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Reactome graph database: Efficient access to complex pathway data
2018
PLoS Computational Biology
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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
2008
Bioinformatics
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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
2015
Database: The Journal of Biological Databases and Curation
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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
2021
Database: The Journal of Biological Databases and Curation
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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
2018
Journal of Allergy and Clinical Immunology
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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
2008
Nucleic Acids Research
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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
2021
Database: The Journal of Biological Databases and Curation
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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
2011
BMC Systems Biology
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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
2012
Nucleic Acids Research
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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
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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]
2017
Msphere
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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
2022
Nucleic Acids Research
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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
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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
2004
Nucleic Acids Research
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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
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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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