Text Search

YMDB supports advanced Google-like searching using a powerful search engine based on the Lucene query language. YMDB text search supports boolean logic (AND, OR, NOT operations ). To match a string exactly, place quotes around your search term (for example "acetic acid" will only match the acetic followed by acid, it will not match acetic or acid alone). You can also search using "wild cards" by inserting a "*" in your search term. For example, searching for "acet*" will match all words starting with "acet". In addition, text search supports parenthetical groupings, and prepended +plus and -minus operators.

Example Description
"glutamic acid" AND glutamine Find all metabolites containing both "glutamic acid" and glutamine
("linoleic acid" OR glutamine) AND NOT "pyroglutamic acid" Find all metabolites containing linoleic acid, glutamine or both, but not containing pyroglutamic acid
"acetic acid" Find all metabolites where the entire term "acetic acid" is found.
acid AND description:pathway Find all metabolites containing acid and pathway in their description
name:*amine AND description:proteinogenic Find all metabolites ending with amine with proteinogenic in their description

As the last 2 examples demonstrate, YMDB text query also supports a high-level search interface allowing you to narrow your search to specific metabolite fields. To use this interface, simply enter the field name followed by a semi-colon(:) and your query term. For example, to search for metabolites where the description contains "fatty acid" you would search for description:"fatty acid". You can also combine different fields in a given search, for example, to find all metabolites with acid in their name and with fatty acid in their description search for description:"fatty acid" AND name:acid.
Alternatively, queries can be generated via the advanced search bar which simplifies the process of generating complex queries. Currently, only the following metabolite and protein fields are searchable using these methods:

Metabolite Fields

Title/Description Field
YMDB ID ymdb_id
Metabolite Name name
CAS Number cas
Cellular Location cellular_locations
ChEBI ID chebi_id
Chemical Formula formula
Chemical IUPAC Name iupac
Description description
Formal Charge charge
H2O Solubility (experimental) experimental_water_solubility
H2O Solubility (predicted) predicted_water_solubility
InChI Identifier inchi
InChI Key inchikey
KEGG Compound ID kegg_id
LogP (experimental) experimental_logp
LogP (predicted) predicted_logp
Melting Point (°C) melting_point
Metabolite Synonyms synonym
Molecular Weight (average) average_mass
Molecular Weight (monoisotopic) mono_mass
PubChem Compound ID pubchem_id
SMILES smiles
State state
Synthesis Reference synthesis_reference
Traditional IUPAC Name traditional_iupac
Wikipedia Link wikipedia_link
pKa pka

Protein Fields

Title/Description Field
Chromosome Location chromosome
GO Classification go_classification
GenBank Gene ID genbank_gene_id
GenBank Protein ID genbank_protein_id
Gene Name gene_name
GeneCard ID genecard_id
General Function general_function
Location cellular_location
Locus locus
Molecular Weight molecular_weight
Number of Residues residue_count
PDB Accession pdb_id
Pathways pathway_name
Pfam Domain Function Identifier pfam_identifier
Pfam Domain Function Name pfam_name
Protein ID id
Protein Name name
Signals signals
Specific Function specific_function
Synonyms synonym
Theoretical pI theoretical_pi
Transmembrane Regions transmembrane_regions
UniProt ID uniprot_id
UniProt Name uniprot_name