 in Athens, Greece: Open PHACTS: A Data Platform for Drug Discovery.
2014-03-20 Open PHACTS - A Data Platform for Drug Discovery
A data platform is proposed for drug discovery that would lower industry firewalls and enable pre-competitive data integration, analysis, and reuse across pharmaceutical companies. The platform would integrate external research data from literature, databases, and other sources on compounds, targets, pathways, and diseases. It would provide data integration and analysis tools through a firewalled database system and applications. The goal is to advance drug discovery by allowing multiple companies to access and build upon the same large foundation of pre-competitive research data.
Sourcing high quality online data resources for computational toxicology
Sourcing high quality online data resources for computational toxicologyUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The internet continues to offer increased access to chemistry data that may be of value to scientists interested in populating systems containing reference toxicology data as well as to provide data for the development of predictive models. This presentation will give an overview of some of the various sources of data available via the internet, provide an overview of some of the challenges associated with gathering high-quality data and discuss methods by which to mesh together disparate data sources.Structure identification approaches using the EPA CompTox Chemicals Dashboard...
Structure identification approaches using the EPA CompTox Chemicals Dashboard...US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
The document discusses how the EPA's CompTox Chemicals Dashboard can be used to support mass spectrometry analyses for structure identification. The Dashboard contains data on over 800,000 chemicals including properties, lists, and links to other resources. It allows searching by formula, structure, and mass to find related chemicals. Candidate structures can be ranked using metadata. Predicted mass spectra from over 800,000 structures may also be accessible. The Dashboard integrates data to help identify unknown chemicals detected by mass spectrometry.An Integrated Approach To Drug Discovery Using Parallel Synthesis
An Integrated Approach To Drug Discovery Using Parallel Synthesis. The history of parallel chemistry for lead discovery at Pfizer Sandwich from begining to outsourcing
ChemSpider – An Online Database and Registration System Linking the Web
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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. 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 chemists. We will discuss some of the challenges associated with validating data quality and examine how ChemSpider is a part of the new “semantic web for chemistry”. ChemSpider has also spawned a number of additional projects include ChemSpider SyntheticPages for hosting openly peer-reviewed chemical synthesis articles, Learn Chemistry Wiki for students learning chemistry and SpectraSchool for learning spectroscopy.Exploiting PubChem for Drug Discovery
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==== Abstract ====
PubChem (https://pubchem.ncbi.nlm.nih.gov) is a popular chemical information resource, visited by millions of unique users per month. It contains chemical data from more than 700 data sources and disseminates these data to the public free of charge. Arguably, it is the largest source of publicly available chemical information, containing more than 250 million depositor-provided substance descriptions, 100 million unique chemical structures, and 260 million bioactivity outcomes from one million assays covering around ten thousand unique protein target sequences. This presentation provides an overview of PubChem’s data, tools, and services useful for drug discovery.
The immense quantity of bioactivity data in PubChem can be used to develop computational models to predict bioactivities of small molecules. While these data are primarily generated from high-throughput screening (HTS), they also include a substantial amount of bioactivity information extracted from peer-reviewed journal articles. In addition, through data integration with other databases, PubChem has a wide range of annotations useful for drug discovery, including pharmacology, toxicology, drug target, metabolism, chemical vendors, scientific articles, patents, and many others.
PubChem supports various types of chemical structure searches, including identity, 2-D and 3-D similarity, substructure, superstructure, and molecular formula. It also provides multiple programmatic access routes, including E-Utilities, Power User Gateway (PUG), PUG-SOAP, PUG-REST, and PUG-View, allowing one to build an automated workflow that takes advantage of information contained in PubChem. In addition, through PubChemRDF, users can integrate PubChem data with their own.
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- 5. Concepts Chemical compounds Biological targets Pathways Diseases Tissues
- 7. ChEMBL DrugBank Gene Ontology Wikipathways UniProt ChemSpider ChEMBL Target Class ConceptWiki ChEBI DisGeNet neXtProt Data Sources ENZYME FDA adverse events
- 9. Registering for API keys API Overview Entry Points: URLs API Results Getting Started with Compounds Going Further Open PHACTS API Basics
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- 15. Response template legend for API calls results
- 16. API calls: Concept types
- 17. Many filtering options per call
- 18. Specific calls exposing filtering parameters
- 20. API Entry Points: URLs https://dev.openphacts.org/docs/1.5
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