Changes between Version 4 and Version 5 of PhyloWS_workgroup

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Timestamp:
2008/02/12 10:44:01 (10 years ago)
Author:
hlapp
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  • PhyloWS_workgroup

    v4 v5  
    1313 * Start a reference implementation, for example based on data in BioSQL 
    1414 
    15 Gathering of use-cases and task-oriented requirements has started at http://evoinfo.nescent.org/PhyloWS.  
     15Gathering of use-cases and task-oriented requirements has started at http://evoinfo.nescent.org/PhyloWS. 
     16 
     17The Open Space discussion centered on the following issues: 
     18 * The OTU (Operational Taxonomic Unit) perspective is an important use-case.  
     19  * Gene tree analysis: similar to the Zmasek et al (2007) paper, one may want to build alignments and phylogenetic trees for all ortholog families of a  gene family, or a pathway. After loading the trees into a database, one could then query the database for those gene trees that support a certain species phylogeny, for example the Ecdysizoan hypothesis. 
     20   * Problem: the query topology will be given with either gene name labels, or species name labels, but the labels of the trees will be OTUs. 
     21   * Hence, each OTU needs to be linked to the gene name(s) and taxon names, and it needs to be possible to specify that matching tree nodes use the linked taxon or gene names.  
     22