-
1
-
-
47149113155
-
Ontology Design Patterns for bio-ontologies: A case study on the Cell Cycle Ontology
-
Aranguren ME, Antezana E, Kuiper M, Stevens R. Ontology Design Patterns for bio-ontologies: a case study on the Cell Cycle Ontology. BMC Bioinform. 2008, 9(Suppl 5):S1.
-
(2008)
BMC Bioinform.
, vol.9
, pp. S1
-
-
Aranguren, M.E.1
Antezana, E.2
Kuiper, M.3
Stevens, R.4
-
2
-
-
0034069495
-
Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium
-
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000, 25(1):25-9.
-
(2000)
Nat Genet.
, vol.25
, Issue.1
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
Butler, H.5
Cherry, J.M.6
Davis, A.P.7
-
3
-
-
33846064113
-
NCBI GEO: Mining tens of millions of expression profiles-database and tools update
-
Database issue
-
Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, Kim IF, Soboleva A, Tomashevsky M, Edgar R. NCBI GEO: mining tens of millions of expression profiles-database and tools update. Nucleic Acids Res. 2007, 35(Database issue):D760-65.
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. D760-D765
-
-
Barrett, T.1
Troup, D.B.2
Wilhite, S.E.3
Ledoux, P.4
Rudnev, D.5
Evangelista, C.6
Kim, I.F.7
Soboleva, A.8
Tomashevsky, M.9
Edgar, R.10
-
4
-
-
48349143030
-
Biomedical ontologies in action: Role in knowledge management, data integration and decision support
-
Bodenreider O. Biomedical ontologies in action: role in knowledge management, data integration and decision support. Yearb Med Inform. 2008, 67-79.
-
(2008)
Yearb Med Inform.
, pp. 67-79
-
-
Bodenreider, O.1
-
5
-
-
0036594338
-
Conceptual data modeling for bioinformatics
-
Bornberg-Bauer E, Paton NW. Conceptual data modeling for bioinformatics. Brief Bioinform. 2002, 3:166-80.
-
(2002)
Brief Bioinform.
, vol.3
, pp. 166-180
-
-
Bornberg-Bauer, E.1
Paton, N.W.2
-
6
-
-
18344396568
-
Minimum information about a microarray experiment (MIAME)-toward standards for microarray data
-
Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J et al. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet. 2001, 29(4):365-71.
-
(2001)
Nat Genet.
, vol.29
, Issue.4
, pp. 365-371
-
-
Brazma, A.1
Hingamp, P.2
Quackenbush, J.3
Sherlock, G.4
Spellman, P.5
Stoeckert, C.6
Aach, J.7
-
7
-
-
36049034216
-
A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence
-
Conenello GM, Zamarin D, Perrone LA, Tumpey T, Palese P. A single mutation in the PB1-F2 of H5N1 (HK/97) and 1918 influenza A viruses contributes to increased virulence. PLoS Pathog. 2007, 3(10):1414-21.
-
(2007)
PLoS Pathog.
, vol.3
, Issue.10
, pp. 1414-1421
-
-
Conenello, G.M.1
Zamarin, D.2
Perrone, L.A.3
Tumpey, T.4
Palese, P.5
-
8
-
-
38449089399
-
Chalkboard: Ontology-based pathway modeling and qualitative inference of disease mechanisms
-
Cook DL, Wiley JC, Gennari JH. Chalkboard: ontology-based pathway modeling and qualitative inference of disease mechanisms. Pac Symp Biocomput. 2007, 16-27.
-
(2007)
Pac Symp Biocomput.
, pp. 16-27
-
-
Cook, D.L.1
Wiley, J.C.2
Gennari, J.H.3
-
9
-
-
33846036710
-
The Stanford Microarray Database: Implementation of new analysis tools and open source release of software
-
Database issue
-
Demeter J, Beauheim C, Gollub J, Hernandez-Boussard T, Jin H, Maier D, Matese JC et al. The Stanford Microarray Database: implementation of new analysis tools and open source release of software. Nucleic Acids Res. 2007, 35(Database issue):D766-70.
