-
1
-
-
35948989284
-
The OBO foundry: coordinated evolution of ontologies to support biomedical data integration
-
Smith B., Ashburner M., et al. The OBO foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol 2007, 25(11):1251-1255. http://obofoundry.org/.
-
(2007)
Nat Biotechnol
, vol.25
, Issue.11
, pp. 1251-1255
-
-
Smith, B.1
Ashburner, M.2
-
2
-
-
77950362881
-
Current progress in patient-specific modeling
-
Neal M.L., Kerckhoffs R.C. Current progress in patient-specific modeling. Brief Bioinform 2010, 11:111-126.
-
(2010)
Brief Bioinform
, vol.11
, pp. 111-126
-
-
Neal, M.L.1
Kerckhoffs, R.C.2
-
3
-
-
33644877164
-
BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems
-
Database issue
-
Le Novere N., Bornstein B., et al. BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Res 2006, 34(Database issue):D689-D691. http://www.ebi.ac.uk/biomodels/.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Le Novere, N.1
Bornstein, B.2
-
4
-
-
51749096446
-
The CellML model repository
-
Lloyd C.M., Lawson J.R., Hunter P.J., Nielsen P.F. The CellML model repository. Bioinformatics 2008, 24(18):2122-2123. http://www.cellml.org/models.
-
(2008)
Bioinformatics
, vol.24
, Issue.18
, pp. 2122-2123
-
-
Lloyd, C.M.1
Lawson, J.R.2
Hunter, P.J.3
Nielsen, P.F.4
-
5
-
-
79952038807
-
-
JSim Model Archive
-
JSim Model Archive, http://physiome.org/jsim/models/.
-
-
-
-
6
-
-
0037336350
-
Integration from proteins to organs: the Physiome Project
-
Hunter P.J., Borg T.K. Integration from proteins to organs: the Physiome Project. Nat Rev Mol Cell Biol 2003, 4(3):237-243.
-
(2003)
Nat Rev Mol Cell Biol
, vol.4
, Issue.3
, pp. 237-243
-
-
Hunter, P.J.1
Borg, T.K.2
-
7
-
-
79952042969
-
-
Virtual Physiological Human - Network of Excellence home page
-
Virtual Physiological Human - Network of Excellence home page, http://www.vph-noe.eu/home/.
-
-
-
-
8
-
-
75549092202
-
Chemical entities of biological interest: an update
-
de Matos P., Alcantara R., et al. Chemical entities of biological interest: an update. Nucleic Acids Res 2010, 38(Database issue):D249-D254. http://www.ebi.ac.uk/chebi/.
-
(2010)
Nucleic Acids Res
, vol.38
, Issue.DATABASE ISSUE
-
-
de Matos, P.1
Alcantara, R.2
-
9
-
-
75849153303
-
-
The Universal Protein Resource (UniProt) in Nucleic Acids Res 2010;38(Database issue):D142-8
-
The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res 2010;38(Database issue):D142-8. http://www.uniprot.org.
-
(2010)
-
-
-
10
-
-
0034069495
-
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
-
Ashburner M., Ball C.A., et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25(1):25-29. http://www.geneontology.org/.
-
(2000)
Nat Genet
, vol.25
, Issue.1
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
-
11
-
-
0033982936
-
KEGG: kyoto encyclopedia of genes and genomes
-
Kanehisa M., Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000, 28(1):27-30. http://www.genome.ad.jp/kegg/.
-
(2000)
Nucleic Acids Res
, vol.28
, Issue.1
, pp. 27-30
-
-
Kanehisa, M.1
Goto, S.2
-
12
-
-
0842283371
-
A reference ontology for bioinformatics: the foundational model of anatomy
-
Rosse C., Mejino J.L.V. A reference ontology for bioinformatics: the foundational model of anatomy. J Biomed Inform 2003, 36:478-500.
