-
1
-
-
33751430005
-
An agent- and ontology-based system for integrating public gene, protein, and disease databases
-
DOI 10.1016/j.jbi.2006.02.014, PII S1532046406000323
-
Alonso-Calvo, R., Maojo, V., Billhardt, H., Martin-Sanchez, F., Garca-Remesal, M. and Prez-Rey, D. (2007) 'An agent-and ontology-based system for integrating public gene, protein, and disease databases', Journal of Biomedical Informatics, Vol. 40, No. 1, pp. 17-29. (Pubitemid 44821016)
-
(2007)
Journal of Biomedical Informatics
, vol.40
, Issue.1
, pp. 17-29
-
-
Alonso-Calvo, R.1
Maojo, V.2
Billhardt, H.3
Martin-Sanchez, F.4
Garcia-Remesal, M.5
Perez-Rey, D.6
-
2
-
-
0025183708
-
Basic local alignment search tool
-
Altschul, S. F., Gish, W., Miller, W., Myers, E. W. and Lipman, D. J. (1990) 'Basic local alignment search tool', J. Mol. Biol., Vol. 215, pp. 403-410.
-
(1990)
J. Mol. Biol.
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
3
-
-
21944445759
-
An ontology for cell types
-
Bard, J., Rhee, S. Y. and Ashburner, M. (2005) 'An ontology for cell types', Genome Biol, Vol. 6, No. 2, p. R21, [http://dx.doi.org/10.1186/gb-2005- 6-2-r21].
-
(2005)
Genome Biol
, vol.6
, Issue.2
-
-
Bard, J.1
Rhee, S.Y.2
Ashburner, M.3
-
4
-
-
58149187893
-
The GOA database in 2009 - An integrated gene ontology annotation resource
-
Barrell, D., Dimmer, E., Huntley, R. P., Binns, D., O'Donovan, C. and Apweiler, R. (2009) 'The GOA database in 2009 - an integrated Gene Ontology Annotation resource', Nucleic Acids Research, Vol. 37, pp. D396-D403.
-
(2009)
Nucleic Acids Research
, vol.37
-
-
Barrell, D.1
Dimmer, E.2
Huntley, R.P.3
Binns, D.4
O'Donovan, C.5
Apweiler, R.6
-
5
-
-
38549164691
-
GenBank
-
DOI 10.1093/nar/gkm929
-
Benson, D. A., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J. and Wheeler, D. L. (2008) 'GenBank', Nucleic Acids Res., Vol. 36, Database issue, pp. D25-D30, Epub 2007 December 11. (Pubitemid 351149691)
-
(2008)
Nucleic Acids Research
, vol.36
, Issue.SUPPL. 1
-
-
Benson, D.A.1
Karsch-Mizrachi, I.2
Lipman, D.J.3
Ostell, J.4
Wheeler, D.L.5
-
6
-
-
0017411710
-
The protein data bank: A computer based archival file for macromolecular structures
-
Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer Jr., E. F., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T. and Tasumi, M. (1977) 'The protein data bank: a computer-based archival file for macromolecular structures', J. Mol. Biol., Vol. 112, pp. 535-542. (Pubitemid 8109216)
-
(1977)
Journal of Molecular Biology
, vol.112
, Issue.3
, pp. 535-542
-
-
Bernstein, F.C.1
Koetzle, T.F.2
Williams, G.J.B.3
-
7
-
-
33646256547
-
Beyond the data deluge: Data integration and bio-ontologies
-
Epub 2006 February 21
-
Blake, J. A. and Bult, C. J. (2006) 'Beyond the data deluge: data integration and bio-ontologies', J. Biomed. Inform., Vol. 39, No. 3, pp. 314-20, Epub 2006 February 21.
-
(2006)
J. Biomed. Inform.
, vol.39
, Issue.3
, pp. 314-320
-
-
Blake, J.A.1
Bult, C.J.2
-
8
-
-
77954520814
-
SNPRanker: A tool for identification and scoring of SNPs associated to target genes
-
doi: 10.2390/biecoll-jib-2010-138. PMID: 20375450
-
Calabria, A., Mosca, E., Viti, F., Merelli, I. and Milanesi, L. (2010) 'SNPRanker: a tool for identification and scoring of SNPs associated to target genes', J. Integr. Bioinform., Vol. 7, No. 3, doi: 10.2390/biecoll-jib-2010-138. PMID: 20375450.
