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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 $