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. D766-D770
-
-
Demeter, J.1
Beauheim, C.2
Gollub, J.3
Hernandez-Boussard, T.4
Jin, H.5
Maier, D.6
Matese, J.C.7
-
10
-
-
34248588368
-
Ontology development for biological systems: Immunology
-
Diehl AD, Lee JA, Scheuermann RH, Blake JA. Ontology development for biological systems: immunology. Bioinformatics. 2007, 23(7):913-15.
-
(2007)
Bioinformatics.
, vol.23
, Issue.7
, pp. 913-915
-
-
Diehl, A.D.1
Lee, J.A.2
Scheuermann, R.H.3
Blake, J.A.4
-
11
-
-
39649103642
-
The BRIDG project: A technical report
-
Fridsma DB, Evans J, Hastak S, Mead CN. The BRIDG project: a technical report. J Am Med Inform Assoc. 2008, 15(2):130-37.
-
(2008)
J Am Med Inform Assoc.
, vol.15
, Issue.2
, pp. 130-137
-
-
Fridsma, D.B.1
Evans, J.2
Hastak, S.3
Mead, C.N.4
-
12
-
-
34447271298
-
National Institute of Allergy and Infectious Diseases bioinformatics resource centers: New assets for pathogen informatics
-
Greene JM, Collins F, Lefkowitz EJ, Roos D, Scheuermann RH, Sobral B, Stevens R, White O, Di Francesco V. National Institute of Allergy and Infectious Diseases bioinformatics resource centers: new assets for pathogen informatics. Infect Immun. 2007, 75(7):3212-19.
-
(2007)
Infect Immun.
, vol.75
, Issue.7
, pp. 3212-3219
-
-
Greene, J.M.1
Collins, F.2
Lefkowitz, E.J.3
Roos, D.4
Scheuermann, R.H.5
Sobral, B.6
Stevens, R.7
White, O.8
Di Francesco, V.9
-
13
-
-
0346801873
-
Gene Ontology Consortium. The Gene Ontology (GO) database and informatics resource
-
Database issue
-
Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K et al. Gene Ontology Consortium. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 2004, 32(Database issue):D258-61.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. D258-D261
-
-
Harris, M.A.1
Clark, J.2
Ireland, A.3
Lomax, J.4
Ashburner, M.5
Foulger, R.6
Eilbeck, K.7
-
14
-
-
0037342537
-
The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models
-
Hucka M, Bolouri H, Finney A, Sauro H, Doyle JHK, Arkin A, Bornstein B et al. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics. 2003, 19:524-31.
-
(2003)
Bioinformatics.
, vol.19
, pp. 524-531
-
-
Hucka, M.1
Bolouri, H.2
Finney, A.3
Sauro, H.4
Doyle, J.H.K.5
Arkin, A.6
Bornstein, B.7
-
15
-
-
35148889036
-
The functional genomics experiment model (FuGE): An extensible framework for standards in functional genomics
-
Jones AR, Miller M, Aebersold R, Apweiler R, Ball CA, Brazma A, Degreef J et al. The functional genomics experiment model (FuGE): an extensible framework for standards in functional genomics. Nat Biotechnol. 2007, 25(10):1127-33.
-
(2007)
Nat Biotechnol.
, vol.25
, Issue.10
, pp. 1127-1133
-
-
Jones, A.R.1
Miller, M.2
Aebersold, R.3
Apweiler, R.4
Ball, C.A.5
Brazma, A.6
Degreef, J.7
-
16
-
-
40349100409
-
MIRIAM Resources: Tools to generate and resolve robust cross-references in systems biology
-
Laibe C, Le Novere N. MIRIAM Resources: tools to generate and resolve robust cross-references in systems biology. BMC Systems Biol. 2007, 1:58.
-
(2007)
BMC Systems Biol.
