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                              BioMart DAS Adaptor

A.  Introduction

    The BioMart DAS ProServer Adaptor can be used to turn any existing
    BioMart Dataset into one or more DAS Sources that can be utilized
    by any DAS compatible client.  To do this, simply install the
    biomart.pm module into the ProServer SourceAdaptor directory,
    add a BioMart DAS compatible Importable-Exportable pair to the
    DatasetConfig.xml document which describes the dataset, and create
    a ProServer ini-file to configure the server.  Once the ProServer
    process is started using the ini-file, the source is available,
    without any programming.

B.  Installation

    1.  Install ProServer:  If you haven't already done so, download the
        Perl software as described in the ProServer installation guide.
        The guide is available from

        http://www.ensembl.org/info/data/external_data/das/proserver-guide.pdf

    2.  Install the BioMart ProServer Adaptor: Copy (or link) biomart.pm
        to the Bio/Das/ProServer/SourceAdaptor directory within the
        ProServer directory tree.

    3.  Install MartJ: If you haven't already done so, download the
        latest stable version of the MartJ binaries from ##TODO##URL##,
        and follow the installation instructions provided.  You will
        need to use the MartEditor Configuration tool which is included
        in this package to edit your DatasetConfig.xml files.

C.  Deploying a BioMart DAS Source

    1.  Create BioMart DAS compatible Importable-Exportable pairs: Each
        BioMart Dataset can serve multiple BioMart DAS Sources, using
        one Importable-Exportable pair (e.g., both having the same
        linkName) for each source.  Use the MartEditor Java Mart
        Configuration tool to edit the DatasetConfig.xml document for
        your mart and dataset.  To be BioMart DAS compatible, your
        Importable must contain an ordered list of 1 to 3 filters in its
        filters attribute.  The order of these filters must correspond
        to the following functional ordering:

            segment, start, end (segment required)

        The actual internalNames for these filters can be determined by
        the deployer.  A BioMart DAS compatible Exportable can contain
        between 3 and 10 attributes in its attributes list.  The order
        of the attributes in this list must correspond functionally
        with the order of the DAS feature hash keys specified in the
        feature_keys attribute of the ini-file (see below).  Again, the
        actual internalNames of these attributes can be determined by
        the deployer.  See the Examples section below for more details.

    2.  Create a ProServer ini configuration File:  Each ProServer
        instance can serve multiple DAS Sources from a single ini
        configuration file.  These can consist of any sources
        programmatically served by any SourceAdaptor plugin that the
        server has installed.  A BioMart DAS Source Specification uses
        the following template (note all attributes are required):

; Name of the source in the URL for the request.
[source_name]

; Instruct the ProServer instance to make this source available.
state          = on

; Instruct the ProServer instance to use the biomart.pm SourceAdaptor.
adaptor        = biomart

; Provide the biomart source with a MartRegistry.xml configuration file.
registryPath   = /pathTo/MartRegistry.xml

; Instruct the BioMart source to use the following mart and dataset in
; the above Registry file.
mart           = name of mart
dataset        = name of dataset

; Instruct the BioMart source to use the Exportable-Importable pair with
; the following linkName.
linkName       = linkname

; Map each attribute in the Exportable attributes list (in order) to its
; corresponding DAS Feature hash key.  All DAS Exportables must define
; 'id','type', and 'method' attributes.  They can also define 'start',
; 'end', 'ori', 'phase','score', 'note', and 'link' attributes.
feature_keys = id,type,method,not

  3.    Start the ProServer:

            /pathTo/ProServer/eg/proserver -c /pathTo/inifile.ini

D.  Examples

    1.  Simple Single Gene DAS compliant Source Dataset
        specification: Mart myMart contains Dataset myDataset, which
        contains:

        -   Filters corresponding to chromosome, start coordinate,
            and end coordinate, with internalNames myGenesChromosome,
            myGenesStart, and myGenesEnd, respectively.

        -   Attributes corresponding to gene ID, gene start,
            gene end, gene type, gene annotation method, and
            orientation, with internalNames myGenesId, myGenesStart,
            myGenesEnd, myGenesType, myGenesMethod, myGenesOrientation,
            respectively.

        A.  Create the Importable with the following fields (the other
            fields may be required, but are not formally specified in
            the BioMart DAS specification, see the BioMart Documentation
            for more details):

            linkName : myGeneDasLink
            filters  : myGenesChromosome,myGenesStart,myGenesEnd

        B.  Create the Exportable with the following fields (same caveat
            as in the Importable):

            linkName   : myGeneDasLink
            attributes : myGenesId,myGenesStart,myGenesEnd,myGenesType,myGenesMethod,myGenesOrientation

        C.  Export the DatasetConfig.xml to the Mart Database.

        D.  Create the ProServer ini-file somewhere on the file system
            where the ProServer server can access it.  Create the
            following entry (see the ProServer documentation for further
            details of the ini-file requirements):

[my_new_mart_gene_das]
state          = on
adaptor        = biomart
registryPath   = /myHome/configs/myMartRegistry.xml
mart           = myMart
dataset        = myDataset
linkName       = myGeneDasLink
feature_keys   = id,start,end,type,method,ori


    2.  Dataset serving a Gene DAS Source, and a Non-positional DAS
        Source: Mart myMart, Dataset myDataset contains:

        -   Filters corresponding to gene ID, chromosome, start
            coordinate, and end coordinate, with internalNames
            myGenesId, myGenesChromosome, myGenesStart, and myGenesEnd,
            respectively.

        -   Attributes corresponding to gene ID, gene start, gene
            end, gene type, gene annotation method, orientation, and
            mouse homologous gene ID with internalNames myGenesId,
            myGenesStart, myGenesEnd, myGenesType, myGenesMethod,
            myGenesOrientation, and myGenesMouseHomologId, respectively.

        A.  Create the Gene DAS Importable with the following fields:

            linkName : myGeneDasLink
            filters  : myGenesChromosome,myGenesStart,myGenesEnd

        B.  Create the Gene DAS Exportable with the following fields:

            linkName   : myGeneDasLink
            attributes : myGenesId,myGenesStart,myGenesEnd,myGenesType,myGenesMethod,myGenesOrientation

        C.  Create the Non-positional DAS Importable with the following
            fields:

            linkName   : myNPDasLink
            filters    : myGenesId

        D.  Create the Non-positional DAS Exportable with the following
            fields:

            linkName   : myNPDasLink
            attributes : myGenesId,myGenesType,myGenesMethod,myGenesMouseHomologId

        E.  Export the DatasetCofig.xml to the Mart Database.

        F.  Create the ProServer ini-file with the following two
            entries:

[my_new_mart_gene_das]
state          = on
adaptor        = biomart
registryPath   = /myHome/configs/myMartRegistry.xml
mart           = myMart
dataset        = myDataset
linkName       = myGeneDasLink
feature_keys   = id,start,end,type,method,ori

[my_new_mart_np_das]
state          = on
adaptor        = biomart

; Note server can use the same MartRegistry.xml document, mart, or
; dataset to configure multiple sources.
registryPath   = /myHome/configs/myMartRegistry.xml
mart           = myMart
dataset        = myDataset

linkName       = myNPDasLink

; Note the lack of start and end, and the use of the 'note' field to
; designate the mouse homologue ID.
feature_keys   = id,type,method,note


$Id: README,v 1.1.1.1 2006-11-22 20:31:00 arek Exp $