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.
Search by fields
Click the red All button to get a dropdown menu with the list of the searchable fields.
| Field | Subfield | Description |
|---|---|---|
| All | Search in any field (equivalent to a simple text search) | |
| Reaction participants | ChEBI small molecule | Search small molecule by name, synonym, chemical class or identifier (the CHEBI: prefix should not be used as part of the identifier) |
| Rhea macromolecule | Search macromolecules (proteins, nucleic acids or Rhea polymer) by name or identifier (the RHEA-COMP: prefix should not be used as part of the identifier) | |
| InChIKey | Search by full or partial InChIKey | |
| Rhea reaction [id] | Search by Rhea identifier (no prefix) | |
| PubMed | Search by PubMed identifier (no prefix) | |
| Enzyme classification | Search by complete or partial EC number | |
| Reaction status | Approved | Reviewed reactions chemically balanced for mass and charge |
| Preliminary | Reviewed reactions with incomplete knowledge (possibly not balanced) | |
| Cross-references | EcoCyc | Search by EcoCyc reaction identifier |
| MetaCyc | Search by MetaCyc reaction identifier | |
| KEGG | Search by KEGG reaction identifier | |
| M-CSA/MACiE | Search by M-CSA/MACiE reaction identifier | |
| Reactome | Search by Reactome reaction identifier (Hsa only) | |
| Cas number | Search by CAS registry number (compound) | |
| Beilstein | Search by Beilstein registry number (compound) | |
| Reaction types | Transport reactions | To retrieve transport reactions |
| Involving proteins | To retrieve reactions with participants that are proteins | |
| Involving nucleic acids | To 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