RDF data access
WARNING - new RDF schema has been deployed and documentation is being updated at the monet.
MolMeDB RDF dataset can be accessed in three ways:
- bulk download of the database as RDF file in one of supported formats (RDF/XML, N-Triples and Turtle),
- IRI dereference,
- querying MolMeDB SPARQL endpoint.
MolMeDB SPARQL endpoint together with example queries is described HERE. Other two options are described below. MolMeDB Vocabulary can be accessed as XML document via https://rdf.molmedb.upol.cz/vocabulary.
Bulk download
MolMeDB RDF database is free to download as RDF files from Google Drive. Files are available in gzip-compressed RDF/XML, N-Triples and Turtle formats. After the extraction, data can be loaded into a triple store (e.g. Virtuoso) to run your local instance of the RDF database.
Download links
- RDF/XML
- Turtle
- N-Triples
IRI dereference
MolMeDB RDF IRIs can be resolved to document describing the resource in multiple formats. Hash IRIs are used for MolMeDB Vocabulary and 303 IRIs are used for resources described in the dataset.
MolMeDB Vocabulary
MolMeDB Vocabulary uses hash IRIs. This means the prefix of an IRI identifies the vocabulary and is separated by "#" character from the local name.
For example, the term
https://rdf.molmedb.upol.cz/vocabulary#MembraneModel
has a prefix
https://rdf.molmedb.upol.cz/vocabulary
and local name
MembraneModel
IRIs of terms from the vocabulary can be resolved using GET request. The response body is an XML document containing the whole vocabulary.
Note
Local part of IRI (after "#") is ignored during resolution. This means that vocabulary XML file can be obtained with or without any local part. Local names serve only to identify the term from the vocabulary.
MolMeDB RDF domains
MolMeDB RDF uses 303 (or slash) IRIs to identify described resources. 303 IRIs have prefixes common to an ontology, database or domain and a local name after the last '/' character. For example, caffeine has IRI
https://identifiers.org/molmedb/MM00040
where
https://identifiers.org/molmedb/
is prefix common for IRIs of all molecules in the dataset and MM00040 is a local name identifying caffeine in particular.
GET request against IRI with an invalid local part leads to a response with 404 (Not found) status code.
We are using redirect during IRI resolution
To describe a resource, e.g. caffeine, we need to identify it first. The description can be written into a document, but we need to keep in mind that caffeine and document describing caffeine are two distinct resources that are not interchangeable. For example, you can describe the molecular weight of caffeine, but the molecular weight of caffeine document is complete nonsense. Thus we keep identifiers separate https://identifiers.org/molmedb/MM00040 for caffeine and https://molmedb.upol.cz/mol/MM00040 for a document describing it.
Format of the returned document is decided according to the Accept header of the GET request (for more info, see the REST API document). HTML, RDF/XML, N-Triples and Turtle formats are currently supported for RDF-related requests.
The HTML format is recommended for clients requesting a human-readable format. Basic molecule info is returned as MolMeDB web page and the rest of URIs are dereferenced to HTML tables describing triples in which a particular IRI occurs as a subject or object.
Warning, HTML output may not be complete.
Considering the high number of triples in which some IRIs occur, we set a limit of 100 lines per HTML document. Please use another output data format mentioned above to obtain a complete list.
RDF/XML, N-Triples and Turtle documents are complete RDF representations describing all the triples in which particular URIs occur. Documents in these three formats are suitable for automated processing.
Table 1. Accept headers and their corresponding formats supported by MolMeDB REST API for RDF-related requests.
| Accept header | Format |
|---|---|
| text/html | HTML |
| application/rdf+xml | RDF/XML |
| application/n-triples | N-Triple |
| text/turtle | Turtle |
IRI list by the described resource
This section provides a comprehensive list of IRI patterns for each resource type described by MolMeDB RDF. Each IRI definition is supplemented by an explanation of what that particular IRI means and an example IRI of that pattern.
