Department of Bioinformatics - BiGCaT

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2 Οκτ 2013 (πριν από 3 χρόνια και 9 μήνες)

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Semantic WikiPathways

Andra Waagmeester

Department of Bioinformatics
-

BiGCaT

2

Overview


Introduction to WikiPathways


GPML


Pathway to RDF conversion


Vocabularies used


Obtaining identifiers URIs pathways and
pathway elements


Example queries


Identifier mapping


Department of Bioinformatics
-

BiGCaT

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WikiPathways


Curated by the community


Built on top of
Mediawiki

framework


Live demo


Department of Bioinformatics
-

BiGCaT

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GPML
-

GenMAPP Pathway Markup
Language


XML
-
based format.


XML representation of GenMAPP MAPP
format


Recognised by WikiPathways, Pathvisio
and Cytoscape




Department of Bioinformatics
-

BiGCaT

5


Department of Bioinformatics
-

BiGCaT

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Pathway to RDF conversion

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-

BiGCaT

7

WP to RDF conversion

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-

BiGCaT

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Vocabularies used


Internal (
vocabularies.wikipathways.org
)


GPML


WP


External


Biopax3


Bibo


Foaf


tbd



Department of Bioinformatics
-

BiGCaT

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Identifiers.org


Providing resolvable persistent URIs.


Based on Miriam
(
http://www.ebi.ac.uk/miriam
)


Textual Pathway identifiers (xrefs)
converted to identifiers.org uri through
the miriam api

Department of Bioinformatics
-

BiGCaT

10

Example query (1)

List pathways and their species

SELECT DISTINCT ?organism ?label

WHERE {


?concept wp:organism ?organism .


?organism rdfs:label ?label .


}


http://sparqlbin.com/#4f91f23a032a87cc46c5a526a6da673a



Department of Bioinformatics
-

BiGCaT

11

Example query (2)

List all datasource currently captured in WikiPathways
and count the number of entries per data source:


SELECT DISTINCT ?datasource count(?datasource) as
?numberEntries

WHERE {


?concept dc:source ?datasource .

}

ORDER BY DESC(?numberEntries)


http://sparqlbin.com/#a86569fa8a5ae4b004fdf2432b3ce98c



Department of Bioinformatics
-

BiGCaT

12

Example query (3)

Extract the amount of pathways edited
per contributor

SELECT DISTINCT

?contributor COUNT(?pathway)
as

?pathwaysEdited

WHERE {



?pathway dc:contributor

?contributor

}

ORDER BY DESC(?pathwaysEdited)



Department of Bioinformatics
-

BiGCaT

13

Example query n

Extracting Inchi out of ChEMBL

SELECT ?concept ?inchi ?pathway ?identifier


WHERE {


?concept dcterms:isPartOf ?pathway .


?concept dc:source "ChEMBL compound"^^xsd:string .


?concept dc:identifier ?identifier .


SERVICE <http://rdf.farmbio.uu.se/chembl/sparql>{


?s rdfs:label ?chidentifier .


?s <http://www.blueobelisk.org/chemistryblogs/inchi>
?inchi .}

FILTER (xsd:string(?chidentifier)= xsd:string(?identifier)) .

}

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-

BiGCaT

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Federated query


Required unified URIs


Identifier mapping

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-

BiGCaT

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Identifier mapping


Data enrichment


Query expansion


Unified identifier conversion

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BiGCaT

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Data enrichment

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BiGCaT

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Unified Identifiers

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BiGCaT

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Query expansion

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BiGCaT

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Acknowledgements


the Innovative Medicines Initiative Joint
(n
°
115191, FP7/2007
-
2013)


The NIH National Institute for General Medical
Sciences (R01
-
GM100039)


Department of Bioinformatics
-

BiGCaT

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Acknowledgement

Gladstone Institute


Alex Pico

Maastricht University


Martina
Kutmon


Egon

Willighagen


Chris
Evelo

Manchester University


Alasdair Gray


Christian
BreninkMeijer



Department of Bioinformatics
-

BiGCaT

21

Resources:


WikiPathways:
www.wikipathways.org


Pathvisio:
www.pathvisio.org


RDF:
rdf.wikipathways.org


SPARQL:
sparql.wikipathways.org


Vocabularies:
vocabularies.wikipathways.org


BridgeDb:
www.bridgeDb.org


IMS:
ondex2.cs.man.ac.uk:9090/QueryExpander/)