Disclaimer
The research leading to these results has received support from the
Innovative Medicines Initiative (IMI)
Joint Undertaking under grant agreement n° 115191, resources of which
are composed of financial contribution from the European Union's
Seventh Framework Programme (FP7/2007-2013) and EFPIA companies’ in
kind contribution.
Intended audience
This dataset and linkset description specification is intended
for data providers who want to publish their data as RDF, and link it
to other datasets. A basic knowledge of RDF is assumed.
Details for converting a dataset and publishing it as RDF are given
in the Open PHACTS RDF guidelines specification [[OPS-RDF]].
Vocabularies for Describing Datasets and Mapping Relationships
In this section, we introduce the vocabularies that will be used for
capturing the dataset descriptions and the mappings between the
datasets.
Vocabulary of Interlinked Datasets (VoID)
The Vocabulary of Interlinked Datasets (VoID) [[!VOID]] is a
W3C interest group note that specifies a vocabulary for describing
the metadata about a dataset and its relationship with other
datasets. The vocabulary builds upon existing metadata
vocabularies, e.g. Dublin Core Terms [[DCTERMS]], and captures four
categories of metadata:
-
General Metadata:
This is general information about the dataset, e.g. the name
and a description, together with who publishes the dataset, and
when it was created.
-
Access Metadata:
This provides details of how to access the dataset, e.g. a
SPARQL endpoint to query the dataset or a file where the dataset
can be downloaded.
-
Structural Metadata:
This provides details of how the dataset is modelled, i.e. the
vocabularies used and the topics covered in the dataset.
-
Mapping Metadata:
This provides details of the mappings of instances in the
dataset to instances in another dataset.
Dataset
The VoID specification [[VOID]] defines a dataset
to be, "a set of RDF triples that are published, maintained or
aggregated by a single provider." The dataset itself may
contain logical subsets, which can be captured in the VoID
description of the dataset, e.g. ChEMBL can be split into subsets
for compounds, targets, etc.
The information captured about a dataset focuses on the general
metadata, access, metadata, and the structural metadata.
Linksets
The VoID specification [[VOID]] defines a link to
be, "an RDF triple whose subject and object are described in
different datasets." The links capture the mapping of an
identifier in one dataset to be related to an identifier in another
dataset. VoID is agnostic to the relationship to use: possible
predicates are given in the next section.
The VoID specification defines a linkset to be,
"a collection of such RDF links between two datasets." The
linkset captures details of the links, i.e. the datasets that are
linked and the relationship, as well as the metadata associated
with the links, e.g. provenance information about who created the
mapping and the specific versions of the datasets related. The VoID
specification enables a separation between (1) the datasets
involved in a linkset, and (2) who publishes the linkset.
Note that a VoID linkset is defined to link two datasets via
a single link predicate
(void:linkPredicate).
As such, there can
exist multiple linksets relating the same pair of datasets, as
illustrated in the figure below. The
figure depicts four distinct linksets: two sourced from ChemSpider
depicted in blue which use different link predicates; one sourced
from ChEMBL depicted in red; and one sourced from a third party
depicted in green. Each of the linksets uses a different link
relationship. Those shown with a double arrow head are symmetric
while those with just a single arrow are directional links.
Expressing Mapping Relationships
A mapping is expressed as a VoID link, i.e. it is an RDF triple
that relates an identifier in one dataset with an identifier in
another dataset with some predicate which provides the meaning of
the mapping. A justification for the mapping, e.g. two chemical
compounds are deemed equivalent as they have the same InChI key, is
expressed with the link in the linkset metadata.
Mapping Vocabularies
The mapping predicate captures the way in which the two
identifiers are related. The mapping should respect the
semantics of the relationship, e.g. the
owl:sameAs
relationship must only be used when the two identifiers are
completely interchangeable.
Standard, and widely used, generic mapping relationships are given
in the table below. (A fuller mapping ontology is given in
[[Halpin2010]], but it is expected that the main relationships used
will be those given in the table.)
Note that there are domain specific relationship that may also be
used to express the relationship between two data instances. For
example, ChEBI provides a set of relationships including for
example
http://purl.obolibrary.org/obo#has_part
and
http://purl.obolibrary.org/obo#is_conjugate_acid_of.