How to read IRI pattern description?
| Method | Describes which HTTP method must be used while requesting the given IRI resolution. |
| IRI pattern |
Specifies the suffix of the URI determining a named resource. A final IRI is created by combining the server address prefix https://rdf.molmedb.upol.cz with the corresponding pattern. For example, IRI with a pattern /interaction/membrane<id> is called at address https://rdf.molmedb.upol.cz/interaction/membrane<id>. Molecules are exception to this, using pattern starting https://identifiers.org/molmedb/ instead. |
| Parameters | Describes possible parameters which can be used for query specification. All parameters can be inserted as part of the IRI (e.g. parameter id in the previous example). |
| Output formats | Describes possible output formats of the data returned from the server. For more info on how to set the output format of your request, please see Output formats. |
MolMeDB vocabulary terms
Terms from MolMedb Vocabulary.
| Method | GET |
| IRI pattern | /vocabulary#<local_name> |
| Parameters |
Note that the local name parameter does not affect the response, but options are listed here for completeness. AbsorbtionWavelength peak absorption wavelength ContactAngle contact angle with the membrane DepthOfMinima depth of minima within a membrane FluorescenceLifetime time a fluorophore spends in the excited state before emitting a photon and returning to the ground state FluorescenceWavelength peak fluorescence wavelength InhibitionAssay result of the assay whether the measured entity acts as an inhibitor of the target enzyme kcalMol kilocalorie per mol LogK logarithm of partition coefficient membrane/water LogPerm logarithm of membrane permeability MembrameModel model of biological membrane PenetrationBarrier penetration barrier (maximum-minimum) PKm -log Km, where Km is the concentration of substrate at ½ Vmax, according to the Henri-Michaelis-Menten kinetic model PositionOfMinima position of minima along the membrane normal from the membrane centre QuantumYield number of times a specific event occurs per photon absorbed by the system SubstrateBindingAssay result of the assay whether the measured entity acts as a substrate of the target enzyme |
| Output formats | XML (default) |
Example
Term for membrane model. Returns MolMeDB Vocabulary (in XML format only)
https://rdf.molmedb.upol.cz/vocabulary#MembraneModel
Part of returned vocabulary XML document describing Membrane Model
...
<owl:Class rdf:about="http://rdf.molmedb.upol.cz/vocabulary#MembraneModel">
<rdfs:subClassOf
rdf:resource="http://www.bioassayontology.org/bao#BAO_0003114"/>
...
<owl:Class>
...
...
<owl:Class rdf:about="http://rdf.molmedb.upol.cz/vocabulary#MembraneModel">
<rdfs:subClassOf
rdf:resource="http://www.bioassayontology.org/bao#BAO_0003114"/>
...
<owl:Class>
...Substance
Substance record. Use https://identifiers.org/molmedb/ prefix instead of the standard MolMeDB RDF one.
| Method | GET |
| IRI pattern | https://identifiers.org/molmedb/<mmdb_identifier> |
| Parameters | mmdb_identifier [string] (required) - MolMeDB compound identifier (e.g. MM00040). |
| Output formats |
HTML (default) RDF/XML N-Triples Turtle |
Example
Returns caffeine molecule detail
https://identifiers.org/molmedb/MM00040
Part of RDF/XML document describing caffeine.
<?xml version="1.0" encoding="UTF-8"?>
<rdf:RDF
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:ns5="http://purl.org/dc/terms/"
xmlns:ns3="http://www.w3.org/2004/02/skos/core#"
xmlns:ns2="http://semanticscience.org/resource/"
xmlns:ns1="http://www.w3.org/2000/01/rdf-schema#"
xmlns:ns4="http://www.bioassayontology.org/bao#"
>
<rdf:Description rdf:about="https://identifiers.org/molmedb/MM00040">
<rdf:type rdf:resource="http://www.bioassayontology.org/bao#BAO_0000076"/>
...
