Retrieve a list of biomolecules (identifiers):



Find biomolecules based on identifiers.

Query directly your biomolecules list of interest using their identifiers, separated by comma.
MatrixDB identifier, UniProt Access number, gene name, Complex portal identifier, ChEBI identifier and GlyTouCan identifier are accepted.



This query will display a unique results table.
Example: P28300,CPX-1714








Build a list of biomolecules:



Enter free text, biomolecule identifier(s), name(s) or gene(s) separated by comma. Words separated by space will be taken as a single term.



This query will display two results tables:

  • Primary Hits: Query found in the 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)

Build a list of biomolecules annotated with
UniProtKB/Swiss-Prot keywords and / or Gene Ontology terms of interest:



Enter free text, keyword identifier and / or GO identifier separated by comma. Words separated by space will be taken as a single term.



This query will display two results tables:

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

Build a list of biomolecules cited in publications of interest:



Enter free text and / or PMID separated by comma.



This query will display two results tables:

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

Build a list of biomolecules related to diseases of interest:



Enter free text, OMIM identifier(s) and / or uniprot disease identifier(s) separated by comma. Words separated by space will be taken as a single term.



This query will display two results tables:

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

Examples: Ehlers-Danlos - Cerebral vessels - Fibrosis - Neonatal - 226650 (OMIM) - DI-00085 (UniProt) - Kidney,Liver (both) - Kidney,Liver (at least one)


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.

Two options are available to query several terms separated by comma: returning results matching necessarily all the terms or returning results matching at least one of the terms. By default, the option is "all terms", but the other one can be check instead. Words separated by space will be taken as a single term.

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!