Queries

This section describes the queries that have been (or are to be) implemented for the Phenoscape data services, in addition to the execution details of each queries on the PostgreSQL database on Darwin.

Status (Jan 20, 09)

The first iteration of the Web Services module for the Phenoscape project (the SICB prototype) was demonstrated at the SICB meeting in Boston, MA in January 2009. This module allowed database searches for Anatomical Entities (Anatomical Entity Services) and Genes (Gene Services). Searches for Taxa (Taxon Services) are to be implemented in the next iteration which will be a part of the next Phenoscape version to be demonstrated at the ASIH meeting in Portland, OR (the ASIH prototype) in July, 2009.

Testing by the Phenoscape project stakeholders (Paula, Todd, and Monte) at the SICB meeting revealed that Anatomy and Gene Services were functional, but their execution was very slow in terms of time. As a result, the data retrieval strategy used in the SICB prototype is being examined for bottlenecks and these details are presented here.

Summary

Queries are assembled in a Java program and dispatched through a connection to the database, and executed at the database end. For brevity's sake, the Java program is called the client side and the database side is called the backend henceforth. The query modules on the client-side interface with the database in the backend to execute the queries. The data retrieved by these query executions are then processed at the client-side. There are two possible bottlenecks in this scheme: one at the client-side and the other at the backend.

The backend bottleneck is the more likely of the two. This is because the query has to be transmitted through the connection from the client side to the backend, then executed at the backend (a process in itself which is not discussed here), and the retrieved results sent back over the connection to the client side. All this takes time, which eventually adds up. As a case in point, the query execution strategy implemented for the SICB prototype spawns a multitude of queries. The execution of each of these queries takes up time to connect, retrieve the results, and transfer them back to the client side. Therefore, a new strategy that tries to obtain all the required data in one query (or a very limited number of queries) is being tested as of now. Details of both the old and new strategies can be found in the linked pages

To test the efficiency of the new queries, more methods need to be added to the OBD Shard libraries, the projects have to be compiled and linked prior to testing. This is to be done over the next two weeks from now (Jan 20, 09). The details of these strategies can also be found here.

Database details

• Last updated: Jan 02, 2009
• Size: ~ 600 MB

Anatomical Entity Services

Queries on anatomical entities retrieve information on the qualities that inhere in them, the taxa that exhibit these entity-quality (or more correctly, character-state) combinations. Querying strategies to retrieve this information from the OBD database leverage a number of relation instances which are stored in the OBD database. These are detailed below

Relations of interest

Post compositions of Entities and Qualities are used to relate taxa and phenotypes through the exhibits relation as shown in (1). <javascript> Taxon exhibits inheres_in(Quality, Entity) -- (1) </javascript> In addition, the OBD database also contains information relating post composed phenotypes to both the Quality and the Entity by different relations as shown in (2) and (3) respectively

<javascript> inheres_in(Quality, Entity) is_a Quality -- (2) inheres_in(Quality, Entity) inheres_in Entity -- (3) </javascript> Quality can be either a Value or an Attribute (beside other slims) and is related to these by the in_subset_of relation as shown in (4) <javascript> Quality in_subset_of Slim -- (4) </javascript>

Qualities and Anatomical entities are subclassed in the PATO and TAO hierarchies respectively as shown in (5) and (6) <javascript> Value is_a Attribute -- (5) Sub Anatomical Feature is_a Anatomical Feature -- (6) </javascript>

• The details of these queries can be found here

• The details of these queries can be found here

Gene Services

The querying strategy for the Gene Services module of SICB prototype is identical to the strategy for the Anatomy Services module. This strategy also involves the spawning of multiple queries, which add to the backend bottleneck. The only difference in this case is this strategy leverages the relationships between genes and genotypes and then, the genotypes and phenotypes (as shown in (1) and (2) below to retrieve the desired information.

<javascript> Gene has_allele Genotype -- (1) Genotype exhibits inheres_in(Quality, Entity) -- (2) </javascript>

Taxon Services

These will be implemented for the first time in the ASIH prototype