Linking Linked Data CSHALS2013

Expert Bioinformatics from Bioinformatics Experts

Linking Linked Data

Linked Data to Integrated Data


Put your data on the web make a pretty web site later.


Now we can ask questions like this...

What members of a target pathway are already targeted in other diseases?

Target

PathwayDisease

Protein

Compound

Target Pathway Disease

Chembl Uniprot Reactome OMIM


Because we have lots of data exposed as RDF

Mim:Phenotype

Uniprot:ProteinBioPAX:Protein


What do you do when you have to add data...


Or connect SPARQL endpoints?

RDF != Linked Data


Is your data 5* ?

Linked data is essential to actually connect the semantic web. It is quite easy to do with a little thought, and becomes second nature. Various common sense considerations determine when to make a link and when not to.


Example openflydata to BioCycWhat genes are differentially expressed in the hindgut and are there any pathways associated with those genes?● Use FlyAtlas at openflydata.org for tissue specific expression profiles. ● Use FlyCyc from BioCyc.● Then SPARQL


Problem: Node URIs<http://openflydata.org/id/flyatlas/affyid/1616608_a_at> <http://purl.org/NET/flyatlas/schema#gene> <http://openflydata.org/id/flybase/feature/FBgn0001128> .

<http://biocyc.org/biopax/biopax-level3#UnificationXref202209><http://www.biopax.org/release/biopax-level3.owl#xref><http://biocyc.org/biopax/biopax-level3#Protein202210>

.<http://biocyc.org/biopax/biopax-level3#UnificationXref202209><http://www.biopax.org/release/biopax-level3.owl#db>

FlyCyc.

<http://biocyc.org/biopax/biopax-level3#UnificationXref202209><http://www.biopax.org/release/biopax-level3.owl#id>

FBGN0001128.


CONSTRUCT { ?x

RDFS:seeAlso `bif:sprintf_iri ("http://identifiers.org/flybase/%s", ?id)`

}WHERE { ?x BP:unificationxref ?xref . ?xref BP:id ?id . ?blank BP:db "FlyCyc"^^xsd:string}

Integration Level 1Use Identifiers.org


Integration Level 2 adding property characteristics

BP = <http://www.biopax.org/release/biopax-level3.owl#>

BP:Protein BP:controls BP:Catalysis

BP:Catalysis BP:controls BP:BioChemicalReaction

BP:Protein BP:controls BP:BioChemicalReaction

CONSTRUCT {?x GB:controlledBy ?y }WHERE

{ ?x BP:controls ?catalysis . ?catalysis BP:controls ?y }


Integration Level 3 class subsumption

FlyA = <http://purl.org/NET/flyatlas/schema#>

flywebflyatlas:1616608_a_at a flyatlas:ProbeData

BP = <http://www.biopax.org/release/biopax-level3.owl#>

flyatlas:ProbeData rdfs:subClassOf BP:DNARegion

CONSTRUCT {?x a BP:DNARegion }WHERE

{ ?x a flyatlas:ProbeData }


Connect BiochemicalReactions to Expression Values

SELECT ?name ?id ?meanWHERE{ ?reaction a BP:BiochemicalReaction . ?reaction BP:standardName ?name . ?reaction GB:controlledBy ?protein . ?protein a BP:Protein . ?protein BP:xref ?id . ?probe a BP:DNARegion . ?probe BP:xref ?id . ?probe flyatlas:l_fatbody ?blank . ?blank flyatlas:mean ?mean}LIMIT 5

No Reasoner – just a few SPARQL CONSTRUCTs


Client Architecture


SELECT distinct ?classWHERE{ ?s a ?class . ?s ?p ?o }

>100

chembl:Activitychembl:Assaychembl:AssayCategorychembl:AssayTargetLinkchembl:ChemicalCompoundchembl:DrugTargetchembl:LiteratureCitationdailymed:drugsdrugbank:Drugdrugbank:DrugInteractiondrugbank:EnzymeLinkdrugbank:ExternalIdentifierdrugbank:ExternalLinkdrugbank:LiteratureCitationdrugbank:Moleculedrugbank:OrganismSpeciesdrugbank:Patentdrugbank:ProteinSequencedrugbank:TargetLinkentrez:EnsemblReferenceentrez:Genepdb:Moleculepdb:Structurepubmed:Chemicalpubmed:Citationpubmed:DatabankReference

Vocabularies in Linked DataWhat does the linked data cloud know about Drugs....


Create a tighter more unified “view” under one schema


Unified Vocabulary What does the linked data cloud know about Drugs....


Map Classes and Properties into a single instantiated view


Before Query

SELECT *WHERE{?s drugb:calculatedInChIKey ?inchiD . ?s a drugb:Drug . ?c a Chembl:ChemicalCompund . ?c chembl:standardInChIKey ?inchiC .FILTER regex(?inchiD, ?inchiC)}


After Query

SELECT *where{?s a GB:Drug .?s GB:inchiKey ?inchi . }


Linked Data Architecture


Creating fixed “views” of Linked Data

When the use of integrated data is fixed e.g. an API or application, Linked Data can be expensive:

– Changes to data requires significant recoding

– Multiple Schemas make queries long and inefficient

• A view or middle layer of data used by the API, changes to data are managed by the view and the API is minimally disturbed

– Views are easier to query

– Views are faster to query

• Client gets the best of both worlds a tight view of data for API queries while still having all the advantages of a linked data strategy.


Summary

● Exposing data as RDF does not equal Linked Data● Making data linked is not hard

– Node IRI's– Unifying Classes– Transitive closure of Properties

● A little semantics goes a long way (no reasoner required)● Creating “Views” from one schema to another is not hard.

– But should be easier


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Linking Linked Data CSHALS2013

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