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Items: 1 to 20 of 38

1.

Retrieval, alignment, and clustering of computational models based on semantic annotations.

Schulz M, Krause F, Le Novère N, Klipp E, Liebermeister W.

Mol Syst Biol. 2011 Jul 19;7:512. doi: 10.1038/msb.2011.41.

2.

JSBML: a flexible Java library for working with SBML.

Dräger A, Rodriguez N, Dumousseau M, Dörr A, Wrzodek C, Le Novère N, Zell A, Hucka M.

Bioinformatics. 2011 Aug 1;27(15):2167-8. doi: 10.1093/bioinformatics/btr361. Epub 2011 Jun 22.

3.

Semantic Web integration of Cheminformatics resources with the SADI framework.

Chepelev LL, Dumontier M.

J Cheminform. 2011 May 16;3:16. doi: 10.1186/1758-2946-3-16.

4.

Semantics-based composition of EMBOSS services.

Lamprecht AL, Naujokat S, Margaria T, Steffen B.

J Biomed Semantics. 2011 Mar 7;2 Suppl 1:S5. doi: 10.1186/2041-1480-2-S1-S5.

5.

The Biomedical Resource Ontology (BRO) to enable resource discovery in clinical and translational research.

Tenenbaum JD, Whetzel PL, Anderson K, Borromeo CD, Dinov ID, Gabriel D, Kirschner B, Mirel B, Morris T, Noy N, Nyulas C, Rubenson D, Saxman PR, Singh H, Whelan N, Wright Z, Athey BD, Becich MJ, Ginsburg GS, Musen MA, Smith KA, Tarantal AF, Rubin DL, Lyster P.

J Biomed Inform. 2011 Feb;44(1):137-45. doi: 10.1016/j.jbi.2010.10.003. Epub 2010 Oct 16.

6.

The BioPAX community standard for pathway data sharing.

Demir E, Cary MP, Paley S, Fukuda K, Lemer C, Vastrik I, Wu G, D'Eustachio P, Schaefer C, Luciano J, Schacherer F, Martinez-Flores I, Hu Z, Jimenez-Jacinto V, Joshi-Tope G, Kandasamy K, Lopez-Fuentes AC, Mi H, Pichler E, Rodchenkov I, Splendiani A, Tkachev S, Zucker J, Gopinath G, Rajasimha H, Ramakrishnan R, Shah I, Syed M, Anwar N, Babur O, Blinov M, Brauner E, Corwin D, Donaldson S, Gibbons F, Goldberg R, Hornbeck P, Luna A, Murray-Rust P, Neumann E, Ruebenacker O, Samwald M, van Iersel M, Wimalaratne S, Allen K, Braun B, Whirl-Carrillo M, Cheung KH, Dahlquist K, Finney A, Gillespie M, Glass E, Gong L, Haw R, Honig M, Hubaut O, Kane D, Krupa S, Kutmon M, Leonard J, Marks D, Merberg D, Petri V, Pico A, Ravenscroft D, Ren L, Shah N, Sunshine M, Tang R, Whaley R, Letovksy S, Buetow KH, Rzhetsky A, Schachter V, Sobral BS, Dogrusoz U, McWeeney S, Aladjem M, Birney E, Collado-Vides J, Goto S, Hucka M, Le Novère N, Maltsev N, Pandey A, Thomas P, Wingender E, Karp PD, Sander C, Bader GD.

Nat Biotechnol. 2010 Sep;28(9):935-42. doi: 10.1038/nbt.1666. Epub 2010 Sep 9. Erratum in: Nat Biotechnol. 2010 Dec;28(12):1308. Nat Biotechnol. 2012 Apr;30(4):365. Reubenacker, Oliver [corrected to Ruebenacker, Oliver].

7.

Enzyme kinetics informatics: from instrument to browser.

Swainston N, Golebiewski M, Messiha HL, Malys N, Kania R, Kengne S, Krebs O, Mir S, Sauer-Danzwith H, Smallbone K, Weidemann A, Wittig U, Kell DB, Mendes P, Müller W, Paton NW, Rojas I.

FEBS J. 2010 Sep;277(18):3769-79. doi: 10.1111/j.1742-4658.2010.07778.x. Epub 2010 Aug 3.

8.

Annotation of SBML models through rule-based semantic integration.

Lister AL, Lord P, Pocock M, Wipat A.

