Gene ontology (GO) annotation was derived from batch queries of the Database for Annotation, Visualization, and Integrated Discovery (DAVID) Bioinformatics tool or manually through individual NCBI Entrez Gene queries [ 32, 33].
Gene ontology (GO) annotation was derived from batch queries of the DAVID Bioinformatics tool or manually through individual NCBI Entrez Gene queries [ 25, 26].
Probesets were assigned to gene model (poplar genome v1.1, http://genome.jgi-psf.org/poplar/poplar.home.html) using the batch query of NetAffx Analysis Center http://www.affymetrix.com/analysis/index.affx, poplar database query at JGI and similarity researches at NCBI http://www.ncbi.nlm.nih.gov[ 28].
The gene ontology of the genes used in each predictor, as discovered by performing a Batch Query on the Affymetrix website (www.affymetrix.com), included a plethora of genes and pathways thought to be important in cancer pharmacology and biology (Table S1).
Second, a batch query of up to 600 genes can be used to interrogate categories of data from different screens to provide a summary of each gene over the large-scale screening projects within the database.
We also made a subset of polymorphisms from a set of 12,399 CVS (group [S]) by a batch query to the HapMap dataset.
Furthermore, MGD can provide bulk access to certain kinds of information through the Batch Query tool, or the BioMart [3] and InterMine [4] databases.
We also plan to include additional functionality like search options and batch query into the database in future revisions.
Though some may provide facilities for batch query, the users in many instances need to employ external scripts for querying and post-processing the relevant data.
However, for genome-wide comparisons involving multiple queries (batch query), the search is a challenge.