Mapping Justifications
A key feature of the Open PHACTS platform is its ability to allow
multiple views of the linked data which is achieved by applying
scientific lenses over the data [[OPS-LENSES]]. For
example, when performing an early stage exploratory task it is
desirable to retrieve as much data as possible and as such the
system enables the use of a lens whereby compounds are matched on
their structural skeleton. Once the research has progressed further,
the need for stricter relationships becomes apparent and the
structure lens is switched for one which matches compounds on their
full chemical structure, i.e. including their charges and
stereo-chemistry.
The ability to classify linksets for use under different scientific
lenses relies on the justification given in the linkset. A set of
vocabulary terms for providing justifications are given in
Appendix A.3.
Example
The following example declares that the ChemSpider α-Ketoisovaleric
acid concept with the CSID
48 shares many properties with the ChEMBL 3-Methyl-2-oxobutanoic
acid concept with the ChEMBL-RDF
ChEMBL ID CHEMBL146554. The relationship is drawn from
ChemSpider based on the compounds sharing the same structure based
on their InChI Keys (in this case the compound has the same InChI
Key QHKABHOOEWYVLI-UHFFFAOYSA-N in both data sets.). Only the
triples directly related to declaring the link are given in the
example.
@prefix chembl: <http://linkedchemistry.info/chembl/chemblid/> .
:cs2chembl_inchi void:linkPredicate skos:exactMatch .
:cs2chembl_inchi dul:expresses <http://semanticscience.org/resource/CHEMINF_000059> .
<http://rdf.chemspider.com/48> skos:exactMatch chembl:CHEMBL146554 .
Describing Datasets
We assume that an RDF representation of the dataset has been generated
according to the Open PHACTS RDF Guidelines [[OPS-RDF]]. This section
describes the information that must appear in the VoID description
for the dataset.
It is recommended that the generation of the VoID description for a
dataset is carried out as part of the creation of the RDF version of
the dataset. To help understand some of the principles of the VoID
description, that is to help you get started there is a
VoID
Generator which supports the creation of dataset descriptions.
Provenance and Version
Version
-
Must declare the version of the dataset using the
pav:version predicate, where this exists for
the dataset.
-
Should link back to the previous version of the dataset using the
pav:previousVersion predicate.
Not all dataset have the notion of a version number. Where the
dataset does have this notion, it must be given in the
description. For other datasets, the versioning information will
be inferred by the last modified date provided as part of the
provenance information.
Provenance of Data Origin
Details of the origin of the data must be provided using one of the
following groups of predicates.
-
If the dataset and its description are accessed from their
original location, then the the following metadata must be
available from the VoID description at that site:
Note that we require both
dcterms:created and
dcterms:modified to be declared. This ensures that
we know which version of the dataset has been used.
-
If the dataset has been retrieved from another location,
i.e. it has already been published as RDF and this is a
replica of that data, then the following metadata must
be given:
-
If the dataset is imported from another data source, i.e.
the knowledge content is unchanged but the format of the
data has been changed (e.g. XML to RDF transformation), then
the following metadata must be given:
-
If the dataset is derived from another data source, i.e.
the knowledge content has changed, then the following
metadata must be provided:
Note that the object of the pav:xxxBy predicate is
a URI.
We currently do not require a specific form of URI for capturing
the details of a person or entity. Future versions of this
specification may recommend the use of ORCID Identifiers
[[ORCID]].
-
Should declare the software used to create the RDF
representation of the dataset using the
pav:createdWith predicate.
Distinguishing Subsets
Data source
-
If the dataset contains distinguishable subsets, then these
should be declared using the
void:subset predicate.
Metadata that is common between the subsets can be declared for the
parent only. However, the subsets allow for more specific linking
between datasets and for providing details of the subject.
In the VoID note [[VOID]], the void:subset property
is used for both subset of and has subset. The
declared semantics for the property is has subset. Within
Open PHACTS, the property must be used with the has subset
semantics.
For more details see
Section 4.4 of the VoID Specification.
Vocabularies, Topics, and
Example Resources
Dataset Vocabularies
-
Should declare the vocabularies and ontologies that encode
the data using the
void:vocabulary predicate.
For more details see
Section 4.3 of the VoID Specification.
Dataset Topics
Multiple topics can be declared. If the data is split into
subsets, then the topics should be associated with the subsets.
BioPortal [[BioPortalWeb]] [[BioPortal]] can be used to search for
suitable vocabulary terms for topics. DBPedia URIs may also be used.
