ORDB

ORDB provides a centralized repository of olfactory receptor and olfactory receptor-like gene and protein sequences, automating acquisition from GenBank and SWISS-PROT and structuring sequence metadata for olfactory research.

Key Features:

• Automated sequence acquisition: Automates downloading of relevant sequences from web sources including GenBank and SWISS-PROT.
• HTML parsing and extraction: Uses HTML parsing techniques to extract sequence and annotation information from source pages.
• Metadata correlation: Correlates extracted data with existing metadata in the ORDB knowledge base.
• Unstructured-to-structured transformation: Transforms unstructured text into structured records aligned with the database architecture.
• EAV/CR data encoding: Encodes structured data using an entity attribute value with classes and relationship (EAV/CR) model.
• Population methods: Supports batch, automatic, and semi-automatic population modes for importing data.
• XML import: Leverages extensible markup language (XML) for encoding imported documents.
• SenseLab integration: Integrates structured data within the broader SenseLab project framework.

Scientific Applications:

• Sequence repository and curation: Centralized cataloging and management of olfactory receptor gene and protein sequences for research.
• Metadata structuring for olfaction research: Structuring unstructured sequence and annotation text to support downstream analyses of olfactory receptors.
• Integrated datasets for sequence analysis: Provision of integrated sequence and metadata resources to support analysis of genetic and protein sequences associated with olfaction.

Methodology:

Automated downloading from GenBank and SWISS-PROT; HTML parsing for data extraction; correlation of extracted data with existing ORDB metadata; transformation of unstructured text into structured records encoded using an EAV/CR model; data import via batch, automatic, or semi-automatic population methods using XML.