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Reactome: An integrated expert model of human molecular processes and access toolkit

Bernard de Bono, Imre Vastrik, Peter D'Eustachio, Esther Schmidt, Gopal Gopinath, David Croft, Marc Gillespie, Bijay Jassal, Suzanna Lewis, Lisa Matthews, Guanming Wu, Ewan Birney (+1 others)
2007 Journal of Integrative Bioinformatics  
Reactome (http://www.reactome.org) is an open-access project that collaborates with field experts to integrate their pathway knowledge into a single quality-checked human model.  ...  SummaryThe behaviour of pervasive molecular processes in human biology can be studied through the large-scale modeling of the molecular events that define them.  ...  Acknowledgements We gratefully acknowledge all authoring and reviewing biologists who provide their expertise and resources for the annotation and quality assessment of the Reactome model, and Geeta Joshi-Tope  ... 
doi:10.1515/jib-2007-84 fatcat:a2bb4t4pfrduvnavqzmmwioykq

The Reactome pathway Knowledgebase

Antonio Fabregat, Konstantinos Sidiropoulos, Phani Garapati, Marc Gillespie, Kerstin Hausmann, Robin Haw, Bijay Jassal, Steven Jupe, Florian Korninger, Sheldon McKay, Lisa Matthews, Bruce May (+10 others)
2015 Nucleic Acids Research  
The Reactome Knowledgebase (www.reactome.org) provides molecular details of signal transduction, transport, DNA replication, metabolism and other cellular processes as an ordered network of molecular transformations  ...  --an extended version of a classic metabolic map, in a single consistent data model.  ...  ACKNOWLEDGEMENT We are grateful to Ewan Birney for his advice and support, and to the many expert scientists who have collaborated with us as external authors and reviewers of Reactome content.  ... 
doi:10.1093/nar/gkv1351 pmid:26656494 pmcid:PMC4702931 fatcat:ikxhcsslzrfeziyzq2p6qadvay

An evidence-based knowledgebase of pulmonary arterial hypertension to identify genes and pathways relevant to pathogenesis

Min Zhao, Eric D. Austin, Anna R. Hemnes, James E. Loyd, Zhongming Zhao
2014 Molecular Biosystems  
Acknowledgements We thank Ms Rebecca Hiller Posey for polishing an earlier draft of the manuscript.  ...  The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.  ...  To facilitate experimental access to existent animal models, we also collected all the mouse and rat knockout or abnormal expression models for PAH-related genes from literature.  ... 
doi:10.1039/c3mb70496c pmid:24448676 pmcid:PMC3950334 fatcat:fklh6i74ybgjreoybgxqhrfrv4

Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing

Girum Fitihamlak Ejigu, Jaehee Jung
2020 Biology  
We highlight visualization tools that immensely aid the annotation process and the contributions of the scientific community to the annotation.  ...  This information will improve our understanding of general aspects of life and evolution and improve our ability to diagnose genetic disorders.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/biology9090295 pmid:32962098 pmcid:PMC7565776 fatcat:gdaxbwygqnaapiqisyf56ajpea

DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes

J. Pinero, N. Queralt-Rosinach, A. Bravo, J. Deu-Pons, A. Bauer-Mehren, M. Baron, F. Sanz, L. I. Furlong
2015 Database: The Journal of Biological Databases and Curation  
DisGeNET integrates expert-curated databases with text-mined data, covers information on Mendelian and complex diseases, and includes data from animal disease models.  ...  Hence, DisGeNET offers one of the most comprehensive collections of human gene-disease associations and a valuable set of tools for investigating the molecular mechanisms underlying diseases of genetic  ...  Funding for open access charge: Instituto de Salud Carlos III-Fondo Europeo de Desarrollo Regional (PI13/00082).  ... 
doi:10.1093/database/bav028 pmid:25877637 pmcid:PMC4397996 fatcat:rf3dotjr2bbz3odfwvsuefnlli

A human functional protein interaction network and its application to cancer data analysis

