MetaCyc Metabolic Pathway Database
Quick Search
Search
Database Search
Advanced Database Search
Browse
Pathways
Compounds
Reactions
MetaCyc Home Home
About MetaCyc
MetaCyc User's Guide
Help
Database Overview
Graphical Overview
Querying Examples
Literature Curation Process
Publications
Release Notes
Submit Your Pathways
Advisory Board
Contributors
Services
Software/Data Download
  including:
    BioPAX format
    SBML format
User Support
Subscribe to Mailing List
Feedback
SRI AI Center
Carnegie Institution of Washington

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 Query section of the query page to search MetaCyc for all objects (proteins, reactions, genes, etc [more]) that contain the words "kinase" and "fructose":

MetaCyc Query Top Page

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.

MetaCyc Query Hits

[top]
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):

MetaCyc Query Top Page
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:IE Find function

MetaCyc Ontology Browsing

STEP 3: That selection expands into the collections of pathways involved in glycolysis:

MetaCyc - List of Pathways Involved in Glycolysis

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:

MetaCyc - Display Pathways Involved in Glycolysis

[top]
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)":

MetaCyc Query Top Page for Gene Querying
OUTCOME: That query would immediately retrieve MetaCyc's entry for that gene:

MetaCyc Gene Entry

[top]

BioCyc | EcoCyc | MetaCyc | HumanCyc
SRI International 333 Ravenswood Avenue, Menlo Park, CA 94025-3493
SRI International is an independent, nonprofit corporation.
Privacy policy Disclaimer