Related Experiment Video
Updated: Jun 4, 2026

Databases to Efficiently Manage Medium Sized, Low Velocity, Multidimensional Data in Tissue Engineering
Published on: November 22, 2019
MolMeDB RDF: transforming a relational database about biological membranes to the RDF format to increase
Dominik Martinát1, Jakub Juračka2, Jakub Galgonek3
1Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, 17. Listopadu 12, 771 46, Olomouc, Czech Republic. dominik.martinat@upol.cz.
None:
Data on molecular behaviour within biological membrane models are pivotal for predictive pharmacology, particularly for modelling bioavailability and target engagement. MolMeDB provides a curated collection of such compound-membrane interaction data. To facilitate automated reasoning and data federation, we present a semantic transformation of MolMeDB into Resource Description Framework (RDF) format, exposed through a public SPARQL endpoint. The resulting schema incorporates community-standard ontologies-including those utilised by PubChem and ChEMBL-to maximise semantic interoperability and enable complex, cross-database federated queries.Scientific contributionMolMeDB RDF provides data on interactions between molecules and membranes and molecules and transporters in machine readable graph format with links to other RDF databases. SPARQL endpoint servicing this dataset enables flexible federated querying including structural queries utilizing SACHEM.
Related Concept Videos
Rab Cascades
Rab Proteins
Rab proteins switch between a cytosolic, GDP-bound inactive state and a membrane-anchored, GTP-bound active state. By themselves, Rabs show slow rates of GDP/GTP exchange and GTP hydrolysis. Thus, Rab proteins are considered...
Membrane Fluidity
Mosaic nature of the membrane
The mosaic characteristic of the membrane helps the plasma membrane remain fluid. The integral proteins and lipids exist as separate but loosely-attached molecules in the membrane. The membrane is a relatively...
Insertion of Multi-pass Transmembrane Proteins in the RER
The multipass transmembrane proteins are the type IV integral membrane proteins with multiple topogenic sequences determining their spatial arrangement in the ER membrane. Nearly all multipass proteins lack a cleavable signal sequence and use...
Insertion of Single-pass Transmembrane Proteins in the RER
Integral transmembrane proteins possess transmembrane and extra membrane domains. The transmembrane domains are primarily made of 20-25 hydrophobic amino acids arranged in a helical secondary confirmation. These...
Export of Misfolded Proteins out of the ER
