-
1
-
-
84893331818
-
Data management strategies for multinational large-scale systems biology projects
-
Wruck W, Peuker M, Regenbrecht CR: Data management strategies for multinational large-scale systems biology projects. Brief Bioinform 2012.
-
(2012)
Brief Bioinform
-
-
Wruck, W.1
Peuker, M.2
Regenbrecht, C.R.3
-
2
-
-
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, Binz PA, Bogue M, Booth T, et al: Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechnol 2008, 26:889-896.
-
(2008)
Nat Biotechnol
, vol.26
, 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
Binz, P.A.8
Bogue, M.9
Booth, T.10
-
3
-
-
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, Ansorge W, Ball CA, Causton HC, et al: Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 2001, 29:365-371.
-
(2001)
Nat Genet
, vol.29
, pp. 365-371
-
-
Brazma, A.1
Hingamp, P.2
Quackenbush, J.3
Sherlock, G.4
Spellman, P.5
Stoeckert, C.6
Aach, J.7
Ansorge, W.8
Ball, C.A.9
Causton, H.C.10
-
4
-
-
80053057733
-
The SEEK: a platform for sharing data and models in systems biology
-
Wolstencroft K, Owen S, du PF, Krebs O, Mueller W, Goble C, Snoep JL: The SEEK: a platform for sharing data and models in systems biology. Methods Enzymol 2011, 500:629-655.
-
(2011)
Methods Enzymol
, vol.500
, pp. 629-655
-
-
Wolstencroft, K.1
Owen, S.2
du, P.F.3
Krebs, O.4
Mueller, W.5
Goble, C.6
Snoep, J.L.7
-
5
-
-
82955207226
-
openBIS: a flexible framework for managing and analyzing complex data in biology research
-
Bauch A, Adamczyk I, Buczek P, Elmer FJ, Enimanev K, Glyzewski P, Kohler M, Pylak T, Quandt A, Ramakrishnan C, et al: openBIS: a flexible framework for managing and analyzing complex data in biology research. BMC Bioinformatics 2011, 12:468.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 468
-
-
Bauch, A.1
Adamczyk, I.2
Buczek, P.3
Elmer, F.J.4
Enimanev, K.5
Glyzewski, P.6
Kohler, M.7
Pylak, T.8
Quandt, A.9
Ramakrishnan, C.10
-
6
-
-
33646743767
-
The Gaggle: an open-source software system for integrating bioinformatics software and data sources
-
Shannon PT, Reiss DJ, Bonneau R, Baliga NS: The Gaggle: an open-source software system for integrating bioinformatics software and data sources. BMC Bioinformatics 2006, 7:176.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 176
-
-
Shannon, P.T.1
Reiss, D.J.2
Bonneau, R.3
Baliga, N.S.4
-
7
-
-
67649595544
-
MIMAS 3.0 is a Multiomics Information Management and Annotation System
-
Gattiker A, Hermida L, Liechti R, Xenarios I, Collin O, Rougemont J, Primig M: MIMAS 3.0 is a Multiomics Information Management and Annotation System. BMC Bioinformatics 2009, 10:151.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 151
-
-
Gattiker, A.1
Hermida, L.2
Liechti, R.3
Xenarios, I.4
Collin, O.5
Rougemont, J.6
Primig, M.7
-
8
-
-
84989276702
-
-
XperimentR. [http://www3.imperial.ac.uk/bioinfsupport/resources/data_management/xperimentr].
-
-
-
-
9
-
-
84983119904
-
ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level
-
Rocca-Serra P, Brandizi M, Maguire E, Sklyar N, Taylor C, Begley K, Field D, Harris S, Hide W, Hofmann O, et al: ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level. Bioinformatics 2010, 26:2354-2356.