Guanming Wu, Xin Feng, Lincoln Stein
2010 Genome Biology  
Conclusions: We have built a highly reliable functional interaction network upon expert-curated pathways and applied this network to the analysis of two genome-wide GBM and several other cancer data sets  ...  domain interaction, Gene Ontology (GO) annotations and text-mined protein interactions, which cover close to 50% of the human proteome.  ...  The data and data model from the Reactome project form the basis of this work.  ... 
doi:10.1186/gb-2010-11-5-r53 pmid:20482850 pmcid:PMC2898064 fatcat:vntehsevq5gcrfppuzcikesvde

Visualization and analysis of a cardio vascular disease- and MUPP1-related biological network combining text mining and data warehouse approaches

Björn Sommer, Evgeny S Tiys, Benjamin Kormeier, Klaus Hippe, Sebastian J Janowski, Timofey V Ivanisenko, Anatoly O Bragin, Patrizio Arrigo, Pavel S Demenkov, Alexey V Kochetov, Vladimir A Ivanisenko, Nikolay A Kolchanov (+1 others)
2010 Journal of Integrative Bioinformatics  
However, analysis and interpretation of this data needs application of efficient computational techniques and systems biology approaches.  ...  In this publication, the combination of different techniques to create such a network associated with an abstract cell environment is discussed in order to gain insights into the functional as well as  ...  Data integration Since industrial research of molecular biology questions starting with the Human Genome Project, one of the main challenges in bioinformatics is the integration of molecular data.  ... 
doi:10.2390/biecoll-jib-2010-148 pmid:21068463 fatcat:jqncp27t5jfdpd5uahr4vccefq

Visualization and Analysis of a Cardio Vascular Diseaseand MUPP1-related Biological Network combining Text Mining and Data Warehouse Approaches

Björn Sommer, Evgeny S. Tiys, Benjamin Kormeier, Klaus Hippe, Sebastian J. Janowski, Timofey V. Ivanisenko, Anatoly O. Bragin, Patrizio Arrigo, Pavel S. Demenkov, Alexey V. Kochetov, Vladimir A. Ivanisenko, Nikolay A. Kolchanov (+1 others)
2010 Journal of Integrative Bioinformatics  
However, analysis and interpretation of this data needs application of efficient computational techniques and systems biology approaches.  ...  In this publication, the combination of different techniques to create such a network associated with an abstract cell environment is discussed in order to gain insights into the functional as well as  ...  Data integration Since industrial research of molecular biology questions starting with the Human Genome Project, one of the main challenges in bioinformatics is the integration of molecular data.  ... 
doi:10.1515/jib-2010-148 fatcat:m7bfudz475fb5hs4zov5aukjqu

EndoNet: an information resource about regulatory networks of cell-to-cell communication

J. Donitz, B. Goemann, M. Lize, H. Michael, N. Sasse, E. Wingender, A. P. Potapov
2007 Nucleic Acids Research  
Whenever expression, synthesis and/or secretion of another hormone are part of this response, it renders the corresponding cell an internal node of the resulting network.  ...  Therefore, the database covers the hierarchy of cellular organization of tissues and organs as it has been modeled in the Cytomer ontology, which has now been directly embedded into EndoNet.  ...  This system thus allows for making an integral analysis of human regulatory pathways by means of significantly extended level of molecular details (23, 24) .  ... 
doi:10.1093/nar/gkm940 pmid:18045786 pmcid:PMC2238947 fatcat:icpv6in4mzbylelzygo2j64uka

BY-COVID- D2.1 - Initial data and metadata harmonisation at domain level to enable fast responses to COVID-19

