Abstract
Motivation: The interaction between drugs and their targets, often proteins, and between antibodies and their targets, is important for planning and analyzing investigational and therapeutic interventions in many biological systems. Although drug-target and antibody-target datasets are available in separate databases, they are not publicly available in an integrated bioinformatics resource. As medical therapeutics, especially in cancer, increasingly uses targeted drugs and measures their effects on biomolecular profiles, there is an unmet need for a user-friendly toolset that allows researchers to comprehensively and conveniently access and query information about drugs, antibodies and their targets.Summary: The PiHelper framework integrates human drug-target and antibody-target associations from publicly available resources to help meet the needs of researchers in systems pharmacology, perturbation biology and proteomics. PiHelper has utilities to (i) import drug- and antibody-target information; (ii) search the associations either programmatically or through a web user interface (UI); (iii) visualize the data interactively in a network; and (iv) export relationships for use in publications or other analysis tools.Availability: PiHelper is a free software under the GNU Lesser General Public License (LGPL) v3.0. Source code and documentation are at http://bit.ly/pihelper. We plan to coordinate contributions from the community by managing future releases.Contact: pihelper@cbio.mskcc.org
Highlights
In cancer biology, systems pharmacology and perturbation biology, researchers designing targeted drug experiments often need to choose targeted drugs and antibodies of interest for their experimental studies
Drug- and antibody-target databases are valuable resources and are increasingly publicly available in computable formats. This information is in separate databases that use mostly incompatible formats, making it difficult to integrate data across different resources
Once the database is populated through the admin tool, the exporter component can be used to export all drug and antibody data to a tab-delimited text format (TSV)
Summary
Systems pharmacology and perturbation biology, researchers designing targeted drug experiments often need to choose targeted drugs and antibodies of interest for their experimental studies. For such studies, drug- and antibody-target databases are valuable resources and are increasingly publicly available in computable formats. Drug- and antibody-target databases are valuable resources and are increasingly publicly available in computable formats This information is in separate databases that use mostly incompatible formats, making it difficult to integrate data across different resources. We believe PiHelper will facilitate hypothesis generation and design of new experiments by enabling researchers to access and query integrated drug-target and antibody-target data from multiple resources in an automatic way
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