-
(2010)
Bioinformatics
, vol.26
, pp. 2354-2356
-
-
Rocca-Serra, P.1
Brandizi, M.2
Maguire, E.3
Sklyar, N.4
Taylor, C.5
Begley, K.6
Field, D.7
Harris, S.8
Hide, W.9
Hofmann, O.10
-
10
-
-
70449732423
-
BASE-2nd generation software for microarray data management and analysis
-
Vallon-Christersson J, Nordborg N, Svensson M, Hakkinen J: BASE-2nd generation software for microarray data management and analysis. BMC Bioinformatics 2009, 10:330.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 330
-
-
Vallon-Christersson, J.1
Nordborg, N.2
Svensson, M.3
Hakkinen, J.4
-
11
-
-
79952319218
-
LabKey Server: an open source platform for scientific data integration, analysis and collaboration
-
Nelson EK, Piehler B, Eckels J, Rauch A, Bellew M, Hussey P, Ramsay S, Nathe C, Lum K, Krouse K, et al: LabKey Server: an open source platform for scientific data integration, analysis and collaboration. BMC Bioinformatics 2011, 12:71.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 71
-
-
Nelson, E.K.1
Piehler, B.2
Eckels, J.3
Rauch, A.4
Bellew, M.5
Hussey, P.6
Ramsay, S.7
Nathe, C.8
Lum, K.9
Krouse, K.10
-
12
-
-
84860631606
-
DIPSBC-data integration platform for systems biology collaborations
-
Dreher F, Kreitler T, Hardt C, Kamburov A, Yildirimman R, Schellander K, Lehrach H, Lange BM, Herwig R: DIPSBC-data integration platform for systems biology collaborations. BMC Bioinformatics 2012, 13:85.
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 85
-
-
Dreher, F.1
Kreitler, T.2
Hardt, C.3
Kamburov, A.4
Yildirimman, R.5
Schellander, K.6
Lehrach, H.7
Lange, B.M.8
Herwig, R.9
-
13
-
-
84858057633
-
XCEDE: an extensible schema for biomedical data
-
Gadde S, Aucoin N, Grethe JS, Keator DB, Marcus DS, Pieper S: XCEDE: an extensible schema for biomedical data. Neuroinformatics 2012, 10:19-32.
-
(2012)
Neuroinformatics
, vol.10
, pp. 19-32
-
-
Gadde, S.1
Aucoin, N.2
Grethe, J.S.3
Keator, D.B.4
Marcus, D.S.5
Pieper, S.6
-
14
-
-
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, Hardy N, Hermjakob H, Hubbard SJ, et al: The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics. Nat Biotechnol 2007, 25:1127-1133.
-
(2007)
Nat Biotechnol
, vol.25
, 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
Hardy, N.8
Hermjakob, H.9
Hubbard, S.J.10
-
15
-
-
84871812701
-
Data Integration in Bioinformatics: Current Efforts and Challenges
-
Zhang Z, Bajic B, Yu J, Cheung KH, Townsend JP: Data Integration in Bioinformatics: Current Efforts and Challenges. InTech 2011, 41-57.
-
(2011)
InTech
, pp. 41-57
-
-
Zhang, Z.1
Bajic, B.2
Yu, J.3
Cheung, K.H.4
Townsend, J.P.5
-
16
-
-
2942547885
-
The distributed annotation system
-
Dowell RD, Jokerst RM, Day A, Eddy SR, Stein L: The distributed annotation system. BMC Bioinformatics 2001, 2:7.
-
(2001)
BMC Bioinformatics
, vol.2
, pp. 7
-
-
Dowell, R.D.1
Jokerst, R.M.2
Day, A.3
Eddy, S.R.4
Stein, L.5
-
17
-
-
23144453296
-
Integrating protein annotation resources through the Distributed Annotation System
-
Olason PI: Integrating protein annotation resources through the Distributed Annotation System. Nucleic Acids Research 2013, 33: W468-W471.
-
(2013)
Nucleic Acids Research
, vol.33
, pp. W468-W471
-
-
Olason, P.I.1
-
18
-
-
84859350703
-
The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*
-
Katayama T, Arakawa K, Nakao M, Ono K, Aoki-Kinoshita KF, Yamamoto Y, Yamaguchi A, Kawashima S, Chun HW, Aerts J, et al: The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*. J Biomed Semantics 2010, 1:8.
