Prospective Queries

We would like to implement an advanced search engine -- something like a Wolfram Alpha for biology.

Expected queries:

• Gene ID
• Technical terms
• Phrase search (e.g. ortholog genes of gene A)
• DNA or protein sequence
• :

From  TREC Genomics Trac:

• <T1>What [ANTIBODIES] have been used to detect protein TLR4?
• <T2>What [BIOLOGICAL SUBSTANCES] have been used to measure toxicity in response to cytarabine?
• <T3>What [CELL OR TISSUE TYPES] express members of the mammalian TIM gene family?
• <T4>What [DISEASES] are associated with lysosomal abnormalities in the nervous system?
• <T5>What [DRUGS] have been tested in mouse models of Alzheimer's disease?
• <T6>What centrosomal [GENES] are implicated in diseases of brain development?
• <T7>What [MOLECULAR FUNCTIONS] does helicase protein NS3 play in HCV (Hepatitis C virus)?
• <T8>What [MUTATIONS] in apolipoprotein genes are associated with disease?
• <T9>Which [PATHWAYS] are possibly involved in the disease ADPKD?
• <T10>What [PROTEINS] does epsin1 interact with during endocytosis?
• <T11>What Streptococcus pneumoniae [STRAINS] are resistent to penicillin and erythromycin?
• <T12>What [SIGNS OR SYMPTOMS] of anxiety disorder are related to lipid levels?
• <T13>What [TOXICITIES] are associated with cytarabine?
• <T14>What [TUMOR TYPES] are associated with Rb1 mutations?

From  FlyMine Templates:

• Disease [Human] --> Genes + D. melanogaster homologues (filter on BLAST E-Value).
  • For a specified human disease, show all associated human genes and their Drosophila homologues as identified with BLAST. Results are filtered by a specified E-Value, the lower the E-Value, the better the match. (Data Source: Homophila).

• EST clone [A. gambiae] --> Chromosomal location + Gene + D. melanogaster orthologue + Pathway.
  • For a particular A. gambiae EST clone, show its chromosomal location, the corresponding A. gambiae gene, the D. melanogaster orthologue and the pathway. (Data Source: VectorBase?, InParanoid?, KEGG, Reactome, FlyReactome?).

From participants:

• Q: I have a set of predicted genes from a newly sequenced genome of a Theileria species. What is a unique characteristic of this set from the view point of the biological pathway? Is it natural that this organism lacks thiolase in the mevalonate pathway? (Toshiaki Katayama)

• To resolve this sample question, we need taxonomically classified list of biological modules in the pathway filled with a phylogenetic profile of orthologous genes among related species. Then we can confirm its absence with protein2genome mapping, predicted sub cellular localization of the enzyme, knowledge on reaction in the organelle (apicoplast) from related journal articles and reviews. Most of components are already in databases but none of them are semantically linked with each other.