The Experts below are selected from a list of 11271 Experts worldwide ranked by ideXlab platform
Stephen H. Bryant - One of the best experts on this subject based on the ideXlab platform.
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Finding Potential Multitarget Ligands Using PubChem.
Methods in molecular biology (Clifton N.J.), 2018Co-Authors: Sunghwan Kim, Benjamin A. Shoemaker, Evan E Bolton, Stephen H. BryantAbstract:PubChem ( https://PubChem.ncbi.nlm.nih.gov ) is a key chemical information resource, developed and maintained by the US National Institutes of Health. The present chapter describes how to find potential multitarget ligands from PubChem that would be tested in further experiments. While the protocol presented here uses PubChem's Web-based interfaces to allow users to follow it interactively, it can also be implemented in computer software by using programmatic access interfaces to PubChem (such as PUG-REST or E-Utilities).
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PubChem BioAssay: A Decade's Development toward Open High-Throughput Screening Data Sharing.
SLAS discovery : advancing life sciences R & D, 2017Co-Authors: Yanli Wang, Tiejun Cheng, Stephen H. BryantAbstract:High-throughput screening (HTS) is now routinely conducted for drug discovery by both pharmaceutical companies and screening centers at academic institutions and universities. Rapid advance in assay development, robot automation, and computer technology has led to the generation of terabytes of data in screening laboratories. Despite the technology development toward HTS productivity, fewer efforts were devoted to HTS data integration and sharing. As a result, the huge amount of HTS data was rarely made available to the public. To fill this gap, the PubChem BioAssay database (https://www.ncbi.nlm.nih.gov/pcassay/) was set up in 2004 to provide open access to the screening results tested on chemicals and RNAi reagents. With more than 10 years’ development and contributions from the community, PubChem has now become the largest public repository for chemical structures and biological data, which provides an information platform to worldwide researchers supporting drug development, medicinal chemistry study,...
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PubChem BioAssay: 2017 update
Nucleic acids research, 2016Co-Authors: Yanli Wang, Paul A Thiessen, Benjamin A. Shoemaker, Jiyao Wang, Stephen H. Bryant, Tiejun Cheng, Asta Gindulyte, Jian ZhangAbstract:PubChem's BioAssay database (https://PubChem.ncbi.nlm.nih.gov) has served as a public repository for small-molecule and RNAi screening data since 2004 providing open access of its data content to the community. PubChem accepts data submission from worldwide researchers at academia, industry and government agencies. PubChem also collaborates with other chemical biology database stakeholders with data exchange. With over a decade's development effort, it becomes an important information resource supporting drug discovery and chemical biology research. To facilitate data discovery, PubChem is integrated with all other databases at NCBI. In this work, we provide an update for the PubChem BioAssay database describing several recent development including added sources of research data, redesigned BioAssay record page, new BioAssay classification browser and new features in the Upload system facilitating data sharing.
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Similar compounds versus similar conformers: complementarity between PubChem 2-D and 3-D neighboring sets
Journal of cheminformatics, 2016Co-Authors: Sunghwan Kim, Evan E Bolton, Stephen H. BryantAbstract:Background PubChem is a public repository for biological activities of small molecules. For the efficient use of its vast amount of chemical information, PubChem performs 2-dimensional (2-D) and 3-dimensional (3-D) neighborings, which precompute “neighbor” relationships between molecules in the PubChem Compound database, using the PubChem subgraph fingerprints-based 2-D similarity and the Gaussian-shape overlay-based 3-D similarity, respectively. These neighborings allow PubChem to provide the user with immediate access to the list of 2-D and 3-D neighbors (also called “Similar Compounds” and “Similar Conformers”, respectively) for each compound in PubChem. However, because 3-D neighboring is much more time-consuming than 2-D neighboring, how different the results of the two neighboring schemes are is an important question, considering limited computational resources.
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Cheminformatics analysis of the AR agonist and antagonist datasets in PubChem.
Journal of cheminformatics, 2016Co-Authors: Ming Hao, Stephen H. Bryant, Yanli WangAbstract:Background As one of the largest publicly accessible databases for hosting chemical structures and biological activities, PubChem has been processing bioassay submissions from the community since 2004. With the increase in volume for the deposited data in PubChem, the diversity and wealth of information content also grows. Recently, the Tox21 program, has deposited a series of pairwise data in PubChem regarding to different mechanism of actions (MOA), such as androgen receptor (AR) agonist and antagonist datasets, to study cell toxicity. To the best of our knowledge, little work has been reported from cheminformatics study for these especially pairwise datasets, which may provide insight into the mechanism of actions of the compounds and relationship between chemical structures and functions, as well as guidance for lead compound selection and optimization. Thus, to fill the gap, we performed a comprehensive cheminformatics analysis, including scaffold analysis, matched molecular pair (MMP) analysis as well as activity cliff analysis to investigate the structural characteristics and discontinued structure–activity relationship of the individual dataset (i.e., AR agonist dataset or AR antagonist dataset) and the combined dataset (i.e., the common compounds between the AR agonist and antagonist datasets).