, vol.1
, pp. 58
-
-
Laibe, C.1
Le Novere, N.2
-
17
-
-
33745062476
-
Alliance for cellular signaling. Components of the antigen processing and presentation pathway revealed by gene expression microarray analysis following B cell antigen receptor (BCR) stimulation
-
Lee JA, Sinkovits RS, Mock D, Rab EL, Cai J, Yang P, Saunders B, Hsueh RC, Choi S, Subramaniam S, Scheuermann RH. Alliance for cellular signaling. Components of the antigen processing and presentation pathway revealed by gene expression microarray analysis following B cell antigen receptor (BCR) stimulation. BMC Bioinform. 2006, 7:237.
-
(2006)
BMC Bioinform.
, vol.7
, pp. 237
-
-
Lee, J.A.1
Sinkovits, R.S.2
Mock, D.3
Rab, E.L.4
Cai, J.5
Yang, P.6
Saunders, B.7
Hsueh, R.C.8
Choi, S.9
Subramaniam, S.10
Scheuermann, R.H.11
-
18
-
-
53049110682
-
MIFlowCyt: The minimum information about a flow cytometry experiment
-
Lee JA, Spidlen J, Atwater S, Boyce K, Cai J, Crosbie N, Dalphin M et al. MIFlowCyt: the minimum information about a flow cytometry experiment. Cytometry: Part A. 2008, 73(10):926-30.
-
(2008)
Cytometry: Part A.
, vol.73
, Issue.10
, pp. 926-930
-
-
Lee, J.A.1
Spidlen, J.2
Atwater, S.3
Boyce, K.4
Cai, J.5
Crosbie, N.6
Dalphin, M.7
-
19
-
-
28644433993
-
Minimum information requested in the annotation of biochemical models (MIRIAM)
-
Le Novère N, Finney A, Hucka M, Bhalla US, Campagne F, Collado-Vides J, Crampin EJ et al. Minimum information requested in the annotation of biochemical models (MIRIAM). Nat Biotechnol. 2005, 23(12):1509-15.
-
(2005)
Nat Biotechnol.
, vol.23
, Issue.12
, pp. 1509-1515
-
-
Le Novère, N.1
Finney, A.2
Hucka, M.3
Bhalla, U.S.4
Campagne, F.5
Collado-Vides, J.6
Crampin, E.J.7
-
20
-
-
2442595958
-
CellML: Its future, present and past
-
Lloyd C, Halstead M, Nielsen P. CellML: its future, present and past. Prog Biophy Mol Biol. 2004, 85:433-50.
-
(2004)
Prog Biophy Mol Biol.
, vol.85
, pp. 433-450
-
-
Lloyd, C.1
Halstead, M.2
Nielsen, P.3
-
21
-
-
21544461263
-
PAX of mind for pathway researchers
-
Luciano J. PAX of mind for pathway researchers. Drug Discovery Today. 2005, 10(13):937-42.
-
(2005)
Drug Discovery Today.
, vol.10
, Issue.13
, pp. 937-942
-
-
Luciano, J.1
-
22
-
-
33846681448
-
Modular organization of protein interaction networks
-
Luo F, Yang Y, Chen CF, Chang R, Zhou J, Scheuermann RH. Modular organization of protein interaction networks. Bioinformatics. 2007, 23(2):207-14.
-
(2007)
Bioinformatics.
, vol.23
, Issue.2
, pp. 207-214
-
-
Luo, F.1
Yang, Y.2
Chen, C.F.3
Chang, R.4
Zhou, J.5
Scheuermann, R.H.6
-
23
-
-
62749121141
-
Knowledge-data integration for temporal reasoning in a clinical trial system
-
O’Connor MJ, Shankar RD, Parrish DB, Das AK. Knowledge-data integration for temporal reasoning in a clinical trial system. Int J Med Inform. 2009, 78:577-85.
-
(2009)
Int J Med Inform.
, vol.78
, pp. 577-585
-
-
O’Connor, M.J.1
Shankar, R.D.2
Parrish, D.B.3
Das, A.K.4
-
24
-
-
33846039701
-
ArrayExpress-a public database of microarray experiments and gene expression profiles
-
Database issue
-
Parkinson H, Kapushesky M, Shojatalab M, Abeygunawardena N, Coulson R, Farne A, Holloway E et al. ArrayExpress-a public database of microarray experiments and gene expression profiles. Nucleic Acids Res. 2007, 35(Database issue):D747-50.
