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Documentation for DAS entry_points service

Retrieve the List of Entry Points for a Data Source

Scope: Reference servers.

Command: entry_points

Format: 

PREFIX/das/DSN/entry_points

Description: This query returns the list of sequence entry points available and their sizes in base pairs.

Arguments:

ref
The ref is argument has been RE-ESTABLISHED, since it is needed for the new services. It is necessary to request a list of available alignments, or to retreive a list of available chains and models for a structure entry.

type (deprecated)
For ACEDB servers, the type parameter provides the class of the reference sequence, Sequence by default. DEPRECATED

Response:

The response to the entry_points command is the "DASEP" XML-formatted document:

Format: 

<?xml version="1.0" standalone="no"?>
<!doctype dasep system "http://www.biodas.org/dtd/dasep.dtd">
<dasep>
<entry_points href="url" version="X.XX"query="ref">

    <segment id="id1" start="start1" stop="stop1" type="type" orientation="+">descriptive text</segment>

    <segment id="id2" start="start2" stop="stop2" type="type" orientation="+">descriptive text</segment>
    <segment id="id3" start="start3" stop="stop3" type="type" orientation="+">descriptive text</segment>

    ...
  </entry_points>
</dasep>

Element:<!doctype>

(required; one only)

The doctype indicates which formal DTD specification to use. For the entry_points query, the doctype DTD is "http://www.biodas.org/dtd/dasep.dtd".

Element:<DASEP>

(required, one only)

The appropriate doctype and root tag is DASEP.

Element:<entry_points>

(required, only one) There is a single <ENTRY_POINTS> tag. It has a version number (required) in the form "N.NN". Whenever the DNA of the entry point changes, the version number should change as well.

Attributes:

attribute:href

(required) attribute echoes the URL query that was used to fetch the current document.

attribute:query

(optional) is the ref argument used to fetch the current document. It is needed for alignments and structure servers to specify for which object the available alignments, chains, and models should be listed. The alignment "subject" ids are provided in the <SEGMENT> section.

Element:<segment>

(optional; zero or more) Each segment contains the attributes

attribute:id

(required) The id is a unique identifier, which can be used as the reference ID in further requests to DAS.

attribute:start

(required) The start and stop indicate the start and stop positions of the segment.

attribute:stop

(required) The start and stop indicate the start and stop positions of the segment.

attribute:orientation

(optional) Orientation is one of "+" or "-" and indicates the strandedness of the segment (use "+" if the segment is not intrinsically ordered).
For alignments the

attribute:id

(optional)is specifying the id of the alignment subject.

attribute:subparts

(optional) if this attribute is present and has the value "yes", it indicates that the segment has subparts.

attribute:type

(optional) If this attribute is present, it can be used to describe the type of the segment (for future compatibility with Sequence Ontology-based feature typing).

For compatibility with older versions of the specification, the <SEGMENT> tag can use a size attribute rather than start and stop, and can omit the orientation attribute: 


      <SEGMENT id="id" size="123456">
In this case, the start is implied to be "1" and the stop is implied to be the same as the length. Note: The result from the entry points requests does not carry sufficient information to reconstruct a complex sequence assembly. Instead, use the features request with a category of "component". See Fetching Sequence Assemblies.