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Searching BioCyc
Ron Caspi
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Help is One Click Away!
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The Web Account System
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The Web Account System
Creating a web
account enables you
to:
Save
Object Groups
Define
page formatting
preferences
Define
Overview layout
preferences
Save
organism groups for
comparative analysis
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Save Organism Groups with Web Accounts
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Note the My Lists tab on the
multi-organism selector for
comparative analyses.
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When you perform comparative
analyses, you can easily save
groups of organisms for re-using
at a later time.
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Define a Favorite Database with Web Accounts
If you create a web
account, you can define
a favorite database that
will be opened by
default when you login
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Searching
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Why the Need for Dedicated Search Tools
Search BioCyc for “L-arginine”
2080 results
Need to have specific
tools for finding exactly
what we search for.
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BioCyc Searches
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Multiple searches available for finding information in different
ways
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The easiest searches to use are fairly coarse
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Start by selecting database to search
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Simplest search: Quick Search
 At upper right of most pages
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Selecting the Database
You can only search one database at a time*!
* With the exception of Google searches
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Click on word “change” under
Search menu or under Quick
Search button
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In resulting selector, choose a
PGDB
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Start typing a word in organism
name
Click on letter to navigate to
organisms starting with that letter
Click a frequently used PGDB
Select by Taxonomy
All subsequent searches will
apply to that database
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The Quick Search Box
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What can you type here:
 Gene names (dnaA )
 Compound name (L-lysine)
 Pathway name (peptidoglycan biosynthesis)
 Reaction name (lysine decarboxylase)
 Protein name (peptidase)
 EC number (1.3.1.26)
 Organism name (Escherichia coli)
 Frame ID (CPLX-8024)
 GO term (0006086)
 Links to other databases (O33998)
 An exact term using the format (Peptidase D search:exact)
 Limited term (hydrogen type:compound)
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What doesn’t work:
 Exact text using the Google format (“peptidase D”)
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Quick Search Results
 Results
are divided into
multiple categories
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Examples of searches performed by users of
the BioCyc website:
Successful
Ascorbate
EC 3.4.17.5
Sigma factor
Polysulfide reductase
Entner-Doudoroff pathway
Cyanobacteria
DnaA
Unsuccessful
pheV
Transmembrane helix 6
3.4.24.B11
ABC cobalt transporter
affinity of DnaA
A simple auto-correction mechanism tries to correct typos. For
example, searching for “sacrosine” will find “sarcosine”.
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Quick Gene Search
 Useful
when only interested in genes.
 For
example, compare the results when searching for
“dnaA” by using the Quick Search and Gene Search
buttons.
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The Search Menu
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Search Menu
 Object-specific searches
 Advanced search
 Ontologies search
 Google search
 BLAST search
 Search of full-text articles (EcoCyc only)
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Google This Site
The BioCyc site is indexed by Google
You can launch a Google text search from:
1. Search → Google This Site
2. The alternative searches box that appears on Quick
Search results pages
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Object-Specific Searches
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The first four items in the search
menu provide a medium-level search
interface against single types of
objects
Use of filtering
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Click on triangles at the
left to expand or hide
filters
Note that if a filter is
hidden it will not be used
in a search
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Compound Search
All buttons – quick way to get complete lists
 Examples for compound searching:
 List
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Search Genes/Proteins/RNAs
All buttons – quick way to get complete lists
 Extensive filtering options
 List
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Search Pathways
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Advanced Search
 The
BioVelo query language
 SAQP: Structured Advanced Query Page
 Permits the definition of complex searches without mastering
BioVelo.
To learn more about
the advanced query
interface, see online
documentation.
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Sequence Search by BLAST
unusual here – a regular BLAST interface
that permits BLASTing sequences against BioCyc
PGDBs.
 The results are linked to the PGDB gene/protein
pages
 Nothing
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Growth Media and Phenotype
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The desktop version of
Pathway Tools allows
definition of growth
media, gene knockout
growth information,
and growth data for
phenotype microarray
plates.
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EcoCyc-Specific Searches: Growth Media
Search for growth
media based on:
name
compounds
present
compounds not
present
observed growth
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EcoCyc-Specific Searches: Textpresso
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Mining E. coli literature poses special
challenges – because almost every molecular
biology paper references E. coli
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The solution – EcoCyc Textpresso! An E. coli
only collection of literature
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30,000 full-text articles and 6,500 abstracts.
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Full text literature searches
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Results presented at bottom of page
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