DASx3DEM
Available services:
The Distributed Annotation System (DAS) is a REST-based Web Services system that allows distribution and integration of biological information by providing features for a wide rage of biological entities: genes, proteins, structures, etc. DASx3DEM uses a client-server pattern to provide the structural 3D models maintained at the Electron Microscopy DataBase (EMDB) together with their related information (annotations).
This way, the 3D-EM models are the reference data where annotations are located representing the known features for a particular macromolecule. Accessing other biological entities is also possible as far as a relation between coordinate systems exists, serving as an alignment method. In DASx3DEM the hybrid models resulting from fitting models at the atomic resolution level (as those in PDB) into the volume maps from
A project proposing the translation of the REST services into SOAP-RPC services is now under development.
See an overview of the architecture in the attached picture.
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Test #1: DASx3DEM test : DAS dsn command.
This test checks whether or not DASx3DEM system is up and running.
The DAS dsn command request a list of data sources available at the site.
It issues a request to the URL: http://www.biocomp.cnb.csic.es:9000/das/dsn
The server response is an XML document with the list of active DAS services and their base URL locations.
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<?xml version="1.0" standalone="no"?>
<?xml-stylesheet type="text/xsl" href="http://biocomp.cnb.csic.es:9000/das/xsl=dsn.xsl"?>
Test #2: DASx3DEM test : Reference service - entry_points command.
This test checks whether the reference service of the DASx3DEM system is up and running.
The DAS entry_points command requests a list of 3D-EM models available at the site.
This test issues a request to the URL: http://biocomp.cnb.csic.es:9000/das/3DEM/entry_points
The server response is an XML document with the list of entry points, 3D-EM models in this case.
Service consumers can use this list to search for an entry and set a new request for more detailed information on a particular 3D-EM model.
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Test #3: DASx3DEM test : Reference service - volmap command.
This test checks whether DASx3DEM is up and running.
The DAS volmap command requests information for a particular 3D-EM model (volume map) from the EMDB data base.
This test issues a request to the URL: http://biocomp.cnb.csic.es:9000/das/3DEM/volmap?query=EMD1134
The server response is an XML document with basic information on the requested entry.
Service consumers can use the LINK element content of the response (which is an URL) in order to retrieve the file containing the volume map for the 3D-EM model.
Test #4: DASx3DEM test : Alignment service - entry_points command.
This test checks whether the alignment service of the DASx3DEM system is up and running.
The DAS entry_points command requests a list of entries available at the site.
This test issues a request to the URL: http://biocomp.cnb.csic.es:9000/das/3DEM_Fitting/entry_points
The server response is an XML document with the list of entry points, in this case hybrid models obtained by fitting PDB structures within 3D-EM volumes.
Test #5: DASx3DEM test : Annotation service - features command.
This test checks whether the annotation service of the DASx3DEM system is up and running.
The DAS features command requests a list of annotations known for a requested entry.
This test issues a request to the URL: http://biocomp.cnb.csic.es:9000/das/3DEM_EMDB/features?segment=EMD1017
The server response is an XML document with the list of annotations with known features for a 3D-EM model, in this case.
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