</rdf:Description>
<rdf:Description rdf:about="https://rdf.molmedb.upol.cz/interaction/int453">
<ns4:BAO_0090012 rdf:resource="https://identifiers.org/molmedb/MM00040"/>
</rdf:Description>
...
</rdf:RDF>
<?xml version="1.0" encoding="UTF-8"?>
<rdf:RDF
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:ns5="http://purl.org/dc/terms/"
xmlns:ns3="http://www.w3.org/2004/02/skos/core#"
xmlns:ns2="http://semanticscience.org/resource/"
xmlns:ns1="http://www.w3.org/2000/01/rdf-schema#"
xmlns:ns4="http://www.bioassayontology.org/bao#"
>
<rdf:Description rdf:about="https://identifiers.org/molmedb/MM00040">
<rdf:type rdf:resource="http://www.bioassayontology.org/bao#BAO_0000076"/>
...
</rdf:Description>
<rdf:Description rdf:about="https://rdf.molmedb.upol.cz/interaction/int453">
<ns4:BAO_0090012 rdf:resource="https://identifiers.org/molmedb/MM00040"/>
</rdf:Description>
...
</rdf:RDF>Substance - attributes
Description of a particular attribute of a substance specified by its MolMeDB ID.
| Method | GET |
| IRI pattern | /substance/<mmdb_identifier>_<attribute> |
| Parameters |
mmdb_identifier [string] (required) - MolMeDB compound identifier attribute [string] (required) - Compound attribute can be one of the following: - smiles - SMILES identifier - nchikey - InChIKey identifier - molecular_weight - average molecular weight - logp - logarithm of octanol-water partition coefficient - pubchem - PubChem identifier - drugbank - DrugBank identifier - chembl - ChEMBL identifier - pdb - wwPDB ligand identifier - chebi - ChEBI identifier - mmdbid - MolMeDB identifier |
| Output formats |
HTML (default) RDF/XML N-Triples Turtle |
Example
Returns SMILES record of Caffeine (MM00040) molecule
https://rdf.molmedb.upol.cz/substance/MM00040_smiles
Turtle document describing SMILES record of Caffeine
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix sio: <http://semanticscience.org/resource/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
<https://rdf.molmedb.upol.cz/substance/MM00040_smiles> rdf:type
sio:CHEMINF_000018;
sio:SIO_000300 "Cn1c(=O)c2c(ncn2C)n(C)c1=O"^^xsd:string .
<https://identifiers.org/molmedb/MM00040> sio:SIO_000008 <https://rdf.molmedb.upol.cz/substance/MM00040_smiles> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix sio: <http://semanticscience.org/resource/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
<https://rdf.molmedb.upol.cz/substance/MM00040_smiles> rdf:type
sio:CHEMINF_000018;
sio:SIO_000300 "Cn1c(=O)c2c(ncn2C)n(C)c1=O"^^xsd:string .
<https://identifiers.org/molmedb/MM00040> sio:SIO_000008 <https://rdf.molmedb.upol.cz/substance/MM00040_smiles> .
Membrane
Membrane description.
| Method | GET |
| IRI pattern | /interaction/membrane<id> |
| Prameters | id [int] (required) - Membrane ID. |
| Output formats |
HTML (default) RDF/XML N-Triples Turtle |
Example
Returns detail of membrane with ID=1
https://rdf.molmedb.upol.cz/interaction/membrane1
Part of N-Triples document describing membrane with ID=1
<https://rdf.molmedb.upol.cz/interaction/membrane1>
<http://www.w3.org/1999/02/22-rdf-syntax-ns#type>
<https://rdf.molmedb.upol.cz/vocabulary#MembraneModel>.
<https://rdf.molmedb.upol.cz/interaction/membrane1> <http://www.w3.org/2000/01/rdf-schema#label>
"DMPC"^^<http://www.w3.org/2001/XMLSchema#string>.