-
(2010)
J Biomed Semantics
, vol.1
, pp. 8
-
-
Katayama, T.1
Arakawa, K.2
Nakao, M.3
Ono, K.4
Aoki-Kinoshita, K.F.5
Yamamoto, Y.6
Yamaguchi, A.7
Kawashima, S.8
Chun, H.W.9
Aerts, J.10
-
19
-
-
58149383792
-
Solutions for data integration in functional genomics: a critical assessment and case study
-
Smedley D, Swertz MA, Wolstencroft K, Proctor G, Zouberakis M, Bard J, Hancock JM, Schofield P: Solutions for data integration in functional genomics: a critical assessment and case study. Brief Bioinform 2008, 9:532-544.
-
(2008)
Brief Bioinform
, vol.9
, pp. 532-544
-
-
Smedley, D.1
Swertz, M.A.2
Wolstencroft, K.3
Proctor, G.4
Zouberakis, M.5
Bard, J.6
Hancock, J.M.7
Schofield, P.8
-
20
-
-
0037935183
-
BioMOBY: an open source biological web services proposal
-
Wilkinson MD, Links M: BioMOBY: an open source biological web services proposal. Brief Bioinform 2002, 3:331-341.
-
(2002)
Brief Bioinform
, vol.3
, pp. 331-341
-
-
Wilkinson, M.D.1
Links, M.2
-
21
-
-
84989336667
-
BioRegistry: Automatic Extraction of Metadata for Biological Database Retrieval and Discovery
-
Devignes MD, Franiatte P, Messai N, Bresso E, Napoli A, Smail-Tabbone M: BioRegistry: Automatic Extraction of Metadata for Biological Database Retrieval and Discovery. International Journal of Metadata, Semantics and Ontologies.
-
International Journal of Metadata, Semantics and Ontologies
-
-
Devignes, M.D.1
Franiatte, P.2
Messai, N.3
Bresso, E.4
Napoli, A.5
Smail-Tabbone, M.6
-
22
-
-
84989326666
-
-
BioRegistry. [http://bioregistry.loria.fr].
-
-
-
-
23
-
-
0036036947
-
Data Integration: A Theoretical Perspective
-
Lenzerini M: Data Integration: A Theoretical Perspective. ACM PODS 2002, 233-246.
-
(2002)
ACM PODS
, pp. 233-246
-
-
Lenzerini, M.1
-
24
-
-
0242493835
-
Knowledge representation for information integration
-
Rousset MC, Reynaud C: Knowledge representation for information integration. Information Systems 2014, 3-22.
-
(2014)
Information Systems
, pp. 3-22
-
-
Rousset, M.C.1
Reynaud, C.2
-
25
-
-
73649086918
-
A metadata approach for clinical data management in translational genomics studies in breast cancer
-
Papatheodorou I, Crichton C, Morris L, Maccallum P, Davies J, Brenton JD, Caldas C: A metadata approach for clinical data management in translational genomics studies in breast cancer. BMC Med Genomics 2009, 2:66.
-
(2009)
BMC Med Genomics
, vol.2
, pp. 66
-
-
Papatheodorou, I.1
Crichton, C.2
Morris, L.3
Maccallum, P.4
Davies, J.5
Brenton, J.D.6
Caldas, C.7
-
26
-
-
65649108623
-
Modeling genomic data with type attributes, balancing stability and maintainability
-
Busch N, Wedemann G: Modeling genomic data with type attributes, balancing stability and maintainability. BMC Bioinformatics 2009, 10:97.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 97
-
-
Busch, N.1
Wedemann, G.2
-
27
-
-
84865499790
-
A Minimum Data Set for Sharing Biobank Samples, Information, and Data: MIABIS
-
Norlin L, Fransson MN, Eriksson M, Merino-Martinez R, Anderberger M, Kurtovic S, Litton JE: A Minimum Data Set for Sharing Biobank Samples, Information, and Data: MIABIS. Biopreservation and Biobanking 2012, 10:343-348.
