1. SRI International Bioinformatics 1 The Structured Advanced Query Page Tomer Altman Bioinformatics Research Group SRI, International February 1, 2008

2. 1 SRI International Bioinformatics 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

3. SRI International Bioinformatics 1 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.

4. SRI International Bioinformatics 1 The Structured Advanced Query Page 'Advanced', in that it allows you to ask more advanced and complicated queries than the basic search interface. '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 (www.biocyc.org/query.html), or from your own Pathway Tools webserver.

5. SRI International Bioinformatics 1 SAQP Architecture The SAQP is built on top of a high-level functional declarative language called BioVelo (Mario Latendresse, SRI), which is built on top of Pathway Tools. 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.

6. SRI International Bioinformatics 1 The Structure of the SAQP: Database specification Class specification 'Where' constraints on attributes of classes Output attributes description Data format (HTML vs TXT)

7. SRI International Bioinformatics 1 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.

8. SRI International Bioinformatics 1 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.

9. SRI International Bioinformatics 1 Example #2: 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.

10. SRI International Bioinformatics 1 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 protein name, the experimental molecular weight, and the pI.

11. SRI International Bioinformatics 1 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.

12. SRI International Bioinformatics 1 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.