http://biodas.open-bio.org/w/index.php?title=DAS/2.1/Spec/Get-Genomic/Sources&feed=atom&action=historyDAS/2.1/Spec/Get-Genomic/Sources - Revision history2024-03-29T02:23:40ZRevision history for this page on the wikiMediaWiki 1.29.3http://biodas.open-bio.org/w/index.php?title=DAS/2.1/Spec/Get-Genomic/Sources&diff=643&oldid=prevSteveC: Updated lead description of this page, incorporating page link back to top-level get-genome spec.2008-10-31T01:28:35Z<p>Updated lead description of this page, incorporating page link back to top-level get-genome spec.</p>
<table class="diff diff-contentalign-left" data-mw="interface">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr style='vertical-align: top;' lang='en'>
<td colspan='2' style="background-color: white; color:black; text-align: center;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 01:28, 31 October 2008</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1" >Line 1:</td>
<td colspan="2" class="diff-lineno">Line 1:</td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>'''<big><del class="diffchange diffchange-inline">DAS/2.1 Sources Document Specification</big>'''</del></div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>'''<big>[[DAS/2.1/Spec/Get-Genomic|<ins class="diffchange diffchange-inline">DAS/2.1</ins>]] <ins class="diffchange diffchange-inline">Sources Document Specification for Genome Data Retrieval</big></ins>'''</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div> </div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del class="diffchange diffchange-inline">* '''</del>[[DAS/2.1/Spec/Get-Genomic|<del class="diffchange diffchange-inline">Retrieving DAS2 genomic sequence and annotation feature records</del>]]'''</div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div> </div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>==Overview==</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>==Overview==</div></td></tr>
</table>SteveChttp://biodas.open-bio.org/w/index.php?title=DAS/2.1/Spec/Get-Genomic/Sources&diff=642&oldid=prevSteveC: Updated links to point at version 2.1 pages2008-10-31T01:23:49Z<p>Updated links to point at version 2.1 pages</p>
<table class="diff diff-contentalign-left" data-mw="interface">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr style='vertical-align: top;' lang='en'>
<td colspan='2' style="background-color: white; color:black; text-align: center;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 01:23, 31 October 2008</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1" >Line 1:</td>
<td colspan="2" class="diff-lineno">Line 1:</td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>'''<big>DAS/2 Sources Document Specification</big>'''</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>'''<big>DAS/2<ins class="diffchange diffchange-inline">.1 </ins>Sources Document Specification</big>'''</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>* <del class="diffchange diffchange-inline">'''General specification:</del>''' [[DAS/2/Spec/Get-Genomic|Retrieving DAS2 genomic sequence and annotation feature records]]</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>* '''[[DAS/2<ins class="diffchange diffchange-inline">.1</ins>/Spec/Get-Genomic|Retrieving DAS2 genomic sequence and annotation feature records]]<ins class="diffchange diffchange-inline">'''</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l381" >Line 381:</td>
<td colspan="2" class="diff-lineno">Line 381:</td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>given capability.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>given capability.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The [[DAS/2/Spec/Get-Genome/Segments|segments]] portion of the specification describes in</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The [[DAS/2<ins class="diffchange diffchange-inline">.1</ins>/Spec/Get-Genome/Segments|segments]] portion of the specification describes in</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>more detail how the FORMAT and SUPPORTS elements are used.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>more detail how the FORMAT and SUPPORTS elements are used.</div></td></tr>