-
(2012)
Biopreservation and Biobanking
, vol.10
, pp. 343-348
-
-
Norlin, L.1
Fransson, M.N.2
Eriksson, M.3
Merino-Martinez, R.4
Anderberger, M.5
Kurtovic, S.6
Litton, J.E.7
-
28
-
-
70449449013
-
Semantic web data warehousing for caGrid
-
McCusker JP, Phillips JA, Gonzalez BA, Finkelstein A, Krauthammer M: Semantic web data warehousing for caGrid. BMC Bioinformatics 2009, 10(Suppl 10):S2.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. S2
-
-
McCusker, J.P.1
Phillips, J.A.2
Gonzalez, B.A.3
Finkelstein, A.4
Krauthammer, M.5
-
29
-
-
70349983268
-
A System for Information Management in BioMedical Studies-SIMBioMS
-
Krestyaninova M, Zarins A, Viksna J, Kurbatova N, Rucevskis P, Neogi SG, Gostev M, Perheentupa T, Knuuttila J, Barrett A, et al: A System for Information Management in BioMedical Studies-SIMBioMS. Bioinformatics 2009, 25:2768-2769.
-
(2009)
Bioinformatics
, vol.25
, pp. 2768-2769
-
-
Krestyaninova, M.1
Zarins, A.2
Viksna, J.3
Kurbatova, N.4
Rucevskis, P.5
Neogi, S.G.6
Gostev, M.7
Perheentupa, T.8
Knuuttila, J.9
Barrett, A.10
-
31
-
-
84864925958
-
An ICT infrastructure to integrate clinical and molecular data in oncology research
-
Segagni D, Tibollo V, Dagliati A, Zambelli A, Priori SG, Bellazzi R: An ICT infrastructure to integrate clinical and molecular data in oncology research. BMC Bioinformatics 2012, 13(Suppl 4):S5.
-
(2012)
BMC Bioinformatics
, vol.13
, pp. S5
-
-
Segagni, D.1
Tibollo, V.2
Dagliati, A.3
Zambelli, A.4
Priori, S.G.5
Bellazzi, R.6
-
32
-
-
84867072947
-
A repository based on a dynamically extensible data model supporting multidisciplinary research in neuroscience
-
Corradi L, Porro I, Schenone A, Momeni P, Ferrari R, Nobili F, Ferrara M, Arnulfo G, Fato MM: A repository based on a dynamically extensible data model supporting multidisciplinary research in neuroscience. BMC Med Inform Decis Mak 2012, 12:115.
-
(2012)
BMC Med Inform Decis Mak
, vol.12
, pp. 115
-
-
Corradi, L.1
Porro, I.2
Schenone, A.3
Momeni, P.4
Ferrari, R.5
Nobili, F.6
Ferrara, M.7
Arnulfo, G.8
Fato, M.M.9
-
33
-
-
84989313026
-
-
JSON (JavaScript Object Notation). [http://www.json.org/].
-
-
-
-
34
-
-
84989342245
-
-
MyBatis. [https://code.google.com/p/mybatis/].
-
-
-
-
35
-
-
62149144693
-
Beyond the Data Deluge
-
Bell G, Hey T: Beyond the Data Deluge. Science 2009, 323:1297-1298.
-
(2009)
Science
, vol.323
, pp. 1297-1298
-
-
Bell, G.1
Hey, T.2
-
36
-
-
84989335190
-
-
DNA Sequencing Cost. [http://www.genome.gov/sequencingcosts/].
-
-
-
-
37
-
-
84989342248
-
-
iRODS. [https://www.irods.org].
-
-
-
-
38
-
-
84989300544
-
-
jQuery.dForm. [http://daffl.github.io/jquery.dform/].
-
-
-
-
39
-
-
34547830867
-
Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks
-
Lim WK, Wang K, Lefebvre C, Califano A: Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks. Bioinformatics 2007, 23:i282-i288.
