Text search
Content:
- Introduction
- How does the text search work?
- What can you search?
- Search by reaction participants
- Name and synonyms
- Identifier
- Chemical structure (InChiKey)
- Biological or chemical role
- Refine search for participant
- Search by enzymes that catalyze a reaction
- Search by Gene Ontology
- Search by identifiers of metabolic resources
- Search by bibliographic citations
- Combining search terms with Boolean operators (AND, OR, NOT)
- Related pages
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, Gene Ontology terms, 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 simple text search looks for matches of your query term(s) in the entire content of the Rhea database. With an Advanced text search you can limit your search to a particular search field.
The text search exploits ontological relationships whenever your query term matches a concept from one of the ontologies used in Rhea. You can change this default behaviour and execute an exact search by using the corresponding option in the Advanced text search.
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 identifier | Prefix | Example |
|---|---|---|
| ChEBI | chebi | chebi:16113 |
| RHEA-COMP | rhea-comp | rhea-comp:10594 |
| CAS Registry Number | cas | cas:57-88-5 |
| Beilstein Registry Number | beilstein | beilstein: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
The page Where can I find information about the enzymes that catalyze Rhea reactions? provides an overview about enzyme related information.
EC number
Rhea reactions are only linked to complete EC numbers, but you can search them by each of the four levels of the enzyme classification. You must use the prefix ec before the EC number.
Examples:
| Query | Result |
|---|---|
| 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:2.1.1.160 | reactions catalyzed by Caffeine synthase |
You can also filter search results by the seven main classes of the enzyme classification.
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:
| Query | Result |
|---|---|
| P32483 or uniprot:P32483 | reactions catalyzed by the enzyme described in UniProt entry P32483 |
| uniprot:* | reactions catalyzed by enzymes described in UniProt entries |
Search by Gene Ontology
Rhea reactions are linked to Gene Ontology (GO) 'Molecular Function' concepts. You can simply enter a GO identifier or name, but it is better to use the prefix go to limit your search to that field.
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.
| Resource | Prefix | Query | |
|---|---|---|---|
| RHEA | rhea | rhea:42796 | |
| KEGG | kegg | kegg:R01716 | |
| MetaCyc | metacyc | metacyc:PABASYN-RXN | |
| EcoCyc | ecocyc | ecocyc:PABASYN-RXN | |
| Reactome (Hsa) | reactome | reactome:R-HSA-193706.1 | |
| M-CSA/MACiE | macie | macie: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.