A list of common terms relevant for Open PHACTS is given in
Appendix A.1.
For more details see
Section 2.5 of the VoID Specification.
Example Resources
Multiple resources can be declared. If the data is split into
subsets, then the example resources should be associated with the
subsets.
For more details see
Section 4.1 of the VoID Specification.
Dataset Access
Data Dump
-
Must provide the location of a dataset dump using the
void:dataDump predicate.
For more details see
Section 3.3 of the VoID Specification.
SPARQL Endpoint
For more details see
Section 3.2 of the VoID Specification.
Dataset Update Frequency
The terms from the Frequency Vocabulary have been reproduced in
Appendix A.2.
Other metadata that can be associated with a dataset may be
included, see the VoID specification [[VOID]] for additional
properties that may be incorporated. The dataset may also have a
provenance graph associated with it providing more detailed
information about the creation, authorship, and derivation of the
dataset. This provenance graph should be expressed using the W3C
Provenance Ontology [[PROV-O]].
Describing Linksets
A linkset is itself a dataset, and as such should provide the
metadata about its content and how it was created. The metadata
associated with a link is essential for enabling its reuse by others.
It enables a consumer of the link to understand which datasets are
linked (including which version), who claimed the link, under what
circumstances, and which (if any) tools were used to generate the link
(e.g. [[SILK]]).
Target Datasets
Note that the object of the above predicates are the URIs of the
respective datasets as declared in a VoID description. The datasets
may themselves be a subset of a larger dataset. Where the datasets
do not provide a VoID description, the minimal required information
must be provided in the linkset description. This is detailed in
Section 5.5.
For more details see
Section 5.1 of the VoID Specification.
Link Relationship
For more details see
Section 5.3 of the VoID Specification.
Link Justification
-
Must declare the reason/circumstance under which the link holds
using the
dul:expresses predicate and an object
from an open vocabulary.
The link justification provides the reason/circumstance why
instances in the two datasets can be considered equivalent.
For example, two chemical compounds have the same InChI Key or
have the same chemical formula.
Need to ensure that by using dul:expresses we are not
inferring other contradictory consequences.
Currently recommended vocabulary terms for the justification can be
found in Appendix A.3.
Provenance
Subset
-
If the linkset is a subset of another dataset, then
this must be declared using the
void:subset predicate.
Note that the dataset URI is the subject of the
void:subset triple and the linkset URI is the object.
If the dataset VoID description contains the declaration, there is
no need to repeat it in the linkset document. However, the linkset
documents can be used to declare additional subsets. A subset
inherits properties from its parent.
For more details see
Section 5.2 of the VoID Specification.
Link Source
-
Must declare how the links were asserted.
-
Manually asserted links are declared using the
authorship properties:
-
Computer derived links are declared by asserting the
tool used to generate the links using the property
pav:createdWith.
Additional information about the settings used when running an
automated link generation tool such as Silk [[SILK]] can be
captured in an associated provenance graph encoded using PROV-O
[[PROV-O]].
Linkset Creation Details
-
Must declare who created the linkset, i.e. encoded the
knowledge into triples or operated the computer generation tool,
with the property
pav:createdBy.
-
Must declare when the linkset was created using the
pav:createdOn predicate.
In this version of the specification, it is assumed that the creator
of the linkset has accessed the most recent version of the dataset.
Linkset Version
-
Must declare a version number for the linkset when this exists
using the
pav:version predicate.
-
Should link back to the previous version of the linkset using the
pav:previousVersion predicate.
Linkset Statistics
-
Should declare the number of links in the linkset using the
void:triples predicate.
Providing the number of triples included in the linkset allows for
applications using the linkset to validate that the entire linkset
has been successfully loaded.
For more details see
Section 4.6 of the VoID Specification.
Minimal Dataset Description
A linkset should point to the dataset descriptions of the datasets
that it uses. These descriptions should be provided by the dataset
provider as part of the dataset publishing process [[OPS-RDF]].
However, there are occasions when one or both of the linked
datasets do not provide a VoID dataset description. The following
set of properties must then be provided in the linkset document.
Other properties may also be given.
Deploying and Exchanging VoID Documents
The two preceeding sections have prescribed the metadata required to
describe datasets and the linksets that inter-relate them. This section
outlines the expected deployment and exchange mechanisms and should be
read in conjunction with
Section 6 of the VoID specification for more details.