-
(2003)
J Biomed Inform
, vol.36
, pp. 478-500
-
-
Rosse, C.1
Mejino, J.L.V.2
-
13
-
-
73949106573
-
-
Bridging biological ontologies and biosimulation: the ontology of physics for biology. In: AMIA Annual Symposium, Washington, DC;
-
Cook DL, Mejino Jr JV, Neal ML, Gennari JH. Bridging biological ontologies and biosimulation: the ontology of physics for biology. In: AMIA Annual Symposium, Washington, DC; 2008. p. 136-40.
-
(2008)
, pp. 136-40
-
-
Cook, D.L.1
Mejino, J.V.2
Neal, M.L.3
Gennari, J.H.4
-
14
-
-
72949116593
-
Linking human diseases to animal models using ontology-based phenotype annotation
-
Washington N.L., Haendel M.A., et al. Linking human diseases to animal models using ontology-based phenotype annotation. PLoS Biol 2009, 7(11):e1000247.
-
(2009)
PLoS Biol
, vol.7
, Issue.11
-
-
Washington, N.L.1
Haendel, M.A.2
-
15
-
-
79952038289
-
-
Basic Formal Ontology (BFO)
-
Basic Formal Ontology (BFO), http://www.ifomis.org/bfo.
-
-
-
-
16
-
-
61949441759
-
Advances in semantic representation for multiscale biosimulation: a case study in merging models
-
Neal M.L., Gennari J.H., Arts T., Cook D.L. Advances in semantic representation for multiscale biosimulation: a case study in merging models. Pac Symp Biocomput 2009, 14:305-315.
-
(2009)
Pac Symp Biocomput
, vol.14
, pp. 305-315
-
-
Neal, M.L.1
Gennari, J.H.2
Arts, T.3
Cook, D.L.4
-
17
-
-
79952038571
-
-
Personal communication from Sauro H, and Butterworth
-
Personal communication from Sauro H, and Butterworth E, 2009.
-
(2009)
-
-
-
18
-
-
33845501360
-
Coupling of a 3D finite element model of cardiac ventricular mechanics to lumped systems models of the systemic and pulmonic circulation
-
Kerckhoffs R.C., Neal M.L., et al. Coupling of a 3D finite element model of cardiac ventricular mechanics to lumped systems models of the systemic and pulmonic circulation. Ann Biomed Eng 2007, 35(1):1-18.
-
(2007)
Ann Biomed Eng
, vol.35
, Issue.1
, pp. 1-18
-
-
Kerckhoffs, R.C.1
Neal, M.L.2
-
19
-
-
28644433993
-
Minimum information requested in the annotation of biochemical models (MIRIAM)
-
Le Novere N., Finney A., et al. Minimum information requested in the annotation of biochemical models (MIRIAM). Nat Biotechnol 2005, 23(12):1509-1515.
-
(2005)
Nat Biotechnol
, vol.23
, Issue.12
, pp. 1509-1515
-
-
Le Novere, N.1
Finney, A.2
-
20
-
-
77949508535
-
Annotation and merging of SBML models with semanticSBML
-
Krause F., Uhlendorf J., et al. Annotation and merging of SBML models with semanticSBML. Bioinformatics 2010, 26(3):421-422. http://www.semanticsbml.org.
-
(2010)
Bioinformatics
, vol.26
, Issue.3
, pp. 421-422
-
-
Krause, F.1
Uhlendorf, J.2
-
21
-
-
70449350595
-
Saint: a lightweight integration environment for model annotation
-
Lister A., Pocock M., Taschuk M., Wipat A. Saint: a lightweight integration environment for model annotation. Bioinformatics 2009, 25(22):3026-3027.
-
(2009)
Bioinformatics
, vol.25
, Issue.22
, pp. 3026-3027
-
-
Lister, A.1
Pocock, M.2
Taschuk, M.3
Wipat, A.4
-
22
-
-
23344454612
-
Experimental and in silico analyses of glycolytic flux control in bloodstream form Trypanosoma brucei
-
BioModels link
-
Albert M.A., Haanstra J.R., et al. Experimental and in silico analyses of glycolytic flux control in bloodstream form Trypanosoma brucei. J Biol Chem 2005, 280(31):28306-28315. BioModels link: http://www.ebi.ac.uk/biomodels-main/BIOMD0000000211.
