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Reactome graph database: Efficient access to complex pathway data

Antonio Fabregat, Florian Korninger, Guilherme Viteri, Konstantinos Sidiropoulos, Pablo Marin-Garcia, Peipei Ping, Guanming Wu, Lincoln Stein, Peter D'Eustachio, Henning Hermjakob, Timothée Poisot
2018 PLoS Computational Biology  
Reactome graph database: Efficient access to complex pathway data PLOS Computational Biology | https://doi.  ...  The Neo4j graph database and its query language, Cypher, provide efficient access to the complex Reactome data model, facilitating easy traversal and knowledge discovery.  ...  Fabregat A, Korninger F, Viteri G, Sidiropoulos K, Marin-Garcia P, Ping P, et al. (2018) Reactome graph database: Efficient access to complex pathway data.  ... 
doi:10.1371/journal.pcbi.1005968 pmid:29377902 pmcid:PMC5805351 fatcat:7znckpg5a5cnrfeekcmakdieyy

PathCase: pathways database system

B. Elliott, M. Kirac, A. Cakmak, G. Yavas, S. Mayes, E. Cheng, Y. Wang, C. Gupta, G. Ozsoyoglu, Z. Meral Ozsoyoglu
2008 Bioinformatics  
PathCase is now available for three different datasets, namely, KEGG pathways data, sample pathways from the literature and BioCyc pathways for humans.  ...  over the web is important to facilitate ongoing biological research.  ...  Wang Foundation to the Center for  ... 
doi:10.1093/bioinformatics/btn459 pmid:18728044 fatcat:25jn4wwelzahlp235bygmz2hha

Comparison of human cell signaling pathway databases—evolution, drawbacks and challenges

Saikat Chowdhury, Ram Rup Sarkar
2015 Database: The Journal of Biological Databases and Curation  
Based on two major characteristics, pathway information and technical details, freely accessible data from commercial and academic databases are examined to understand their evolution and enrichment.  ...  To advance this study, during the past two decades, systematic collections of pathway data from experimental studies have been compiled and distributed freely by several databases, which also integrate  ...  For example, REACTOME uses two types of API service: SOAP and RESTful to access and download the REACTOME data remotely.  ... 
doi:10.1093/database/bau126 pmid:25632107 pmcid:PMC4309023 fatcat:b6y4vbdg7rfdrac5z3htaxdcji

An overview of graph databases and their applications in the biomedical domain

Santiago Timón-Reina, Mariano Rincón, Rafael Martínez-Tomás
2021 Database: The Journal of Biological Databases and Curation  
From early graph models to more recent native graph databases, the landscape of implementations has evolved to cover enterprise-ready requirements.  ...  With this evidence, we conclude that the available graph database management systems are fit to support data-intensive, integrative applications, targeted at both basic research and exploratory tasks closer  ...  On the other hand, the new graph model provides more straightforward ways to perform complex queries over metabolic pathways.  ... 
doi:10.1093/database/baab026 pmid:34003247 pmcid:PMC8130509 fatcat:xku5npedwzgs3ayzsuvz6iattq

Interleukins and their signaling pathways in the Reactome biological pathway database

Steve Jupe, Keith Ray, Corina Duenas Roca, Thawfeek Varusai, Veronica Shamovsky, Lincoln Stein, Peter D'Eustachio, Henning Hermjakob
2018 Journal of Allergy and Clinical Immunology  
Objective-Reactome was established as a freely accessible knowledge base of human biological pathways.  ...  Although this might be sufficient to be interpreted by an expert reader, the lack of detail makes such pathways less useful and difficult to understand for anyone unfamiliar with the area and of limited  ...  Reactome content is available programmatically through a REpresentational State Transfer (REST)-based content service and as a Neo4J graph database.  ... 
doi:10.1016/j.jaci.2017.12.992 pmid:29378288 pmcid:PMC5927619 fatcat:oy2ctphdqbehffj37pps24hsi4

ConsensusPathDB—a database for integrating human functional interaction networks

Atanas Kamburov, Christoph Wierling, Hans Lehrach, Ralf Herwig
2008 Nucleic Acids Research  
We describe the database schema and the methods used for data integration.  ...  Current knowledge of these interactions is dispersed in more than 200 databases, each having a specific focus and data format.  ...  ACKNOWLEDGEMENTS We are grateful to the interaction database providers ( Table 1 ) that allowed automated access to their databases.  ... 
doi:10.1093/nar/gkn698 pmid:18940869 pmcid:PMC2686562 fatcat:xaeqf3acsjgalo6vb7fymcu3pm

Large-scale regulatory and signaling network assembly through linked open data

M Lefebvre, A Gaignard, M Folschette, J Bourdon, C Guziolowski
2021 Database: The Journal of Biological Databases and Curation  
These databases can be automatically queried to reconstruct regulatory and signaling networks.  ...  difficulty of recovering logical flows in biological pathways.  ...  Acknowledgement The authors would like to thank Nathalie Théret and Vincent Legagneux for providing experimental data and their biological expertise for the 'Results' section.  ... 
doi:10.1093/database/baaa113 pmid:33459761 pmcid:PMC7812716 fatcat:qtxpgtgljvb4hdmck6i3w4yzwy