VoID documents describing datasets and linksets must contain a
metadata block describing the VoID document using the following
properties:
Of course, other properties may also be declared, e.g. a title using
dcterms:title. For more details, see
Section 6.2 of
the VoID specification [[VOID]].
An example is given below for the ChemSpider deployment. Note the
use of an empty-string relative URI (<>) as a syntactic
shortcut for the URI of the document that contains the statements.
<> a void:DatasetDescription ;
dcterms:title "ChemSpider VoID Description"^^xsd:string ;
pav:createdBy <http://www.chemspider.com/> ;
pav:createdOn "2012-05-02T13:50:34Z"^^xsd:dateTime;
pav:lastUpdateOn "2012-08-10T13:52:12Z"^^xsd:dateTime;
foaf:primaryTopic :chemSpiderDataset .
Deploying VoID Descriptions
Several mechanisms for deploying VoID descriptions are given in
Section 6 of the
VoID Note [[VOID]].
Deploying a Dataset Description
For datasets that are being published in their own domain, with
dereferenceable URIs, then we recommend placing the dataset's
VoID description in the root directory in a file called
void.ttl, with a local "hash URI" for the dataset
(and any subsets). For example, for ChemSpider we would have a
URI such as
http://rdf.chemspider.com/void.ttl#chemSpiderDataset.
When the code is being hosted on an external service, then the
VoID descriptor should be provided in the dataset's home
directory. For example, for the RDF encoding of ChEMBL this
would be
http://linkedchemistry.info/chembl/void.ttl#chembl-rdf.
Examples of the VoID descriptors are given in
Appendix A.
Each RDF document containing the data should then contain a
backlink to the dataset descriptor. For example, the ChEMBL-RDF
molecule m1, there would be the triple:
<http://linkedchemistry.info/chembl/chemblid/molecule/m1> void:inDataset
<http://linkedchemistry.info/chembl/chemblid/void.ttl#chembl-rdf_compounds> .
Deploying a Linkset Description
For the purposes of Open PHACTS, it is anticipated that
linksets will be materialised as separate documents from the
datasets. This is to allow their loading into the identity
mapping service [[IMS]]. These linkset files will contain
the metadata about the linkset as well as the links.
It is also permitted to separate the link triples from the
linkset metadata. In this case, the file containing the links
must provide a link back to the linkset desription using the
void:inDataset predicate. The example below
shows how a set of links can refer back to the linkset
description given in the ChEMBL-RDF VoID description file.
<> void:inDataset <http://linkedchemistry.info/chembl/chemblid/void.ttl#chembl-rdf_targets-uniprot-linkset> .
<http://linkedchemistry.info/chembl/target/t1> skos:exactMatch <http://purl.uniprot.org/uniprot/O43451> .
...
External VoID Files
Tooling being developed within Open PHACTS should support the
predicates stated in this document. However, they should also be
able to read VoID files from external sources that do not comply
completely with this specification, but do comply with the VoID
standard [[VOID]]. An example would be the use of the
void:target predicate instead of the
void:subjectsTarget and
void:objectsTarget predicates. Such usage should
not be the norm and should result in warnings being generated.
Example Dataset VoID Descriptors
ChemSpider VoID Descriptor
The ChemSpider site already has a VoID descriptor available from
http://rdf.chemspider.com/void.rdf. This has been created with
a previous version of the VoID specification. Below is a suggested
updated version which conforms with the requirements of this
specification.
@prefix : <http://rdf.chemspider.com/void.ttl#>.
@prefix dcterms: <http://purl.org/dc/terms/>.
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix freq: <http://purl.org/cld/freq/> .
@prefix pav: <http://purl.org/pav/>.
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>.
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>.
@prefix skos: <http://www.w3.org/2004/02/skos/core#>.
@prefix voag: <http://voag.linkedmodel.org/schema/voag#> .
@prefix void: <http://rdfs.org/ns/void#>.
@prefix xsd: <http://www.w3.org/2001/XMLSchema#>.
# Metadata about this file
<http://rdf.chemspider.com/void.ttl>
a void:DatasetDescription;
dcterms:title "A VoID Description of the ChemSpider Dataset"@en;
dcterms:description
"""This is an example VoID description for the ChemSpider dataset.