-
(2005)
J Biol Chem
, vol.280
, Issue.31
, pp. 28306-28315
-
-
Albert, M.A.1
Haanstra, J.R.2
-
23
-
-
79952043748
-
-
OBO Relationship Ontology
-
OBO Relationship Ontology, http://www.obofoundry.org/ro/.
-
-
-
-
24
-
-
79952041500
-
-
Turtle: Terse RDF Triple Language
-
Turtle: Terse RDF Triple Language, http://www.w3.org/TeamSubmission/turtle/.
-
-
-
-
25
-
-
79952043500
-
-
BioModels Database: A Database of Annotated Published Models
-
BioModels Database: A Database of Annotated Published Models, http://www.ebi.ac.uk/biomodels/.
-
-
-
-
26
-
-
79952042243
-
-
NCBO BioPortal
-
NCBO BioPortal, http://bioportal.bioontology.org/.
-
-
-
-
27
-
-
79952040924
-
-
Personal communication from Noy N
-
Personal communication from Noy N.
-
-
-
-
28
-
-
40549119235
-
Integration of multi-scale biosimulation models via light-weight semantics
-
Gennari J.H., Neal M.L., Carlson B.E., Cook D.L. Integration of multi-scale biosimulation models via light-weight semantics. Pac Symp Biocomput 2008, 13:414-425.
-
(2008)
Pac Symp Biocomput
, vol.13
, pp. 414-425
-
-
Gennari, J.H.1
Neal, M.L.2
Carlson, B.E.3
Cook, D.L.4
-
29
-
-
0346361658
-
The PROMPT suite: interactive tools for ontology merging and mapping
-
Noy N.F., Musen M.A. The PROMPT suite: interactive tools for ontology merging and mapping. Int J Human-Computer Studies 2003, 59(6):983-1024.
-
(2003)
Int J Human-Computer Studies
, vol.59
, Issue.6
, pp. 983-1024
-
-
Noy, N.F.1
Musen, M.A.2
-
30
-
-
69949157393
-
Biophysical annotation and representation of CellML models
-
Wimalaratne S.M., Halstead M.D.B., et al. Biophysical annotation and representation of CellML models. Bioinformatics 2009, 25(17):2263.
-
(2009)
Bioinformatics
, vol.25
, Issue.17
, pp. 2263
-
-
Wimalaratne, S.M.1
Halstead, M.D.B.2
-
31
-
-
80052699329
-
MIREOT: the minimum information to reference an external ontology term
-
Courtot M., Gibson F., et al. MIREOT: the minimum information to reference an external ontology term. Proc Int Conf Biomed Ontol 2009, 87-90.
-
(2009)
Proc Int Conf Biomed Ontol
, pp. 87-90
-
-
Courtot, M.1
Gibson, F.2
-
32
-
-
20844433631
-
Using ontologies to describe mouse phenotypes
-
Gkoutos G.V., Green E.C., et al. Using ontologies to describe mouse phenotypes. Genome Biol 2005, 6(1):R8.
-
(2005)
Genome Biol
, vol.6
, Issue.1
-
-
Gkoutos, G.V.1
Green, E.C.2
-
33
-
-
79952041363
-
-
Adding semantics in kinetics models of biochemical pathways. In: 2nd International ESCEC Symposium on Experimental Standard Conditions on Enzyme Characterizations;
-
Le Novere N, Courtot M, Laibe C. Adding semantics in kinetics models of biochemical pathways. In: 2nd International ESCEC Symposium on Experimental Standard Conditions on Enzyme Characterizations; 2006. http://www.ebi.ac.uk/sbo/.
-
(2006)
-
-
Le Novere, N.1
Courtot, M.2
Laibe, C.3
|