Evan E Bolton - One of the best experts on this subject based on the ideXlab platform.
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PubChem Periodic Table and Element pages: improving access to information on chemical elements from authoritative sources
Chemistry Teacher International, 2020Co-Authors: Sunghwan Kim, Paul A Thiessen, Asta Gindulyte, Jian Zhang, Evan E BoltonAbstract:Abstract PubChem (https://PubChem.ncbi.nlm.nih.gov) is one of the top five most visited chemistry web sites in the world, with more than five million unique users per month (as of March 2020). Many of these users are educators, undergraduate students, and graduate students at academic institutions. Therefore, PubChem has a great potential as an online resource for chemical education. This paper describes the PubChem Periodic Table and Element pages, which were recently introduced to celebrate the 150th anniversary of the periodic table. These services help users navigate the abundant chemical element data available within PubChem, while providing a convenient entry point to explore additional chemical content, such as biological activities and health and safety data available in PubChem Compound pages for specific elements and their isotopes. The PubChem Periodic Table and Element pages are also available as widgets, which enable web developers to display PubChem’s element data on web pages they design. The elemental data can be downloaded in common file formats and imported into data analysis programs (e.g., spreadsheet software, like Microsoft Excel and Google Sheets, and computer scripts, such as python and R). Overall, the PubChem Periodic Table and Element pages improve access to chemical element data from authoritative sources.
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PUG-View: programmatic access to chemical annotations integrated in PubChem
Journal of cheminformatics, 2019Co-Authors: Sunghwan Kim, Paul A Thiessen, Tiejun Cheng, Asta Gindulyte, Jian Zhang, Evan E BoltonAbstract:PubChem is a chemical data repository that provides comprehensive information on various chemical entities. It contains a wealth of chemical information from hundreds of data sources. Programmatic access to this large amount of data provides researchers with new opportunities for data-intensive research. PubChem provides several programmatic access routes. One of these is PUG-View, which is a Representational State Transfer (REST)-style web service interface specialized for accessing annotation data contained in PubChem. The present paper describes various aspects of PUG-View, including the scope of data accessible through PUG-View, the syntax for formulating a PUG-View request URL, the difference of PUG-View from other web service interfaces in PubChem, and its limitations and usage policies.
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Finding Potential Multitarget Ligands Using PubChem.
Methods in molecular biology (Clifton N.J.), 2018Co-Authors: Sunghwan Kim, Benjamin A. Shoemaker, Evan E Bolton, Stephen H. BryantAbstract:PubChem ( https://PubChem.ncbi.nlm.nih.gov ) is a key chemical information resource, developed and maintained by the US National Institutes of Health. The present chapter describes how to find potential multitarget ligands from PubChem that would be tested in further experiments. While the protocol presented here uses PubChem's Web-based interfaces to allow users to follow it interactively, it can also be implemented in computer software by using programmatic access interfaces to PubChem (such as PUG-REST or E-Utilities).
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PubChem chemical structure standardization
Journal of Cheminformatics, 2018Co-Authors: Volker Hähnke, Sunghwan Kim, Evan E BoltonAbstract:PubChem is a chemical information repository, consisting of three primary databases: Substance, Compound, and BioAssay. When individual data contributors submit chemical substance descriptions to Substance, the unique chemical structures are extracted and stored into Compound through an automated process called structure standardization. The present study describes the PubChem standardization approaches and analyzes them for their success rates, reasons that cause structures to be rejected, and modifications applied to structures during the standardization process. Furthermore, the PubChem standardization is compared to the structure normalization of the IUPAC International Chemical Identifier (InChI) software, as manifested by conversion of the InChI back into a chemical structure. The observed rejection rate for substances processed by PubChem standardization was 0.36%, which is predominantly attributed to structures with invalid atom valences that cannot be readily corrected without additional information from contributors. Of all structures that pass standardization, 44% are modified in the process, reducing the count of unique structures from 53,574,724 in substance to 45,808,881 in compound as identified by de-aromatized canonical isomeric SMILES. Even though the processing time is very low on average (only 0.4% of structures have individual standardization time above 0.1 s), total standardization time is completely dominated by edge cases: 90% of the time to standardize all structures in PubChem substance is spent on the 2.05% of structures with the highest individual standardization time. It is worth noting that 60% of the structures obtained from PubChem structure standardization are not identical to the chemical structure resulting from the InChI (primarily due to preferences for a different tautomeric form). Standardization of chemical structures is complicated by the diversity of chemical information and their representations approaches. The PubChem standardization is an effective and efficient tool to account for molecular diversity and to eliminate invalid/incomplete structures. Further development will concentrate on improved tautomer consideration and an expanded stereocenter definition. Modifications are difficult to thoroughly validate, with slight changes often affecting many thousands of structures and various edge cases. The PubChem structure standardization service is accessible as a public resource ( https://PubChem.ncbi.nlm.nih.gov/standardize ), and via programmatic interfaces.
