Assigning feature relationships in Chado

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Assigning feature relationships in Chado

Akiff Manji
Hi everyone,

I've recently put together a Chado database to store bacterial genome sequences in the form of multi fasta files. I've been using the perl bulk loader scripts (gmod_fasta2gff3.pl gmod_bulkoad_gff3.pl) to upload the sequences to the database. Everything works pretty well and I'm able to tag attributes into the feature property tables. In fact currently we have been using only the feature prop table to assign contigs from an mfasta file to a genome. This essentially creates the same name entry for every single contig we upload for a particular genome.

I realize this is not the approach to be taking, and rather we should be defining relationships according to the RDF model and the feature_relationship table. My question is, how exactly can we add these relationships on the sequence file uploads (ie. without having to later define the relationships with SQL)? What is the usual approach to implementing relationships within the Chado database? Is there a bulk uploader that does this?

Cheers,

Akiff Manji



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Re: Assigning feature relationships in Chado

Scott Cain
Hi Akiff,

Generally, the only relationships that get created automatically by the GFF bulk loader are those that are defined in the GFF file using the Parent and Derives_from tags.  If all you want is a part_of relationship, you could use the Parent tag to make that happen.  If you want something else, you could use a custom tag (whose value would end up in featureprop) and then write a pgsql function to make the changes after the loading is done.  If you have Tripal, it is also possible that you could use the generic table loader in Tripal to do it in one go, but I'm not sure.

Scott



On Mon, May 6, 2013 at 4:48 PM, Akiff Manji <[hidden email]> wrote:
Hi everyone,

I've recently put together a Chado database to store bacterial genome sequences in the form of multi fasta files. I've been using the perl bulk loader scripts (gmod_fasta2gff3.pl gmod_bulkoad_gff3.pl) to upload the sequences to the database. Everything works pretty well and I'm able to tag attributes into the feature property tables. In fact currently we have been using only the feature prop table to assign contigs from an mfasta file to a genome. This essentially creates the same name entry for every single contig we upload for a particular genome.

I realize this is not the approach to be taking, and rather we should be defining relationships according to the RDF model and the feature_relationship table. My question is, how exactly can we add these relationships on the sequence file uploads (ie. without having to later define the relationships with SQL)? What is the usual approach to implementing relationships within the Chado database? Is there a bulk uploader that does this?

Cheers,

Akiff Manji



------------------------------------------------------------------------------
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"Graph Databases" is the definitive new guide to graph databases and
their applications. This 200-page book is written by three acclaimed
leaders in the field. The early access version is available now.
Download your free book today! http://p.sf.net/sfu/neotech_d2d_may
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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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leaders in the field. The early access version is available now.
Download your free book today! http://p.sf.net/sfu/neotech_d2d_may
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Re: Assigning feature relationships in Chado

Akiff Manji
In reply to this post by Akiff Manji

That's perfect.. Solved everything. Btw, really impressed with the prompt responses.

Thanks again for your help

Akiff

On 2013-05-06 2:48 PM, "Akiff Manji" <[hidden email]> wrote:
Hi everyone,

I've recently put together a Chado database to store bacterial genome sequences in the form of multi fasta files. I've been using the perl bulk loader scripts (gmod_fasta2gff3.pl gmod_bulkoad_gff3.pl) to upload the sequences to the database. Everything works pretty well and I'm able to tag attributes into the feature property tables. In fact currently we have been using only the feature prop table to assign contigs from an mfasta file to a genome. This essentially creates the same name entry for every single contig we upload for a particular genome.

I realize this is not the approach to be taking, and rather we should be defining relationships according to the RDF model and the feature_relationship table. My question is, how exactly can we add these relationships on the sequence file uploads (ie. without having to later define the relationships with SQL)? What is the usual approach to implementing relationships within the Chado database? Is there a bulk uploader that does this?

Cheers,

Akiff Manji



------------------------------------------------------------------------------
Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and
their applications. This 200-page book is written by three acclaimed
leaders in the field. The early access version is available now.
Download your free book today! http://p.sf.net/sfu/neotech_d2d_may
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