The Structured Advanced Query Page

Tomer Altman

Bioinformatics Research Group

SRI, International

February 1, 2008

Introduction

BioVelo is a query language

Like SQL but simpler and easier to learn

Documentation: http://biocyc.org/bioveloLanguage.html

Free-Form Advanced Query Page allows Web submission of BioVelo queries

Structured Advanced Query Page (SAQP)

Web page for interactively constructing advanced queries to PGDBs

Queries are translated to BioVelo and sent to the PGDB

SAQP: http://biocyc.org/query.html

Documentation: http://biocyc.org/webQueryDoc.html

Why a query interface?

Allow a structured way to access the rich data representation stored in a PGDB.

Most advanced databases have a high-level, declarative method of access (i.e., SQL).

Provides an intermediate level of access between graphically browsing the PGDB and programmatically processing the data using Lisp.

The Structured Advanced Query Page

'Advanced', in that it is built on top of a high-level functional declarative language called BioVelo (Mario Latendresse, SRI).

'Structured', in that it is a dynamic HTML form, that provides greater ease in crafting queries, but trades flexibility and power for simplicity (FFAQP).

'Page', in that it is primarily accessed via the web interface for BioCyc, or from your own Pathway Tools webserver.

The Structure of the SAQP:

Database specification

Class specification

'Where' constraints on attributes of classes

Output attributes description

Data format (HTML vs TXT)

Example #1:

A simple query usually consists of querying a particular database about a particular class.

Find all the proteins in E. coli K-12.

Structure of the Results

A line that shows the equivalent BioVelo expression that the SAQP generated to answer the query.

A HTML table of the results, with the corresponding entries hyperlinked to the matching Pathway Tools webpages.

If a text data format was requested, then a tab-delimited text file is generated, with just the table data.

Example #2:

Find all the proteins of E. coli K-12 for which the DNA-FOOTPRINT-SIZE is smaller than 10.

Example #3:

In EcoCyc, display polypeptides constrained by experimentally determined molecular weight and isoelectric point.

The experimental molecular weight should be between 50 and 100 kD.

The pI should be less than 7.

Example #4:

The SAQP allows for specifying quantifiers on relations between PGDB classes.

Extending example #3, now we want only proteins where at least one of the genes that encodes the protein to be within the first 500 kilobases of the E. coli chromosome.

Example #5: Queries with Several Components

Performs a 'Cartesian product' of the classes from each search component.

Search for all pathways of E. coli that also exist in H. pilori, strains 26995 and HPAG1.

Tomer Altman

2008-02-01T10:02:22