Browse > Article
http://dx.doi.org/10.5808/GI.2009.7.4.208

IdMapper: A Java Application for ID Mapping across Multiple Cross-referencing Providers  

Lee, Hoo-Keun (Lee Gil Ya Cancer and Diabetes Institute, Gachon University of Medicine and Science)
Kim, Hyeon-Jin (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)
Abstract
We developed an identifier mapping application for bioinformatics research in Java programming language. It is easy to use and provides many usability functionalities that are expected as essentials for a professional application. It supports three widely used mapping services and can convert many ids from one source database into many target databases at once. Id mapping across service providers is possible by remapping the resultant ids. Because it adheres to the NetBeans platform architecture, it can be incorporated into other NetBeans platform applications as an id mapping provider without adaption or modification.
Keywords
ID mapping; java; netbeans; rich client; web services;
Citations & Related Records
Times Cited By KSCI : 2  (Citation Analysis)
연도 인용수 순위
1 Alibes, A., Yankilevich, P., Ca\tilde{n}ada, A., and Díaz-Uriarte, R. (2007). IDconverter and ICDlight: Convertsion and annotation of gene and protein IDs. BMC Bioinformatics 8, 9   DOI   PUBMED
2 BioClipse. http://www.bioclipse.net.
3 Cote, R.G., Jones, P., Martens, L., Kerrien, S., Reisinger, F., Lin, Q., Leinonen, R., Apweiler, R., and Jermjakob, H. (2007). The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases. BMC Bioinformatics 8, 401   DOI   PUBMED
4 InstantJChem. http://www.chemaxon.com/instantjchem/
5 JAX-WS. https://jax-ws.dev.java.net/
6 Kim, C., Choi, J., and Yoon, S. (2008). Microarray data analysis of perturbed pathways in breast cancer tissues. Genomics & Informatics 6, 210-222   DOI
7 NetBeans Platform. http://platform.netbeans.org
8 Pruitt, K.D., Tatusova, T., and Maglott, D.R. (2007). NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucl. Acids Res. 35, D61-65   DOI   ScienceOn
9 Sun Java. http://java.sun.com
10 ChipInspector. http://www.genomatix.de/products/ChipInspector/index.html
11 Quantitative Biology Tool. http://www.semanticbits.com/what_ we_do/software_solutions/qbt.php
12 The Uniprot Consortium (2008). The universal protein resource (UniProt). Nucl. Acids Res. 36, D190-195   DOI   ScienceOn
13 BridgeDb. http://www.bridgedb.org
14 SwingLabs. http://swinglabs.org
15 Huang, D.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   PUBMED
16 Bussey, K.J., Kane, D., Sunshine, M., Narasimhan, S., Nishizuka, S., Reinhold, W.C., Zeeberg, B., Ajay, W., and Weinstein, J.N. (2003). MatchMiner: a tool for batch navigation among gene and gene product identifiers. Genome Biology 4, R27   DOI   PUBMED
17 Kim, K., Chung, H., Jeung, H., Shin, J., Kim, T., and Rha, S. (2006). Significant gene selection using integrated microarray data set with batch effect. Genomics & Informatics 4, 103-109
18 Povey, S., Lovering, R., Bruford, E., Wright, M., Lush,M., and Wain, H. (2001). The HUGO Gene Nomenclature Committee (HGNC). Hum. Genet. 109, 678-680   DOI   ScienceOn
19 Flicek, P., Aken, B.L., Beal, K., Ballester, B., Caccamo, M., Chen, Y., Clarke, L., Coates, G., Cunningham, F., Cutts, T., Down, T., Dyer, S.C., Eyre, T., Fitzgerald, S., Fernandez-Banet, J., Gräf, S., Haider, S., Hammond, M., Holland, R., Howe, K.L., Howe, K., Johnson, N., Jenkinson, A., K\ddot{a}h\ddot{a}ri, A., Keefe, D., Kokocinski, F., Kulesha, E., Lawson, D., Longden, I., Megy, K., Meidl, P., Overduin, B., Parker, A., Pritchard, B., Prlic, A., Rice, S., Rios, D., Schuster, M., Sealy, I., Slater, G., Smedley, D., Spudich, G., Trevanion, S., Vilella, A.J., Vogel, J., White, S., Wood, M., Birney, E., Cox, T., Curwen, V., Durbin, R., Fernandez-Suarez, X.M., Herrero, J., Hubbard, T.J.P., Kasprzyk, A., Proctor, G., Smith, J., Ureta-Vidal, A., and Searle, S. (2008). Ensembl 2008. Nucl. Acids Res. 36, D707-714   DOI   ScienceOn
20 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
21 SpectraSuite. http://www.oceanoptics.com/Products/spectrasuite. asp
22 Smedley, D., Haider, S., Ballester, B., Holland, R., London, D., Thorisson, G., and Kasprzyk, A. (2009). BioMart-biological queries made easy. BMC Genomics 10, 22   DOI   PUBMED   ScienceOn
23 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. Nucl. Acids Res. 34, W626-W631   DOI   PUBMED   ScienceOn
24 Waegele B., Dunger-Kaltenbach I., Fobo G., Montrone C., Mewes, H.W., and Ruepp, A. (2009). CRONOS: the crossreference navigation server. Bioinformatics 25, 141-143   DOI   ScienceOn