-
(2010)
J. Integr. Bioinform.
, vol.7
, Issue.3
-
-
Calabria, A.1
Mosca, E.2
Viti, F.3
Merelli, I.4
Milanesi, L.5
-
9
-
-
58149185126
-
BRENDA, AMENDA and FRENDA the enzyme information system: New content and tools in 2009
-
Database issue
-
Chang, A., Scheer, M., Grote, A., Schomburg, I. and Schomburg, D. (2009) 'BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009', Nucleic Acids Res., Vol. 37, Database issue, pp. D588-D592 [http://dx.doi.org/10.1093/nar/gkn820].
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Chang, A.1
Scheer, M.2
Grote, A.3
Schomburg, I.4
Schomburg, D.5
-
10
-
-
44949099405
-
Similar genes discovery system (SGDS): Application for predicting possible pathways by using GO semantic similarity measure
-
Chiang, J. H., Ho, S. H. and Wang, W. H. (2008) 'Similar genes discovery system (SGDS): Application for predicting possible pathways by using GO semantic similarity measure', Expert Systems with Applications, Vol. 35, No. 3, pp. 1115-1121.
-
(2008)
Expert Systems with Applications
, vol.35
, Issue.3
, pp. 1115-1121
-
-
Chiang, J.H.1
Ho, S.H.2
Wang, W.H.3
-
11
-
-
33645348241
-
The ontology lookup service, a lightweight cross-platform tool for controlled vocabulary queries
-
Cote, R. G., Jones, P., Apweiler, R. and Hermjakob, H., (2006) 'The ontology lookup service, a lightweight cross-platform tool for controlled vocabulary queries', BMC Bioinformatics, Vol. 7, No. 1, p. 97.
-
(2006)
BMC Bioinformatics
, vol.7
, Issue.1
, pp. 97
-
-
Cote, R.G.1
Jones, P.2
Apweiler, R.3
Hermjakob, H.4
-
12
-
-
33847103869
-
Measuring semantic similarity between Gene Ontology terms
-
DOI 10.1016/j.datak.2006.05.003, PII S0169023X06000875, Business Process Management Where business processes and web services meet
-
Couto, F. M., Silva, M. J. and Coutinho, P. M. (2007) 'Measuring semantic similarity between Gene Ontology terms', Data and Knowledge Engineering, Vol. 61, No. 1, pp. 137-152. (Pubitemid 46282157)
-
(2007)
Data and Knowledge Engineering
, vol.61
, Issue.1
, pp. 137-152
-
-
Couto, F.M.1
Silva, M.J.2
Coutinho, P.M.3
-
13
-
-
80052905398
-
Exploitation of a 3D-oriented ontology for choosing the representative proteins in protein surfaces comparison
-
2010 INRIA Sophia Antipolis - Méditerranée, France
-
Cozzi, P., Viti, F., Merelli, I. and Milanesi, L. (2010) 'Exploitation of a 3D-oriented ontology for choosing the representative proteins in protein surfaces comparison', FOCUS K3D Conference on Semantic 3D Media and Content 11th and 12th February, 2010 INRIA Sophia Antipolis - Méditerranée, France.
-
(2010)
FOCUS K3D Conference on Semantic 3D Media and Content 11th and 12th February
-
-
Cozzi, P.1
Viti, F.2
Merelli, I.3
Milanesi, L.4
-
14
-
-
38349071755
-
Toward an ontological database for subcellular neuroanatomy
-
Gupta, A., Larson, S. D., Condit, C., Gupta, S., Fong, L., Chen, L. and Martone, M. E. (2007) 'Toward an ontological database for subcellular neuroanatomy', Advances in Conceptual Modeling - Foundations and Applications, Lecture Notes in Computer Science, Vol. 4802, pp. 64-73.
