Difference between revisions of "DAS - Distributed Annotation System"
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"The distributed annotation system (DAS) is a client-server system in which a single client integrates information from multiple servers. It allows a single machine to gather up genome annotation information from multiple distant web sites, collate the information, and display it to the user in a single view. Little coordination is needed among the various information providers." - Wikipedia
 
"The distributed annotation system (DAS) is a client-server system in which a single client integrates information from multiple servers. It allows a single machine to gather up genome annotation information from multiple distant web sites, collate the information, and display it to the user in a single view. Little coordination is needed among the various information providers." - Wikipedia
  
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parts.mit.edu is a valid DAS server.
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The DAS interface to the Registry can provide sequence and feature information about any part in the Registry.
  
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DAS information is available via the HTTP protocol. Note that only the Registry at Registry is registered with the
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DASDY service at this time.
  
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The DAS interface to the Registry can provide sequence and feature information about any part in the Registry.
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==DAS DSN Server==
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'''https://parts.igem.org/das/dsn'''
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* parts.igem.org is a valid DAS server it will return the XML for the list of DAS services available on the server.
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==DAS Protein Annotation Server==
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'''https://parts.igem.org/das/protein_annotations/entry_points'''
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* A list of protein coding sequence parts that have swissprot numbers and can be understood by the DAS system.
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'''https://parts.igem.org/das/protein_annotations/types'''
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* A list of the types that are valid for protein_annotations
  
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DAS information is available via the HTTP protocol.
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'''https://parts.igem.org/das/protein_annotations/features?selection=UniprotNumber'''
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* Identification that the sequence exists
  
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(NOTE: the das interface in only operating on parts.mit.edu at this time.)
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'''https://parts.igem.org/das/protein_annotations/dna?selection=PartName:firstbase,lastbase'''
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*Returns XML containing the sequence for the given part from the firstbase to the last base specified
  
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http://parts.mit.edu/das/dsn will return the XML for the list of DAS services available on the server.
 
  
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Server protein_annotations:
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==DAS Parts Server==
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http://parts.mit.edu/protein_annotations/entry_points
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    A list of protein coding sequence parts that have swissprot numbers and can be understood by the DAS system.
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http://parts.mit.edu/protein_annotations/types
 
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    A list of the types that are valid for protein_annotations
 
  
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http://parts.mit.edu/das/protein_annotations/features?selection=UniprotNumber
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'''https://parts.igem.org/das/parts/entry_points'''
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    Identification that the sequence exists
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* Returns an XML list of all available parts in the registry. The information includes the part name and sequence length.
  
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http://parts.mit.edu/das/protein_annotations/dna?selection=PartName:firstbase,lastbase
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'''https://parts.igem.org/das/parts/features?segment=PartName'''
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    Returns XML containing the sequence for the given part from the firstbase to the last base specified
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* Returns easy to read XML listing each feature in the part.
  
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'''https://parts.igem.org/das/parts/dna?segment=PartName'''
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* Returns the easy to read XML listing of the entire sequence for the part
  
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Server parts
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'''https://parts.igem.org/das/parts/features?segment=PartName:firstbase,lastbase'''
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* Returns easy to read XML listing each feature in the part between firstbase and lastbase.
  
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http://parts.mit.edu/das/parts/entry_points
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'''https://parts.igem.org/das/parts/dna?segment=PartName:firstbase,lastbase'''
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    Returns an XML list of all available parts in the registry. The information includes the part name and sequence length.
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* Returns the easy to read XML listing of the sequence for the part between firstbase and lastbase.
  
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http://parts.mit.edu/das/parts/features?segment=PartName:firstbase,lastbase
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===Questions and comments:===
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    Returns easy to read XML listing each feature in the part between firstbase and lastbase.
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'''[[User:Vincent|Vincent]] 14:06, 20 July 2009 (UTC)''':
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It is great for the Part Registry to provide a DAS description of the parts. It really helps to build Software tools and routines to deal with part-related data. However, the available information is still pretty sparse. How can the community support this effort ? 
  
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http://parts.mit.edu/das/dna?segment=PartName:firstbase,lastbase
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I have also some more technical question about the DAS server:
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    Returns the easy to read XML listing of the sequence for the part
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* Which DAS server is used ? LDAS or something else ?
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* Is the DAS feed compliant with DAS version 1.53, or something else ?
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* DAS provides interesting features to describe DNA sequence assemblies (using the component category for example). But the current Registry DAS service doesn't seem to implement that option. Is there a reason for this ? It would be a very useful feature.
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* So far, it looks like only one [https://parts.igem.org/das/parts/types/ category] is used (translational). Is there a reason for this ?

Latest revision as of 14:06, 20 July 2009

"The distributed annotation system (DAS) is a client-server system in which a single client integrates information from multiple servers. It allows a single machine to gather up genome annotation information from multiple distant web sites, collate the information, and display it to the user in a single view. Little coordination is needed among the various information providers." - Wikipedia

The DAS interface to the Registry can provide sequence and feature information about any part in the Registry.

DAS information is available via the HTTP protocol. Note that only the Registry at Registry is registered with the DASDY service at this time.

DAS DSN Server

https://parts.igem.org/das/dsn

  • parts.igem.org is a valid DAS server it will return the XML for the list of DAS services available on the server.

DAS Protein Annotation Server

https://parts.igem.org/das/protein_annotations/entry_points

  • A list of protein coding sequence parts that have swissprot numbers and can be understood by the DAS system.

https://parts.igem.org/das/protein_annotations/types

  • A list of the types that are valid for protein_annotations

https://parts.igem.org/das/protein_annotations/features?selection=UniprotNumber

  • Identification that the sequence exists

https://parts.igem.org/das/protein_annotations/dna?selection=PartName:firstbase,lastbase

  • Returns XML containing the sequence for the given part from the firstbase to the last base specified


DAS Parts Server

https://parts.igem.org/das/parts/entry_points

  • Returns an XML list of all available parts in the registry. The information includes the part name and sequence length.

https://parts.igem.org/das/parts/features?segment=PartName

  • Returns easy to read XML listing each feature in the part.

https://parts.igem.org/das/parts/dna?segment=PartName

  • Returns the easy to read XML listing of the entire sequence for the part

https://parts.igem.org/das/parts/features?segment=PartName:firstbase,lastbase

  • Returns easy to read XML listing each feature in the part between firstbase and lastbase.

https://parts.igem.org/das/parts/dna?segment=PartName:firstbase,lastbase

  • Returns the easy to read XML listing of the sequence for the part between firstbase and lastbase.

Questions and comments:

Vincent 14:06, 20 July 2009 (UTC): It is great for the Part Registry to provide a DAS description of the parts. It really helps to build Software tools and routines to deal with part-related data. However, the available information is still pretty sparse. How can the community support this effort ?

I have also some more technical question about the DAS server:

  • Which DAS server is used ? LDAS or something else ?
  • Is the DAS feed compliant with DAS version 1.53, or something else ?
  • DAS provides interesting features to describe DNA sequence assemblies (using the component category for example). But the current Registry DAS service doesn't seem to implement that option. Is there a reason for this ? It would be a very useful feature.
  • So far, it looks like only one category is used (translational). Is there a reason for this ?