Page-Om Equivalent For Snps

Question

[User 6659]

Hello

Are there any object models for storing information about SNPs and their annotations i.e. something equivalent to PAGE-OM that was designed for genotype to phenotype experiments for SNPs?

thanks

Answer 1

[Pierre Lindenbaum]

I know the NCBI model: ftp://ftp.ncbi.nlm.nih.gov/snp/specs/docsum_3.1.xsd

To store such information I would use RDF (but would it scale ?) or a document- oriented database (couchdb, mongodb etc... )

UPDATE: FLEXIBILITY: i would use a document oriented software because for such a database, your schema will change every time (new annotations, new way to structure your data...). For example it will be far more easier/straightforward to store your data as JSON like

{
"name":"rs25",
"mapping":
  [
  {
  build:"build36",
  positions:[{"chromosome":"chr1",position:987987},{"chromosome":"chr2",position:9879}]
  },
  {
  build:"build37",
  positions:[{"chromosome":"chr1",position:987997},{"chromosome":"chr2",position:9869}]
  }
  ],
comments:[{"autor":"pierre","date":"2011-02-28","text":"Hello world"}]
}

instead of creating... how many SQL tables?

••RDF**: is a way to store your object as a set of triples: subject/predicate/object.

You can start by storing it using JENA or another simple RDF datastore and querying it using SPARQL. However, as I said before, i don't know if it would be a suitable way to store something like dbSNP.

[User 6659]

I've never used RDF. Presumably an RDF schema can be mapped to a relational database? why would you consider a document oriented database? i know in gwas there are lots of documents you might want to store but not so much in snp annotation. What documents could there be?

[Pierre Lindenbaum]

JENA, the RDF library for Java stores the RDF triples in a relational database. However trying to transform the content of a RDF documents to a set of classes/tables wouldn't have much interest.

Answer 2

[Andrea_Bio]

Much of the PAGE-OM model is suitable for the information you require. It has classes to store variants, alleles, their genomic locations and their effects upon transcripts and translations. It also has classes to model the effect on protein function.

You may also want to look at

1. the recommendations of the Human Variome project
2. Polymorphism Markup Language
3. Variation Ontology (VariO) and VarioML
4. The Gen2Phen project and their working documents