Table 1 Comparison of ontology-based query interfaces. This table shows a comparison of OntoDas with existing systems designed to facilitate ontology-based queries, using various criteria
From: OntoDas – a tool for facilitating the construction of complex queries to the Gene Ontology
Criterion | AmiGO | MartView | GViewer | DOPE | Flamenco | OntoDas |
|---|---|---|---|---|---|---|
1. Problem domains: | Gene Ontology (25 K terms) to multi-species gene DB (2 M entries) | Gene Ontology (25 K terms), individual species gene DBs (30 K entries each) | Gene Ontology (25 K terms), several others (5 K each); rat gene and QTL data (9 K entries) | EMTREE ontology (50 K terms), custom literature DB (10 M entries) | image metadata thesauri (4 K terms each); image databases (35 K entries each) | Gene Ontology (25 K terms) to multi-species gene DB (2 M entries) |
2. Types of queries: | single term only; narrowing by evidence code, species. | multiple terms, only one term, evidence code per ontology. Only one species per query | AND, OR, NOT over several ontologies; no species/evidence code narrowing | AND queries of any number of terms; no narrowing criteria | AND queries across any number of terms; only one term per orthogonal ontology; supplementation with keyword search | AND queries across any number of terms |
3. Initial term finding: | forms, tree navigation | QuickGO browse, search, but no tie-in with MartView interface | no support | Form with intelligent term suggestion; tree navigation | keyword search, dynamic tree navigation | not yet implemented |
4. Combination finding: | no support | no support | no support | valid combinations with first term shown, but limited support for 3 or more | all valid combinations with current query displayed, also size of result set (query previewing) | extensive; all valid combinations displayed, as well as size of result set (query previewing) |
5. Display of results: | paged table, links to detail on each query, links to external information. | simplistic but configurable to be richer; spreadsheet export | highly visual SVG; no table but proprietary spreadsheet export | interactive, visual cluster map; problems with scalability | page-able table, links to detail on each entry, ability to construct new queries from annotations of entry | table with links out; paging and CSV download not yet implemented |
6. User involvement: | minimal, though possibly via mailing list | no evidence of any | no evidence of any | usability evaluation post- development | multiple cycles of testing, re-development, evaluated against a baseline | extensive participatory design throughout the life cycle |
7. Technologies: | web-based: Perl, MySQL | web-based: Perl, BioMart | web-based: Java JSP and Oracle 9i PL/SQL | Desktop-based: Java/Swing, ClusterMap, Sesame RDF store | Web-based: Python WebWare, MySQL, Java/Lucene optional | Web-based: Ajax (MochiKit and others), Python TurboGears, MySQL, web services |