Reciprocally, such PubChem/PubMed direct links will also allow PubMed users to immediately access assay results, hence facilitating information integration by PubChem and other NCBI resources. It started in 2004 serving as a public repository for information generated from chemogenomic, medicinal chemistry and functional genomics research. PubChem assigns a unique PubChem BioAssay accession (AID) to each of the imported bioassay records, and provides cross-links to the respective ChEMBL web pages. 2016 Sep;11(9):843-55. doi: 10.1080/17460441.2016.1216967. Similarly, PubChem now allows other types of cross-reference, such as those to PubMed, GenBank or NCBI Probe databases, to be specified per each tested substance. Contributions from some other organizations were described previously (1). Thank you for submitting a comment on this article. For example, … The table includes SID,CID, structure, bioactivity outcome, score and active concentration value if available, Complete data table for given AID, including all deposited test results, An interface for constructing an Entrez query, An interface for reviewing search history and combining search results, Chemical structure and bioassay submission tool, BioActivity Summary presented from the assay point of view, BioActivity Summary presented from the compound point of view, BioActivity Summary presented from the target point of view, BioActivity information for a single SID or CID. doi: 10.1093/nar/gkp965. These tools allow users to retrieve assay descriptions and data, review related bioassays, compare bioactivity data from multiple experiments and explore structure–activity relationship. PubChem: a public information system for analyzing bioactivities of small molecules. 2020 Sep 23;1(8):100107. doi: 10.1016/j.patter.2020.100107. Analysis of the Interaction between Polygenic Risk Score and Calorie Intake in Obesity in the Korean Population. A snapshot of the Document Summary (DocSum) page returned from an Entrez Search for ‘tylenol’ against the PubChem Compound database. PubChem (http://pubchem.ncbi.nlm.nih.gov) is a public repository for biological activity data of small molecules and RNAi reagents. -, Wang Y.L., Bolton E., Dracheva S., Karapetyan K., Shoemaker B.A., Suzek T.O., Wang J.Y., Xiao J.W., Zhang J., Bryant S.H. There is a great variation in complexity of bioassay depositions ranging from very large primary screens with simple endpoints to assays containing dose–response data points or even multiple bioactivity outcomes. Accordingly, the deposition system has been further developed and allows the submission of such information for all types of screening data. The PubChem Deposition Gateway supports chemical and assay data submission through a web-based system at http://pubchem.ncbi.nlm.nih.gov/deposit/. 2015 Jul 1;43(W1):W605-11. This blast page allows you to blast a given set of protein sequences to find matches to those protein targets in the PubChem BioAssay database. Nucleic Acids Res. Tracking frequent updates to deposited bioassay records represents another challenge as depositors may add additional test results or provide a complete replacement for the entire assay data set. These bioassay depositions provide protein target references to a list of different protein records in Entrez Protein database. Also, as a repository, PubChem constantly optimizes and develops its deposition system answering many demands of both high- and low-volume depositors. The deposition system also allows bulk data upload via private FTP accounts. A list of web-based bioactivity analysis tools and their URLs are summarized in Table 1, which can also be accessed from the PubChem web page at http://pubchem.ncbi.nlm.nih.gov/assay. PubChem allows one to download bioassay records in ASN, XML and ‘comma-separated values’ (CSV) formats. 4. Saudi J Biol Sci. Furthermore, the BioAssay Summary service provides a central entry point to a set of data analysis tools for the bioactive compounds identified in the assay. Vol. A full list of indexed fields and filters, such as assay name, description, protocol, target description, readout name and tested chemical name, are documented at the PubChem Help page (http://pubchem.ncbi.nlm.nih.gov/help.html#PubChemindex). PubChem extended Entrez's ‘auto-complete’ feature to the BioAssay database which covers several index fields including ‘JournalName’, ‘ProteinTargetName’, ‘TaxonomyName’ and data ‘SourceName’. It also provides a description of the database’s data standard and basic utilities facilitating information access and use for new users. 2010 Jan;38(Database issue):D255-66. To meet the increasing demand from public users and from rapid growth of data volume and complexity, PubChem maintains and develops its service to the community as a public data repository by optimizing and expanding its bioassay data model for supporting broader types of information, by developing infrastructure to ensure database scalability, by improving deposition system to ease information exchange, and by enhancing search, retrieval, analysis and download tools. In addition, the ‘Related BioAssays’ section lists assays that may be related to the one under review and links to further detailed summary over the bioassay relationship. An overview of the PubChem BioAssay resource. Building PubChem BioAssay Database; 5. The order of the compound Ids is the same as the data files. Tracking source names and source identifiers is very important for PubChem as they can be used as terms in generating Entrez queries. It provides searchable descriptions of each bioassay, including descriptions of the conditions and readouts specific to that screening procedure. In light of this problem, the PubChem BioAssay database, an open-access repository providing the bioactivity information of compounds that were already tested on a biological target, is now a recommended source for data set construction. Matching hits will have "dose-response" curve gif icons which links to corresponding entries in Entrez PCAssay. A bioassay test result is always linked to a substance with a unique PubChem substance accession (SID), making it necessary for depositors to submit substance record prior to bioassay data. PubChem's bioassay data are integrated into the NCBI Entrez information retrieval system, thus making PubChem data searchable and accessible by Entrez queries. Most of the high-throughput screen data sets in PubChem contain bioactivity outcome specification, e.g. This feature can be accessed on the ‘Advanced’ page, where selecting the ‘JournalName’ field and entering ‘med’ in the ‘Search Builder’ input box will bring up a list of journal names including ‘Journal of Medicinal Chemistry’, ‘European Journal of Medicinal Chemistry’ etc., for example. The BioAssay database contains over one million biological assay experiments containing more than 229 million bioactivity outcomes. Meanwhile, such a semi-structured data model allows PubChem to accommodate a greater diversity of information content critical to multiple research communities. Published by Oxford University Press on behalf of Nucleic Acids Research 2015. 2012;40:D400–D412. PubChem's BioAssay Database. PubChem's bioassay data are integrated into the NCBI Entrez information retrieval system, thus making PubChem data searchable and accessible by Entrez queries. This new web interface can be accessed by following the download icon on a BioAssay Entrez DocSum page (Figure 2) to export records identifies based on a user's search criteria. For each assay, PubChem now provides a BioAssay Record page (formerly called the Assay Summary page), which displays information provided by the data contributor about the assay as well as annotations and links to tools that support data interpretation … Organism(s) covered: -Tag - Target: Metabolite, Chemical compound: Tag - Information type: Method, Image/Movie, … A technical improvement has been made to deposition account management: establishment of stable Data Source Identifier and modifiable Data Source Name (DSN). One can also use the ‘Cited Publication’ menu on the Limits page to search assays associated with a selected journal. Supporting simultaneous submission of such diverse set of data types and sizes from multiple depositors requires interface flexibility and multi-thread processing infrastructure. PUG-SOAP and PUG-REST: web services for programmatic access to chemical information in PubChem. The target-centric page (Figure 3C) provides a summary for the assay experiments associated with a protein target. PubChem: integrated platform of small molecules and biological activities. The Substance database contains chemical information deposited by individual data contributors to PubChem, and the Compound database stores unique chemical structures extracted from the Substance database. Users can pick a search field given in the ‘Search Field Tags’ section or build up a complex query using other input boxes on the page. Oxford University Press is a department of the University of Oxford. PubChem allows depositors to provide updates to their records. 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