Text search

Content:

Introduction

The home page of the Rhea website provides a search box to query its content with a full-text search. You can search Rhea reactions by their participants, enzymes that catalyze the reaction, identifiers of metabolic resources and bibliographic citations. The Rhea search always returns a result table with the reactions that match your query.

Please, read the introduction Searching Rhea and use the advanced text search if you need help to restrict your query to a particular search field or to combine fields with logical operators.

How does the text search work?

The text search exploits the ChEBI ontology:

  1. A query term is searched in the names and synomyms of ChEBI's chemical entities and in their biological or chemical role.
  2. Each ChEBI entity that matches the query term is then used to identifiy Rhea reaction participants that are described using either:
    • that entity.
    • a more specific form of that entity, i.e. one that is linked to it via one or several is a relationships.
    • the major microspecies at pH 7.3 of that entity.

Searching with a compound class

Example: lipid

A search for lipid returns reactions with a participant that is described using a ChEBI entity whose name or synonyms contain the term lipid, e.g. hepta-acyl lipid A (CHEBI:87048), or that is a more specific form of such an entity, e.g. lipid (CHEBI:18059) is a compound class that is not directly used in Rhea, but its more specific forms a fatty acid (CHEBI:28868), 8(R)-HPETE (CHEBI:57447) and O-(S-fatty acylpantetheine-4'-phosphoryl)-L-serine residue (CHEBI:138651), the reactive part of a fatty acyl-[ACP] (RHEA-COMP:14125), are used and thus found by this search.

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Searching with different protonation states

The ChEBI ontology describes each protonation state of a given compound (neutral, protonated, zwitterionic, tautomeric) with a separate class and links related classes by specific relationships (is conjugate acid of, is conjugate base of, is tautomer of). Rhea uses only those ChEBI entities that describe the form that is the major microspecies at pH 7.3 and it links this entity via has_major_microspecies_at_pH_7_3 relationships to the other forms.

Example: D-alanine

D-alanine has two groups, an amino group and a carboxylic acid group, that each can be (de)protonated. The different protonation states are described by 4 linked ChEBI entities:

A search that matches any of these 4 entities will return the same result, the reactions that use the major microspecies at pH 7.3 (CHEBI:57416).

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What can you search?

Search by reaction participants

Name and synonyms

You can search reaction participants by their names and synonyms. Beware that your query may match more than you expect, and the results are not always obvious when you search with a synonym of the name that is used in Rhea. You can use the section 'Refine search' in the menu on the left to check the participants that your query finds and then refine your search.

Identifier

You can search reaction participants by their ChEBI or RHEA-COMP identifiers, as well as by their CAS and Beilstein registry numbers.

Type of identifierPrefixExample
ChEBIchebichebi:16113
RHEA-COMPrhea-comprhea-comp:10594
CAS registry numbercascas:57-88-5
Beilstein registry numberbeilsteinbeilstein:2060565
Chemical structure (InChiKey)

You can search reaction participants by their InChiKey.

An InChiKey is composed of three blocks that are separated by a dash:

  • Block 1 encodes the molecular skeleton
  • Block 2 encodes the stereochemistry
  • Block 3 encodes the charge

Example: VFRROHXSMXFLSN-SLPGGIOYSA-L

This InChIKey encodes aldehydo-D-glucose 6-phosphate (CHEBI:57584). A search with VFRROHXSMXFLSN-SLPGGIOYSA-L returns all Rhea reactions with a participant that is related to CHEBI:57584.

If you are not interested in charge and stereochemistry, you can search with a partial InChIKey that consists only of block 1. In this case it is safer to use the prefix inchikey to ensure that your query string is searched only in that field: inchikey:VFRROHXSMXFLSN

Biological or chemical role

The ChEBI ontology describes the biological or chemical roles of some of its chemical entities and these can be queried in the text search by their name or ChEBI identifier.

Example: antifungal

A search for the term antifungal identifies all the ChEBI roles that match antifungal, such as antifungal agent (CHEBI:35718), antifungal drug (CHEBI:86327), etc., and uses them to retrieve reactions with participants that have one of these roles (assigned either directly or to a more generic participant).

See Searching Rhea

Refine search for participant

Your search term(s) will likely match several participants when you search by name, synomym or role. If this is the case, you will see the section 'Refine search' in the menu on the left of the result table with link(s) that let you choose the participant(s) you meant to search.

Example: caffeine

If you search for caffeine and then click the link 'Choose molecule for caffeine >>' you will see a molecule with the name caffeine (the one you likely meant to search), but also a molecule named 1,3,7-trimethylurate that was found because of its synonym 8-oxo-caffeine. You can now click the link 'x reaction(s)' of the molecule for which you meant to search to retrieve the reactions in which it participates.

Search by enzymes that catalyze a reaction

Visit our document Where can I find information about the enzymes that catalyze Rhea reactions? to get the whole picture.

EC number

You can search each of the four levels of the enzyme classification. You must use the prefix ec before the EC number.

Examples:

QueryResult
ec:*reactions linked to EC numbers
ec:2 or ec:2.-.-.-reactions catalyzed by Transferases
ec:2.1 or ec:2.1.-.-reactions catalyzed by Transferases transferring one-carbon groups
ec:2.1.1 or ec:2.1.1.-reactions catalyzed by Methyltransferases
ec:2.1.1.160reactions catalyzed by Caffeine synthase
UniProtKB accession

You can simply enter a UniProtKB accession, but it is better to use the prefix uniprot to limit your search to that field.

Examples:

QueryResult
P32483 or uniprot:P32483reactions catalyzed by the enzyme described in UniProt entry P32483
uniprot:*reactions catalyzed by enzymes described in UniProt entries

Search by identifiers of metabolic resources

You can simply enter an identifier, but it is better to prefix it to limited your search to that field.

ResourcePrefixQuery
RHEArhearhea:42796
KEGGkeggkegg:R01716
MetaCycmetacycmetacyc:PABASYN-RXN
EcoCycecocycecocyc:PABASYN-RXN
Reactome (Hsa)reactomereactome:R-HSA-193706.1
MACiE/M-CSAmaciemacie:M0283

Search by bibliographic citations

You can simply enter a PubMed identifier to find reactions that were curated from the cited article, but it is better to use the prefix pubmed to limit your search to that field.

Examples: 29867142, pubmed:29867142

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.