Advanced text search

Content:

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.

image

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:

  1. select the suggestion: chebi:"L-glutamate 5-semialdehyde [58066]"
  2. 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.

image

Examples:

Search fields

Field nameExample queryQuery builder field > subfield labelDescription
chebi, chebi_exactchebi:59871, chebi_exact:59871Reaction participants > ChEBI small moleculeSearch small molecule by name, synonym, chemical class or identifier
rhea-comprhea-comp:10594Reaction participants > Rhea macromoleculeSearch macromolecules (proteins, nucleic acids or Rhea polymer) by name or identifier
inchikeyinchikey:VFRROHXSMXFLSNInChIKeySearch by full or partial InChIKey
rhearhea:42796Rhea reaction [id]Search by Rhea identifier
uniprotuniprot:P32483UniProtKB ACSearch by UniProtKB accession
pubmedpubmed:29867142PubMedSearch by PubMed identifier
ecec:2.1.1.160Enzyme classification [EC]Search by complete or partial EC number
go, go_exactgo:0003884, go_exact:0003884Gene Ontology [GO]Search by Gene Ontology (GO) 'Molecular Function' name or identifier
statusstatus:approvedReaction status > ApprovedSearch reviewed reactions chemically balanced for mass and charge
statusstatus:preliminaryReaction status > PreliminarySearch reviewed reactions with incomplete knowledge (possibly not balanced)
ecocycecocyc:PABASYN-RXNCross-references > EcoCycSearch by EcoCyc identifier
metacycmetacyc:PABASYN-RXNCross-references > MetaCycSearch by MetaCyc identifier
reactomereactome:R-HSA-193706.1Cross-references > ReactomeSearch by Reactome (Hsa) identifier
keggkegg:R01716Cross-references > KEGGSearch by KEGG identifier
maciemacie:M0283Cross-references > M-CSA/MACiESearch by M-CSA/MACiE identifier
cascas:57-88-5Cross-references > CAS numberSearch by CAS Registry Number
beilsteinbeilstein:2060565Cross-references > BeilsteinSearch by Beilstein Registry Number
transporttransport:yesReaction types > Transport reactionsSearch transport reactions
hasproteinhasprotein:yesReaction types > Involving proteinsSearch reactions with participants that are proteins
hasnucleotidehasnucleotide:yesReaction types > Involving nucleic acidsSearch 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:

  • AND retrieves reactions that include all the search terms.
  • OR retrieves reactions that include at least one of the search terms.
  • NOT excludes 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]"