It is derived from the existing VoID description and updating it to the latest
version of the VoID specification."""@en;
pav:createdBy <http://www.cs.man.ac.uk/~graya/me.ttl>;
pav:createdOn "2012-05-02T14:48:03Z"^^xsd:dateTime;
pav:lastUpdateOn "2012-08-10T09:32:49Z"^^xsd:dateTime;
pav:derivedFrom <http://rdf.chemspider.com/void.rdf>;
foaf:primaryTopic :chemSpiderDataset;
.
# Description of the ChemSpider dataset
:chemSpiderDataset
# General metadata
a void:Dataset;
dcterms:title "ChemSpider"@en;
dcterms:description "ChemSpider's Public Dataset"@en;
foaf:homepage <http://rdf.chemspider.com/>;
foaf:page <http://www.chemspider.com/>;
dcterms:license <http://www.chemspider.com/Disclaimer.aspx>;
void:uriSpace "http://rdf.chemspider.com/"^^xsd:string;
#Provenance
dcterms:publisher <http://www.chemspider.com/>;
dcterms:created "2007-03-01T00:00:00"^^xsd:dateTime;
dcterms:modified "2012-10-16T00:00:00"^^xsd:dateTime;#Subsets
void:subset :chemSpiderDataset_chembl_subset,:chemSpiderDataset_drugbank_subset;
#Vocabularies, topics, resources
void:vocabulary <http://purl.org/dc/elements/1.1/>,
<http://purl.org/dc/terms/>,
<http://www.openarchives.org/ore/terms/>,
<http://www.polymerinformatics.com/ChemAxiom/ChemDomain.owl#>,
<http://xmlns.com/foaf/0.1/>;
dcterms:subject <http://dbpedia.org/resource/Molecule>;
void:exampleResource <http://rdf.chemspider.com/2157>;
#Dataset Access
void:sparqlEndpoint <http://rdf.chemspider.com/sparql>;
#Update Frequency
voag:frequencyOfChange freq:continuous;
#Other Metadata
# Technical features
void:feature <http://www.w3.org/ns/formats/RDF_XML>;
# Dataset statistics
void:triples "1157624328"^^xsd:nonNegativeInteger;
.
:chemSpiderDataset_chembl_subset
#General Metadata
a void:Dataset;
dcterms:title "ChemSpider ChEMBL Subset"@en;
dcterms:description "The slice of ChemSpider data that corresponds to ChEMBL molecules."@en;
#Provenance
pav:retrievedFrom <ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_13/chembl_13.sdf.gz>;
pav:retrievedOn "2012-08-02T10:23:56Z"^^xsd:dateTime;
pav:retrievedBy <http://www.chemspider.com/> ;
#Dataset Access
void:dataDump <https://www.dropbox.com/sh/6zboa8z9i9vrzyl/7NxayhkUH0/ChEMBL20120731.zip>;
.
# Description of the ChemSpider subset relating to DrugBank
:chemSpiderDataset_drugbank_subset
#General Metadata
a void:Dataset;
dcterms:title "ChemSpider DrugBank Subset"@en;
dcterms:description "Data corresponding to DrugBank."@en;
#Provenance
pav:retrievedFrom <http://www.drugbank.ca/system/downloads/current/structures/all.sdf.zip>;
pav:retrievedOn "2012-08-02T10:24:06Z"^^xsd:dateTime;
pav:retrievedBy <http://www.chemspider.com/> ;
#Dataset Access
void:dataDump <https://www.dropbox.com/sh/6zboa8z9i9vrzyl/qcFZzbLM77/DrugBank20120731.zip>;
.
ChEMBL-RDF VoID Descriptor
Below we provide the VoID document for the ChEMBL-RDF dataset, which
is a conversion of the ChEMBL database. The VoID file would be
located at
http://linkedchemistry.info/void.ttl.
@prefix : <http://linkedchemistry.info/void.ttl#>.
@prefix dcterms: <http://purl.org/dc/terms/>.
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix freq: <http://purl.org/cld/freq/> .
@prefix pav: <http://purl.org/pav/>.
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>.
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>.
@prefix skos: <http://www.w3.org/2004/02/skos/core#>.
@prefix voag: <http://voag.linkedmodel.org/schema/voag#> .
@prefix void: <http://rdfs.org/ns/void#>.
