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G-Links: a gene-centric link acquisition service

Kazuki Oshita, Masaru Tomita, Kazuharu Arakawa
2015 F1000Research  
We aim to solve this problem with a service named G-Links, 1) by gathering resource URI information from 130 databases and 30 web services in a gene-centric manner so that users can retrieve all available  ...  This data integration issue is one of the key challenges in bioinformatics.  ...  However, data integration is a much deeper problem than just data aggregation. Literature review The authors might mention earlier link-based aggregators, BioMOBY. e.g. Gene centricity  ... 
doi:10.12688/f1000research.5754.2 pmid:26673001 pmcid:PMC4670005 fatcat:6vtzac5n6fbwpitovp5sq2uokm

Protein Bioinformatics Infrastructure for the Integration and Analysis of Multiple High-Throughput "omics" Data

Chuming Chen, Peter B. McGarvey, Hongzhan Huang, Cathy H. Wu
2010 Advances in Bioinformatics  
In this paper, we present the challenges in high-throughput "omics" data integration and analysis, introduce a protein-centric approach for systems integration of large and heterogeneous high-throughput  ...  a major challenge which requires advanced computational methods and bioinformatics infrastructures for integration, mining, visualization, and comparative analysis to facilitate data-driven hypothesis  ...  The authors would like to thank the anonymous reviewers for their constructive comments on the manuscript.  ... 
doi:10.1155/2010/423589 pmid:20369061 pmcid:PMC2847380 fatcat:poilhj6yvvhk7oy45v6ryhroge

G-Links: a gene-centric link acquisition service

Kazuki Oshita, Masaru Tomita, Kazuharu Arakawa
2014 F1000Research  
We aim to solve this problem with a service named G-Links, 1) by gathering resource URI information from 130 databases and 30 web services in a gene-centric manner so that users can retrieve all available  ...  This data integration issue is one of the key challenges in bioinformatics.  ...  Acknowledgements The development of web services described in this work was significantly facilitated by the DBCLS BioHackathon 2012 hosted by the National Bioscience Database Center/Database Center for  ... 
doi:10.12688/f1000research.5754.1 pmid:26673001 pmcid:PMC4670005 fatcat:md5fsjfmv5bh5jmgdg7xkmnjja

An Integrative Bioinformatics Framework for Genome-scale Multiple Level Network Reconstruction of Rice

Lili Liu, Qian Mei, Zhenning Yu, Tianhao Sun, Zijun Zhang, Ming Chen
2013 Journal of Integrative Bioinformatics  
Integration of different regulatory information levels of an organism is expected to provide a good way for mapping genotypes to phenotypes.  ...  This provides a reference for understanding genotype-phenotype relationship of rice, and for analysis of its molecular regulatory network.  ...  Acknowledgements The authors would like to thank all the publicly available data sets and the scientists behind them. This work was supported by the National Natural Sciences Foundation of China  ... 
doi:10.1515/jib-2013-223 fatcat:lvpladsbifdpjpn232ng5fsimi

An integrative bioinformatics framework for genome-scale multiple level network reconstruction of rice

Lili Liu, Qian Mei, Zhenning Yu, Tianhao Sun, Zijun Zhang, Ming Chen
2013 Journal of Integrative Bioinformatics  
Integration of different regulatory information levels of an organism is expected to provide a good way for mapping genotypes to phenotypes.  ...  This provides a reference for understanding genotype-phenotype relationship of rice, and for analysis of its molecular regulatory network.  ...  Acknowledgements The authors would like to thank all the publicly available data sets and the scientists behind them. This work was supported by the National Natural Sciences Foundation of China  ... 
doi:10.2390/biecoll-jib-2013-223 pmid:23563093 fatcat:dfetaonsfbfoteq3vaisfrbzga

DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis

Brad T Sherman, Da Huang, Qina Tan, Yongjian Guo, Stephan Bour, David Liu, Robert Stephens, Michael W Baseler, H Clifford Lane, Richard A Lempicki
2007 BMC Bioinformatics  
Analysts usually need to visit many of these bioinformatics databases in order to integrate comprehensive annotation information for their genes, which becomes one of the bottlenecks, particularly for  ...  For a given gene list, it not only provides the quick accessibility to a wide range of heterogeneous annotation data in a centralized location, but also enriches the level of biological information for  ...  Acknowledgements The authors are grateful to the referees for their constructive comments and thank David Bryant in the ABCC group for web server support.  ... 
doi:10.1186/1471-2105-8-426 pmid:17980028 pmcid:PMC2186358 fatcat:c4prreos5nhfbhkeiwn62zuxym

Interaction networks for identifying coupled molecular processes in microbial communities

Magnus Bosse, Alexander Heuwieser, Andreas Heinzel, Ivan Nancucheo, Hivana Melo Barbosa Dall'Agnol, Arno Lukas, George Tzotzos, Bernd Mayer
2015 BioData Mining  
, in turn offering a data matrix for analyzing the molecular basis of cooperative phenomena.  ...  Conclusions: Analyzing the entangled molecular processes of a microbial community on the level of segmented, gene-centric interaction networks allows identification of core molecular processes and functionalities  ...  Data structures holding the PATRIC ID as central identified are populated with annotation and interaction information, including ortholog mapping for adding to comprehensiveness in annotation.  ... 
doi:10.1186/s13040-015-0054-4 pmid:26180552 pmcid:PMC4502522 fatcat:qhe3f6luqrfg7fpiij3uepf44m

Trans-Omics: How To Reconstruct Biochemical Networks Across Multiple 'Omic' Layers

Katsuyuki Yugi, Hiroyuki Kubota, Atsushi Hatano, Shinya Kuroda
2016 Trends in Biotechnology  
24 We propose "trans-omic" analysis for reconstructing global biochemical networks 25 across multiple omic layers by use of both multi-omic measurements and computational 26 data integration.  ...  To overcome 7 the lack of comprehensiveness and the information gap regarding interaction across 8 multiple omic layers, an approach for reconstructing molecular networks by connecting 9 multiple omic  ...  ., et al. (2000) Toward a protein-protein interaction map of the budding yeast: A 24 comprehensive system to examine two-hybrid interactions in all possible combinations between 25 the yeast proteins.  ... 
doi:10.1016/j.tibtech.2015.12.013 pmid:26806111 fatcat:4vfmjxezyzaoloh6n25cgkdchu

Challenges and Solutions in Proteomics

Hongzhan Huang, Hem Shukla, Cathy Wu, Satya Saxena
2007 Current Genomics  
using a comprehensive sequence library and functional interpretation using integrated data.  ...  To facilitate functional and pathway discovery for large-scale proteomic data, we have developed an integrated proteomic expression analysis system, iProXpress, which facilitates protein identification  ...  ACKNOWLEDGEMENT This research was supported in part by the Intramural Research Program of the NIH, National Institute on Aging and the NIH grants U01-HG02712 and HHSN2662004000-61C to the Protein Information  ... 
doi:10.2174/138920207780076910 pmid:18645629 pmcid:PMC2474689 fatcat:aszmx7uqkrcojdcxp5zswx3vxu

Ongoing and future developments at the Universal Protein Resource

2010 Nucleic Acids Research  
UniProt provides a mapping service to convert common gene IDs and protein IDs (such as NCBI's gi number and Entrez Gene ID) to UniProtKB AC/ID and vice versa.  ...  ID mapping is essential to support data interoperability among disparate data sources and enables the integration and querying of data from heterogeneous molecular biology databases.  ... 
doi:10.1093/nar/gkq1020 pmid:21051339 pmcid:PMC3013648 fatcat:vhmcewdzlrfndn3fmtafewqbxa

Systems Integration of Biodefense Omics Data for Analysis of Pathogen-Host Interactions and Identification of Potential Targets