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An update on PUG-REST: RESTful interface for programmatic access to PubChem.
Nucleic acids research, 2018Co-Authors: Sunghwan Kim, Paul A Thiessen, Tiejun Cheng, Evan E BoltonAbstract:PubChem (https://PubChem.ncbi.nlm.nih.gov) is one of the largest open chemical information resources available. It currently receives millions of unique users per month on average, serving as a key resource for many research fields such as cheminformatics, chemical biology, medicinal chemistry, and drug discovery. PubChem provides multiple programmatic access routes to its data and services. One of them is PUG-REST, a Representational State Transfer (REST)-like web service interface to PubChem. On average, PUG-REST receives more than a million requests per day from tens of thousands of unique users. The present paper provides an update on PUG-REST since our previous paper published in 2015. This includes access to new kinds of data (e.g. concise bioactivity data, table of contents headings, etc.), full implementation of synchronous fast structure search, support for assay data retrieval using accession identifiers in response to the deprecation of NCBI's GI numbers, data exchange between PUG-REST and NCBI's E-Utilities through the List Gateway, implementation of dynamic traffic control through throttling, and enhanced usage policies. In addition, example Perl scripts are provided, which the user can easily modify, run, or translate into another scripting language.
Sunghwan Kim - One of the best experts on this subject based on the ideXlab platform.
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PubChem in 2021: new data content and improved web interfaces.
Nucleic acids research, 2020Co-Authors: Sunghwan Kim, Benjamin A. Shoemaker, Jie Chen, Tiejun Cheng, Asta Gindulyte, Paul A ThiessenAbstract:PubChem (https://PubChem.ncbi.nlm.nih.gov) is a popular chemical information resource that serves the scientific community as well as the general public, with millions of unique users per month. In the past two years, PubChem made substantial improvements. Data from more than 100 new data sources were added to PubChem, including chemical-literature links from Thieme Chemistry, chemical and physical property links from SpringerMaterials, and patent links from the World Intellectual Properties Organization (WIPO). PubChem's homepage and individual record pages were updated to help users find desired information faster. This update involved a data model change for the data objects used by these pages as well as by programmatic users. Several new services were introduced, including the PubChem Periodic Table and Element pages, Pathway pages, and Knowledge panels. Additionally, in response to the coronavirus disease 2019 (COVID-19) outbreak, PubChem created a special data collection that contains PubChem data related to COVID-19 and the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
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PubChem Periodic Table and Element pages: improving access to information on chemical elements from authoritative sources
Chemistry Teacher International, 2020Co-Authors: Sunghwan Kim, Paul A Thiessen, Asta Gindulyte, Jian Zhang, Evan E BoltonAbstract:Abstract PubChem (https://PubChem.ncbi.nlm.nih.gov) is one of the top five most visited chemistry web sites in the world, with more than five million unique users per month (as of March 2020). Many of these users are educators, undergraduate students, and graduate students at academic institutions. Therefore, PubChem has a great potential as an online resource for chemical education. This paper describes the PubChem Periodic Table and Element pages, which were recently introduced to celebrate the 150th anniversary of the periodic table. These services help users navigate the abundant chemical element data available within PubChem, while providing a convenient entry point to explore additional chemical content, such as biological activities and health and safety data available in PubChem Compound pages for specific elements and their isotopes. The PubChem Periodic Table and Element pages are also available as widgets, which enable web developers to display PubChem’s element data on web pages they design. The elemental data can be downloaded in common file formats and imported into data analysis programs (e.g., spreadsheet software, like Microsoft Excel and Google Sheets, and computer scripts, such as python and R). Overall, the PubChem Periodic Table and Element pages improve access to chemical element data from authoritative sources.
