Integrative Bioinformatics: How To Integrate My Queries?

Question

[Chong Tang]

Hey guys!

Just a newbie in bioinformatics. I have a problem about integrative bioinformatics: how to combine those database to make my queries more efficiency?

Is there any browser or interface which can help me to search multiple databases while only input one query?

[Sean Davis]

There is no such magic box for all queries for all databases. However, if you let us know which databases and which queries, it will make it easier to know what to say.

[Chong Tang]

Haha. I think you are right. I just want to know if there's any useful search engine to combine search. It's just my thoughts. Thank you!

[gabanyi]

You can give our data aggregation website a try, thought we limit ourselves to proteins that have been structurally determined (or are in the process of being so). http://sbkb.org

One query (sequence for example), and it returns descriptors or links or both. Good luck!

Answer 1

[Pierre Lindenbaum]

As Sean said, there is no such magic box for all queries for all databases, nevertheless you could have a look at bio2rdf to get an idea of what is a Integrative database.

http://www.ncbi.nlm.nih.gov/pubmed/18472304

J Biomed Inform. 2008 Oct;41(5):706-16. doi: 10.1016/j.jbi.2008.03.004.

Bio2RDF: towards a mashup to build bioinformatics knowledge systems.

Belleau F, Nolin MA, Tourigny N, Rigault P, Morissette J.

or look at the tools provided by the NCBI http://www.ncbi.nlm.nih.gov/books/NBK25500/

[kanwarjag]

Looks like a question from a pure biologist. We face this magic question all the time. Still lot of investigators (folks) think bioinformatics is nothing just put is your list in computer and it will make nice figures for your Nature paper. Sean is right No magic box sorry

[DG]

Luckily enough biologists know it isn't simple, so they continue to hire bioinformaticians in their departments :)

[Chong Tang]

Thank you. Just learnt something about RDF this semester. Now I'll read for more things about it this summer. Thank you!

Answer 2

[Michael Schubert]

Bio2rdf is good when you want to integrate your own database with other databases that have got an rdf interface.

If you just want to combine different databases in specific queries take a look at http://www.ebi.ac.uk/rdf/ - they have got SPARQL endpoints for 6 major databases, with examples on how to query them.

Jupp S et al. The EBI RDF Platform: Linked Open Data for the Life Sciences. Bioinformatics (2014).

RDF is an emerging technology for describing, publishing and linking life science data. As a major provider of bioinformatics data and services, the European Bioinformatics Institute (EBI) is committed to making data readily accessible to the community in ways that meet existing demand. The EBI RDF platform has been developed to meet an increasing demand to coordinate RDF activities across the institute and provides a new entry point to querying and exploring integrated resources available at the EBI.

e.g.

Query 4 **Show expression for ENSG00000129991 (TNNI3) with its GO annotations from Uniprot (Federated query to http://beta.sparql.uniprot.org/sparql)**

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX obo: <http://purl.obolibrary.org/obo/>
PREFIX sio: <http://semanticscience.org/resource/>
PREFIX efo: <http://www.ebi.ac.uk/efo/>
PREFIX atlas: <http://rdf.ebi.ac.uk/resource/atlas/>
PREFIX atlasterms: <http://rdf.ebi.ac.uk/terms/atlas/>

PREFIX upc:<http://purl.uniprot.org/core/>
PREFIX identifiers:<http://identifiers.org/ensembl/>

SELECT distinct ?valueLabel ?goid ?golabel 
WHERE { 
?value rdfs:label ?valueLabel .
?value atlasterms:isMeasurementOf ?probe  .
?probe atlasterms:dbXref identifiers:ENSG00000129991  .
?probe atlasterms:dbXref ?uniprot .
SERVICE <http://beta.sparql.uniprot.org/sparql> {   
?uniprot a upc:Protein  .
?uniprot upc:classifiedWith ?keyword  .
?keyword rdfs:seeAlso ?goid  .
?goid rdfs:label ?golabel  .
}   
}

Keep in mind that this is only one example. Check the website for more.

Results are here.