-
(2007)
Advances in Conceptual Modeling - Foundations and Applications, Lecture Notes in Computer Science
, vol.4802
, pp. 64-73
-
-
Gupta, A.1
Larson, S.D.2
Condit, C.3
Gupta, S.4
Fong, L.5
Chen, L.6
Martone, M.E.7
-
15
-
-
38549107891
-
The 20 years of PROSITE
-
DOI 10.1093/nar/gkm977
-
Hulo, N., Bairoch, A., Bulliard, V., Cerutti, L., Cuche, B., De Castro, E., Lachaize, C., Langendijk-Genevaux, P. S. and Sigrist, C. J. A. (2007) 'The 20 years of PROSITE', Nucleic Acids Res., Vol. 36, Database issue, pp. D245-D249. (Pubitemid 351149730)
-
(2008)
Nucleic Acids Research
, vol.36
, Issue.SUPPL. 1
-
-
Hulo, N.1
Bairoch, A.2
Bulliard, V.3
Cerutti, L.4
Cuche, B.A.5
De Castro, E.6
Lachaize, C.7
Langendijk-Genevaux, P.S.8
Sigrist, C.J.A.9
-
17
-
-
73949108731
-
Annotating breast cancer microarray samples using ontologies
-
Liu, H., Li, X., Yoon, V. and Clarke, R. (2008) 'Annotating breast cancer microarray samples using ontologies', AMIA Annu. Symp. Proc., Vol. 6, pp. 414-418.
-
(2008)
AMIA Annu. Symp. Proc.
, vol.6
, pp. 414-418
-
-
Liu, H.1
Li, X.2
Yoon, V.3
Clarke, R.4
-
18
-
-
80052875954
-
Imagebased surface matching algorithm oriented to structural biology
-
23 March, IEEE computer Society Digital Library
-
Merelli, I., Cozzi, P., D'Agostino, D., Clematis, A. and Milanesi, L. (2010) 'Imagebased surface matching algorithm oriented to structural biology', IEEE/ACM Transactions on Computational Biology and Bioinformatics, 23 March, IEEE computer Society Digital Library.
-
(2010)
IEEE/ACM Transactions on Computational Biology and Bioinformatics
-
-
Merelli, I.1
Cozzi, P.2
D'Agostino, D.3
Clematis, A.4
Milanesi, L.5
-
19
-
-
84935851696
-
Nervous system database (NSD): Data integration spanning molecular and system levels
-
Pilsen, Czech Republic, doi: 10.3389/conf.neuro.11.2009.08.121
-
Mosca, E., Alfieri, R., Viti F., Merelli, I. and Milanesi, L. (2009) 'Nervous System Database (NSD): data integration spanning molecular and system levels', Frontiers in Neuroinformatics. Conference Abstract: 2nd INCF Congress of Neuroinformatics, Pilsen, Czech Republic, doi: 10.3389/conf.neuro.11.2009.08. 121.
-
(2009)
Frontiers in Neuroinformatics. Conference Abstract: 2nd INCF Congress of Neuroinformatics
-
-
Mosca, E.1
Alfieri, R.2
Viti, F.3
Merelli, I.4
Milanesi, L.5
-
20
-
-
77953015096
-
A multilevel data integration resource for breast cancer study
-
Mosca, E., Alfieri, R., Merelli, I., Viti, F., Calabria, A. and Milanesi, L. (2010) 'A multilevel data integration resource for breast cancer study', BMC Syst Biol., Vol. 3, No. 4, p. 76.
-
(2010)
BMC Syst Biol.
, vol.3
, Issue.4
, pp. 76
-
-
Mosca, E.1
Alfieri, R.2
Merelli, I.3
Viti, F.4
Calabria, A.5
Milanesi, L.6
-
21
-
-
38449100150
-
Framework for a protein ontology
-
doi:10.1186/1471-2105-8-S9-S1
-
Natale, D. A., Arighi, C. N., Barker, W. C., Blake, J., Chang, T. C., Hu, Z., Liu, H., Smith, B. and Wu, C. H. (2007) 'Framework for a protein ontology', BMC Bioinformatics, Vol. 8, Suppl. 9, p. S1, doi:10.1186/1471-2105-8-S9-S1.
