I was planning to add XMLRPC resources on biodb2 for UCSC annotations after I finish including ~ 300 pairwise alignments, but not yet. I think we could divide this into two types, MySQL version using public mysql database and Collection version downloaded from UCSC website (.sql and .txt.gz files). For MySQL version, we could identify "type" of table by "desc" SQL syntax and supply convenient method to query/retrieve annotations from public mysql server, just like ensembl module by Jenny. For Collection version, we could download .sql file from web and parse/identify table types, then add AnnotationDB by reading .txt.gz files.
I think I could do the Collection version and add to the biodb2 XMLRPC server. Proposed table will be Gene prediction, Repeats, SNP tables. -- Namshin Kim On Tue, Sep 1, 2009 at 4:01 PM, Christopher Lee <[email protected]> wrote: > > > On Aug 31, 2009, at 7:03 PM, Jenny Qing Qian wrote: > > > As the ensembl database, the ucsc database has various kinds of > > annotation feature tables like exons and genes. I am not sure > > whether they also have a seq_region table. I assume they directly > > map their annotations to their reference genomes, not via > > contigs... If this is the case, then we could just simplify the > > seqregion.py and work out the mapping. Agree? > > > > There is no seqregion table. > > > > Thanks. That helps to simplify the case. If they don't store the > > sequences at contig-level in a separate table, they probably don't > > need a seqregion table for coordinates transformation. > > I'd expect that UCSC would map the Ensembl annotations directly onto > their own assembly (i.e. no more seq_region; "stop the madness!"), and > it sounds like that's what they've actually done. If you can identify > a few candidate tables in their MySQL server that store gene and exon > annotations, we can quickly do an experiment to see how hard it would > be to plug these annotations into Pygr. I bet it'll be > straightforward, and could be good to include in the tutorial. > > -- Chris > > > > --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "pygr-dev" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/pygr-dev?hl=en -~----------~----~----~----~------~----~------~--~---
