Literature DB >> 34132740

libOmexMeta: Enabling semantic annotation of models to support FAIR principles.

Ciaran Welsh1, David P Nickerson2, Anand Rampadarath2, Maxwell L Neal3, Herbert M Sauro1, John H Gennari4.   

Abstract

SUMMARY: As the number and complexity of biosimulation models grows, so do demands for tools that can help users better understand models and make those models more findable, shareable and reproducible. Consistent model annotation is a step toward these goals. Both models and tools are written in a variety of different languages; thus, the community has recognized the need for standard, language-independent methods for annotation. Based on the Computational Modeling in Biology Network (COMBINE) community consensus, we introduce an open-source, cross-platform software library for semantic annotation of models. AVAILABILITY: libOmexMeta is freely available at https://github.com/sys-bio/libOmexMeta under the Apache License 2.0. A live demonstration is at github.com/sys-bio/pyomexmeta-binder-notebook. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
© The Author(s) (2021). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Entities:  

Year:  2021        PMID: 34132740      PMCID: PMC8665746          DOI: 10.1093/bioinformatics/btab445

Source DB:  PubMed          Journal:  Bioinformatics        ISSN: 1367-4803            Impact factor:   6.931


  8 in total

1.  COPASI--a COmplex PAthway SImulator.

Authors:  Stefan Hoops; Sven Sahle; Ralph Gauges; Christine Lee; Jürgen Pahle; Natalia Simus; Mudita Singhal; Liang Xu; Pedro Mendes; Ursula Kummer
Journal:  Bioinformatics       Date:  2006-10-10       Impact factor: 6.937

2.  Tellurium: An extensible python-based modeling environment for systems and synthetic biology.

Authors:  Kiri Choi; J Kyle Medley; Matthias König; Kaylene Stocking; Lucian Smith; Stanley Gu; Herbert M Sauro
Journal:  Biosystems       Date:  2018-07-25       Impact factor: 1.973

3.  The Physiome Model Repository 2.

Authors:  Tommy Yu; Catherine M Lloyd; David P Nickerson; Michael T Cooling; Andrew K Miller; Alan Garny; Jonna R Terkildsen; James Lawson; Randall D Britten; Peter J Hunter; Poul M F Nielsen
Journal:  Bioinformatics       Date:  2011-01-06       Impact factor: 6.937

4.  OpenCOR: a modular and interoperable approach to computational biology.

Authors:  Alan Garny; Peter J Hunter
Journal:  Front Physiol       Date:  2015-02-06       Impact factor: 4.566

Review 5.  Harmonizing semantic annotations for computational models in biology.

Authors:  Maxwell Lewis Neal; Matthias König; David Nickerson; Göksel Mısırlı; Reza Kalbasi; Andreas Dräger; Koray Atalag; Vijayalakshmi Chelliah; Michael T Cooling; Daniel L Cook; Sharon Crook; Miguel de Alba; Samuel H Friedman; Alan Garny; John H Gennari; Padraig Gleeson; Martin Golebiewski; Michael Hucka; Nick Juty; Chris Myers; Brett G Olivier; Herbert M Sauro; Martin Scharm; Jacky L Snoep; Vasundra Touré; Anil Wipat; Olaf Wolkenhauer; Dagmar Waltemath
Journal:  Brief Bioinform       Date:  2019-03-22       Impact factor: 11.622

6.  COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project.

Authors:  Frank T Bergmann; Richard Adams; Stuart Moodie; Jonathan Cooper; Mihai Glont; Martin Golebiewski; Michael Hucka; Camille Laibe; Andrew K Miller; David P Nickerson; Brett G Olivier; Nicolas Rodriguez; Herbert M Sauro; Martin Scharm; Stian Soiland-Reyes; Dagmar Waltemath; Florent Yvon; Nicolas Le Novère
Journal:  BMC Bioinformatics       Date:  2014-12-14       Impact factor: 3.169

7.  The FAIR Guiding Principles for scientific data management and stewardship.

Authors:  Mark D Wilkinson; Michel Dumontier; I Jsbrand Jan Aalbersberg; Gabrielle Appleton; Myles Axton; Arie Baak; Niklas Blomberg; Jan-Willem Boiten; Luiz Bonino da Silva Santos; Philip E Bourne; Jildau Bouwman; Anthony J Brookes; Tim Clark; Mercè Crosas; Ingrid Dillo; Olivier Dumon; Scott Edmunds; Chris T Evelo; Richard Finkers; Alejandra Gonzalez-Beltran; Alasdair J G Gray; Paul Groth; Carole Goble; Jeffrey S Grethe; Jaap Heringa; Peter A C 't Hoen; Rob Hooft; Tobias Kuhn; Ruben Kok; Joost Kok; Scott J Lusher; Maryann E Martone; Albert Mons; Abel L Packer; Bengt Persson; Philippe Rocca-Serra; Marco Roos; Rene van Schaik; Susanna-Assunta Sansone; Erik Schultes; Thierry Sengstag; Ted Slater; George Strawn; Morris A Swertz; Mark Thompson; Johan van der Lei; Erik van Mulligen; Jan Velterop; Andra Waagmeester; Peter Wittenburg; Katherine Wolstencroft; Jun Zhao; Barend Mons
Journal:  Sci Data       Date:  2016-03-15       Impact factor: 6.444

8.  BioModels: expanding horizons to include more modelling approaches and formats.

Authors:  Mihai Glont; Tung V N Nguyen; Martin Graesslin; Robert Hälke; Raza Ali; Jochen Schramm; Sarala M Wimalaratne; Varun B Kothamachu; Nicolas Rodriguez; Maciej J Swat; Jurgen Eils; Roland Eils; Camille Laibe; Rahuman S Malik-Sheriff; Vijayalakshmi Chelliah; Nicolas Le Novère; Henning Hermjakob
Journal:  Nucleic Acids Res       Date:  2018-01-04       Impact factor: 16.971

  8 in total
  2 in total

1.  Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology.

Authors:  Anna Niarakis; Dagmar Waltemath; James Glazier; Falk Schreiber; Sarah M Keating; David Nickerson; Claudine Chaouiya; Anne Siegel; Vincent Noël; Henning Hermjakob; Tomáš Helikar; Sylvain Soliman; Laurence Calzone
Journal:  Brief Bioinform       Date:  2022-07-18       Impact factor: 13.994

2.  NLIMED: Natural Language Interface for Model Entity Discovery in Biosimulation Model Repositories.

Authors:  Yuda Munarko; Dewan M Sarwar; Anand Rampadarath; Koray Atalag; John H Gennari; Maxwell L Neal; David P Nickerson
Journal:  Front Physiol       Date:  2022-02-24       Impact factor: 4.566

  2 in total

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