Advanced text search

Content:

Introduction

The advanced text search allows you to search in specific fields of the Rhea database. This is useful when you search with an ambiguous term, for instance a numeric record identifier that may exist in several fields.

The advanced text search also allows you to combine query terms with logical operators (AND, OR, NOT).

You can access the Advanced query builder from the home page or from any page, by clicking the link Advanced search next to the text search box.

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Search by fields

Click the red All button to get a dropdown menu with the list of the searchable fields.

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FieldSubfieldDescription
AllSearch in any field (equivalent to a simple text search)
Reaction participantsChEBI small moleculeSearch small molecule by name, synonym, chemical class or identifier (the CHEBI: prefix should not be used as part of the identifier)
Rhea macromoleculeSearch macromolecules (proteins, nucleic acids or Rhea polymer) by name or identifier (the RHEA-COMP: prefix should not be used as part of the identifier)
InChIKeySearch by full or partial InChIKey
Rhea reaction [id]Search by Rhea identifier (no prefix)
PubMedSearch by PubMed identifier (no prefix)
Enzyme classificationSearch by complete or partial EC number
Reaction statusApprovedReviewed reactions chemically balanced for mass and charge
PreliminaryReviewed reactions with incomplete knowledge (possibly not balanced)
Cross-referencesEcoCycSearch by EcoCyc reaction identifier
MetaCycSearch by MetaCyc reaction identifier
KEGGSearch by KEGG reaction identifier
M-CSA/MACiESearch by M-CSA/MACiE reaction identifier
ReactomeSearch by Reactome reaction identifier (Hsa only)
Cas numberSearch by CAS registry number (compound)
BeilsteinSearch by Beilstein registry number (compound)
Reaction typesTransport reactionsTo retrieve transport reactions
Involving proteinsTo retrieve reactions with participants that are proteins
Involving nucleic acidsTo retrieve reactions with participants that are nucleic acids (RNAs or DNAs)

Please, read the document Text search for details on each field.

Term suggestion

When you start typing in the text box of a "Reaction participants > ChEBI small molecule" field, a non-exhaustive list of possible matches is presented to help you find a participant by name or synonym. To search for a participant that is not listed, just finish typing its name and then click the Search button.

Tips

  • Identifiers (ID) should be given without prefix.
    Examples:
    - Select Reaction participants, then ChEBI small molecule field and enter 29748 to retrieve reactions involving CHEBI:29748.
    - Select Rhea reaction [id] field, then enter 52368 to retrieve reactions involving RHEA:52368.
  • The use of wildcard (*) is allowed
    For instance, you can select Enzyme classification [EC] field, then enter the asterisk character * to retrieve all reactions referenced by any EC number.
    Similarly, select UniProtKB AC field, then enter * in order to retrieve reactions referenced by any UniProtKB enzymes.
  • Difference between result searches
    You may obtain different results depending if you select (or not) a ChEBI identifier from the autocomplete list.
    For instance,
    1. Reaction participants > ChEBI small molecule:'L-glutamate 5-semialdehyde' without autocompletion
    will give you more results than
    2. Reaction participants > ChEBI small molecule:'L-glutamate 5-semialdehyde' + selection of 'L-glutamate 5-semialdehyde [CHEBI:58066]' proposed by autocompletion.

The first search is a text search, it will also return reactions with N-acetyl-L-glutamate 5-semialdehyde.

Use cases

Logical operator AND

Search for methyl transferase reactions involving SAM as methyl donor

RNA and DNA methyl transferases share structural motifs required to transfer methyl groups from S-adenosyl-L-methionine (SAM) to nucleic acid.
If you want to retrieve all reactions that involve both S-adenosyl-L-methionine and S-adenosyl-L-homocysteine

Advanced search
AND Reaction participants > ChEBI small molecule:S-adenosyl-L-methionine [59789]
AND Reaction participants > ChEBI small molecule:S-adenosyl-L-homocysteine [57856]

The corresponding query is
query: chebi:"S-adenosyl-L-methionine [59789]" chebi:"S-adenosyl-L-homocysteine [57856]"

Click query to get the results.

You may also be interested to list the reactions that use S-adenosyl-L-methionine but not S-adenosyl-L-homocysteine

query: chebi:"S-adenosyl-L-methionine [59789]" NOT chebi:"S-adenosyl-L-homocysteine [57856]"

Click here: chebi:"S-adenosyl-L-methionine [59789]" NOT chebi:"S-adenosyl-L-homocysteine [57856]" to get the results.

How to find enzymes that hydrolyze cholesterol esters?

See document How to find enzymes that hydrolyze cholesterol esters? to get another example with an AND search

Logical operator NOT

How to find enzymes that convert some diacyl-sn-glycerol (DAG) to some triacyl-sn-glycerol (TAG)?

See tutorial How to link chemical search results to enzyme data? to get an example with a NOT search