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The Structured Advanced Query Page

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Title: The Structured Advanced Query Page


1
The Structured Advanced Query Page
  • Mario Latendresse
  • Tomer Altman
  • Bioinformatics Research Group
  • SRI International
  • March, 2014

SRI International Bioinformatics
1
2
Introduction
  • Structured Advanced Query Page (SAQP)?
  • Web page for interactively constructing advanced
    and precise queries to PGDBs
  • SAQP is not available on Ptools desktop
  • Queries are translated to BioVelo and sent to
    the server for processing
  • Top Menu Bar command Search -gt Advanced Search
  • http//biocyc.org/query.shtml
  • Documentation http//biocyc.org/webQueryDoc.shtm
    l
  • BioVelo is a query language
  • Like SQL but simpler and no updates allowed
  • Documentation http//biocyc.org/bioveloLanguage.
    shtml
  • Free-Form Advanced Query Page (FFAQP) allows Web
    submission of BioVelo queries

SRI International Bioinformatics
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3
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.

SRI International Bioinformatics
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The Structured Advanced Query Page
  • 'Structured it is a dynamic HTML form, that
    provides greater ease in crafting queries, but
    trades flexibility and power for simplicity
    (FFAQP).
  • 'Advanced it allows to write more precise
    queries than the basic search interface.
  • 'Page it is accessed via the Web interface for
    BioCyc (www.biocyc.org/query.shtml), or from your
    own Pathway Tools web server.

SRI International Bioinformatics
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5
SAQP Architecture
  • The SAQP is built on top of a high-level
    functional declarative language called BioVelo,
    which is built on top of Pathway Tools.
  • BioVelo was designed at SRI
  • On every result page, you will see the equivalent
    BioVelo code that was generated from the SAQP,
    which, in turn, generated the results.
  • You don't need to know anything about BioVelo to
    use the SAQP, but it might be helpful later if
    you need the ability to write even more
    complicated queries using the Free Form Advanced
    Query Page (FFAQP).

SRI International Bioinformatics
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How to Use the SAQP
  • 1. Database and class selection then adding
    conditions
  • 2. Selection of attributes to output (columns)
  • 3. Select the output data format (HTML vs TXT)?
  • 4. Click the Submit Query button
  • Documentation about each attribute is displayed
    by mousing over its name once selected

SRI International Bioinformatics
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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
  • Display the protein names

SRI International Bioinformatics
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Structure of the Results
  • A line that shows the equivalent BioVelo
    expression that the SAQP generated to answer the
    query
  • A button to create a SmartTable from the result
  • A HTML table of the results, with the
    corresponding entries hyperlinked to the matching
    Pathway Tools Web pages
  • Sorting can be applied on each column
  • If a text data format was requested, then a
    tab-delimited text file is generated, with just
    the table data

SRI International Bioinformatics
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Example 2,
  • We will add a condition to example 1
  • Find all the proteins of E. coli K-12 for which
    the DNA-FOOTPRINT-SIZE is smaller than 10
  • Display the protein name, and the DNA footprint
    size.

SRI International Bioinformatics
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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
  • Display the polypeptide name, the experimental
    molecular weight, and the pI

SRI International Bioinformatics
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Example 4
  • The SAQP allows for specifying quantifiers on
    relations between PGDB classes
  • Extending example 3 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.

SRI International Bioinformatics
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Exercises
  • 1) Find all genes of E. coli that contain trp
    in their name.
  • 2) Find all genes in MetaCyc that have more than
    one product. Output the gene names and product
    names.
  • 3) Find all reactions in E. coli which have the
    reactant (i.e., the left side) acetaldehyde.
  • 4) Find all monomers in E. coli. A monomer has no
    components.
  • 5) Find all reactions in MetaCyc that have more
    than 4 reactants.
  • 6) Find all metabolic pathways, in MetaCyc, that
    have more than 5 reactions. Output the reaction
    lists as well as the pathway names.

SRI International Bioinformatics
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Introduction to BioVelo
  • BioVelo is based on set and list comprehension.
  • In Mathematics, a set comprehension describes a
    set of values as in x x in Prime, x gt 100
  • The output is 'x', the body has a generator 'x in
    Prime' and a condition 'x gt 100'. Several
    conditions and several generators could be used.
  • BioVelo used a concise syntax
  • 1) output-expression generator, condition,
    ...
  • 2) a generator has the form v ?
    databaseclass
  • 3) a condition uses logical and relational
    operators

SRI International Bioinformatics
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Examples of BioVelo Queries
  • r r lt- ecolireactions
  • pname p lt- ecoliproteins
  • p?name plt- ecoliproteins
  • p?name p lt- ecoliproteins,
    pdna-footprint-size lt 10
  • (g?name, gleft-end-position) g lt-
    ecoligenes,

  • gleft-end-position lt 153000
  • (g?name, k) glt- ecoligenes, k
    abs(gleft-end-position gright-end-position)1,
    k lt 200
  • (r?name, c?name) rlt- ecolireactions, clt-
    rleft, c in rright

SRI International Bioinformatics
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