title: Interfaces to PeptideAtlas: a case study of standard data access systems.
abstract: Access to public data sets is important to the scientific community as a resource to develop new experiments or validate new data. Projects such as the PeptideAtlas, Ensembl and The Cancer Genome Atlas (TCGA) offer both access to public data and a repository to share their own data. Access to these data sets is often provided through a web page form and a web service API. Access technologies based on web protocols (e.g. http) have been in use for over a decade and are widely adopted across the industry for a variety of functions (e.g. search, commercial transactions, and social media). Each architecture adapts these technologies to provide users with tools to access and share data. Both commonly used web service technologies (e.g. REST and SOAP), and custom-built solutions over HTTP are utilized in providing access to research data. Providing multiple access points ensures that the community can access the data in the simplest and most effective manner for their particular needs. This article examines three common access mechanisms for web accessible data: BioMart, caBIG, and Google Data Sources. These are illustrated by implementing each over the PeptideAtlas repository and reviewed for their suitability based on specific usages common to research. BioMart, Google Data Sources, and caBIG are each suitable for certain uses. The tradeoffs made in the development of the technology are dependent on the uses each was designed for (e.g. security versus speed). This means that an understanding of specific requirements and tradeoffs is necessary before selecting the access technology.
authors.affiliation: Institute for Systems Biology, Seattle, WA 98109, USA.
authors.forename: Sarah
authors.initials: S
authors.lastname: Killcoyne
authors.forename: Jeremy
authors.initials: J
authors.lastname: Handcock
authors.forename: Thomas
authors.initials: T
authors.lastname: Robinson
authors.forename: Eric W
authors.initials: EW
authors.lastname: Deutsch
authors.forename: John
authors.initials: J
authors.lastname: Boyle
mesh_terms: D030541:Databases, Genetic; D016678:Genome; D023281:Genomics; D016247:Information Storage and Retrieval / Q000379:methods; D020407:Internet; D010455:Peptides / Q000737:chemistry*; D012984:Software
chemical_list: D010455:Peptides