Literature DB >> 22199389

PathVisio-Validator: a rule-based validation plugin for graphical pathway notations.

Kumar Chandan1, Martijn P van Iersel, Mirit I Aladjem, Kurt W Kohn, Augustin Luna.   

Abstract

PURPOSE: The PathVisio-Validator plugin aims to simplify the task of producing biological pathway diagrams that follow graphical standardized notations, such as Molecular Interaction Maps or the Systems Biology Graphical Notation. This plugin assists in the creation of pathway diagrams by ensuring correct usage of a notation, and thereby reducing ambiguity when diagrams are shared among biologists. Rulesets, needed in the validation process, can be generated for any graphical notation that a developer desires, using either Schematron or Groovy. The plugin also provides support for filtering validation results, validating on a subset of rules, and distinguishing errors and warnings.

Mesh：

Year:  2011        PMID： 22199389      PMCID： PMC3307104          DOI： 10.1093/bioinformatics/btr694

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  8 in total

1.  The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.

Authors:  M Hucka; A Finney; H M Sauro; H Bolouri; J C Doyle; H Kitano; A P Arkin; B J Bornstein; D Bray; A Cornish-Bowden; A A Cuellar; S Dronov; E D Gilles; M Ginkel; V Gor; I I Goryanin; W J Hedley; T C Hodgman; J-H Hofmeyr; P J Hunter; N S Juty; J L Kasberger; A Kremling; U Kummer; N Le Novère; L M Loew; D Lucio; P Mendes; E Minch; E D Mjolsness; Y Nakayama; M R Nelson; P F Nielsen; T Sakurada; J C Schaff; B E Shapiro; T S Shimizu; H D Spence; J Stelling; K Takahashi; M Tomita; J Wagner; J Wang
Journal:  Bioinformatics       Date:  2003-03-01       Impact factor: 6.937

2.  Editing, validating and translating of SBGN maps.

Authors:  Tobias Czauderna; Christian Klukas; Falk Schreiber
Journal:  Bioinformatics       Date:  2010-07-13       Impact factor: 6.937

3.  PathVisio-MIM: PathVisio plugin for creating and editing Molecular Interaction Maps (MIMs).

Authors:  Augustin Luna; Margot L Sunshine; Martijn P van Iersel; Mirit I Aladjem; Kurt W Kohn
Journal:  Bioinformatics       Date:  2011-06-02       Impact factor: 6.937

4.  A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method.

Authors:  Augustin Luna; Evrim I Karac; Margot Sunshine; Lucas Chang; Ruth Nussinov; Mirit I Aladjem; Kurt W Kohn
Journal:  BMC Bioinformatics       Date:  2011-05-17       Impact factor: 3.169

5.  The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways.

Authors:  Luca Beltrame; Enrica Calura; Razvan R Popovici; Lisa Rizzetto; Damariz Rivero Guedez; Michele Donato; Chiara Romualdi; Sorin Draghici; Duccio Cavalieri
Journal:  Bioinformatics       Date:  2011-06-07       Impact factor: 6.937

6.  The BioPAX community standard for pathway data sharing.

Authors:  Emek Demir; Michael P Cary; Suzanne Paley; Ken Fukuda; Christian Lemer; Imre Vastrik; Guanming Wu; Peter D'Eustachio; Carl Schaefer; Joanne Luciano; Frank Schacherer; Irma Martinez-Flores; Zhenjun Hu; Veronica Jimenez-Jacinto; Geeta Joshi-Tope; Kumaran Kandasamy; Alejandra C Lopez-Fuentes; Huaiyu Mi; Elgar Pichler; Igor Rodchenkov; Andrea Splendiani; Sasha Tkachev; Jeremy Zucker; Gopal Gopinath; Harsha Rajasimha; Ranjani Ramakrishnan; Imran Shah; Mustafa Syed; Nadia Anwar; Ozgün Babur; Michael Blinov; Erik Brauner; Dan Corwin; Sylva Donaldson; Frank Gibbons; Robert Goldberg; Peter Hornbeck; Augustin Luna; Peter Murray-Rust; Eric Neumann; Oliver Ruebenacker; Oliver Reubenacker; Matthias Samwald; Martijn van Iersel; Sarala Wimalaratne; Keith Allen; Burk Braun; Michelle Whirl-Carrillo; Kei-Hoi Cheung; Kam Dahlquist; Andrew Finney; Marc Gillespie; Elizabeth Glass; Li Gong; Robin Haw; Michael Honig; Olivier Hubaut; David Kane; Shiva Krupa; Martina Kutmon; Julie Leonard; Debbie Marks; David Merberg; Victoria Petri; Alex Pico; Dean Ravenscroft; Liya Ren; Nigam Shah; Margot Sunshine; Rebecca Tang; Ryan Whaley; Stan Letovksy; Kenneth H Buetow; Andrey Rzhetsky; Vincent Schachter; Bruno S Sobral; Ugur Dogrusoz; Shannon McWeeney; Mirit Aladjem; Ewan Birney; Julio Collado-Vides; Susumu Goto; Michael Hucka; Nicolas Le Novère; Natalia Maltsev; Akhilesh Pandey; Paul Thomas; Edgar Wingender; Peter D Karp; Chris Sander; Gary D Bader
Journal:  Nat Biotechnol       Date:  2010-09-09       Impact factor: 54.908

7.  Presenting and exploring biological pathways with PathVisio.

Authors:  Martijn P van Iersel; Thomas Kelder; Alexander R Pico; Kristina Hanspers; Susan Coort; Bruce R Conklin; Chris Evelo
Journal:  BMC Bioinformatics       Date:  2008-09-25       Impact factor: 3.169

8.  WikiPathways: pathway editing for the people.

Authors:  Alexander R Pico; Thomas Kelder; Martijn P van Iersel; Kristina Hanspers; Bruce R Conklin; Chris Evelo
Journal:  PLoS Biol       Date:  2008-07-22       Impact factor: 8.029
  8 in total
  4 in total

1.  Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment.

Authors:  Anwesha Bohler; Lars M T Eijssen; Martijn P van Iersel; Christ Leemans; Egon L Willighagen; Martina Kutmon; Magali Jaillard; Chris T Evelo
Journal:  BMC Bioinformatics       Date:  2015-08-23       Impact factor: 3.169

2.  PathVisio 3: an extendable pathway analysis toolbox.

Authors:  Martina Kutmon; Martijn P van Iersel; Anwesha Bohler; Thomas Kelder; Nuno Nunes; Alexander R Pico; Chris T Evelo
Journal:  PLoS Comput Biol       Date:  2015-02-23       Impact factor: 4.475

3.  Multifactorial Modes of Action of Arsenic Trioxide in Cancer Cells as Analyzed by Classical and Network Pharmacology.

Authors:  Mona Dawood; Sami Hamdoun; Thomas Efferth
Journal:  Front Pharmacol       Date:  2018-02-27       Impact factor: 5.810

4.  Software support for SBGN maps: SBGN-ML and LibSBGN.

Authors:  Martijn P van Iersel; Alice C Villéger; Tobias Czauderna; Sarah E Boyd; Frank T Bergmann; Augustin Luna; Emek Demir; Anatoly Sorokin; Ugur Dogrusoz; Yukiko Matsuoka; Akira Funahashi; Mirit I Aladjem; Huaiyu Mi; Stuart L Moodie; Hiroaki Kitano; Nicolas Le Novère; Falk Schreiber
Journal:  Bioinformatics       Date:  2012-05-10       Impact factor: 6.937
  4 in total

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