building an annotation library from scratch
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James F. Reid ▴ 610
@james-f-reid-3148
Last seen 7.1 years ago
Hi Guido, you could create a file containing the microRNA ID and it's corresponding Gene ID (NCBI) and then use SQLForge to create a custom annotation package which would use an organism .db0 package. HTH, J. Hooiveld, Guido wrote: > Dear list, > > Question for the more knowledgable people: > A collegue and I would like to create an annotation library based on the > miRBASE content (for the Affymetrix miRNA array). Luckily miRBASE > provides a dump of their data in MySQL format > (ftp://mirbase.org/pub/mirbase/CURRENT/database_files/). We succeeded in > converting the info into a SQLite format, but are now stuck. > Based on the BioC vignettes, we do know that we somehow have to use the > packages AnnotationDbi and SQLForge, but as far as we are able to > understand the packages use the info available in the corresponding > organism .db0 packages. However, it is not clear to us how now to > continue with the mirna.db SQLite file we created. > Any advice is much appreciated! > > Thanks, > Guido > > Code we used to access the conent of mirna.db within R: > >> conn <- dbConnect("SQLite", dbname = "mirna.db") >> dbListTables(conn) > [1] "dead_mirna" "literature_references" > [3] "mirna" "mirna_2_prefam" > [5] "mirna_chromosome_build" "mirna_context" > [7] "mirna_database_links" "mirna_literature_references" > [9] "mirna_mature" "mirna_pre_mature" > [11] "mirna_prefam" "mirna_species" > [13] "mirna_target_links" "mirna_target_url" > [15] "sqlite_sequence" >> dbListFields(conn, "mirna") > Error in sqliteFetch(res, n = n, ...) : > BLOB column handling not implemented >> dbListFields(conn, "dead_mirna") > [1] "mirna_acc" "mirna_id" "previous_id" "forward_to" "comment" > > > > ------------------------------------------------ > Guido Hooiveld, PhD > Nutrition, Metabolism & Genomics Group > Division of Human Nutrition > Wageningen University > Biotechnion, Bomenweg 2 > NL-6703 HD Wageningen > the Netherlands > tel: (+)31 317 485788 > fax: (+)31 317 483342 > internet: http://nutrigene.4t.com <http: nutrigene.4t.com=""/> > email: guido.hooiveld at wur.nl > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
miRNA Annotation Organism db0 AnnotationDbi microRNA miRNA Annotation Organism db0 • 607 views
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Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 5.1 years ago
United States
Hi Guido, There is a new vignette that has been contributed to AnnotationDbi, that you will want to look at soon (it should appear in a day or two). This vignette will explain in detail how to make custom database schemas. The vignette will be called "NewSchema". Many thanks to Gabor Csardi for the nice write-up on this topic. Marc Hooiveld, Guido wrote: > Dear list, > > Question for the more knowledgable people: > A collegue and I would like to create an annotation library based on the > miRBASE content (for the Affymetrix miRNA array). Luckily miRBASE > provides a dump of their data in MySQL format > (ftp://mirbase.org/pub/mirbase/CURRENT/database_files/). We succeeded in > converting the info into a SQLite format, but are now stuck. > Based on the BioC vignettes, we do know that we somehow have to use the > packages AnnotationDbi and SQLForge, but as far as we are able to > understand the packages use the info available in the corresponding > organism .db0 packages. However, it is not clear to us how now to > continue with the mirna.db SQLite file we created. > Any advice is much appreciated! > > Thanks, > Guido > > Code we used to access the conent of mirna.db within R: > > >> conn <- dbConnect("SQLite", dbname = "mirna.db") >> dbListTables(conn) >> > [1] "dead_mirna" "literature_references" > [3] "mirna" "mirna_2_prefam" > [5] "mirna_chromosome_build" "mirna_context" > [7] "mirna_database_links" "mirna_literature_references" > [9] "mirna_mature" "mirna_pre_mature" > [11] "mirna_prefam" "mirna_species" > [13] "mirna_target_links" "mirna_target_url" > [15] "sqlite_sequence" > >> dbListFields(conn, "mirna") >> > Error in sqliteFetch(res, n = n, ...) : > BLOB column handling not implemented > >> dbListFields(conn, "dead_mirna") >> > [1] "mirna_acc" "mirna_id" "previous_id" "forward_to" "comment" > > > > > ------------------------------------------------ > Guido Hooiveld, PhD > Nutrition, Metabolism & Genomics Group > Division of Human Nutrition > Wageningen University > Biotechnion, Bomenweg 2 > NL-6703 HD Wageningen > the Netherlands > tel: (+)31 317 485788 > fax: (+)31 317 483342 > internet: http://nutrigene.4t.com <http: nutrigene.4t.com=""/> > email: guido.hooiveld at wur.nl > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >
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