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PUG-View: programmatic access to chemical annotations integrated in PubChem
Journal of cheminformatics, 2019Co-Authors: Sunghwan Kim, Paul A Thiessen, Tiejun Cheng, Asta Gindulyte, Jian Zhang, Evan E BoltonAbstract:PubChem is a chemical data repository that provides comprehensive information on various chemical entities. It contains a wealth of chemical information from hundreds of data sources. Programmatic access to this large amount of data provides researchers with new opportunities for data-intensive research. PubChem provides several programmatic access routes. One of these is PUG-View, which is a Representational State Transfer (REST)-style web service interface specialized for accessing annotation data contained in PubChem. The present paper describes various aspects of PUG-View, including the scope of data accessible through PUG-View, the syntax for formulating a PUG-View request URL, the difference of PUG-View from other web service interfaces in PubChem, and its limitations and usage policies.
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PubChem 2019 update: improved access to chemical data
Nucleic acids research, 2018Co-Authors: Sunghwan Kim, Benjamin A. Shoemaker, Jie Chen, Tiejun Cheng, Asta Gindulyte, Paul A ThiessenAbstract:PubChem (https://PubChem.ncbi.nlm.nih.gov) is a key chemical information resource for the biomedical research community. Substantial improvements were made in the past few years. New data content was added, including spectral information, scientific articles mentioning chemicals, and information for food and agricultural chemicals. PubChem released new web interfaces, such as PubChem Target View page, Sources page, Bioactivity dyad pages and Patent View page. PubChem also released a major update to PubChem Widgets and introduced a new programmatic access interface, called PUG-View. This paper describes these new developments in PubChem.
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Finding Potential Multitarget Ligands Using PubChem.
Methods in molecular biology (Clifton N.J.), 2018Co-Authors: Sunghwan Kim, Benjamin A. Shoemaker, Evan E Bolton, Stephen H. BryantAbstract:PubChem ( https://PubChem.ncbi.nlm.nih.gov ) is a key chemical information resource, developed and maintained by the US National Institutes of Health. The present chapter describes how to find potential multitarget ligands from PubChem that would be tested in further experiments. While the protocol presented here uses PubChem's Web-based interfaces to allow users to follow it interactively, it can also be implemented in computer software by using programmatic access interfaces to PubChem (such as PUG-REST or E-Utilities).
Yanli Wang - One of the best experts on this subject based on the ideXlab platform.
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PubChem BioAssay: A Decade's Development toward Open High-Throughput Screening Data Sharing.
SLAS discovery : advancing life sciences R & D, 2017Co-Authors: Yanli Wang, Tiejun Cheng, Stephen H. BryantAbstract:High-throughput screening (HTS) is now routinely conducted for drug discovery by both pharmaceutical companies and screening centers at academic institutions and universities. Rapid advance in assay development, robot automation, and computer technology has led to the generation of terabytes of data in screening laboratories. Despite the technology development toward HTS productivity, fewer efforts were devoted to HTS data integration and sharing. As a result, the huge amount of HTS data was rarely made available to the public. To fill this gap, the PubChem BioAssay database (https://www.ncbi.nlm.nih.gov/pcassay/) was set up in 2004 to provide open access to the screening results tested on chemicals and RNAi reagents. With more than 10 years’ development and contributions from the community, PubChem has now become the largest public repository for chemical structures and biological data, which provides an information platform to worldwide researchers supporting drug development, medicinal chemistry study,...
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PubChem BioAssay: 2017 update
Nucleic acids research, 2016Co-Authors: Yanli Wang, Paul A Thiessen, Benjamin A. Shoemaker, Jiyao Wang, Stephen H. Bryant, Tiejun Cheng, Asta Gindulyte, Jian ZhangAbstract:PubChem's BioAssay database (https://PubChem.ncbi.nlm.nih.gov) has served as a public repository for small-molecule and RNAi screening data since 2004 providing open access of its data content to the community. PubChem accepts data submission from worldwide researchers at academia, industry and government agencies. PubChem also collaborates with other chemical biology database stakeholders with data exchange. With over a decade's development effort, it becomes an important information resource supporting drug discovery and chemical biology research. To facilitate data discovery, PubChem is integrated with all other databases at NCBI. In this work, we provide an update for the PubChem BioAssay database describing several recent development including added sources of research data, redesigned BioAssay record page, new BioAssay classification browser and new features in the Upload system facilitating data sharing.