-
(2007)
BMC Bioinformatics
, vol.8
, Issue.9 SUPPL.
-
-
Natale, D.A.1
Arighi, C.N.2
Barker, W.C.3
Blake, J.4
Chang, T.C.5
Hu, Z.6
Liu, H.7
Smith, B.8
Wu, C.H.9
-
22
-
-
29444448122
-
The MeSH translation maintenance system: Structure, interface design, and implementation
-
7-11 September, San Francisco, CA
-
Nelson, S. J., Schopen, M., Savage, A. G., Schulman, J. L. and Arluk, N. (2004) 'The MeSH translation maintenance system: structure, interface design, and implementation', Proceedings of the 11th World Congress on Medical Informatics, 7-11 September, San Francisco, CA.
-
(2004)
Proceedings of the 11th World Congress on Medical Informatics
-
-
Nelson, S.J.1
Schopen, M.2
Savage, A.G.3
Schulman, J.L.4
Arluk, N.5
-
23
-
-
66349110163
-
Annotating the human genome with disease ontology
-
Osborne, J. D., Flatow, J., Holko, M., Lin, S. M., Kibbe, W. A., Zhu, L. J., Danila, M. I., Feng, G. and Chisholm, R. L. (2009) 'Annotating the human genome with disease ontology', BMC Genomics, Vol. 10, Suppl. 1, p. S6, [http://dx.doi.org/10.1186/1471-2164-10-S1-S6].
-
(2009)
BMC Genomics
, vol.10
, Issue.1 SUPPL.
-
-
Osborne, J.D.1
Flatow, J.2
Holko, M.3
Lin, S.M.4
Kibbe, W.A.5
Zhu, L.J.6
Danila, M.I.7
Feng, G.8
Chisholm, R.L.9
-
24
-
-
37849039292
-
A genetic similarity algorithm for searching the gene ontology terms and annotating anonymous protein sequences
-
Othman, R. M., Deris, S. and Illias, R. M. (2008) 'A genetic similarity algorithm for searching the Gene Ontology terms and annotating anonymous protein sequences', J. Biomed. Inform., Vol. 41, No. 1, pp. 65-81.
-
(2008)
J. Biomed. Inform.
, vol.41
, Issue.1
, pp. 65-81
-
-
Othman, R.M.1
Deris, S.2
Illias, R.M.3
-
25
-
-
0029948001
-
SSAP: Sequential structure alignment program for protein structure comparison
-
Orengo, C. A. and Taylor, W. R. (1996) 'SSAP: sequential structure alignment program for protein structure comparison', Methods Enzymol., Vol. 266, pp. 617-635.
-
(1996)
Methods Enzymol.
, vol.266
, pp. 617-635
-
-
Orengo, C.A.1
Taylor, W.R.2
-
26
-
-
0030777303
-
CATH - A hierarchic classification of protein domain structures
-
Orengo, C. A., Michie, A. D., Jones, D. T., Swindells, M. B. and Thornton, J. M. (1997) 'CATH: a hierarchic classification of protein domain structures', Structure, Vol. 5, pp. 1093-1108, ISSN: 0969-2126. (Pubitemid 27393093)
-
(1997)
Structure
, vol.5
, Issue.8
, pp. 1093-1108
-
-
Orengo, C.A.1
Michie, A.D.2
Jones, S.3
Jones, D.T.4
Swindells, M.B.5
Thornton, J.M.6
-
27
-
-
33646832869
-
ONTOFUSION: Ontology-based integration of genomic and clinical databases
-
DOI 10.1016/j.compbiomed.2005.02.004, PII S0010482505000740
-
Perez-Rey, D., Maojo, V., Garca-Remesal, M., Alonso-Calvo, R., Billhardt, H., Martin-Snchez, F. and Sousa, A. (2006) 'ONTOFUSION: ontology-based integration of genomic and clinical databases', Computers in Biology and Medicine, Vol. 36, No. 7, pp. 712-730. (Pubitemid 43776527)
-
(2006)
Computers in Biology and Medicine
, vol.36
, Issue.7-8
, pp. 712-730
-
-
Perez-Rey, D.1
Maojo, V.2
Garcia-Remesal, M.3
Alonso-Calvo, R.4
Billhardt, H.5
Martin-Sanchez, F.6
Sousa, A.7
-
