Lynx web services for annotations and systems analysis of multi-gene disorders.

Dinanath Sulakhe,Bo Feng,Daniela Börnigen,Utpal J Dave,Ian T Foster,Natalia Maltsev,Andrew Taylor,Sandhya Balasubramanian,T Conrad Gilliam,Bingqing Xie

doi:10.1093/nar/gku517

Abstract

Lynx is a web-based integrated systems biology platform that supports annotation and analysis of experimental data and generation of weighted hypotheses on molecular mechanisms contributing to human phenotypes and disorders of interest. Lynx has integrated multiple classes of biomedical data (genomic, proteomic, pathways, phenotypic, toxicogenomic, contextual and others) from various public databases as well as manually curated data from our group and collaborators (LynxKB). Lynx provides tools for gene list enrichment analysis using multiple functional annotations and network-based gene prioritization. Lynx provides access to the integrated database and the analytical tools via REST based Web Services (http://lynx.ci.uchicago.edu/webservices.html). This comprises data retrieval services for specific functional annotations, services to search across the complete LynxKB (powered by Lucene), and services to access the analytical tools built within the Lynx platform.

Highlights

Gaining a greater understanding of molecular mechanisms underlying common multi-gene disorders is a major challenge in biomedical research [1]
We have developed an integrated Lynx platform that consists of a knowledgebase (LynxKB [2]) which periodically collects various classes of biological data in a structured relational database, analytical tools for the analysis of multi-gene lists and a Lynx web services interface which allows users to query and search LynxKB to retrieve annotations and access the analytical tools
In Lynx, we have implemented a large integrated biomedical knowledgebase (LynxKB) and a collection of RESTful web services to access this information in a structured format

Summary

Introduction

Gaining a greater understanding of molecular mechanisms underlying common multi-gene disorders (e.g. autism, schizophrenia, diabetes) is a major challenge in biomedical research [1]. We have developed an integrated Lynx platform that consists of a knowledgebase (LynxKB [2]) which periodically collects various classes of biological data in a structured relational database, analytical tools for the analysis of multi-gene lists and a Lynx web services interface which allows users to query and search LynxKB to retrieve annotations and access the analytical tools. Lynx web services are implemented using REST (Representational State Transfer) architecture to provide a simple interface with multiple request types supported (HTTP GET and POST).

Results

Conclusion