Changes between Version 51 and Version 52 of PhyloWS_workgroup

Show
Ignore:
Timestamp:
2008/02/15 16:40:09 (11 years ago)
Author:
rvos
Comment:

--

Legend:

Unmodified
Added
Removed
Modified
  • PhyloWS_workgroup

    v51 v52  
    4141In a [http://hackathon.dbcls.jp/attachment/wiki/PhyloWS_workgroup/P1070128.JPG white board] exercise the next day, we identified plausible input and output data types for phyloinformatic webservices. Plausibility is defined by our being able to imagine [https://www.nescent.org/wg_evoinfo/PhyloWS#Use_Cases use cases] (no time line for implementation implied, the goal here is to come up with interfaces) 
    4242 * '''Inputs''' - The input data types defined here do not imply pass-by-value, i.e. "One Tree" could be some kind of identifier. In addition, it looks like several services need multiple data types (e.g. a matrix + a tree, in order to return a tree score). Given that accumulate-and-fire (i.e. stateful operations, where you first post a matrix, then a tree) is a Bad Thing, and that tunneling multiple data types in a single attachment or body (e.g. a chunk of nexus/nexml) is also a Bad Thing, it seems that these combinations of data would be submitted as multiple post parameters. 
    43   * '''One Tree''' - exactly one tree, which might function as a query topology, as an input for topology metric calculations, or as something for which associated data (matrices) and metadata might be retrieved 
    44   * '''Pair of Trees''' - exactly two trees, which function as inputs for tree reconciliation (e.g. duplication inference) or for tree-to-tree distance calculations 
    45   * '''Set of Trees''' - input for consensus calculations, or as query topologies 
    46   * '''One OTU''' - exactly one OTU for which associated data (trees or matrices that contain it) and metadata might be retrieved 
    47   * '''Pair of OTUs''' - exactly two OTUs, as input for topological queries (MRCA) and calculations (patristic distance) 
    48   * '''Set of OTUs''' - input for topological queries (MRCA) and for which data (trees or matrices that contain them) and metadata might be retrieved 
    49   * '''One Node''' - input for tree traversal operations (parent, children) and for which metadata might be retrieved 
    50   * '''Pair of Nodes''' - input for topological queries (MRCA) and calculations (patristic distance) 
    51   * '''Set of Nodes''' - input for topological queries (MRCA) 
    52   * '''One Character''' - exactly one character (matrix column) for which calculations are performed (variability) and metadata is retrieved 
    53   * '''Set of Characters''' - input as filter predicate, to retrieve OTUs that contain recorded states for the characters 
    54   * '''One Character State Sequence''' - for which metadata is retrieved 
    55   * '''Pair of Character State Sequences''' - as input for pairwise alignments, as input to calculate pairwise divergence 
    56   * '''Set of Character State Sequences''' - as input for multiple sequence alignment 
    57   * '''Character State Matrix''' - as input for inference (of one tree or set of trees), as input for calculations (average sequence divergence) and for which metadata is retrieved 
     43  * ''One Tree'' - exactly one tree, which might function as a query topology, as an input for topology metric calculations, or as something for which associated data (matrices) and metadata might be retrieved 
     44  * ''Pair of Trees'' - exactly two trees, which function as inputs for tree reconciliation (e.g. duplication inference) or for tree-to-tree distance calculations 
     45  * ''Set of Trees'' - input for consensus calculations, or as query topologies 
     46  * ''One OTU'' - exactly one OTU for which associated data (trees or matrices that contain it) and metadata might be retrieved 
     47  * ''Pair of OTUs'' - exactly two OTUs, as input for topological queries (MRCA) and calculations (patristic distance) 
     48  * ''Set of OTUs'' - input for topological queries (MRCA) and for which data (trees or matrices that contain them) and metadata might be retrieved 
     49  * ''One Node'' - input for tree traversal operations (parent, children) and for which metadata might be retrieved 
     50  * ''Pair of Nodes'' - input for topological queries (MRCA) and calculations (patristic distance) 
     51  * ''Set of Nodes'' - input for topological queries (MRCA) 
     52  * ''One Character'' - exactly one character (matrix column) for which calculations are performed (variability) and metadata is retrieved 
     53  * ''Set of Characters'' - input as filter predicate, to retrieve OTUs that contain recorded states for the characters 
     54  * ''One Character State Sequence'' - for which metadata is retrieved 
     55  * ''Pair of Character State Sequences'' - as input for pairwise alignments, as input to calculate pairwise divergence 
     56  * ''Set of Character State Sequences'' - as input for multiple sequence alignment 
     57  * ''Character State Matrix'' - as input for inference (of one tree or set of trees), as input for calculations (average sequence divergence) and for which metadata is retrieved 
    5858 
    5959 * '''Outputs''' - In addition to the mirroring the inputs described above, some 'primitives' may be required: 
    60   * '''Int''' - an integer, for things such as topology metrics (node counts) tree-to-tree distances (in branch moves) node distances (in number of nodes in between), character state counts, sequence divergence (substitution counts, site counts) 
    61   * '''Float''' - a floating point value, for topology metrics (balance, stemminess, resolution) tree-to-tree distances (symmetric difference), patristic distance, sequence divergence 
    62   * '''String''' - for metadata, e.g. descriptions 
    63   * '''Stringvector''' - for metadata, e.g. a set of tags 
     60  * ''Int'' - an integer, for things such as topology metrics (node counts) tree-to-tree distances (in branch moves) node distances (in number of nodes in between), character state counts, sequence divergence (substitution counts, site counts) 
     61  * ''Float'' - a floating point value, for topology metrics (balance, stemminess, resolution) tree-to-tree distances (symmetric difference), patristic distance, sequence divergence 
     62  * ''String'' - for metadata, e.g. descriptions 
     63  * ''Stringvector'' - for metadata, e.g. a set of tags 
    6464  * For all I/O combinations, imagine a [https://www.nescent.org/wg/evoinfo/index.php?title=PhyloWS#Use_Cases use case], move to NESCent wiki 
    6565  * For each use case, classify [https://www.nescent.org/wg/evoinfo/index.php?title=PhyloWS#PhyloWS_Requirements scope and requirements]