PathCase-SB architecture and database design

Ali Cakmak, Xinjian Qi, Sarp A Coskun, Mitali Das, En Cheng, A Cicek, Nicola Lai, Gultekin Ozsoyoglu, Z Ozsoyoglu
2011 BMC Systems Biology  
Conclusions: PathCase-SB architecture and database provide a highly extensible and scalable environment with easy and fast (real-time) access to the data in the database.  ...  PathCase-SB aims to integrate data of selected biological data sources on the web (currently, BioModels database and KEGG), and to provide more powerful and/or new capabilities via the new web-based integrative  ...  Acknowledgements and Funding Authors acknowledge (a) guidance and contributions of (late) Marco Cabrera for his early contributions to PathCase-SB architecture and database design, (b) PathCase-SB design  ... 
doi:10.1186/1752-0509-5-188 pmid:22070889 pmcid:PMC3229461 fatcat:lvc74inelzhnlf2huwpzj4w2ba

RNApathwaysDB—a database of RNA maturation and decay pathways

Kaja Milanowska, Katarzyna Mikolajczak, Anna Lukasik, Marcin Skorupski, Zuzanna Balcer, Magdalena A. Machnicka, Martyna Nowacka, Kristian M. Rother, Janusz M. Bujnicki
2012 Nucleic Acids Research  
Options for data presentation include pathway graphs and tables with enzymes and literature data.  ...  The systematization of data about RNA metabolic pathways and enzymes taking part in RNA maturation and degradation is essential for the full understanding of these processes.  ...  We are indebted to the authors of primary databases and services, whose content could be reused or linked to by RNApathwaysDB.  ... 
doi:10.1093/nar/gks1052 pmid:23155061 pmcid:PMC3531052 fatcat:jlixjxr3wjb7dhbddv6exgssly

GREG-studying transcriptional regulation using integrative graph databases

2020 Database: The Journal of Biological Databases and Curation  
GREG (The Gene Regulation Graph Database) is an integrative database and web resource that allows the user to visualize and explore the network of all above-mentioned interactions for a query transcription  ...  Therefore, the combination of protein-DNA, protein-protein, ncRNA-DNA, ncRNA-protein and DNA-DNA data in a single graph database offers new possibilities regarding generation of biological hypotheses.  ...  We also thank Cliff Meyer from Cistrome and all creators and maintainers of the different databases involved.  ... 
doi:10.1093/database/baz162 pmid:32055858 pmcid:PMC7018612 fatcat:iinpjow6pbbqtl5behmd2dg6sm

Protein Bioinformatics Databases and Resources [chapter]

Chuming Chen, Hongzhan Huang, Cathy H. Wu
2017 Msphere  
As an update to our previously contributed MiMB series chapter [8], we now focus on databases that are aligned with the content of this book and emphasize the types of data stored and related data access  ...  Protein bioinformatics databases can be primarily classified as sequence databases, 2D gel databases, 3D structure databases, chemistry databases, enzyme and pathway databases, family and domain databases  ...  Large dataset or complex analyses can be accessed from MySQL server, Perl and RESTful APIs. Complex cross databases queries are supported by BioMart data mining tool [156] .  ... 
doi:10.1007/978-1-4939-6783-4_1 pmid:28150231 pmcid:PMC5506686 fatcat:rrclcq47p5hqrlffz2v2xexjoy

ERMer: a serverless platform for navigating, analyzing, and visualizing Escherichia coli regulatory landscape through graph database

Zhitao Mao, Ruoyu Wang, Haoran Li, Yixin Huang, Qiang Zhang, Xiaoping Liao, Hongwu Ma
2022 Nucleic Acids Research  
In contrast, graph databases are purposefully developed to execute such deep searches efficiently.  ...  Furthermore, a Q&A module is included to showcase the power of graph databases in answering complex biological questions through simple queries.  ...  Reactome migrates the content from the relational database to a graph database for providing more efficient access to its high-quality curated reaction data (10) .  ... 
doi:10.1093/nar/gkac288 pmid:35489073 fatcat:34axbrde45fzjeqvh2cbidcz6y

RPGeNet v2.0: expanding the universe of retinal disease gene interactions network

2019 Database: The Journal of Biological Databases and Curation  
For the new version, RPGeNet v2.0, the database engine was migrated to Neo4j graph database manager, which speeds up the initial queries and can handle whole interactome data for new ways to query the  ...  of novel candidates to specific retinal or cellular pathways.  ...  Ministry of Economy (BFU2017-83755P) and Generalitat de Catalunya Conflict of interest G.M. and R.G-D. are co-founders and assessors of DBGen, a spin-off of the Universitat de Barcelona dedicated to  ... 
doi:10.1093/database/baz120 pmid:31712826 pmcid:PMC6846243 fatcat:xyww4zdt5bfwtmlrw5lp74ozqm

The Rat Genome Database (RGD): developments towards a phenome database

N. de la Cruz
2004 Nucleic Acids Research  
to efficiently browse and survey research data.  ...  These improvements, combined with the genomic sequence of the rat, have led to a successful year at RGD with over two million page accesses that represent an over 4-fold increase in a year.  ...  to efficiently browse and survey research data.  ... 
doi:10.1093/nar/gki050 pmid:15608243 pmcid:PMC540004 fatcat:gnzke5nrlfbmnikqraddcnazea

Structured reviews for data and knowledge-driven research

2020 Database: The Journal of Biological Databases and Curation  
Database URL: http://ngly1graph.org/. Network data files are at: https://github.com/SuLab/ngly1-graph and source code at: https://github.com/SuLab/bioknowledge-reviewer.  ...  Instead, the knowledge graph we have created enables researchers to query the graph with complex questions, to traverse different domains and databases in one single query and to explore disease-specific  ...  Knowledge graphs make it easy to integrate information from many sources, to explore heterogeneous information within a single data model and to infer new relationships via efficient queries.  ... 
doi:10.1093/database/baaa015 pmid:32283553 pmcid:PMC7153956 fatcat:sk3sogsf2zdktau7d4d5hmjs6u
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