Ontological background
WARNING - new RDF schema has been deployed and documentation is being updated at the monet.
Established biomedical ontologies define most terms for entity classes and predicates used in MolMeDB RDF. Other terms have been newly defined in MolMeDB Vocabulary as subclasses of terms from BioAssay Ontology or Units of Measurement Ontology. All ontologies and terms used in MolMeDB RDF dataset are named by IRI identifiers (listed below in Table 1). Each term has a unique identifier, but it is expected that terms from the same ontology share the same prefix. Large or more complex ontologies and datasets sometimes use collections of multiple prefixes for different domains.
Example
- Terms from MolMeDB Vocabulary use the prefix https://rdf.molmedb.upol.cz/vocabulary#.
- The full IRI for a membrane model is https://rdf.molmedb.upol.cz/vocabulary#MembraneModel, and for a penetration barrier it is https://rdf.molmedb.upol.cz/vocabulary#PenetrationBarrier.
Full IRI identifiers can be quite long and too cumbersome to use in texts and SPARQL queries, so it is common to use CURIE compact syntax, which allows for definition of namespace names as shorthands for prefixes. Compact IRI then consists of a namespace name in the place of a prefix, colon (:) separator and a local part. This documentation uses compact IRIs in most examples.
Example
For MolMeDB vocabulary namespace name mmdbvoc is used in this text. Compact IRI for membrane model is mmdbvoc:MembraneModel, where mmdbvoc stands for the full prefix of the ontology (https://rdf.molmedb.upol.cz/vocabulary#) and MembraneModel is the local part identifying this particular term.
Note that compact IRIs alone are NOT valid IRIs. Any RDF document or SPARQL query using compact syntax needs to define namespace names and their corresponding prefixes. Example of mmdbvoc namespace name definition for MolMeDB Vocabulary in a SPARQL query :
...
PREFIX mmdbvoc: <https://rdf.molmedb.upol.cz/vocabulary#>
...
...
PREFIX mmdbvoc: <https://rdf.molmedb.upol.cz/vocabulary#>
...Table 1: Ontologies, their namespaces and terms used in MolMeDB RDF.
| Ontology | Namespace name | Prefix |
|---|---|---|
| RDF Schema 1.1 |
rdf: rdfs: |
http://www.w3.org/2000/01/rdf-schema# http://www.w3.org/1999/02/22-rdf-syntax-ns |
|
rdf:HTML rdf:type rdfs:comment rdfs:label rdfs:seeAlso |
||
| XML Schema Definition Language | xsd: | http://www.w3.org/2001/XMLSchema# |
|
xsd:int xsd:float xsd:string |
||
| Simple Knowledge Organization System | skos: | http://www.w3.org/2004/02/skos/core# |
| skos:exactMatch | ||
|
Semanticscience Integrated ontology Chemical Information Ontology |
sio: | http://semanticscience.org/resource/ |
|
sio:SIO_000008 has attribute sio:SIO_000089 dataset sio:SIO_000221 has unit sio:SIO_000300 has value sio:CHEMINF_000018 SMILES descriptor sio:CHEMINF_000059 InChIKey sio:CHEMINF_000120 charge sio:CHEMINF_000140 PubChem compound identifier (CID) sio:CHEMINF_000216 average molecular weight descriptor sio:CHEMINF_000251 logP descriptor sio:CHEMINF_000406 DrugBank identifier soi:CHEMINF_000407 ChEBI identifier sio:CHEMINF_000412 ChEMBL identifier sio:CHEMINF_000571 MolMeDB identifier sio:CHEMINF_000572 PDB ligand identifier |
||
| BioAssay Ontology | bao: | http://www.bioassayontology.org/bao# |
|
bao:BAO_0000040 measure group bao:BAO_0000076 screened entity bao:BAO_0000199 pIC50 bao:BAO_0000208 has endpoint bao:BAO_0000209 has measure group bao:BAO_0000212 has assay method bao:BAO_0000283 transporter bao:BAO_0000426 is measure group of bao:BAO_0000559 is endpoint of bao:BAO_0002182 pharmacokinetic assay bao:BAO_0002583 pEC50 bao:BAO_0002753 assay method component bao:BAO_0003008 transporter assay bao:BAO_0090004 has part bao:BAO_0090012 has participant |
||
| REPRODUCE-ME | repr: | https://w3id.org/reproduceme# |
|
repr:hasExperimentalCondition repr:NegativeResult repr:PositiveResult |
||
|
Information Artifact Ontology Units of Measurement Ontology |
obo: | http://purl.obolibrary.org/obo/ |
|
obo:IAO_0000227 terms merged obo:IAO_0000231 has obsolescence reason obo:IAO_0100001 term replaced by obo:UO_0000018 nanometer obo:UO_0000027 degree Celsius obo:UO_0000062 molar obo:UO_0000150 nanosecond obo:UO_0000185 degree obo:UO_0000221 dalton |
||
| EDAM - The ontology of data analysis and management | edam: | http://edamontology.org/ |
| edam:data_2291 UniProt ID | ||
| Experimental Factor Ontology | efo: | http://www.ebi.ac.uk/efo/ |
| efo:EFO_0001702 | ||
| Dublin Core (DC) ontology |
dc: dcterms: |
http://purl.org/dc/elements/1.1/ http://purl.org/dc/terms/ |
|
dc:description dcterms:bibliographicCitation dcterms:BibliographicResource dcterms:isReferencedBy dcterms:references dcterms:source dcterms:subject |
||
| Bibliographic Ontology | bibo: | http://purl.org/ontology/bibo/ |
|
bibo:doi bibo:pmid |
||
|
PubChem RDF ChEMBL RDF ChEBI RDF wwPDB RDF UniProt RDF |
pubchem: chembl: chebi: * uniprot: |
http://rdf.ncbi.nlm.nih.gov/pubchem/compound/ http://rdf.ebi.ac.uk/resource/chembl/molecule/ http://purl.obolibrary.org/obo/ http://rdf.wwpdb.org/cc/{pdb_ligand_id}/chem_comp/{pdb_ligand_id} http://purl.uniprot.org/uniprot/ |
| Terms from RDF versions of PubChem, ChEMBL, ChEBI, and wwPDB correspond with molecules and terms from UniProt RDF correspond with transporter proteins. The IRI form for ligands in wwPDB does not support the CURIE syntax for compact IRIs. Therefore no namespace name and IRI pattern are shown for wwPDB. | ||
MolMeDB Vocabulary
TBD