Advanced Queries

Welcome to the MatrixDB advanced search interface.

This interface allows finding interactions of a biomolecule (proteins, glycosaminoglycans and matricryptins) or a list of biomolecules by querying various data (left-hand side menu).

Each query will produce "Primary hits" that are most likely relevant, and "Secondary hits" that may also be of interest although their relationship with the query string is less direct. For example the "Publications" type will search for the string of characters (free text) in publication titles and identifiers, yielding a list of Primary hits, and also in publication abstracts, yielding Secondary hits.

Subsequently, biomolecules related to the retrieved annotations, publications or diseases can be added with a single click to the cart, or examined and added individually. By default the biomolecules are restricted to *human* biomolecules involved in *at least one interaction*, but these restrictions can be relaxed by unclicking the relevant checkboxes.

Several independent queries can be performed and their results pooled together to iteratively construct a list of biomolecules. "Show queries history" (in the pink "Current cart" frame) can be used to visualize the list of queries performed along with the biomolecules that they added to the cart, and to delete some queries if needed.

Finally, the interaction network comprising all selected biomolecules and their direct partners can be constructed and analyzed in the MatrixDB Network Navigator by clicking on "Build interaction network" in the pink "Current cart" frame.

This is an experimental interface, any feedback is welcome!


Find biomolecules based on free text

Examples: Heparan sulfate, COL1A1, Alzheimer, P28300, EBI-2431547

This query will display two results tables:

  • Primary Hits: Query found in identifier or name of the biomolecule or in gene name
  • Secondary Hits: Query found in various descriptive fields for the biomolecule (molecular description, function, subcellular location, tissue specificity, protein domain)

UniProtKB/Swiss-Prot keywords & Gene Ontology terms

Find biomolecules annoted with UniProtKB/Swiss-Prot keywords and / or Gene Ontology terms of interest

Examples: Angiogenesis, Aging, Structural constituent, Osteogenesis, KW-0272, GO:0043062

This query will display two results tables:

  • Primary Hits: Query found in annotation identifier or name
  • Secondary Hits Query found in annotation description


Find biomolecules cited in publications of interest

Examples: Matricellular protein, Glycosaminoglycan, Basement membrane, 15181153 (PMID)

This query will display two results tables:

  • Primary Hits: Query found in PMID or publication title
  • Secondary Hits: Query found in publication abstract


Find biomolecules related to diseases of interest

Examples: Ehlers-Danlos, Osteoarthritis, Fibrosis, Kidney, Neonatal, 226650 (OMIM identifier) DI-00085 (UniProt identifier)

This query will display two results tables:

  • Primary Hits: Query found in disease identifier or name
  • Secondary Hits: Query found in disease description