building an annotation library from scratch
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Guido Hooiveld ★ 3.0k
@guido-hooiveld-2020
Last seen 1 day ago
Wageningen University, Wageningen, the …
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@wur.nl [[alternative HTML version deleted]]
miRNA Annotation db0 AnnotationDbi miRNA Annotation db0 AnnotationDbi • 608 views
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