</table>SteveChttp://biodas.open-bio.org/w/index.php?title=DAS/2.1/Spec/Get-Genomic/Sources&diff=641&oldid=prevSteveC: DAS/2/Spec/Get-Genomic/Sources moved to DAS/2.1/Spec/Get-Genomic/Sources: To separate this evolving version of the DAS spec from the frozen DAS/2 version.2008-10-31T00:53:24Z<p><a href="/wiki/DAS/2/Spec/Get-Genomic/Sources" class="mw-redirect" title="DAS/2/Spec/Get-Genomic/Sources">DAS/2/Spec/Get-Genomic/Sources</a> moved to <a href="/wiki/DAS/2.1/Spec/Get-Genomic/Sources" title="DAS/2.1/Spec/Get-Genomic/Sources">DAS/2.1/Spec/Get-Genomic/Sources</a>: To separate this evolving version of the DAS spec from the frozen DAS/2 version.</p>
<table class="diff diff-contentalign-left" data-mw="interface">
<tr style='vertical-align: top;' lang='en'>
<td colspan='1' style="background-color: white; color:black; text-align: center;">← Older revision</td>
<td colspan='1' style="background-color: white; color:black; text-align: center;">Revision as of 00:53, 31 October 2008</td>
</tr><tr><td colspan='2' style='text-align: center;' lang='en'><div class="mw-diff-empty">(No difference)</div>
</td></tr></table>SteveChttp://biodas.open-bio.org/w/index.php?title=DAS/2.1/Spec/Get-Genomic/Sources&diff=640&oldid=prevSteveC: Importing text from the Sources sections of the original das2_get.html2008-10-30T08:14:49Z<p>Importing text from the Sources sections of the original das2_get.html</p>
<p><b>New page</b></p><div>'''<big>DAS/2 Sources Document Specification</big>'''<br />
<br />
* '''General specification:''' [[DAS/2/Spec/Get-Genomic|Retrieving DAS2 genomic sequence and annotation feature records]]<br />
<br />
<br />
==Overview==<br />
<br />
A DAS server supplies information about genomic sequence data sources.<br />
The collection of all sources, each data source, and each version of a<br />
data source are accessible through a URL. All three classes of URLs<br />
return a document of content-type 'application/x-das-sources+xml'<br />
though likely with differing amounts of detail. A 'versioned source'<br />
request returns information only about a specific version of a data<br />
source. A 'source' request returns the list of all the versioned<br />
source data for that source. A 'sources' request returns the list of<br />
all the source data, including all the versioned source data.<br />
<br />
The URLs might not be distinct. For example, a server with only one<br />
version of one data source may use the same URL for all three<br />
documents, and a server for a single organism may use the same URL for<br />
the 'sources' and 'source' documents.<br />
<br />
Most servers will list only the data sources provided by that server.<br />
Some servers combine the sources documents from other servers into a<br />
single document. These registry servers act as a centralized index<br />
and reduce configuration and network overhead. A registry server uses<br />
the same sources format as an annotation server.<br />
<br />
Here is an example of a simple sources document which makes no<br />
distinction between the three sources categories. It, like the other<br />
new DAS formats, is in XML. All of the DAS elements are in the XML<br />
namespace <tt>http://biodas.org/documents/das2</tt>. This namespace<br />
is reserved and authors of DAS extensions may not create new XML<br />
elements in it.<br />
<br />
===Example request and response===<br />
<br />
<P>Request:</P><br />
<blockquote class="url"><br />
http://www.example.com/das/genome/yeast.xml<br />
</blockquote><br />
<br />
<P>Response:</P><br />
<pre class="speclist">Content-Type: application/x-das-sources+xml<br />
<br />
&lt;?xml version="1.0" encoding="UTF-8"?&gt;<br />
&lt;SOURCES xmlns="http://biodas.org/documents/das2"<br />
xml:base="http://www.example.com/das/genome/"&gt;<br />
<br />
&lt;SOURCE uri="yeast.xml" title="Saccharomyces cerevisiae (Baker's yeast) genome"<br />
doc_href="http://www.example.com/yeast.html"&gt;<br />
&lt;VERSION uri="yeast.xml" created="2005-12-05"&gt;<br />
&lt;COORDINATES uri="http://sanger.ac.uk/das-registry/yeast-32-gene"<br />
taxid="4932" source="Gene_ID" authority="SGD32" version="3"/&gt;<br />
&lt;CAPABILITY type="features" query_uri="features.xml" /&gt;<br />
&lt;CAPABILITY type="types" query_uri="types.xml"/&gt;<br />
&lt;/VERSION&gt;<br />
&lt;/SOURCE&gt;<br />
<br />
&lt;/SOURCES&gt;<br />
</pre><br />
<br />
All identifiers and href attributes in DAS documents follow the <br />
[http://www.w3.org/TR/xmlbase/ XML Base specification] when<br />
