PubChem BioAssay: 2017 update - PubMed (original) (raw)

. 2017 Jan 4;45(D1):D955-D963.

doi: 10.1093/nar/gkw1118. Epub 2016 Nov 29.

Affiliations

PubChem BioAssay: 2017 update

Yanli Wang et al. Nucleic Acids Res. 2017.

Abstract

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.

Published by Oxford University Press on behalf of Nucleic Acids Research 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US.

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Figures

Figure 1.

Figure 1.

A bioassay record (AID 1510,

https://pubchem.ncbi.nlm.nih.gov/bioassay/1510

). (A) The overview of the record page. The table of contents provides quick navigation to a list of sections shown on the page. Each section has an anchor and its URL can be used for widget embedding. (B) Selected sections: Data Table, Same-Project BioAssays and BioAssay Annotations.

Figure 2.

Figure 2.

The PubChem BioAssay Classification Tree (

https://pubchem.ncbi.nlm.nih.gov/classification/#hid=80

). A hierarchical display is provided, which can be navigated and explored by expanding to the sub-trees upon clicking on the triangle icon formula image. A click on the numbers on a node (showing the count of BioAssay records with that annotation) leads to a report in Entrez for the associated assay records.

Figure 3.

Figure 3.

Collective and cross-assay bioactivity data for a specific gene target in the PubChem BioAssay database (

https://pubchem.ncbi.nlm.nih.gov/assay/bioactivity.html?geneid=1956

). The filters at the top of the web page may be used to drill down to a subset of interest. For example, using the filters provided under the ‘Substance Types’ section, one may retrieve the RNAi data by clicking on ‘RNAi (34)’. The ‘Primary drug (385)’ filter in the section allows the retrieval of the bioactivity data for drugs that were developed to specifically target the query protein/gene, while the ‘Drug (1646)’ filter retrieves bioactivity for any drugs in general which were tested in the assays. This latter filter allows one to identify drug molecules that show experimental evidence (based on PubChem BioAssay data) for binding or affecting the query protein/gene target so that their potential for drug repositioning (against the query protein/gene target) may be further explored. Drug and target information supporting these two filters were obtained from annotations in the DrugBank.

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