Literature DB >> 17132622

Representing, storing and accessing molecular interaction data: a review of models and tools.

Lena Strömbäck1, Vaida Jakoniene, He Tan, Patrick Lambrix.   

Abstract

One important aim within systems biology is to integrate disparate pieces of information, leading to discovery of higher-level knowledge about important functionality within living organisms. This makes standards for representation of data and technology for exchange and integration of data important key points for development within the area. In this article, we focus on the recent developments within the field. We compare the recent updates to the three standard representations for exchange of data SBML, PSI MI and BioPAX. In addition, we give an overview of available tools for these three standards and a discussion on how these developments support possibilities for data exchange and integration.

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Mesh:

Year:  2006        PMID: 17132622     DOI: 10.1093/bib/bbl039

Source DB:  PubMed          Journal:  Brief Bioinform        ISSN: 1467-5463            Impact factor:   11.622


  11 in total

1.  Kinetic Modeling using BioPAX ontology.

Authors:  Oliver Ruebenacker; Ion I Moraru; James C Schaff; Michael L Blinov
Journal:  Proceedings (IEEE Int Conf Bioinformatics Biomed)       Date:  2007-11-02

2.  Integration of biological networks and gene expression data using Cytoscape.

Authors:  Melissa S Cline; Michael Smoot; Ethan Cerami; Allan Kuchinsky; Nerius Landys; Chris Workman; Rowan Christmas; Iliana Avila-Campilo; Michael Creech; Benjamin Gross; Kristina Hanspers; Ruth Isserlin; Ryan Kelley; Sarah Killcoyne; Samad Lotia; Steven Maere; John Morris; Keiichiro Ono; Vuk Pavlovic; Alexander R Pico; Aditya Vailaya; Peng-Liang Wang; Annette Adler; Bruce R Conklin; Leroy Hood; Martin Kuiper; Chris Sander; Ilya Schmulevich; Benno Schwikowski; Guy J Warner; Trey Ideker; Gary D Bader
Journal:  Nat Protoc       Date:  2007       Impact factor: 13.491

3.  The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*.

Authors:  Toshiaki Katayama; Kazuharu Arakawa; Mitsuteru Nakao; Keiichiro Ono; Kiyoko F Aoki-Kinoshita; Yasunori Yamamoto; Atsuko Yamaguchi; Shuichi Kawashima; Hong-Woo Chun; Jan Aerts; Bruno Aranda; Lord Hendrix Barboza; Raoul Jp Bonnal; Richard Bruskiewich; Jan C Bryne; José M Fernández; Akira Funahashi; Paul Mk Gordon; Naohisa Goto; Andreas Groscurth; Alex Gutteridge; Richard Holland; Yoshinobu Kano; Edward A Kawas; Arnaud Kerhornou; Eri Kibukawa; Akira R Kinjo; Michael Kuhn; Hilmar Lapp; Heikki Lehvaslaiho; Hiroyuki Nakamura; Yasukazu Nakamura; Tatsuya Nishizawa; Chikashi Nobata; Tamotsu Noguchi; Thomas M Oinn; Shinobu Okamoto; Stuart Owen; Evangelos Pafilis; Matthew Pocock; Pjotr Prins; René Ranzinger; Florian Reisinger; Lukasz Salwinski; Mark Schreiber; Martin Senger; Yasumasa Shigemoto; Daron M Standley; Hideaki Sugawara; Toshiyuki Tashiro; Oswaldo Trelles; Rutger A Vos; Mark D Wilkinson; William York; Christian M Zmasek; Kiyoshi Asai; Toshihisa Takagi
Journal:  J Biomed Semantics       Date:  2010-08-21

4.  Qualitative translation of relations from BioPAX to SBML qual.

Authors:  Finja Büchel; Clemens Wrzodek; Florian Mittag; Andreas Dräger; Johannes Eichner; Nicolas Rodriguez; Nicolas Le Novère; Andreas Zell
Journal:  Bioinformatics       Date:  2012-08-24       Impact factor: 6.937

5.  Identification of candidate repurposable drugs to combat COVID-19 using a signature-based approach.

Authors:  Sinead M O'Donovan; Ali Imami; Hunter Eby; Nicholas D Henkel; Justin Fortune Creeden; Sophie Asah; Xiaolu Zhang; Xiaojun Wu; Rawan Alnafisah; R Travis Taylor; James Reigle; Alexander Thorman; Behrouz Shamsaei; Jarek Meller; Robert E McCullumsmith
Journal:  Sci Rep       Date:  2021-02-24       Impact factor: 4.379

6.  Pathway databases and tools for their exploitation: benefits, current limitations and challenges.

Authors:  Anna Bauer-Mehren; Laura I Furlong; Ferran Sanz
Journal:  Mol Syst Biol       Date:  2009-07-28       Impact factor: 11.429

7.  MetNet Online: a novel integrated resource for plant systems biology.

Authors:  Yves Sucaet; Yi Wang; Jie Li; Eve Syrkin Wurtele
Journal:  BMC Bioinformatics       Date:  2012-10-15       Impact factor: 3.169

Review 8.  Getting started in biological pathway construction and analysis.

Authors:  Ganesh A Viswanathan; Jeremy Seto; Sonali Patil; German Nudelman; Stuart C Sealfon
Journal:  PLoS Comput Biol       Date:  2008-02       Impact factor: 4.475

9.  Challenges in Reproducibility, Replicability, and Comparability of Computational Models and Tools for Neuronal and Glial Networks, Cells, and Subcellular Structures.

Authors:  Tiina Manninen; Jugoslava Aćimović; Riikka Havela; Heidi Teppola; Marja-Leena Linne
Journal:  Front Neuroinform       Date:  2018-05-01       Impact factor: 4.081

10.  Oxytocin's anti-inflammatory and proimmune functions in COVID-19: a transcriptomic signature-based approach.

Authors:  Ali S Imami; Sinead M O'Donovan; Justin F Creeden; Xiaojun Wu; Hunter Eby; Cheryl B McCullumsmith; Kerstin Uvnäs-Moberg; Robert E McCullumsmith; Elissar Andari
Journal:  Physiol Genomics       Date:  2020-08-18       Impact factor: 3.107

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