Peter B. McGarvey, Hongzhan Huang, Raja Mazumder, Jian Zhang, Yongxing Chen, Chengdong Zhang, Stephen Cammer, Rebecca Will, Margie Odle, Bruno Sobral, Margaret Moore, Cathy H. Wu (+1 others)
2009 PLoS ONE  
Underlying this approach is a data warehouse with comprehensive protein + gene identifier and name mappings and annotations extracted from over 100 molecular databases.  ...  The Biodefense Resource Center (www.proteomicsresource.org) has developed a bioinformatics framework, employing a protein-centric approach to integrate and support mining and analysis of the large and  ...  Protein-Centric Data Integration The key design principal in the Resource Center is protein-centric data integration.  ... 
doi:10.1371/journal.pone.0007162 pmid:19779614 pmcid:PMC2745575 fatcat:y4asrpywyfhy5ppbrknppx34nu

Drug repositoning or target repositioning: a structural perspective of drug-target-indication relationship for available repurposed drugs [article]

Daniele Parisi, Melissa Francisca Adasme, Anastasia Sveshnikova, Yves Moreau, Michael Schroeder
2019 bioRxiv   pre-print
between an old and new indication, a target-centric one, which links a known target and its established drug to a new indication, or a drug-centric approach, which connects a known drug to a new target  ...  Although many of those cases are products of serendipitous findings, repositioning opportunities can be uncovered systematically by following either a disease-centric approach, as a result of a close relation  ...  Retrieval of molecular drug targets data A list of Molecular Drug Targets (MDT) was collected from the "Comprehensive map of molecular drug targets" provided by Santos et al. 39 , where authors curated  ... 
doi:10.1101/715094 fatcat:62f27u3u55cbvchznzh5urbux4

miRTargetLink—miRNAs, Genes and Interaction Networks

Maarten Hamberg, Christina Backes, Tobias Fehlmann, Martin Hart, Benjamin Meder, Eckart Meese, Andreas Keller
2016 International Journal of Molecular Sciences  
We developed miRTargetLink, a tool for automating respective analysis procedures that are frequently applied.  ...  As a showcase for miRTargetLink, we analyze targets of five cardiac miRNAs. miRTargetLink is freely available without restrictions at www.ccb.uni-saarland.de/mirtargetlink.  ...  Originally implemented as a search tool for recurring instances of neighboring genes [1] , STRING v10 has become a comprehensive protein-protein interaction database containing predicted and validated  ... 
doi:10.3390/ijms17040564 pmid:27089332 pmcid:PMC4849020 fatcat:62g6dabtyjemlkeuhx4bx7c6ja

Drug repositioning or target repositioning: a structural perspective of drug-target-indication relationship for available repurposed drugs

Daniele Parisi, Melissa F. Adasme, Anastasia Sveshnikova, Sarah Naomi Bolz, Yves Moreau, Michael Schroeder
2020 Computational and Structural Biotechnology Journal  
Lastly, a drug-centric approach connects a known drug to a new target and its associated indication.  ...  Disease-centric approaches identify close relationships between an old and a new indication. A target-centric approach links a known target and its established drug to a new indication.  ...  To make the text-mining data set compatible with the drug repositioning data set, UniProt IDs were turned into gene IDs using the UniProt API service and MeSH on demand was used to assign indication IDs  ... 
doi:10.1016/j.csbj.2020.04.004 pmid:32419905 pmcid:PMC7215100 fatcat:ycsr7jrrw5csnozhvqfa2jdclq

MSV3d: database of human MisSense variants mapped to 3D protein structure

T.-D. Luu, A.-M. Rusu, V. Walter, R. Ripp, L. Moulinier, J. Muller, T. Toursel, J. D. Thompson, O. Poch, H. Nguyen
2012 Database: The Journal of Biological Databases and Curation  
We present MSV3d (Database of human MisSense Variants mapped to 3D protein structure), a new database that contains detailed annotation of missense variants of all human proteins (20 199 proteins).  ...  The database (http://decrypthon.igbmc.fr/msv3d) is easily accessible through a simple web interface coupled to a powerful query engine and a standard web service.  ...  Acknowledgements The authors are grateful to Serge Uge for his assistance in implementing the local cluster. The IGBMC common services and platforms are acknowledged for assistance.  ... 
doi:10.1093/database/bas018 pmid:22491796 pmcid:PMC3317913 fatcat:yrpykuh6prev3bxaj4jq2wovzm
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