The SNP data and their related annotations were formatted into tables and stored in SorGSD using the MySQL database management system (version 5).
Annotation fields in SBML are formatted in RDF (the resource description Framework ([ 10]. Each such external link entry is annotated with a qualifier (e.g., "is", "isHomologTo", "isDescribedBy", etc).
The effort required to organize community annotation data is significantly reduced using the Apollo-Chado approach because 1) errors arising from mistakes in data entry on web forms are eliminated, 2) annotations produced by community members are formatted in a way that allows direct loading into the Chado database.
Retrieved gene set and annotations are optionally filtered in the third step according to user input, and are formatted in the specified output format in the last step.
Annotations are automatically formatted to the PAF standard.
Using the platform, organizations can collect, enhance, publish, enable commenting and annotation, and report on their open data no matter in what format it's formatted.
The GEP gene annotations are in BED format, and most of the gene characteristics (e.g., gene size, coding exon size) were determined using BEDTools (Quinlan and Hall 2010) and custom scripts.
In the NaviCell annotation format, annotations are structured in sections, each grouping a specific type of information.
GEO annotations are in free-text format and a certain concept is frequently presented in different ways by different scientists, making it difficult to organize and compare data generated from different research institutions.
In both cases, the annotations are saved in the same format (RDF) providing a way to easily compute metrics.