<https://rdf.molmedb.upol.cz/interaction/membrane1>
<http://www.w3.org/1999/02/22-rdf-syntax-ns#type>
<https://rdf.molmedb.upol.cz/vocabulary#MembraneModel>.
<https://rdf.molmedb.upol.cz/interaction/membrane1> <http://www.w3.org/2000/01/rdf-schema#label>
"DMPC"^^<http://www.w3.org/2001/XMLSchema#string>.Membrane interaction
Membrane interaction assay record.
| Method | GET |
| IRI pattern | /interaction/int<id> |
| Parameters | ID is a number corresponding to the id of a membrane interaction. |
| Output formats |
HTML (default) RDF/XML N-Triples Turtle |
Example
Returns record of membrane interaction with ID=1
https://rdf.molmedb.upol.cz/interaction/int1
Membrane interaction - measure group
Measure group of membrane interaction assay specified by membrane interaction ID.
| Method | GET |
| IRI pattern | /interaction/measure_group_int<id> |
| Parameters | ID [int] (required) - ID of a membrane interaction |
| Output formats |
HTML (default) RDF/XML N-Triples Turtle |
Example
Returns record of measure group of the membrane interaction with ID=1
https://rdf.molmedb.upol.cz/interaction/measure_group_int1
Membrane interaction - experimental condition
Experimental condition (temperature/charge) at which assay was conducted.
| Method | GET |
| IRI pattern | /interaction/measure_group_<condition>_int<id> |
| Parameters |
condition [temperature/charge] (required) id [int] (required) - ID o membrane interaction. |
| Output formats |
HTML (default) RDF/XML N-Triples Turtle |
Example
Returns record of temperature at which was the membrane interaction with ID=453 measured
https://rdf.molmedb.upol.cz/interaction/measure_group_temperature_int453
Membrane interaction - endpoint
Value of a specific measurement of a membrane interaction (determined by the interaction ID).
| Method | GET |
| IRI pattern | /interaction/endpoint_<property>_int<id> |
| Parameters |
property [string] (requited) - Can be one of the following: - logk - logarithm of partition coefficient membrane/water - logperm - logarithm of membrane permeability - position - position of minima along the membrane normal from the membrane center - penetration - penetration barrier - water - depth of minima within membrane - theta - contact angle - abs_wl - peak absorbtion wavelength - fluo_wl - peak fluorescence wavelength - qy - quantum yield - lt - fluorescence lifetime id [int] (required) - ID of a membrane interaction. |
| Output formats |
HTML (default) RDF/XML N-Triples Turtle |
Example
Returns record of LogK value of the membrane interaction with ID=1
https://rdf.molmedb.upol.cz/interaction/endpoint_logk_int1
Membrane interaction - standard deviation
Standard deviation of a specific measurement of a membrane interaction determined by the ID.
| Method | GET |
| IRI pattern | /interaction/endpoint_<property>_stdev_int<id> |
| Parameters |
property [string] (requited) - Can be one of the following: - logk - logarithm of partition coefficient membrane/water - logperm - logarithm of membrane permeability - position - position of minima along the membrane normal from the membrane center - penetration - penetration barrier - water - depth of minima within membrane - theta - contact angle - abs_wl - peak absorbtion wavelength - fluo_wl - peak fluorescence wavelength - qy - quantum yield - lt - fluorescence lifetime id [int] (required) - ID of a membrane interaction. |
| Output formats |
HTML (default) RDF/XML N-Triples Turtle |
Example
Returns record of a standard deviation of logPerm value in interaction with ID=1967
https://rdf.molmedb.upol.cz/interaction/endpoint_logperm_stdev_int1967
Membrane interaction - method
Description of a method determined by the ID.
| Method | GET |
| IRI pattern | /interaction/method<id> |
| Parameters | id [int] (required) - Method ID. |
| Output formats |
HTML (default) RDF/XML N-Triples Turtle |
Example
Record of a method with ID=1.