-
(2007)
Bioinformatics
, vol.23
, pp. i282-i288
-
-
Lim, W.K.1
Wang, K.2
Lefebvre, C.3
Califano, A.4
-
40
-
-
57449089331
-
A Web-based and Gridenabled dChip version for the analysis of large sets of gene expression data
-
Corradi L, Fato M, Porro I, Scaglione S, Torterolo L: A Web-based and Gridenabled dChip version for the analysis of large sets of gene expression data. BMC Bioinformatics 2008, 9:480.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 480
-
-
Corradi, L.1
Fato, M.2
Porro, I.3
Scaglione, S.4
Torterolo, L.5
-
41
-
-
84864951415
-
Design of a multi-signature ensemble classifier predicting neuroblastoma patients' outcome
-
Cornero A, Acquaviva M, Fardin P, Versteeg R, Schramm A, Eva A, Bosco MC, Blengio F, Barzaghi S, Varesio L: Design of a multi-signature ensemble classifier predicting neuroblastoma patients' outcome. BMC Bioinformatics 2012, 13(Suppl 4):S13.
-
(2012)
BMC Bioinformatics
, vol.13
, pp. S13
-
-
Cornero, A.1
Acquaviva, M.2
Fardin, P.3
Versteeg, R.4
Schramm, A.5
Eva, A.6
Bosco, M.C.7
Blengio, F.8
Barzaghi, S.9
Varesio, L.10
-
42
-
-
84887170976
-
Logic Learning Machine creates explicit and stable rules stratifying neuroblastoma patients
-
Cangelosi D, Blengio F, Versteeg R, Eggert A, Garaventa A, Gambini C, Conte M, Eva A, Muselli M, Varesio L: Logic Learning Machine creates explicit and stable rules stratifying neuroblastoma patients. BMC Bioinformatics 2013, 14:S12.
-
(2013)
BMC Bioinformatics
, vol.14
, pp. S12
-
-
Cangelosi, D.1
Blengio, F.2
Versteeg, R.3
Eggert, A.4
Garaventa, A.5
Gambini, C.6
Conte, M.7
Eva, A.8
Muselli, M.9
Varesio, L.10
-
43
-
-
33845643077
-
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB
-
Rayner TF, Rocca-Serra P, Spellman PT, Causton HC, Farne A, Holloway E, Irizarry RA, Liu J, Maier DS, Miller M, et al: A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. BMC Bioinformatics 2006, 7:489.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 489
-
-
Rayner, T.F.1
Rocca-Serra, P.2
Spellman, P.T.3
Causton, H.C.4
Farne, A.5
Holloway, E.6
Irizarry, R.A.7
Liu, J.8
Maier, D.S.9
Miller, M.10
-
44
-
-
84989326590
-
-
JIBX. [http://jibx.sourceforge.net/].
-
-
-
-
45
-
-
80052579099
-
Implementing a genomic data management system using iRODS in the Wellcome Trust Sanger Institute
-
Chiang GT, Clapham P, Qi G, Sale K, Coates G: Implementing a genomic data management system using iRODS in the Wellcome Trust Sanger Institute. BMC Bioinformatics 2011, 12:361.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 361
-
-
Chiang, G.T.1
Clapham, P.2
Qi, G.3
Sale, K.4
Coates, G.5
-
46
-
-
84865360567
-
Solutions for biomedical grid computing-Case studies from the D-Grid project Services-MediGRID
-
Dickmann F, Falkner J, Gunia W, Hampe J, Hausmann M, Herrmann A, Kepper N, Knoch TA, Lauterbach S, Lippert J, et al: Solutions for biomedical grid computing-Case studies from the D-Grid project Services-MediGRID. Journal of Computational Science 2012, 3:280-297.
-
(2012)
Journal of Computational Science
, vol.3
, pp. 280-297
-
-
Dickmann, F.1
Falkner, J.2
Gunia, W.3
Hampe, J.4
Hausmann, M.5
Herrmann, A.6
Kepper, N.7
Knoch, T.A.8
Lauterbach, S.9
Lippert, J.10
-
47
-
-
80052821984
-
Science friction: data, metadata, and collaboration
-
Edwards PN, Mayernik MS, Batcheller AL, Bowker GC, Borgman CL: Science friction: data, metadata, and collaboration. Soc Stud Sci 2011, 41:667-690.
-
(2011)
Soc Stud Sci
, vol.41
, pp. 667-690
-
-
Edwards, P.N.1
Mayernik, M.S.2
Batcheller, A.L.3
Bowker, G.C.4
Borgman, C.L.5
|