Tom Giles, Phil Quinlan, Jeroen Belien, Julia Lischke, Laura Portell-Silva, Salvador Capella-Gutierrez, Reagon Karki, Vasso Kalaitzi, Enrique Bernal-Delgado, Antje Keppler
2022 Zenodo  
WP2 will further collate data governance models, metadata descriptions and access mechanisms ensuring full alignment with WP3 on the acquisition, curation and use of metadata from data sources.  ...  Interaction with WP4 will enable the development of tools for processing and harmonising metadata across data sources within the same domain.  ...  (biological processes and molecular function), and pathways (Reactome).  ... 
doi:10.5281/zenodo.7017728 fatcat:3vooduemvzbwxiacgpavusox7q

Comprehensive pathway enrichment analysis workflows: COVID-19 case study

Giuseppe Agapito, Chiara Pastrello, Igor Jurisica
2020 Briefings in Bioinformatics  
to find biomarkers, explainable models and eventually cures.  ...  We aim to provide a comprehensive overview of PEA techniques and the tools that implement them.  ...  and Reactome [12] pathway databases. pathDIP pathDIP [17] is an integrated database of pathways in human, model organisms and domesticated animals, comprising core pathways from major curated pathway  ... 
doi:10.1093/bib/bbaa377 fatcat:aa2xtbxb55g4xp3zav3veu2m4y

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  ...  We also discuss the challenges and opportunities for developing next-generation protein bioinformatics databases and resources to support data integration and data analytics in the Big Data era.  ...  Acknowledgments This work was supported by grants from the National Institutes of Health: U41HG007822 and Delaware-INBRE (P20GM103446).  ... 
doi:10.1007/978-1-4939-6783-4_1 pmid:28150231 pmcid:PMC5506686 fatcat:rrclcq47p5hqrlffz2v2xexjoy

An integrative data analysis platform for gene set analysis and knowledge discovery in a data warehouse framework

Yi-An Chen, Lokesh P. Tripathi, Kenji Mizuguchi
2016 Database: The Journal of Biological Databases and Curation  
We have previously developed TargetMine, an integrated data warehouse optimized for target prioritization.  ...  Data analysis is one of the most critical and challenging steps in drug discovery and disease biology.  ...  Acknowledgements The authors thank the members of the Mizuguchi laboratory for their critical review of the study and the manuscript.  ... 
doi:10.1093/database/baw009 pmid:26989145 pmcid:PMC4795931 fatcat:g32ewsxnb5gq5chad742fww2ia

Consensus and conflict cards for metabolic pathway databases

Miranda D Stobbe, Morris A Swertz, Ines Thiele, Trebor Rengaw, Antoine HC van Kampen, Perry D Moerland
2013 BMC Systems Biology  
Conclusions: C 2 Cards can contribute to ongoing reconciliation efforts by simplifying the identification of consensus and conflicts between pathway databases and lowering the threshold for experts to  ...  As a proof-of-concept, we implemented C 2 Cards Human , as a web application http://www.molgenis.org/c2cards, covering five human pathway databases.  ...  We also thank the anonymous reviewers for their helpful comments and suggestions for improving the presentation and comprehensibility of the paper.  ... 
doi:10.1186/1752-0509-7-50 pmid:23803311 pmcid:PMC3703255 fatcat:zct2aibl4fg2blqxuak6v4xf44

VINEdb: a data warehouse for integration and interactive exploration of life science data

Sridhar Hariharaputran, Thoralf Töpel, Björn Brockschmidt, Ralf Hofestädt, Bioinformatics, Medical Informatics Department, Bielefeld University Library, Publikationsdienste.Ub@Uni-Bielefeld.De, BieColl, Bielefeld University
2008 Journal of Integrative Bioinformatics  
The molecular interactions involved in this and other processes are analyzed and annotated by experts and stored as data in different databases.  ...  Molecular networks that regulate these processes are critical targets for drug development, gene therapy, and metabolic engineering.  ...  However, the upto-dateness of the systems is hard to judge and there is no logging information available on the update process. Reactome [13] is a knowledge base of biological processes.  ... 
doi:10.2390/biecoll-jib-2007-63 dblp:journals/jib/HariharaputranTBH07 fatcat:lhysmhjc75hydeituotepr57aa
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