Changes between Version 5 and Version 6 of Queries

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Timestamp:
2009/12/18 02:29:24 (9 years ago)
Author:
ktym
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  • Queries

    v5 v6  
    1 == Prospective Queries == 
     1== Queries == 
    22 
    3 We would like to implement an advanced search engine -- something like a Wolfram Alpha for biology.  
     3Targeted queries to be resolved by Semantic Web technologies. 
    44 
    5 Expected queries: 
     5One of our goal would be to implement an advanced search engine -- something like a Wolfram Alpha for biology. In this page, we will gather meaningful and challenging queries for the Semantic Web technology and will define some goals of the BioHackathon 2010 from them. 
     6 
     7=== Expected query types === 
     8 
     9Queries may vary from simple google-like keyword or phrase search to biological objects as its input. This section itemize prospected types of query arbitrary. 
     10 
    611 * Gene ID 
    712 * Technical terms 
    8  * Phrase search (e.g. ortholog genes of gene A) 
     13 * Phrase search (e.g. "ortholog genes of gene A") 
    914 * DNA or protein sequence 
    1015 *  : 
    1116 
    12 From [http://ir.ohsu.edu/genomics/2007protocol.html TREC Genomics Trac]: 
     17=== From [http://ir.ohsu.edu/genomics/2007protocol.html TREC Genomics Trac] === 
     18 
     19[http://trec.nist.gov/ TREC] (Text REtreival Conference) held a competition for information extraction (IE) or text mining (TM) researchers and raised following 14 challenging questions to retrieve answering passages automatically. Some of these can also be targets for Semantic Web as well. 
    1320 
    1421 * <T1>What [ANTIBODIES] have been used to detect protein TLR4? 
     
    2734 * <T14>What [TUMOR TYPES] are associated with Rb1 mutations? 
    2835 
    29 From [http://www.flymine.org/release-20.0/templates.do FlyMine Templates]: 
     36 
     37=== From [http://www.flymine.org/release-20.0/templates.do FlyMine Templates] === 
     38 
     39InterMine/FlyMine provides a curated set of typical query templates. As these are checked by the biologists, most of them seems to be meaningful compared to computationally generated queries based on combinations of available resources. 
    3040 
    3141 * Disease [Human] --> Genes + D. melanogaster homologues (filter on BLAST E-Value). 
     
    3646 
    3747 
    38 From participants: 
     48=== From participants === 
     49 
     50Please add your own use cases here: 
    3951 
    4052 * 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)