andy jenkinson, ebi the das protocol. summary of topics technical overview principles of...
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Andy Jenkinson, EBI
The DAS Protocol
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Summary of Topics
• Technical overview
• Principles of communication
• Pros and cons
• DAS capabilities
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DAS Architecture
• A client asks for data from many servers• HTTP requests• identically structured URLs, the same parameters
• Each server behaves in the same way• pre-defined set of behaviours• e.g. provide a sequence, provide annotations of a sequence
• Each server provides different data in the same format• DAS-XML
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DAS Concepts
Reference object• usually a sequence• e.g. “chromosome X” or “NT_025741”
Annotation• information attached to a location within a segment• e.g. “substitution at residue 326 of BRCA1”
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DAS Concepts
Reference server• server that provides “core” reference object data• e.g. GRCh37 sequence data
Annotation server• server that provides annotations of reference objects
Segment• part of a reference object • e.g. “bases 100 to 200 of chromosome X”• ties together annotation and reference servers
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Architectural Overview
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The DAS Protocol
Defines 3 constraints• transport layer: HTTP• query format: constrained REST URLs• response format: constrained XML
Keyword: constrained
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The DAS Protocol
Defines 3 constraints• transport layer: HTTP• query format: constrained REST URLs• response format: constrained XML
![Page 9: Andy Jenkinson, EBI The DAS Protocol. Summary of Topics Technical overview Principles of communication Pros and cons DAS capabilities](https://reader035.vdocument.in/reader035/viewer/2022070306/5516c285550346a25b8b613c/html5/thumbnails/9.jpg)
The DAS Protocol
Defines 3 constraints• transport layer: HTTP• query format: constrained REST URLs• response format: constrained XML
Data transport• Standard HTTP• Includes compression• Some additional headers, e.g. to indicate DAS version
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The DAS Protocol
Defines 3 constraints• transport layer: HTTP• query format: constrained REST URLs• response format: constrained XML
Well-defined query URLs• A client can issue a command
http://das.sanger.ac.uk/das/ccds_mouse/features?segment=...^^^^^^^^^^^^^^^^^^^^^^^ ^^^ ^^^^^^^^^^ ^^^^^^^^ ^^^^^^^^^^^ site prefix das source command arguments
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The DAS Protocol
Defines 3 constraints• transport layer: HTTP• query format: constrained REST URLs• response format: constrained XML
XML format• server responds with a simple XML document
<SEGMENT id=“X” start=“1” end=“100”> <FEATURE id=“exon1”> <TYPE id=“exon”>exon</TYPE>
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Why DAS?
Fast, targeted queries• suitable for visual display
Based on existing simple tech• XML/HTTP/CGI• “dumb server, clever client” - relatively low knowledge
barrier for bioinformaticians with data to expose
Scalable• integrators (client software) get more data for zero cost
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Why not DAS?
One-dimensional queries• query only by sequence position• not by developmental stage, tissue type, etc• (yet)
Constrained generic format• clients aren’t “tailored” to each data source • possible data types are to some extent limited
Not semantically rich• ontology support optional
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Commands: the basics
Sequence• give me the DNA sequence for a given segment of a
reference object• e.g. “bases 100k – 200k of chromosome 15”
Features• give me all annotations offered by the data source that
are attached to a given segment of the sequence
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The sequence command
/das/<source>/sequence?<params>
Parameters:
segment=ID:start,end (one or more)
ID of reference object
Example:
/das/<source>/sequence?segment=X:100,200 ;segment=Y:500,600
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The sequence command
Response:<DASSEQUENCE> <SEQUENCE id="X” start="100” stop="200” version="1.0”> cctgagccagcagtggcaacccaatggggtccctttcca... </SEQUENCE> <SEQUENCE id=”Y” start=”500” stop=”600” version="1.0”> ctggacagcccggaaaatgagctcctcatctctaaccca...</SEQUENCE></DASSEQUENCE>
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The features command
/das/<source>/features?<params>
Parameters:
segment=ID:start,end (one or more)
type=foo (zero or more)
category=bar (zero or more)
Example:
/das/<source>/features?segment=X:100,200 ;segment=Y:500,600 ;type=SNP
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The features command
Response:<DASGFF> <GFF version="1.01" href=”..."> <SEGMENT id="X" start="100" stop="200"> <FEATURE id="X"> <START>100</START> <END>200</END> <TYPE id=”SNP” category=”variation">SNP</TYPE> <METHOD id=”sequencing">sequencing</METHOD> <SCORE>86.4</SCORE> <ORIENTATION>+</ORIENTATION> </FEATURE> ...
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Other Commands
Stylesheet• hints on how to render different types of feature• e.g. “exons as blue boxes, SNPs as red triangles”
/das/<source>/stylesheet
Types• lists the types of feature available
/das/<source>/types
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Metadata
Can make a client that knows how to query a server and parse the response
BUT something missing…• which data sources are available on a server?• which commands does a source support?• what kind of reference objects does it know about?
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The sources command
<server>/das/sources
• Lists a server’s data sources
For each source:• text description• list of “capabilities” (commands)• list of coordinate systems (type of reference object)• etc
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DAS Registry
• third component of DAS• catalogue of DAS sources
Human interface• validate, register, search, view statistics
Programmatic interface• http://www.dasregistry.org/das/sources• http://www.dasregistry.org/das/coordinatesystem• http://www.dasregistry.org/das/organism
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SOA
Registry
Find
ClientBindServer
Publ
ish
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Links
DAS Homepage• http://www.biodas.org/
DAS Specification• http://www.biodas.org/documents/spec-1.6.html
DAS in Ensembl:• http://www.ensembl.org/info/docs/das/index.html
Mailing list:• http://biodas.org/mailman/listinfo/das