SRI International Bioinformatics 1 Searching BioCyc Ron Caspi.

SRI International Bioinformatics1

Searching BioCyc

Ron Caspi

2 SRI International Bioinformatics

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The Web Account System


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


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.


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


Searching


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.


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


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


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”)


Quick Search Results

Results are divided into multiple categories


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”.


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.


The Search Menu

Search Menu Object-specific searches Advanced search Ontologies search Google search BLAST search Search of full-text articles (EcoCyc only)


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


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


Compound Search

List All buttons – quick way to get complete listsExamples for compound searching:


Search Genes/Proteins/RNAs

List All buttons – quick way to get complete listsExtensive filtering options


Search Pathways


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.


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


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


EcoCyc-Specific Searches: Growth MediaSearch for growth media based on:

namecompounds presentcompounds not presentobserved growth


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

SRI International Bioinformatics 1 Searching BioCyc Ron Caspi.

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Transcript of SRI International Bioinformatics 1 Searching BioCyc Ron Caspi.