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Cheminformatics analysis of the AR agonist and antagonist datasets in PubChem.
Journal of cheminformatics, 2016Co-Authors: Ming Hao, Stephen H. Bryant, Yanli WangAbstract:Background As one of the largest publicly accessible databases for hosting chemical structures and biological activities, PubChem has been processing bioassay submissions from the community since 2004. With the increase in volume for the deposited data in PubChem, the diversity and wealth of information content also grows. Recently, the Tox21 program, has deposited a series of pairwise data in PubChem regarding to different mechanism of actions (MOA), such as androgen receptor (AR) agonist and antagonist datasets, to study cell toxicity. To the best of our knowledge, little work has been reported from cheminformatics study for these especially pairwise datasets, which may provide insight into the mechanism of actions of the compounds and relationship between chemical structures and functions, as well as guidance for lead compound selection and optimization. Thus, to fill the gap, we performed a comprehensive cheminformatics analysis, including scaffold analysis, matched molecular pair (MMP) analysis as well as activity cliff analysis to investigate the structural characteristics and discontinued structure–activity relationship of the individual dataset (i.e., AR agonist dataset or AR antagonist dataset) and the combined dataset (i.e., the common compounds between the AR agonist and antagonist datasets).
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Literature information in PubChem: associations between PubChem records and scientific articles.
Journal of cheminformatics, 2016Co-Authors: Sunghwan Kim, Paul A Thiessen, Benjamin A. Shoemaker, Jiyao Wang, Evan E Bolton, Yanli Wang, Tiejun Cheng, Stephen H. BryantAbstract:PubChem is an open archive consisting of a set of three primary public databases (BioAssay, Compound, and Substance). It contains information on a broad range of chemical entities, including small molecules, lipids, carbohydrates, and (chemically modified) amino acid and nucleic acid sequences (including siRNA and miRNA). Currently (as of Nov. 2015), PubChem contains more than 150 million depositor-provided chemical substance descriptions, 60 million unique chemical structures, and 225 million biological activity test results provided from over 1 million biological assay records. Many PubChem records (substances, compounds, and assays) include depositor-provided cross-references to scientific articles in PubMed. Some PubChem contributors provide bioactivity data extracted from scientific articles. Literature-derived bioactivity data complement high-throughput screening (HTS) data from the concluded NIH Molecular Libraries Program and other HTS projects. Some journals provide PubChem with information on chemicals that appear in their newly published articles, enabling concurrent publication of scientific articles in journals and associated data in public databases. In addition, PubChem links records to PubMed articles indexed with the Medical Subject Heading (MeSH) controlled vocabulary thesaurus. Literature information, both provided by depositors and derived from MeSH annotations, can be accessed using PubChem’s web interfaces, enabling users to explore information available in literature related to PubChem records beyond typical web search results.
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PubChem applications in drug discovery: a bibliometric analysis
Drug discovery today, 2014Co-Authors: Tiejun Cheng, Yanli Wang, Yongmei Pan, Ming Hao, Stephen H. BryantAbstract:A bibliometric analysis of PubChem applications is presented by reviewing 1132 research articles. The massive volume of chemical structure and bioactivity data in PubChem and its online services have been used globally in various fields including chemical biology, medicinal chemistry and informatics research. PubChem supports drug discovery in many aspects such as lead identification and optimization, compound-target profiling, polypharmacology studies and unknown chemical identity elucidation. PubChem has also become a valuable resource for developing secondary databases, informatics tools and web services. The growing PubChem resource with its public availability offers support and great opportunities for the interrogation of pharmacological mechanisms and the genetic basis of diseases, which are vital for drug innovation and repurposing.
Paul A Thiessen - One of the best experts on this subject based on the ideXlab platform.
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PubChem in 2021: new data content and improved web interfaces.
