Question: Page-Om Equivalent For Snps
2
gravatar for User 6659
9.9 years ago by
User 6659970
User 6659970 wrote:

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

model snp • 1.4k views
ADD COMMENTlink written 9.9 years ago by User 6659970
3
gravatar for Pierre Lindenbaum
9.9 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum133k wrote:

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.

ADD COMMENTlink modified 16 months ago by _r_am32k • written 9.9 years ago by Pierre Lindenbaum133k

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?

ADD REPLYlink written 9.9 years ago by User 6659970

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.

ADD REPLYlink written 9.9 years ago by Pierre Lindenbaum133k
1
gravatar for Andrea_Bio
9.8 years ago by
Andrea_Bio2.6k
Andrea_Bio2.6k wrote:

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
ADD COMMENTlink written 9.8 years ago by Andrea_Bio2.6k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1109 users visited in the last hour