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ChEMBL-RDF

Dataset ChEMBL-RDF
Licence Creative Commons Attribution-ShareAlike 3.0 Unported (CC-BY-SA 3.0)
Published 14th August 2011
Updated 23rd October 2011
Resources 5425127

ChEMBL-RDF

Creative Commons Attribution-ShareAlike 3.0 Unported (CC-BY-SA 3.0)

This database contains the RDF version of ChEMBL 11 created by Egon Willighagen. All data comes from the ChEMBL database. ChEMBL is a medicinal chemistry database by the team of dr. J. Overington at the EBI, available at http://www.ebi.ac.uk/chembl/.

Full attribution details (including citable papers) can be found at this link: https://github.com/egonw/chembl.rdf . This data set currently contains a subset of the data, until I figured out how to upload all data using curl.

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Default APIs

SPARQL Endpoint

Use the SPARQL 1.0 query language to perform structured queries against a dataset. Useful for performing precise queries against a dataset whose structure you understand.

Sample queries

a
Iker Huerga
08th Sep 2011
Query: 
SELECt DISTINCT ?s WHERE{ ?s a <http://purl.org/ontology/bibo/Journal>. }
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All triples for CHEMBL1
Egon Willighagen
22nd Oct 2011

Returns all triples for CHEMBL1.

Query: 
SELECT * WHERE { ?entry <http://www.w3.org/2000/01/rdf-schema#label> "CHEMBL1" . ?entry ?property ?hasValue . }
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All biological activities for CHEMBL1
Egon Willighagen
06th Nov 2011

Returns all published biological activities for CHEMBL1.

Query: 
PREFIX bibo: <http://purl.org/ontology/bibo/> PREFIX chembl: <http://rdf.farmbio.uu.se/chembl/onto/#> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX cito: <http://purl.org/spar/cito/> PREFIX dc: <http://purl.org/dc/elements/1.1/> SELECT * WHERE { ?mol rdfs:label "CHEMBL1" . ?act chembl:forMolecule ?mol . ?act chembl:type ?type ; cito:citesAsDataSource ?paper ; chembl:standardValue ?value ; chembl:standardUnits ?unit ; chembl:onAssay ?assay . OPTIONAL { ?paper bibo:pmid ?pmid } OPTIONAL { ?paper bibo:doi ?doi } ?assay chembl:hasTarget ?target . OPTIONAL { ?target dc:title ?title } OPTIONAL { ?target dc:identifier ?id } OPTIONAL { ?target chembl:organism ?organism } }
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Citations for a publication by PMID
Egon Willighagen
10th Feb 2012

Returns the the citations to papers identified by a single PubMed ID (via a crafted IRI) and the RDF types of the citing objects (assays and activities).

Query: 
SELECT ?object ?type WHERE { ?paper <http://purl.org/ontology/bibo/pmid> <http://bio2rdf.org/pubmed:15139753> . ?object ?cites ?paper . ?object <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?type . }
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Citations for a publication by DOI
Egon Willighagen
10th Feb 2012

Returns the the citations to papers identified by a single DOI (literal) and the RDF types of the citing objects (assays and activities).

Query: 
SELECT ?object ?type WHERE { ?paper <http://purl.org/ontology/bibo/doi> "10.1016/0960-894X(94)00449-P" . ?object ?cites ?paper . ?object <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?type . }
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Create a sample query

Search API

Perform a free-text search against the text fields indexed in a dataset. Useful when you want to quickly query a dataset but don't know, or need to know its structure.

Lookup API

Retrieve a description of a single resource. Useful for fetching the key properties and relationships of a single entity.

Reconciliation API

Useful for resolving names, labels or codes against a dataset in Kasabi to find links to more data. This API is compatible with the Google Refine tool.

Augmentation API

Pass an RSS 1.0 feed through a dataset, automatically enriching the feed with descriptions of any relevant data sources. Useful for “fishing” data out of datasets without writing queries.

How to Attribute This Dataset

Kasabi provides a quick and easy way to attribute a dataset from any webpage. We think attribution is an important community norm.

To directly embed an attribution message in a webpage, add a script tag that invokes our Attribution API as follows

<script
     type="text/javascript"
     src="http://api.kasabi.com/dataset/chembl-rdf/attribution">
</script>

If you need more flexible options, then read the Attribution API documentation

Contributed APIs

No Contributed APIs available