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TRAIT (TRAnscript Integrated Table): a knowledgebase of human skeletal muscle transcripts.

Stefano Toppo1, Nicola Cannata, Paolo Fontana

  • 1CRIBI, Università di Padova, via Ugo Bassi 58/B, Padova, 35131 Italy.

Bioinformatics (Oxford, England)
|March 26, 2003
PubMed
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The TRAIT knowledgebase integrates transcript data with genomic, protein, and disease information. This system aids in managing and querying extensive biological data for research.

Area of Science:

  • Bioinformatics
  • Genomics
  • Molecular Biology

Background:

  • The TRAIT knowledgebase was initially developed to manage expressed sequence tag (EST)-based gene discovery in human skeletal muscle.
  • This project generated over 4500 independent sequence clusters, highlighting the need for integrated data management.

Purpose of the Study:

  • To create a comprehensive knowledgebase (TRAIT) for integrating diverse biological data.
  • To facilitate efficient querying and analysis of transcriptomic and related genomic information.

Main Methods:

  • Data integration from genome, proteins, ortholog genes, and diseases.
  • Annotation of transcripts using both automatic and manual procedures.
  • Storage of data in a MySQL database with a user-friendly web interface for complex queries.

Related Experiment Videos

Main Results:

  • Successful management of over 4500 independent sequence clusters from a human skeletal muscle gene discovery project.
  • Development of a system for linking known transcripts to public databases and predicting features for unknown transcripts.
  • Implementation of a query system allowing concurrent selection of multiple fields (ontology, expression, map position, protein domains) with ranked results.

Conclusions:

  • The TRAIT knowledgebase provides a robust platform for managing and accessing integrated biological data.
  • The user-friendly interface and ranked results enhance the utility of the knowledgebase for researchers in genomics and molecular biology.