Text-Based Querying | Browsing using Ontologies | Direct Queries
MetaCyc Web Querying Examples
Example 1: Using Text-Based Querying for an Object whose Name is Unknown
[step 1 | step 2]
Suppose you want to find information related to 6-phosphofructokinase but have forgotten its precise name. All you remember is that the enzyme is a kinase involving fructose.
Step 1:Use the Quick Search box that appears at
the top of every MetaCyc web page to search for all objects (proteins, reactions, genes, etc) that contain the words "kinase" and "fructose":
Step 2: Hit "enter" or click the "Quick Search"
button to see hits from
MetaCyc proteins, Gene Ontology terms and reactions that match this query (below).
From there, you can access extensive information about the
proteins, as well as the reactions associated with phosphofructokinase,
by clicking on individual items.
Example 2: Browsing MetaCyc using Ontologies for Pathways Related to Glycolysis
[step 1 | step 2 | step 3 | step 4]
Suppose you wanted to get an overall view of pathways involved in glycolysis.
As part of MetaCyc's curation process [def], all of its pathways are classified according to a pathway ontology [def].
Step 1: Use Metabolism
→ Browse Pathway Ontologies command
(from the Tools menu) to retrieve all high-level pathways (i.e., without retrieving every instance of a pathway subsumed under those headings):
Step 2: In the resulting page,
appropriate root class (for glycolysis, this would be "Generation of precursor
metabolites and energy", and expand it by clicking on the "plus" sign next
to it. Once the list expands, click on Glycolysis:
Step 3: Clicking on "Glycolysis" opens a window that lists the
different pathways that are classified under glycolysis. One of the powerful
features of MetaCyc is the ability to show multiple pathways covering the
variability of metabolic pathways found in nature.
Step 4: Clicking the different links under the Glycolysis class will display the alternative glycolysis pathways found in
different organisms. For example, clicking on
V (Pyrococcus) will result in the following pathway. The summary section below the pathway
diagram will provide information about the pathway, including the types of organisms in which this pathway variant is found.
Example 3: Direct querying of MetaCyc using an Identifier
[step 1 | step 2 | outcome]
Suppose you know the name of a gene (e.g., fruK).
Step 1: You can use either the Quick Search
box at the top of the page, or (to avoid receiving results that are not genes)
you can use the "Search Genes, Proteins orRNAs" command (from the
Tools → Search menu).
Step 2: When the MetaCyc "Gene/Protein/RNA
Search" page appears, type fruK in the text field. As you type, the system will
automatically suggest matches to the text entered so far; for example, after you
typed "fru" the system may suggest genes such as FruB, fruI and
fruK as possible candidates. After you type "fruK", only the fruK
genes in MetaCyc appear as candidates.
As this point you can either click on one of the suggestions before you
submit your query (by clicking on the "Submit Query" button or hitting "Enter"),
in which case you will be taken directly to that object's page, or you may
ignore the suggestions, and submit the query as entered, in which case you will be taken to a page that
lists all possible matches, as shown below.
Outcome: Once you click on an individual gene, you
will be taken to the MetaCyc's entry for that gene: