Advanced text search
Content:
- Introduction
- Advanced search query builder
- Search fields
- Combining search terms with Boolean operators (AND, OR, NOT)
- Related documents
Introduction
The advanced 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. You can also combine several query terms with Boolean operators (AND, OR, NOT).
Once you are familiar with the field names, you can directly enter your field-specific queries into the website's text search box. For occasional usage you may find the advanced search query builder that is shown in the next section helpful.
Advanced search query builder
You can access the advanced search query builder from the home page or from any page by clicking the link Advanced search next to the text search box.
By clicking the red All button, you get a drop-down menu with the list of the search fields. By default the Boolean operator that combines several fields is set to AND, click on it to change this selection.
Search suggestions
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.
You may obtain different results depending on whether you select one of the suggestions or not, e.g. enter L-glutamate 5-semialdehyde into the Reaction participants > ChEBI small molecule field and try:
- select the suggestion: chebi:"L-glutamate 5-semialdehyde [58066]"
- do not select a suggestion: chebi:"L-glutamate 5-semialdehyde"
The second query will give you more results than the first, because it also matches N-acetyl-L-glutamate 5-semialdehyde [CHEBI:29123].
The same functionality is available for the Gene Ontology [GO] field. For instance, if you start to type caffeine, a drop-down menu will appear and suggest GO terms that are mapped to Rhea reactions, e.g. caffeine oxidase activity [GO:0034875].
Wildcards
The wildcard character * is allowed in most search fields, e.g. to retrieve all reactions catalyzed by enzymes described in UniProt entries, select the UniProtKB AC field and enter the wildcard character: uniprot:*
Ontology versus exact search
For searches in ontologies, like ChEBI and the Gene Ontology (GO), the default search uses the ontology's relationships to retrieve Rhea reactions that are directly related to the concepts that match your query, as well as Rhea reactions that are related to concepts that are themselves related to the matching concepts via certain ontological relationships (see this example).
You can choose the corresponding exact option to retrieve only Rhea reactions that are directly related to the concepts that match your query.
Examples:
- chebi:59871 (111 reactions) versus chebi_exact:59871 (8 reactions)
- go:0003884 (3 reactions) versus go_exact:0003884 (1 reaction)
Search fields
| Field name | Example query | Query builder field > subfield label | Description |
|---|---|---|---|
chebi, chebi_exact | chebi:59871, chebi_exact:59871 | Reaction participants > ChEBI small molecule | Search small molecule by name, synonym, chemical class or identifier |
rhea-comp | rhea-comp:10594 | Reaction participants > Rhea macromolecule | Search macromolecules (proteins, nucleic acids or Rhea polymer) by name or identifier |
inchikey | inchikey:VFRROHXSMXFLSN | InChIKey | Search by full or partial InChIKey |
rhea | rhea:42796 | Rhea reaction [id] | Search by Rhea identifier |
uniprot | uniprot:P32483 | UniProtKB AC | Search by UniProtKB accession |
pubmed | pubmed:29867142 | PubMed | Search by PubMed identifier |
ec | ec:2.1.1.160 | Enzyme classification [EC] | Search by complete or partial EC number |
go, go_exact | go:0003884, go_exact:0003884 | Gene Ontology [GO] | Search by Gene Ontology (GO) 'Molecular Function' name or identifier |
status | status:approved | Reaction status > Approved | Search reviewed reactions chemically balanced for mass and charge |
status | status:preliminary | Reaction status > Preliminary | Search reviewed reactions with incomplete knowledge (possibly not balanced) |
ecocyc | ecocyc:PABASYN-RXN | Cross-references > EcoCyc | Search by EcoCyc identifier |
metacyc | metacyc:PABASYN-RXN | Cross-references > MetaCyc | Search by MetaCyc identifier |
reactome | reactome:R-HSA-193706.1 | Cross-references > Reactome | Search by Reactome (Hsa) identifier |
kegg | kegg:R01716 | Cross-references > KEGG | Search by KEGG identifier |
macie | macie:M0283 | Cross-references > M-CSA/MACiE | Search by M-CSA/MACiE identifier |
cas | cas:57-88-5 | Cross-references > CAS number | Search by CAS Registry Number |
beilstein | beilstein:2060565 | Cross-references > Beilstein | Search by Beilstein Registry Number |
transport | transport:yes | Reaction types > Transport reactions | Search transport reactions |
hasprotein | hasprotein:yes | Reaction types > Involving proteins | Search reactions with participants that are proteins |
hasnucleotide | hasnucleotide:yes | Reaction types > Involving nucleic acids | Search reactions with participants that are nucleic acids (RNAs or DNAs) |
Please, read the document Text search for details on each field.
Combining search terms with Boolean operators (AND, OR, NOT)
When you search for multiple terms, e.g. L-glutamate 5-semialdehyde, the search engine retrieves the reactions that contain all your search terms, i.e. it combines them with a Boolean AND operator. You can overwrite this default behaviour by connecting your search terms explicitly with Boolean operators:
ANDretrieves reactions that include all the search terms.ORretrieves reactions that include at least one of the search terms.NOTexcludes reactions that contain the following search term.
The search engine evaluates multiple operators from left to right. You can use parentheses to group terms that should be processed as a unit before being incorporated into the overall search.
Examples:
If you are interested in RNA and DNA methyl transferase reactions that transfer methyl groups from S-adenosyl-L-methionine (SAM) to nucleic acid and want to retrieve all reactions that involve both S-adenosyl-L-methionine AND S-adenosyl-L-homocysteine, enter the following in the 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 query built looks like this:
chebi:"S-adenosyl-L-methionine [59789]" chebi:"S-adenosyl-L-homocysteine [57856]"
You may also be interested to retrieve only the reactions that use S-adenosyl-L-methionine, but NOT S-adenosyl-L-homocysteine. Just change the Boolean operator before your second search field to NOT:
AND Reaction participants > ChEBI small molecule: S-adenosyl-L-methionine [59789]
NOT Reaction participants > ChEBI small molecule: S-adenosyl-L-homocysteine [57856]
The query built now looks like this:
chebi:"S-adenosyl-L-methionine [59789]" NOT chebi:"S-adenosyl-L-homocysteine [57856]"