The Evolution of Standards and Data Management Practices in Systems Biology

Overview

Journal Mol Syst Biol

Specialty Molecular Biology

Date 2015 Dec 25

PMID 26700851

Citations 17

Authors

Natalie J Stanford

Katherine Wolstencroft

Martin Golebiewski

Renate Kania

Nick Juty

Christopher Tomlinson

Stuart Owen

Sarah Butcher

Henning Hermjakob

Nicolas Le Novere

Wolfgang Mueller

Jacky Snoep

Carole Goble

Affiliations

Soon will be listed here.

Citing Articles

Data management challenges for artificial intelligence in plant and agricultural research.

Williamson H, Brettschneider J, Caccamo M, Davey R, Goble C, Kersey P F1000Res. 2023; 10:324.

PMID: 36873457 PMC: 9975417. DOI: 10.12688/f1000research.52204.2.

Systems Biology in ELIXIR: modelling in the spotlight.

Martins Dos Santos V, Anton M, Szomolay B, Ostaszewski M, Arts I, Benfeitas R F1000Res. 2024; 11.

PMID: 36742342 PMC: 9871403. DOI: 10.12688/f1000research.126734.2.

An Early Stage Researcher's Primer on Systems Medicine Terminology.

Zanin M, Aitya N, Basilio J, Baumbach J, Benis A, Behera C Netw Syst Med. 2021; 4(1):2-50.

PMID: 33659919 PMC: 7919422. DOI: 10.1089/nsm.2020.0003.

From whole-mount to single-cell spatial assessment of gene expression in 3D.

Waylen L, Nim H, Martelotto L, Ramialison M Commun Biol. 2020; 3(1):602.

PMID: 33097816 PMC: 7584572. DOI: 10.1038/s42003-020-01341-1.

SBML Level 3: an extensible format for the exchange and reuse of biological models.

Keating S, Waltemath D, Konig M, Zhang F, Drager A, Chaouiya C Mol Syst Biol. 2020; 16(8):e9110.

PMID: 32845085 PMC: 8411907. DOI: 10.15252/msb.20199110.

References

Waltemath D, Adams R, Beard D, Bergmann F, Bhalla U, Britten R . Minimum Information About a Simulation Experiment (MIASE). PLoS Comput Biol. 2011; 7(4):e1001122. PMC: 3084216. DOI: 10.1371/journal.pcbi.1001122. View

Stanford N, Wolstencroft K, Golebiewski M, Kania R, Juty N, Tomlinson C . The evolution of standards and data management practices in systems biology. Mol Syst Biol. 2015; 11(12):851. PMC: 4704484. DOI: 10.15252/msb.20156053. View

Klipp E, Liebermeister W, Helbig A, Kowald A, Schaber J . Systems biology standards--the community speaks. Nat Biotechnol. 2007; 25(4):390-1. DOI: 10.1038/nbt0407-390. View

Wolstencroft K, Owen S, Krebs O, Nguyen Q, Stanford N, Golebiewski M . SEEK: a systems biology data and model management platform. BMC Syst Biol. 2015; 9:33. PMC: 4702362. DOI: 10.1186/s12918-015-0174-y. View

Courtot M, Juty N, Knupfer C, Waltemath D, Zhukova A, Drager A . Controlled vocabularies and semantics in systems biology. Mol Syst Biol. 2011; 7:543. PMC: 3261705. DOI: 10.1038/msb.2011.77. View

Le Novere N, Finney A, Hucka M, Bhalla U, Campagne F, Collado-Vides J . Minimum information requested in the annotation of biochemical models (MIRIAM). Nat Biotechnol. 2005; 23(12):1509-15. DOI: 10.1038/nbt1156. View

Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C . Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet. 2001; 29(4):365-71. DOI: 10.1038/ng1201-365. View

Hucka M, Nickerson D, Bader G, Bergmann F, Cooper J, Demir E . Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative. Front Bioeng Biotechnol. 2015; 3:19. PMC: 4338824. DOI: 10.3389/fbioe.2015.00019. View

Chelliah V, Juty N, Ajmera I, Ali R, Dumousseau M, Glont M . BioModels: ten-year anniversary. Nucleic Acids Res. 2014; 43(Database issue):D542-8. PMC: 4383975. DOI: 10.1093/nar/gku1181. View

10.

Hastings J, de Matos P, Dekker A, Ennis M, Harsha B, Kale N . The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. Nucleic Acids Res. 2012; 41(Database issue):D456-63. PMC: 3531142. DOI: 10.1093/nar/gks1146. View

11.

Ashburner M, Ball C, Blake J, Botstein D, Butler H, Cherry J . Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000; 25(1):25-9. PMC: 3037419. DOI: 10.1038/75556. View