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. D747-D750
-
-
Parkinson, H.1
Kapushesky, M.2
Shojatalab, M.3
Abeygunawardena, N.4
Coulson, R.5
Farne, A.6
Holloway, E.7
-
25
-
-
67650760512
-
FuGEFlow: Data model and markup language for flow cytometry
-
submitted
-
Qian Y, Tchuvatkina D., Spidlen J, Wilkinson P, Garparetto M, Jones AR, Manion FJ, Scheurmann RH, Sekaly RP, and Brinkmann RR. FuGEFlow:data model and markup language for flow cytometry. BMC Bioinform. 2009, submitted.
-
(2009)
BMC Bioinform.
-
-
Qian, Y.1
Tchuvatkina, D.2
Spidlen, J.3
Wilkinson, P.4
Garparetto, M.5
Jones, A.R.6
Manion, F.J.7
Scheurmann, R.H.8
Sekaly, R.P.9
Brinkmann, R.R.10
-
27
-
-
38049144316
-
Biomedical ontologies: A functional perspective
-
Rubin DL, Shah NH, Noy NF. Biomedical ontologies: a functional perspective. Brief Bioinform. 2008, 9(1):75-90.
-
(2008)
Brief Bioinform.
, vol.9
, Issue.1
, pp. 75-90
-
-
Rubin, D.L.1
Shah, N.H.2
Noy, N.F.3
-
28
-
-
22044433259
-
Relations in biomedical ontologies
-
Smith B, Ceusters W, Klagges B, Köhler J, Kumar A, Lomax J, Mungall C, Neuhaus F, Rector AL, Rosse C. Relations in biomedical ontologies. Genome Biol. 2005, 6(5):R46.
-
(2005)
Genome Biol.
, vol.6
, Issue.5
, pp. R46
-
-
Smith, B.1
Ceusters, W.2
Klagges, B.3
Köhler, J.4
Kumar, A.5
Lomax, J.6
Mungall, C.7
Neuhaus, F.8
Rector, A.L.9
Rosse, C.10
-
29
-
-
35948989284
-
The OBO Foundry: Coordinated evolution of ontologies to support biomedical data integration
-
Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ et al. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol. 2007, 25(11):1251-55.
-
(2007)
Nat Biotechnol.
, vol.25
, Issue.11
, pp. 1251-1255
-
-
Smith, B.1
Ashburner, M.2
Rosse, C.3
Bard, J.4
Bug, W.5
Ceusters, W.6
Goldberg, L.J.7
-
30
-
-
38549147460
-
BioHealthBase: Informatics support in the elucidation of influenza virus host pathogen interactions and virulence
-
Database issue
-
Squires B, Macken C, Garcia-Sastre A, Godbole S, Noronha J, Hunt V, Chang R, Larsen CN, Klem E, Biersack K, Scheuermann RH. BioHealthBase:informatics support in the elucidation of influenza virus host pathogen interactions and virulence. Nucleic Acids Res. 2008, 36(Database issue):D497-503.
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. D497-D503
-
-
Squires, B.1
Macken, C.2
Garcia-Sastre, A.3
Godbole, S.4
Noronha, J.5
Hunt, V.6
Chang, R.7
Larsen, C.N.8
Klem, E.9
Biersack, K.10
Scheuermann, R.H.11
-
31
-
-
45749118607
-
Promoting coherent minimum reporting guidelines for biological and biomedical investigations: The MIBBI project
-
Taylor CF, Field D, Sansone SA, Aerts J, Apweiler R, Ashburner M, Ball CA et al. Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechnol. 2008, 26(8):889-96.
-
(2008)
Nat Biotechnol.
, vol.26
, Issue.8
, pp. 889-896
-
-
Taylor, C.F.1
Field, D.2
Sansone, S.A.3
Aerts, J.4
Apweiler, R.5
Ashburner, M.6
Ball, C.A.7
|