@prefix xsd: <http://www.w3.org/2001/XMLSchema#>.
# Metadata about this file
<>
a void:DatasetDescription;
dcterms:title "ChEMBL-RDF VoID Description"@en;
dcterms:description
"""This is the VoID description for a ChEMBL-RDF dataset."""@en;
pav:createdBy <http://egonw.github.com/#me> ;
pav:createdOn "2012-08-12T16:56:07Z"^^xsd:dateTime;
pav:lastUpdateOn "2012-09-14T12:21:12Z"^^xsd:dateTime;
pav:previousVersion <http://semantics.bigcat.unimaas.nl/chembl/v13_ops/chembl-rdf-void.ttl>;
foaf:primaryTopic :chemblrdf_dataset.
:chemblrdf_dataset
# General metadata
a void:Dataset;
dcterms:title "ChEMBL-RDF 13.OPS.2"@en;
dcterms:description "The ChEMBL database in RDF format."@en;
foaf:homepage <http://github.com/egonw/chembl.rdf/>;
foaf:page <http://www.biosharing.org/biodbcore-000015>;
dcterms:license <http://creativecommons.org/licenses/by-sa/3.0/> ;
void:uriSpace "http://linkedchemistry.info/chembl/"^^xsd:string ;
# Provenance
pav:version "v13_ops";
pav:previousVersion <http://semantics.bigcat.unimaas.nl/chembl/v13_ops/chembl-rdf-void.ttl#chemblrdf_dataset>;
pav:importedFrom :chembl_dataset;
pav:importedBy <http://egonw.github.com/#me> ;
pav:importedOn "2012-05-15T15:34:40Z"^^xsd:dateTime;
pav:createdWith <https://github.com/openphacts/chembl.rdf>;
# Subsets
void:subset :chemblrdf_compounds, :chemblrdf_targets ;
# Vocabularies, topics, resources
void:vocabulary
<http://www.w3.org/1999/02/22-rdf-syntax-ns#>,
<http://www.w3.org/2000/01/rdf-schema#>,
<http://www.w3.org/2002/07/owl#>,
<http://www.w3.org/2001/XMLSchema#>,
<http://purl.org/dc/elements/1.1/>,
<http://purl.org/ontology/bibo/>,
<http://xmlns.com/foaf/0.1/>,
<http://purl.org/spar/cito/>,
<http://www.w3.org/2004/02/skos/core#> ,
<http://purl.obolibrary.org/obo#>,
<http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#>,
<http://www.blueobelisk.org/chemistryblogs/>,
<http://www.nmrshiftdb.org/onto#>,
<http://www.ifomis.org/bfo/1.1/snap#>,
<http://semanticscience.org/resource/>,
<http://purl.org/obo/owl/CHEBI#>;
# Update frequency
#Need to verify the update frequency!
voag:frequencyOfChange freq:semiannual;
# Other metadata
void:distinctSubjects "18018451"^^xsd:integer ;
.
:chembl_dataset
# Metadata about the original data source
a dcterms:Dataset;
dcterms:title "ChEMBL"@en;
dcterms:description """ChEMBL is a database of bioactive drug-like small molecules, it contains 2-D structures, calculated properties (e.g. logP, Molecular Weight, Lipinski Parameters, etc.) and abstracted bioactivities (e.g. binding constants, pharmacology and ADMET data)."""@en;
foaf:homepage <http://www.ebi.ac.uk/chembl/>;
dcterms:license <http://creativecommons.org/licenses/by-sa/3.0/> ;
pav:version "13"^^xsd:integer ;
dcterms:publisher <http://www.ebi.ac.uk/chembl/>;
dcterms:created "2012-02-29T00:00:00Z"^^xsd:dateTime;
dcterms:modified "2012-02-29T00:00:00Z"^^xsd:dateTime;
.
:chemblrdf_compounds
# Subset metadata
a void:Dataset ;
dcterms:title "ChEMBL Molecules"@en;
dcterms:description "The subset of ChEMBL data relating to molecules."@en;
void:uriSpace "linkedchemistry.info/chembl/molecule/"^^xsd:string ;
dcterms:subject <http://dbpedia.org/resource/Molecule> ;
void:exampleResource <http://linkedchemistry.info/chembl/molecule/m1>;
void:dataDump <http://semantics.bigcat.unimaas.nl/chembl/v13_ops/compounds.nt.gz> ;
.
