Text-Based Querying | Browsing using Ontologies | Direct Queries
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MetaCyc Web Querying Examples
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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 Query section of the query page to search MetaCyc for all objects (proteins, reactions, genes, etc [more]) that contain the words "kinase" and "fructose":
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STEP 2: Click Submit to see hits from proteins and reactions stored in MetaCyc (below).
From there, you would access extensive information about the protein itself, as well as the reactions associated with phosphofructokinase.
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EXAMPLE #2: Browsing MetaCyc using Ontologies for Pathways Related to Glycolysis
[step 1 | step 2 | step 3]
Suppose you wanted to get an overall view of pathways involved in glycolysis. Thanks for MetaCyc's literature curation process [def], all of its pathways are classified according to a pathway ontology [def].
STEP 1: Use the Browse Ontologies section of the query page, operating against pathways, to retrieve all high-level pathways (i.e., without retrieving every instance of a pathway subsumed under those headings):
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STEP 2: From the overall taxonomy of pathways, click Glycolysis:
hint: you can use your browser's search function to find a particular entry, e.g., ctrl-F in Internet Explorer:
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STEP 3: That selection expands into the collections of pathways involved in glycolysis:
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STEP 4: One of the powerful features of MetaCyc is the ability to show multiple pathways covering the variability of metabolic pathways found in nature. Clicking the different links under the Glycolysis class will display the alternative glycolysis pathways found in different organisms. For example, clicking on Glycolysis I will result in the following:
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EXAMPLE #3: Direct querying of MetaCyc using an Identifier
[step 1 | outcome]
Suppose you know the name of a gene (e.g., fruK).
STEP 1: Use the Query section after selecting "Gene (by name)":
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OUTCOME: That query would immediately retrieve MetaCyc's entry for that gene:
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