SRI International Bioinformatics1
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
Note the My Lists tab on the multi-organism selector for comparative analyses.
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
Multiple searches available for finding information in different ways
The easiest searches to use are fairly coarse
Start by selecting database to search
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
Click on word “change” under Search menu or under Quick Search button
In resulting selector, choose a PGDB
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 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)
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 Unsuccessful Ascorbate pheV EC 3.4.17.5 Transmembrane helix
6 Sigma factor 3.4.24.B11 Polysulfide reductase ABC cobalt transporter Entner-Doudoroff pathway affinity of DnaACyanobacteria 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
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
The first four items in the search menu provide a medium-level search interface against single types of objects
Use of filtering
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
List All buttons – quick way to get complete listsExamples for compound searching:
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Search Genes/Proteins/RNAs
List All buttons – quick way to get complete listsExtensive filtering options
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Search Pathways
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Advanced Search
The BioVelo query languageSAQP: 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
Nothing unusual here – a regular BLAST interface that permits BLASTing sequences against BioCyc PGDBs.
The results are linked to the PGDB gene/protein pages
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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.
Growth Media and Phenotype
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EcoCyc-Specific Searches: Growth MediaSearch for growth media based on:
namecompounds presentcompounds not presentobserved growth
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EcoCyc-Specific Searches: Textpresso
Mining E. coli literature poses special challenges – because almost every molecular biology paper references E. coli
The solution – EcoCyc Textpresso! An E. coli only collection of literature
30,000 full-text articles and 6,500 abstracts.
Full text literature searches
Results presented at bottom of page