Schema driven assignment and implementation of life science identifiers (LSIDs)

J Biomed Inform. 2008 Oct;41(5):730-8. doi: 10.1016/j.jbi.2008.05.014. Epub 2008 Jun 13.

Abstract

Life science identifier (LSID) is a global unique identifier standard intended to help rationalize the unique archival requirements of biological data. We describe LSID implementation architecture such that data managed by a relational database management system may be integrated with the LSID protocol as an add-on layer. The approach requires a database administrator (DBA) to specify an export schema detailing the content and structure of the archived data, and a mapping of the existing database to that schema. This specification can be expressed using SQL view syntax. In effect, we define a SQL-like language for implementing LSIDs. We describe the mapping of the view definition to an implementation as a set of databases triggers and a fixed runtime library. Thus a compiler for a domain-specific language could be written that would reduce the implementation of LSIDs to the task of writing SQL view-like definitions.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Computational Biology / methods*
  • Database Management Systems / organization & administration*
  • Databases, Factual
  • Humans
  • Natural Language Processing*
  • Online Systems / organization & administration
  • Programming Languages
  • Software Design*