J Biomed Semantics. 2010 Jun 22;1 Suppl 1:S3. doi: 10.1186/2041-1480-1-S1-S3.

9.

BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models.

Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C.

BMC Syst Biol. 2010 Jun 29;4:92. doi: 10.1186/1752-0509-4-92.

10.

NeuroML: a language for describing data driven models of neurons and networks with a high degree of biological detail.

Gleeson P, Crook S, Cannon RC, Hines ML, Billings GO, Farinella M, Morse TM, Davison AP, Ray S, Bhalla US, Barnes SR, Dimitrova YD, Silver RA.

PLoS Comput Biol. 2010 Jun 17;6(6):e1000815. doi: 10.1371/journal.pcbi.1000815.

11.

SBRML: a markup language for associating systems biology data with models.

Dada JO, Spasić I, Paton NW, Mendes P.

Bioinformatics. 2010 Apr 1;26(7):932-8. doi: 10.1093/bioinformatics/btq069. Epub 2010 Feb 21.

PMID:
20176582
12.

Cross-product extensions of the Gene Ontology.

Mungall CJ, Bada M, Berardini TZ, Deegan J, Ireland A, Harris MA, Hill DP, Lomax J.

J Biomed Inform. 2011 Feb;44(1):80-6. doi: 10.1016/j.jbi.2010.02.002. Epub 2010 Feb 10.

13.

BioModels.net Web Services, a free and integrated toolkit for computational modelling software.

Li C, Courtot M, Le Novère N, Laibe C.

Brief Bioinform. 2010 May;11(3):270-7. doi: 10.1093/bib/bbp056. Epub 2009 Nov 25.

14.

Annotation and merging of SBML models with semanticSBML.

Krause F, Uhlendorf J, Lubitz T, Schulz M, Klipp E, Liebermeister W.

Bioinformatics. 2010 Feb 1;26(3):421-2. doi: 10.1093/bioinformatics/btp642. Epub 2009 Nov 17.

PMID:
19933161
15.

Saint: a lightweight integration environment for model annotation.

Lister AL, Pocock M, Taschuk M, Wipat A.

Bioinformatics. 2009 Nov 15;25(22):3026-7. doi: 10.1093/bioinformatics/btp523. Epub 2009 Sep 4.

16.

The Systems Biology Graphical Notation.

Le Novère N, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A, Demir E, Wegner K, Aladjem MI, Wimalaratne SM, Bergman FT, Gauges R, Ghazal P, Kawaji H, Li L, Matsuoka Y, Villéger A, Boyd SE, Calzone L, Courtot M, Dogrusoz U, Freeman TC, Funahashi A, Ghosh S, Jouraku A, Kim S, Kolpakov F, Luna A, Sahle S, Schmidt E, Watterson S, Wu G, Goryanin I, Kell DB, Sander C, Sauro H, Snoep JL, Kohn K, Kitano H.

Nat Biotechnol. 2009 Aug;27(8):735-41. doi: 10.1038/nbt.1558. Epub 2009 Aug 7. Erratum in: Nat Biotechnol. 2009 Sep;27(9):864.

PMID:
19668183
17.

libAnnotationSBML: a library for exploiting SBML annotations.

Swainston N, Mendes P.

Bioinformatics. 2009 Sep 1;25(17):2292-3. doi: 10.1093/bioinformatics/btp392. Epub 2009 Jun 26.

18.

BioPortal: ontologies and integrated data resources at the click of a mouse.

Noy NF, Shah NH, Whetzel PL, Dai B, Dorf M, Griffith N, Jonquet C, Rubin DL, Storey MA, Chute CG, Musen MA.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W170-3. doi: 10.1093/nar/gkp440. Epub 2009 May 29.

19.

SBML2L(A)T(E)X: conversion of SBML files into human-readable reports.

Dräger A, Planatscher H, Motsou Wouamba D, Schröder A, Hucka M, Endler L, Golebiewski M, Müller W, Zell A.

Bioinformatics. 2009 Jun 1;25(11):1455-6. doi: 10.1093/bioinformatics/btp170. Epub 2009 Mar 23.

20.

Bridging biological ontologies and biosimulation: the ontology of physics for biology.

Cook DL, Mejino JL, Neal ML, Gennari JH.

AMIA Annu Symp Proc. 2008 Nov 6:136-40.

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