IdBean: a Java GUI application for conversion of biological identifiers |
Lee, Sang-Hyuk
(Division of Molecular Life Sciences, Ewha Womans University)
Kim, Bum-Jin (Division of Molecular Life Sciences, Ewha Womans University) Kim, Hyeon-Jin (Department of Radiology, Seoul National University Hospital) Lee, Hook-Eun (Lee Gil Ya Cancer and Diabetes Institute, Gachon University of Medicine and Science) Yu, Ung-Sik (Lee Gil Ya Cancer and Diabetes Institute, Gachon University of Medicine and Science) |
1 | van Iersel, M. P., Kelder, T., Pico, A. R., Hanspers, K., Coort, S., Conklin, B. R. and Evelo, C. (2008) Presenting and exploring biological pathways with PathVisio. BMC Bioinformatics 9, 399. DOI ScienceOn |
2 | Spjuth, O., Alvarsson, J., Berg, A., Eklund, M., Kuhn, S., Masak, C., Torrance, G., Wagener, J., Willighagen, E. L., Steinbeck, C. and Wikberg, J. E. (2009) Bioclipse 2: a scriptable integration platform for the life sciences. BMC Bioinformatics 10, 397. DOI ScienceOn |
3 | Edinburgh Pathway Editor [http://www.bioinformatics.ed. ac.uk/epe/]. |
4 | Instant JChem [http://www.chemaxon.com/products/instantjchem/]. |
5 | Quantitative Biology Tool [http://www.semanticbits.com/ what_we_do/software_solutions/qbt.php]. |
6 | ChipInspector [http://www.genomatix.de/chipinspector.html]. |
7 | Eclipse [http://www.eclipse.org]. |
8 | NetBeans [http://www.netbeans.org]. |
9 | OSGi [http://www.osgi.org]. |
10 | Iragne, F., Barre, A., Goffard, N. and De Daruvar, A. (2004) AliasServer: a web server to handle multiple aliases used to refer to proteins. Bioinformatics 20, 2331-2332. DOI ScienceOn |
11 | Imanishi, T. and Nakaoka, H. (2009) Hyperlink Management System and ID Converter System: enabling maintenance- free hyperlinks among major biological databases. Nucleic. Acids. Res. 37, W17-W22. DOI ScienceOn |
12 | Jackson library [http://jackson.codehaus.org]. |
13 | httpclient Java library [http://hc.apache.org]. |
14 | SwingX library [http://swinglabs.org]. |
15 | Huang, da W., Sherman, B. T., Stephens, R., Baseler, M. W., Lane, H. C. and Lempicki, R. A. (2008) DAVID gene ID conversion tool. Bioinformation 2, 428-430. DOI ScienceOn |
16 | Waegele, B., Dunger-Kaltenbach, I., Fobo, G., Montrone, C., Mewes, H. W. and Ruepp, A. (2009) CRONOS: the cross-reference navigation server. Bioinformatics 25, 141-143. DOI ScienceOn |
17 | Berriz, G. F. and Roth, F. P. (2008) The Synergizer service for translating gene, protein and other biological identifiers. Bioinformatics 24, 2272-2273. DOI ScienceOn |
18 | Alibes, A., Yankilevich, P., Canada, A. and Diaz-Uriarte, R. (2007) IDconverter and IDClight: conversion and annotation of gene and protein Ids. BMC Bioinformatics 8, 9. DOI |
19 | Khatri, P., Desai, V., Tarca, A. L., Sellamuthu, S., Wildman, D. E., Romero, R. and Draghici, S. (2006) New Onto-Tools: Promoter-Express, nsSNPCounter and Onto-Translate. Nucleic. Acids. Res. 34, W626-W631. DOI ScienceOn |
20 | Cote, R. G., Jones, P., Martens, L., Kerrien, S., Reisinger, F., Lin, Q., Leinonen, R., Apweiler, R. and Hermjakob, H. (2007) The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases. BMC Bioinformatics 8, 401. DOI |
21 | Smedley, D., Haider, S., Ballester, B., Holland, R., London, D., Thorisson, G. and Kasprzyk, A. (2009) BioMartbiological queries made easy. BMC Genomics 10, 22. DOI ScienceOn |
22 | Gene Ontology tools [http://www.geneontology.org/GO.tools.shtml]. |
23 | van Iersel, M. P., Pico, A. R., Kelder, T., Gao, J., Ho, I., Hanspers, K., Conklin, B. R. and Evelo, C. T. (2010) The BridgeDB framework: standardized access to gene, protein and metabolite identifier mapping services. BMC Bioinformatics 11, 5. DOI ScienceOn |
24 | Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B. and Ideker, T. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Research 13, 2498-2504. DOI ScienceOn |
25 | The UniProt Consortium (2009) The Universal Protein Resource (UniProt) 2009. Nucleic. Acids. Res. 37, D169-174. DOI |
26 | Hubbard, T. J., Aken, B. L., Ayling, S., Ballester, B., Beal, K., Bragin, E., Brent, S., Chen, Y., Clapham, P., Clarke, L., Coates, G., Fairley, S., Fitzgerald, S., Fernandez-Banet, J., Gordon, L., Graf, S., Haider, S., Hammond, M., Holland, R., Howe, K., Jenkinson, A., Johnson, N., Kahari, A., Keefe, D., Keenan, S., Kinsella, R., Kokocinski, F., Kulesha, E., Lawson, D., Longden, I., Megy, K., Meidl, P., Overduin, B., Parker, A., Pritchard, B., Rios, D., Schuster, M., Slater, G., Smedley, D., Spooner, W., Spudich, G., Trevanion, S., Vilella, A., Vogel, J., White, S., Wilder, S., Zadissa, A., Birney, E., Cunningham, F., Curwen, V., Durbin, R., Fernandez-Suarez, X. M., Herrero, J., Kasprzyk, A., Proctor, G., Smith, J., Searle, S. and Flicek, P. (2009) Ensembl 2009. Nucleic. Acids. Res. 37, D690-697. DOI ScienceOn |
27 | Maglott, D., Ostell, J., Pruitt, K. D. and Tatusova, T. (2007) Entrez Gene: gene-centered information at NCBI. Nucleic. Acids. Res. 35, D26-31. DOI ScienceOn |
28 | Pruitt, K .D., Tatusova, T., Klimke, W. and Maglott, D. R. (2009) NCBI Reference Sequences: current status, policy and new initiatives. Nucleic. Acids. Res. 37, D32-36. DOI ScienceOn |
29 | Bruford, E. A., Lush, M. J., Wright, M. W., Sneddon, T. P., Povey, S. and Birney, E. (2008) The HGNC Database in 2008: a resource for the human genome. Nucleic. Acids. Res. 36, D445-448. |