A few diagrams to document the RDF schema
A turtle file is available on our FTP

Examples

  1. Retrieve the MNXref metabolite with name N,N-dimethyl-beta-alanine, together with molecular information.
  2. Retrieve the identifiers for N,N-dimethyl-beta-alanine in external databases. This crosslinking of external identifiers is the core of MNXref.
  3. For the KEGG compound C01732, retrieve the MNXref identifier, name and source.
  4. Retrieve the MNXref reaction identifier, that correspond to the KEGG reaction R00703 (lactate dehydrogenase).
  5. List the external identifiers that correspond to the KEGG reaction R00703 (lactate dehydrogenase). This crosslinking of external identifiers is the core of MNXref.
  6. Show the reaction equation catalyzed by lactate dehydrogenase (KEGG reaction R00703). NB: Stochiometric coefficients for substrates are given a negative value
  7. Show the reaction equation for the tartrate/succinate antiporter (rhea:34763). NB: there are two generic compartments here.
  8. Show the reaction equation for ATP synthase (reaction ATPS4m from BiGG). NB: there are two types of protons here, as MetaNetX distinguishes protons used for balancing (MNXM1) from those that are translocated (MNXM01).
  9. List all GSMNs currently in the MetaNetX repository, with their numbers of reactions, chemical, compartments and genes/proteins.
  10. A GSMN is primarily a set of reactions: here are all the reaction equations occurring in bigg_e_coli_core. NB: here the reac label is the one produced while compiling MetaNetX
  11. ...in addition reactions are endowed with a direction, flux bounds and possibly the description of the enzymes that catalyze it.
  12. Given the protein with UniProt accession number P42588 (PAT_ECOLI, putrescine aminotransferase, EC 2.6.1.82) retrieve all reactions and models in which this polypetide appears.
  13. Same as previous but with P0ABU7 as query (Biopolymer transport protein ExbB).