Argos 
& Genome Directories  
& Lucegene ('Lucy Jean') 
A Replicable Genome infOrmation System 
of Common Components

GMOD Meeting, Sept. 2003

D. Gilbert, gilbertd@indiana.edu, http://marmot.bio.indiana.edu/

Lucegene ('Lucy Jean')
for Genome Information Search and Retrieval
[IN BRIEF]

Info. Retrieval for Genomes
* IR text search/retrieval tools tuned for data access, not management
* Good for a wide range of semi-structured and complex structured data 
* Better functional match for textual data common in biology than numeric, table-oriented RDBMS
* Easier to add new data (e.g. SRS parses 100s of existing bio-databanks)

Lucene and LuceGene
* Lucene open-source project at jakarta.apache.org/lucene
* Common text search features: booleans, phrases, word stemming, fuzzy and field range searches, relevance ranking
* Comparable to Glimpse, Exite, WAIS, Isearch, ht/dig, Alta-vista, Google backends
* Author Doug Cutting has written text search engines for Apple and Excite
* LuceGene additions
* Data input adaptors for HTML; XML (e.g. MedLine); FlyBase flatfile; Biosequences (GenBank, EMBL, etc.)
* Basic output formats for XML, HTML via XSLT, Text, Spreadsheet
* Tested with
* 100,000s of FlyBase Genes, References, Game and Chado XML annotations
* euGenes gene summaries & Daphnia Medline, Sequences, HTML documents
* LuceGene/Lucene needs
* Range search improvements (inefficient, dies w/ large range)
* Links/joins among databases
* Output adaptors and work? (or rely on data source formatting)