Bio-medical Ontologies Maintenance and Change Management

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50 E. De Francesco et al. In Figure 7, an example of the synthetic description we adopted is illustrated. In particular, a form is exploited where both the acronym and the full name of the database under analysis are showed. We consider the CryptoDB [35] (Cryptosporidium Genome Resources) database, that is, the genome database of the AIDS-related apicomplexan-parasite, as reported in the brief description below the full name in the form. Also the web-link to the considered database is provided, along with its database features. In particular, CryptoDB is a relational DBMS based on the Genomic Unified Schema (illustrated above, in Section 2.2). All features corresponding to the other analysis criteria are reported. In detail, we highlight that CryptoDB contains information on genes, clone/contig sequences, polymorphism and motifs, and that it stores physical maps, pathways and bibliographic references as well. It supports simple queries and also analysis queries based on similarity search, and allows graphical interaction and sequence based query methods. Additional information are contained in the form about the search criteria supported by each database. In particular, CryptoDB can be queried by using both keywords and map positions as search parameters (map positions require the specification of the positions of chromosomic regions). The result formats supported by CryptoDB are HTML (as all the other genomic databases), FASTA and tab-separated files. It allows the user to download data stored in its repository, but not to submit new data, as specified in the last two field (“submit” and “download”) of the form. 3 Concluding Remarks In this chapter we presented the main results of an analysis we have conducted on 74 genomic databases. Such an analysis has been done mainly focusing on a database technology point of view, by choosing five specific criteria under which all the considered databases have been investigated. Thus, the considered databases have been classified according to such criteria and their synthetic descriptions are given, with the aim of providing a preliminary instrument to access and manage more easily the enormous amount of data coming from the biological repositories. References 1. ArkDB, http://www.thearkdb.org/arkdb//index.jsp 2. AureoList, http://genolist.pasteur.fr/AureoList 3. BeetleBase, http://www.bioinformatics.ksu.edu/BeetleBase 4. Biocyc website, http://biocyc.org 5. Bovilist world-wide web server, http://genolist.pasteur.fr/BoviList 6. Candidadb: Database dedicated to the analysis of the genome of the human fungal pathogen, candida albicans, http://genolist.pasteur.fr/CandidaDB 7. Central aspergilus data repository, www.cadre.man.ac.uk 8. Chado: The gmod database schema, http://www.gmod.org/chado
A Summary of Genomic Databases: Overview and Discussion 51 9. ColiBase, http://colibase.bham.ac.uk 10. Drugbank database, http://redpoll.pharmacy.ualber-ta.ca/drugbank 11. EcoCyc website, http://ecocyc.org 12. Emblnucl.seq.dbstatistics,http://www3.ebi.ac.uk/Services/DBStats 13. Ensembl, www.ensembl.org 14. From sequence to function, an introduction to the kegg project, http://www.genome.jp/kegg/docs/intro.html 15. Graingenes: a database for triticeae and avena, http://wheat.pw.usda.gov/GG2/index.shtm 16. Gus: The gen. unified schema docum, http://www.gusdb.org/documentation.php 17. Hcv polyorotein, http://hepatitis.ibcp.fr/ 18. HumanCyc website, http://humancyc.org 19. LegioList, http://genolist.pasteur.fr/LegioList 20. Leproma, http://genolist.pasteur.fr/Leproma 21. Photolist, http://genolist.pasteur.fr/PhotoList 22. Pylorigene, http://genolist.pasteur.fr/PyloriGene 23. Quant. pcr primer db (qppd), http://web.ncifcrf.gov/rtp/gel/primerdb 24. Rice annotation database, http://golgi.gs.dna.affrc.go.jp/SY-1102/rad 25. Streptopneumolist, http://genolist.pasteur.fr/StreptoPneumoList 26. System biology markup language (sbml), http://www.smbl.org 27. Tcruzidb: An integrated trypanosoma cruzi genome resource, http://tcruzidb.org 28. Wormbase: Db on biology and genome of c.elegans, http://www.wormbase.org/ 29. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J.: Basic local alignment search tool. J. of Mol. Biology 215(3), 403–410 (1990) 30. Bahl, A., et al.: Plasmodb: the plasmodium genome resource. a database integrating experimental and computational data. Nucl. Ac. Res. 31(1), 212–215 (2003) 31. Baxevanis, A.D.: The molecular biology database collection: an update compilation of biological database resource. Nucl. Ac. Res. 29(1), 1–10 (2001) 32. Cherry, J.M., Ball, C., Weng, S., Juvik, G., Schmidt, R., Adler, C., Dunn, B., Dwight, S., Riles, L., Mortimer, R.K., Botstein, D. 33. Iragne, F., Beyne, E., Nikolski, M., Sherman, D., Durrens, P., Souciet, J.-L.: Génolevures complete genomes provide data and tools for comparative genomics of hemiascomycetous yeasts. Nucl. Ac. Res. 34(Database issue), D432– D435 (2006) 34. Galperin, M.Y.: The molecular biology database collection: 2007 update. Nucl. Ac. Res. 35(Database issue), D3–D4 (2007) 35. Heiges, M., Wang, H., Robinson, E., Aurrecoechea, C., Gao, X., Kaluskar, N., Rhodes, P., Wang, S., He, C.Z., Su, Y., Miller, J., Kraemer, E., Kissinger, J.C.: Cryptodb: a cryptosporidium bioinformatics resource update. Nucl. Ac. Res. 34(Database issue), D419–D422 (2006) 36. Hucka, M., Finney, A., Sauro, H.M.: The system biology markup language (sbml): a medium for representation and exchange of biochemical network model. Bioinformatics 19(4), 524–531 (2003) 37. Li, L., Paulsen, I.T., Kissinger, J.C., Gajria, B., Roos, D.S.: Toxodb: accessing the toxoplasma gondii genome. Nucl. Ac. Res. 31(1), 234–236 (2003)
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Amandeep S. Sidhu and Tharam S. Dil
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Amandeep S. Sidhu and Tharam S. Dil
Page 5 and 6: Preface The molecular biology commu
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Page 9 and 10: X Contents Mining Clinical, Immunol
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Page 19 and 20: Towards Bioinformatics Resourceomes
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Bio-medical Ontologies Maintenance
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TextToOnto (Maedche and Volz 2001)
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Extraction of Constraints from Biol
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Classifying Patterns in Bioinformat
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Mining Clinical, Immunological, and
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Substructure Analysis of Metabolic
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entry compound relation subtype com
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Running Time 4500 4000 3500 3000 25
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6 Conclusion Substructure Analysis
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266 J.Y. Chen, S. Taduri, and F. Ll
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Completing the Total Wellbeing Puzz
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296 M. Fernandez, M. Villasana, and
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Genetic Algorithm in Ab Initio Prot
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Author Index Apiletti, Daniele 169
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