:chemblrdf_targets
# Subset metadata
a void:Dataset ;
dcterms:title "ChEMBL Targets"@en;
dcterms:description "The subset of ChEMBL data relating to targets which are single proteins."@en;
void:uriSpace "linkedchemistry.info/chembl/target/"^^xsd:string ;
dcterms:subject <http://dbpedia.org/resource/Protein> ;
void:exampleResource <http://linkedchemistry.info/chembl/target/t1>;
void:dataDump <http://semantics.bigcat.unimaas.nl/chembl/v13_ops/targets.nt.gz> ;
.
Example Linksets
ChemSpider to ChEMBL-RDF Compounds Linkset
Below is the start of the linkset file relating ChemSpider
compounds with ChEMBL-RDF compounds. The linkset reuses the VoID
descriptions already provided for the datasets, but augments these
with additional metadata.
@prefix : <http://linkedchemistry.info/void.ttl>.
@prefix dcterms: <http://purl.org/dc/terms/>.
@prefix dul: <http://www.ontologydesignpatterns.org/ont/dul/DUL.owl#> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix freq: <http://purl.org/cld/freq/> .
@prefix pav: <http://purl.org/pav/>.
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>.
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>.
@prefix skos: <http://www.w3.org/2004/02/skos/core#>.
@prefix voag: <http://voag.linkedmodel.org/schema/voag#> .
@prefix void: <http://rdfs.org/ns/void#>.
@prefix xsd: <http://www.w3.org/2001/XMLSchema#>.
@prefix chembl: <http://linkedchemistry.info/chemblid/> .
# Metadata about this file
<>
a void:DatasetDescription;
dcterms:title "ChEMBL-RDF Compounds to ChemSpider linkset"@en;
dcterms:description """A VoID linkset that links compounds in ChEMBL-RDF
with compounds in ChemSpider."""@en;
pav:createdBy <http://egonw.github.com/#me> ;
pav:createdOn "2012-08-13T15:00:00Z"^^xsd:dateTime ;
pav:lastUpdateOn "2012-09-14T11:15:32Z"^^xsd:dateTime ;
foaf:primaryTopic :chembl-rdf-compounds_cs_linkset ;
.
# Pointer to the subset description in the ChEMBL VoID file
<http://linkedchemistry.info/void.ttl#chemblrdf_compounds>
# Linkset declared as a subset. Inherits properties
void:subset :chembl-rdf-compounds_cs_linkset .
:chembl-rdf-compounds_cs_linkset
# General linkset metadata
a void:Linkset ;
dcterms:title "ChEMBL-RDF Compounds ChemSpider Linkset"@en;
dcterms:description "Linkset relating ChEMBL-RDF compounds to ChemSpider compounds."@en;
#Explicit declaration of license for the linkset is preferred
dcterms:license <http://creativecommons.org/licenses/by-sa/3.0/> ;
# Link information
void:subjectsTarget <http://linkedchemistry.info/void.ttl#chemblrdf_compounds> ;
void:objectsTarget <http://rdf.chemspider.com/void.ttl#chemSpiderDataset_chembl_subset> ;
void:linkPredicate skos:exactMatch ;
dul:expresses <http://semanticscience.org/resource/CHEMINF_000059> ;
# Linkset provenance
pav:authoredOn "2012-02-22T10:59:38Z"^^xsd:dateTime ;
pav:authoredBy <http://www.chemspider.com/> ;
pav:createdBy <http://egonw.github.com/#me> ;
pav:createdOn "2012-05-15T11:29:01Z"^^xsd:dateTime ;
# Linkset statistics
void:triples "1073967"^^xsd:integer ;
.
chembl:CHEMBL1236438 skos:exactMatch <http://rdf.chemspider.com/43> .
chembl:CHEMBL144103 skos:exactMatch <http://rdf.chemspider.com/60> .
#...
An alternative deployment strategy for this linkset would be to
include the linkset metadata in the ChEMBL-RDF VoID description
file as a subset of the ChEMBL-RDF dataset. The linkset metadata
must then include the predicate void:dataDump to point
to the file containing the links. The file containing the links
must include the corresponding predicate void:inDataset
pointing back to the linkset description.