28
-
-
0002016474
-
Semantic Similarity in a Taxonomy: An Information-Based Measure and its Application to Problems of Ambiguity in Natural Language
-
Resnik, P. (1999) 'Semantic similarity in a taxonomy: an information-based measure and its application to problems of ambiguity in natural language', Journal of Artificial Intelligence Research, Vol. 11, pp. 95-130. (Pubitemid 129628761)
-
(1999)
Journal of Artificial Intelligence Research
, vol.11
, pp. 95-130
-
-
Resnik, P.1
-
29
-
-
33748335463
-
A new measure for functional similarity of gene products based on gene ontology
-
Schlicker, A., Domingues, F. S., Rahnenfhrer, J. and Lengauer, T. (2006) 'A new measure for functional similarity of gene products based on gene ontology', BMC Bioinformatics, Vol. 7, p. 302.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 302
-
-
Schlicker, A.1
Domingues, F.S.2
Rahnenfhrer, J.3
Lengauer, T.4
-
30
-
-
35948989284
-
The OBO Foundry: Coordinated evolution of ontologies to support biomedical data integration
-
DOI 10.1038/nbt1346, PII NBT1346
-
Smith, B., Ashburner, M., Rosse, C., Bard, J., Bug, W., Ceusters, W., Goldberg, L. J., Eilbeck, K., Ireland, A., Mungall, C. J., The OBI Consortium, Leontis, N., Rocca-Serra, P., Ruttenberg, A., Sansone, S. A., Scheuermann, R. H., Shah, N., Whetzel, P. L. and Lewis, S. (2007) 'The OBO foundry: coordinated evolution of ontologies to support biomedical data integration', Nature Biotechnology, Vol. 25, pp. 1251-1255, Publushed online: 7 November 2007|doi:10.1038/nbt1346. (Pubitemid 350076511)
-
(2007)
Nature Biotechnology
, 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
Eilbeck, K.8
Ireland, A.9
Mungall, C.J.10
Leontis, N.11
Rocca-Serra, P.12
Ruttenberg, A.13
Sansone, S.-A.14
Scheuermann, R.H.15
Shah, N.16
Whetzel, P.L.17
Lewis, S.18
-
31
-
-
68249085263
-
The gene ontology's referencegenome project: A unified frame work for functional annotation across species
-
The Gene Ontology Consortium
-
The Gene Ontology Consortium (2009) 'The gene ontology's referencegenome project: A unified frame work for functional annotation across species', PLoS Comput Biol, Vol. 5, No. 7, p. e1000431.
-
(2009)
PLoS Comput Biol
, vol.5
, Issue.7
-
-
-
32
-
-
44649133998
-
Ontology-based, tissue microArray oriented, image centered tissue bank
-
PMID: 18460177
-
Viti, F., Merelli, I., Caprera, A., Lazzari, B., Stella, A. and Milanesi, L. (2008) 'Ontology-based, tissue microArray oriented, image centered tissue bank', BMC Bioinformatics, Vol. 9, Suppl. 4, p. S4, PMID: 18460177.
-
(2008)
BMC Bioinformatics
, vol.9
, Issue.4 SUPPL.
-
-
Viti, F.1
Merelli, I.2
Caprera, A.3
Lazzari, B.4
Stella, A.5
Milanesi, L.6
-
33
-
-
34447294237
-
A new method to measure the semantic similarity of GO terms
-
DOI 10.1093/bioinformatics/btm087
-
Wang, J. Z., Du, Z., Payattakool, R., Yu, P. S. and Chen, C. F. (2007) 'A new method to measure the semantic similarity of go terms', Bioinformatics, Vol. 23, No. 10, pp. 1274-1281. (Pubitemid 47050544)
-
(2007)
Bioinformatics
, vol.23
, Issue.10
, pp. 1274-1281
-
-
Wang, J.Z.1
Du, Z.2
Payattakool, R.3
Yu, P.S.4
Chen, C.-F.5
|