Changes between Version 6 and Version 7 of PhyloWS_workgroup

2008/02/12 11:22:45 (11 years ago)



  • PhyloWS_workgroup

    v6 v7  
    2222  * In molecular and comparative genomics applications, one may want to find all trees that have been built for a certain sequence. 
    2323   * Problem: As above, querying by sequence will give the gene name or the sequence accession number to match by, but tree nodes will have OTUs as labels.  
     24 * We discussed whether we need identifiers for OTUs. 
     25  * Pros: Rather than many individual idiosyncratic schemes for encoding sequence ID and taxon (and possibly additional information) into an OTU label, a single identifier could be resolved to the metadata using a common mechanism (such as LSID). Alternatively, one could standardize on a common encoding mechanism, that could then be parsed by a common mechanism. 
     26  * Cons: If using an (presumably opaque) identifier for OTUs, one ought to be able to expect that the same combination of sequence ID, taxon name (where one often implies the other, unless sequence ID is really an ambiguous gene name), and additional metadata (such as allele, population sample, etc) results in the same identifier, in essence necessitating an OTU identifier registry, or a common algorithm for constructing the identifier (which would then no longer be opaque). A standardized encoding mechanism would need to be widely supported and adopted.