https://rdf.molmedb.upol.cz/interaction/method1
Transporter interaction
Transporter interaction assay record.
| Method | GET |
| IRI pattern | /transporter/tra<id> |
| Parameters | id [int] (required) - Transporter interaction ID. |
| Output formats |
HTML (required) RDF/XML N-Triples Turtle |
Example
Returns record of transporter interaction with ID=34644
https://rdf.molmedb.upol.cz/transporter/tra34644
Transporter interaction - measure group
Measure group of transporter interaction assay determined by ID.
| Method | GET |
| IRI pattern | /transporter/measure_group_tra<id> |
| Parameters | id [int] (required) - Transpoter interaction ID. |
| Output formats |
HTML (default) RDF/XML N-Triples Turtle |
Example
Returns record of measure group of the transporter interaction with ID=34644
https://rdf.molmedb.upol.cz/transporter/measure_group_tra34644
Transporter interaction - endpoint
Description of a result for measurement of specified property of a transporter interaction specified by its ID.
| Method | GET |
| IRI pattern | /transporter/endpoint_<property>_tra<id> |
| Parameters |
property [string] (required) - Can be one of the following: - substrate - result on assay whether the compound is a substrate of the transporter - inhibitor - result on assay whether the compound is an inhibitor of the transporter - pkm - pKm - pec50 - pEC50 - pki - pKi - pic50 - pIC50 id [int] (required) is a number corresponding to the id of a transporter interaction. |
| Output formats |
HTML (default) RDF/XML N-Triples Turtle |
Example
Returns record of pIC50 value the transporter interaction with ID=34644
https://rdf.molmedb.upol.cz/transporter/endpoint_pic50_tra34644
Transporter interaction - standard deviation
Standard deviation of result for measurement of a specified property of a transporter interaction specified by its ID.
| Method | GET |
| IRI pattern | /transporter/endpoint_<property>_stdev_tra<id> |
| Parameters |
property [string] (required) - Can be one of the following: - substrate - result on assay whether the compound is a substrate of the transporter - inhibitor - result on assay whether the compound is an inhibitor of the transporter - pkm - pKm - pec50 - pEC50 - pki - pKi - pic50 - pIC50 id [int] (required) is a number corresponding to the id of a transporter interaction. |
| Output formats |
HTML (default) RDF/XML N-Triples Turtle |
Example
Returns descriotion of a standard deviation of pKm for transporter interaction with ID=31403
https://rdf.molmedb.upol.cz/transporter/endpoint_pkm_stdev_tra31403
Reference
Description of a data source providing information for transporter and membrane interactions
| Method | GET |
| IRI pattern | /reference/ref<id> |
| Parameters | id [int] (default) - Internal data source (reference) id. |
| Output formats |
HTML (default) RDF/XML N-Triples Turtle |
Example
Return description of Endo, S., Escher, B. I., & Goss, K. -U. (2011). Capacities of Membrane Lipids to Accumulate Neutral Organic Chemicals, 45(14), 5912-5921. https://doi.org/10.1021/es200855w
https://rdf.molmedb.upol.cz/reference/ref1
Transporter
Transporter IRIs belong to UniProt thus MolMeDB is not responsible for result of their IRI resolution. However they can be resolved in the same way as MolMeDB IRIs. We list them here for the sake of completeness.
Another important point is that documents returned by UniProt IRI resolution DO NOT contain information about their role in MolMeDB. Please refer to the MolMeDB data about transporter interactions to obtain this information.
| Method | GET |
| IRI pattern | http://purl.uniprot.org/uniprot/<id> |
| Parameters | id [int] (required) - UniProt identifier. |
| Output formats |
HTML (default) RDF/XML N-Triples Turtle |
Example
Returns ABCC2 transporter detail.
http://purl.uniprot.org/uniprot/Q92887