We developed, as a part of the data loader, a unified data transformation module to perform such translations.
It was desired, therefore, to add a more generic data loader that required no programming and could be sufficiently flexible to load data into any Chado table.
Data import and storage are handled by the data loader module (Fig. 1C) that either reads a generic text-based data input format or can be fully automated if tailored to the chosen combination of set-up/image processing tool.
Data loader The data loader is responsible for transforming simulation data to the format required for storage in the database system.
Three input parameters, the matrix data loader, the condition pool, and the gene mapping, are fed into the SAGE data filter, the core of the data processing unit.
It is developed to follow the steps typically encountered in a cell migration experiment (Fig. 1 and Table 1) and is composed of three modules: the experiment manager, the data loader and the data analyzer.
For example, the genomic data loader for data from the Broad Institute gathers the contigs, genes and protein sequence data from 3 separate FASTA files and relates the data to information provided in other files of different formats.
Sequences within a superfamily were classified into homologous families based on multiple sequence alignments and phylogenetic trees, as calculated by CLUSTAL W (28). Information on source organism, sequence annotations and sequence was extracted by the sequence data loader of the DWARF system.
Tripal does provide an API for interacting with a Chado database, as well as data loaders (e.g. FASTA, GFF3 and OBO loaders) but interacts directly with the Chado database and does not use BioPerl.
Furthermore, Tripal provides a web-based Chado installer, genomic data loaders, web-based editing of data for organisms, genomic features, biological libraries, controlled vocabularies and stock collections.
Generic CSV/TSV tables can be used for all types of visualizations, and its core provides data loaders for those files.