ChemSpider to DrugBank Linkset
Below is the linkset file relating ChemSpider compounds to DrugBank
drugs. As there is no VoID file available for the DrugBank dataset,
the VoID information is included in the linkset, following the
minimal information prescribed in
Section 5.5. For ChemSpider,
the VoID information is imported from the ChemSpider location.
@prefix : <http://rdf.chemspider.com/void.ttl#>.
@prefix dcterms: <http://purl.org/dc/terms/>.
@prefix dul: <http://www.ontologydesignpatterns.org/ont/dul/DUL.owl> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix freq: <http://purl.org/cld/freq/> .
@prefix pav: <http://purl.org/pav/>.
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>.
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>.
@prefix skos: <http://www.w3.org/2004/02/skos/core#>.
@prefix voag: <http://voag.linkedmodel.org/schema/voag#> .
@prefix void: <http://rdfs.org/ns/void#>.
@prefix xsd: <http://www.w3.org/2001/XMLSchema#>.
# Metadata about this file
<>
a void:DatasetDescription;
dcterms:title "ChemSpider to DrugBank Linkset VoID Description"@en;
dcterms:description
"""This is an example VoID description for a ChemSpider linkset.
The linkset relates ChemSpider identifiers with DrugBank identifiers.
The links have been generated as the chemicals share the same structure."""@en;
pav:createdBy <http://www.cs.man.ac.uk/~graya/me.ttl>;
pav:createdOn "2012-08-13T16:43:25Z"^^xsd:dateTime;
pav:lastUpdateOn "2012-10-16T10:22:43Z"^^xsd:dateTime;
foaf:primaryTopic :chemSpider_drugbank_linkset;
.
# Pointer to the ChemSpider dataset
<http://rdf.chemspider.com/void.ttl#chemSpiderDataset_drugbank_subset>
# declare that the linkset is a subset of ChemSpider
void:subset :chemSpider_drugbank_linkset;
.
# Need to declare dataset metadata about DrugBank as no VoID file
## Note this is just a minimal amount of information as prescribed in Section 5.5
:drugbank_drugs_dataset
# General Dataset Metadata
a void:Dataset;
dcterms:title "DrugBank Drugs Dataset"@en;
dcterms:description "A subset of the DrugBank database containing the information relating to drugs."@en;
foaf:homepage <http://www4.wiwiss.fu-berlin.de/drugbank/>;
foaf:page <http://www.drugbank.ca/>;
dcterms:license <http://www.drugbank.ca/about#cite>;
void:uriSpace "http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugs/"^^xsd:string;
# Provenance and Version
pav:version "3.0";
pav:retrievedOn "2011-11-30T11:01:59Z"^^xsd:dateTime;
pav:retrievedFrom <http://www4.wiwiss.fu-berlin.de/drugbank/drugbank_dump.nt.bz2>;
pav:retrievedBy [
a foaf:Person;
foaf:name "Antonis Loizou"^^xsd:string.
];
.
# Description of the linkset from ChemSpider to DrugBank
:chemSpider_drugbank_linkset
# General Linkset Metadata
a void:Linkset;
dcterms:title "ChemSpider DrugBank Linkset"@en;
dcterms:description "Linkset relating ChemSpider compounds to DrugBank drugs."@en;
dcterms:license <http://creativecommons.org/licenses/by-sa/3.0/> ;
# Link Information
void:subjectsTarget <http://rdf.chemspider.com/void.ttl#chemSpiderDataset_drugbank_subset>;
void:objectsTarget :drugbank_drugs_dataset;
void:linkPredicate skos:exactMatch;
dul:expresses <http://semanticscience.org/resource/CHEMINF_000059>;
# Linkset Provenance
pav:authoredBy <http://www.chemspider.com/>;
pav:authoredOn "2012-02-23T09:08:29Z"^^xsd:dateTime;
pav:createdBy <http://www.cs.man.ac.uk/~graya/me.ttl>;
pav:createdOn "2012-08-13T15:29:31Z"^^xsd:dateTime;
# Linkset statistics
void:triples "6428"^^xsd:nonNegativeInteger;
.
# Location of the triples
## Note that the triples would not contain the void header information as
## that is in this file. I have assumed the same location as the subset
## above, but this needs to change to a correct location.
## The file containing the triples should contain the following backlink
## |uriOfTheData| void:inDataset <http://rdf.chemspider.com/void-example.rdf#chemSpider_drugbank_linkset>.