Nucleic acids research, 2020Co-Authors: Sunghwan Kim, Benjamin A. Shoemaker, Jie Chen, Tiejun Cheng, Asta Gindulyte, Paul A ThiessenAbstract:PubChem (https://PubChem.ncbi.nlm.nih.gov) is a popular chemical information resource that serves the scientific community as well as the general public, with millions of unique users per month. In the past two years, PubChem made substantial improvements. Data from more than 100 new data sources were added to PubChem, including chemical-literature links from Thieme Chemistry, chemical and physical property links from SpringerMaterials, and patent links from the World Intellectual Properties Organization (WIPO). PubChem's homepage and individual record pages were updated to help users find desired information faster. This update involved a data model change for the data objects used by these pages as well as by programmatic users. Several new services were introduced, including the PubChem Periodic Table and Element pages, Pathway pages, and Knowledge panels. Additionally, in response to the coronavirus disease 2019 (COVID-19) outbreak, PubChem created a special data collection that contains PubChem data related to COVID-19 and the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
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PubChem Periodic Table and Element pages: improving access to information on chemical elements from authoritative sources
Chemistry Teacher International, 2020Co-Authors: Sunghwan Kim, Paul A Thiessen, Asta Gindulyte, Jian Zhang, Evan E BoltonAbstract:Abstract PubChem (https://PubChem.ncbi.nlm.nih.gov) is one of the top five most visited chemistry web sites in the world, with more than five million unique users per month (as of March 2020). Many of these users are educators, undergraduate students, and graduate students at academic institutions. Therefore, PubChem has a great potential as an online resource for chemical education. This paper describes the PubChem Periodic Table and Element pages, which were recently introduced to celebrate the 150th anniversary of the periodic table. These services help users navigate the abundant chemical element data available within PubChem, while providing a convenient entry point to explore additional chemical content, such as biological activities and health and safety data available in PubChem Compound pages for specific elements and their isotopes. The PubChem Periodic Table and Element pages are also available as widgets, which enable web developers to display PubChem’s element data on web pages they design. The elemental data can be downloaded in common file formats and imported into data analysis programs (e.g., spreadsheet software, like Microsoft Excel and Google Sheets, and computer scripts, such as python and R). Overall, the PubChem Periodic Table and Element pages improve access to chemical element data from authoritative sources.
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PUG-View: programmatic access to chemical annotations integrated in PubChem
Journal of cheminformatics, 2019Co-Authors: Sunghwan Kim, Paul A Thiessen, Tiejun Cheng, Asta Gindulyte, Jian Zhang, Evan E BoltonAbstract:PubChem is a chemical data repository that provides comprehensive information on various chemical entities. It contains a wealth of chemical information from hundreds of data sources. Programmatic access to this large amount of data provides researchers with new opportunities for data-intensive research. PubChem provides several programmatic access routes. One of these is PUG-View, which is a Representational State Transfer (REST)-style web service interface specialized for accessing annotation data contained in PubChem. The present paper describes various aspects of PUG-View, including the scope of data accessible through PUG-View, the syntax for formulating a PUG-View request URL, the difference of PUG-View from other web service interfaces in PubChem, and its limitations and usage policies.
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PubChem 2019 update: improved access to chemical data
Nucleic acids research, 2018Co-Authors: Sunghwan Kim, Benjamin A. Shoemaker, Jie Chen, Tiejun Cheng, Asta Gindulyte, Paul A ThiessenAbstract:PubChem (https://PubChem.ncbi.nlm.nih.gov) is a key chemical information resource for the biomedical research community. Substantial improvements were made in the past few years. New data content was added, including spectral information, scientific articles mentioning chemicals, and information for food and agricultural chemicals. PubChem released new web interfaces, such as PubChem Target View page, Sources page, Bioactivity dyad pages and Patent View page. PubChem also released a major update to PubChem Widgets and introduced a new programmatic access interface, called PUG-View. This paper describes these new developments in PubChem.
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An update on PUG-REST: RESTful interface for programmatic access to PubChem.
Nucleic acids research, 2018Co-Authors: Sunghwan Kim, Paul A Thiessen, Tiejun Cheng, Evan E BoltonAbstract:PubChem (https://PubChem.ncbi.nlm.nih.gov) is one of the largest open chemical information resources available. It currently receives millions of unique users per month on average, serving as a key resource for many research fields such as cheminformatics, chemical biology, medicinal chemistry, and drug discovery. PubChem provides multiple programmatic access routes to its data and services. One of them is PUG-REST, a Representational State Transfer (REST)-like web service interface to PubChem. On average, PUG-REST receives more than a million requests per day from tens of thousands of unique users. The present paper provides an update on PUG-REST since our previous paper published in 2015. This includes access to new kinds of data (e.g. concise bioactivity data, table of contents headings, etc.), full implementation of synchronous fast structure search, support for assay data retrieval using accession identifiers in response to the deprecation of NCBI's GI numbers, data exchange between PUG-REST and NCBI's E-Utilities through the List Gateway, implementation of dynamic traffic control through throttling, and enhanced usage policies. In addition, example Perl scripts are provided, which the user can easily modify, run, or translate into another scripting language.