resolving partial identifiers and href attributes. In this case the<br />
relative id "yeast.xml" is fully resolved using the xml:base of<br />
"http://www.example.com/das/genome/" to<br />
"http://www.example.com/das/genome/yeast.xml". If the result after<br />
resolving through all the parent xml:base attributes is still a<br />
relative URL then it is resolved once more with respect to the URL<br />
used to fetch the document.<br />
<br />
===Example request and response (complex)===<br />
<br />
Here is an example of a more complicated sources document with<br />
multiple organisms each with multiple versions. Each of the two<br />
source documents (one for each organism) has a distinct URL as does<br />
each of the version for each organism. This is a pure registry server<br />
because the actual annotation data comes from other machines.<br />
<br />
<P>Request:</P><br />
<blockquote class="url"><br />
http://www.biodas.org/known_das_servers<br />
</blockquote><br />
<br />
<P>Response:</P><br />
<pre class="speclist">Content-Type: application/x-das-sources+xml<br />
<br />
&lt;SOURCES xmlns="http://biodas.org/documents/das2"&gt;<br />
&lt;SOURCE uri="http://das.ensembl.org/das/SPICEDS/" title="das_vega_trans"&gt;<br />
&lt;VERSION uri="http://das.ensembl.org/das/SPICEDS/127/" created="2005-05-23"&gt;<br />
&lt;MAINTAINER email="someone@sanger.ac.uk" /&gt;<br />
&lt;COORDINATES uri="http://sanger.ac.uk/das-registry/zv4-25-chr" taxid="7955"<br />
source="Chromosome" authority="ZV4" version="25"<br />
test_range="name=BX255914" /&gt;<br />
&lt;CAPABILITY type="segments"<br />
query_uri="http://www.ebi.ac.uk/das-srv/genome/zebrafish-62" /&gt;<br />
&lt;CAPABILITY type="features"<br />
query_uri="http://das.ensembl.org/das/SPICEDS/127/features"&gt;<br />
&lt;SUPPORTS name="das2queries" /&gt;<br />
&lt;/CAPABILITY&gt;<br />
&lt;CAPABILITY type="types"<br />
query_uri="http://das.ensembl.org/das/SPICEDS/127/types" /&gt;<br />
&lt;/VERSION&gt;<br />
<br />
&lt;VERSION uri="http://das.ensembl.org/das/SPICEDS/128/" created="2005-08-13"&gt;<br />
&lt;MAINTAINER email="someone-else@sanger.ac.uk" /&gt;<br />
&lt;COORDINATES uri="http://sanger.ac.uk/das-registry/zv4-26-chr" taxid="7955"<br />
source="Chromosome" authority="ZV4" version="26"<br />
test_range="name=BX255914" /&gt;<br />
&lt;CAPABILITY type="segments"<br />
query_uri="http://www.ebi.ac.uk/das-srv/genome/zebrafish-62" /&gt;<br />
&lt;CAPABILITY type="features"<br />
query_uri="http://das.ensembl.org/das/SPICEDS/128/features"&gt;<br />
&lt;SUPPORTS name="das2queries" /&gt;<br />
&lt;/CAPABILITY&gt;<br />
&lt;CAPABILITY type="types"<br />
query_uri="http://das.ensembl.org/das/SPICEDS/128/types" /&gt;<br />
&lt;CAPABILITY type="locks" query_uri="http://das.ensembl.org/das/SPICEDS/128/locks" /&gt;<br />
&lt;CAPABILITY type="writeback"<br />
query_uri="http://das.ensembl.org/das/SPICEDS/128/locks" /&gt;<br />
&lt;/VERSION&gt;<br />
&lt;/SOURCE&gt;<br />
<br />
&lt;SOURCE uri="http://www.example.com/das2/mus/sources.xml" title="Mus musculus"&gt;<br />
&lt;VERSION uri="http://www.example.com/das2/mus/42/sources.xml" created="2006-02-11"&gt;<br />
&lt;MAINTAINER email="pied-piper@hamlet.ac.uk" /&gt;<br />
&lt;COORDINATES uri="http://sanger.ac.uk/das-registry/yeast-12-clone" taxid="10090"<br />
source="Clone" authority="Ensembl" test_range="name=AL935121" /&gt;<br />
&lt;CAPABILITY type="features"<br />
query_uri="http://www.example.com/cgi-bin/features-mus-v42.cgi"&gt;<br />
&lt;SUPPORTS name="das2queries" /&gt;<br />
&lt;/CAPABILITY&gt;<br />
&lt;CAPABILITY type="types"<br />
query_uri="http://www.example.com/das2/mus/v42/types.xml" /&gt;<br />
&lt;/VERSION&gt;<br />
&lt;/SOURCE&gt;<br />
&lt;/SOURCES&gt;<br />
</pre><br />
<br />
Each SOURCE id and VERSION id is fetchable. Fetching the URL<br />
"http://das.ensembl.org/das/SPICEDS/" returns a sources document with<br />
the SOURCE record for "das_vega_trans" and both of its VERSION<br />
subelements and fetching "http://das.ensembl.org/das/SPICEDS/128/"<br />
returns a sources document with only the second of its VERSION<br />
subelements.<br />
<br />
DAS documents refer to other documents through URLs. There are no<br />
restrictions on the internal form of the URLs, other than the query<br />
string portion. Server implementers are free to choose URLs which<br />
best fit the architecture needs. For example, a simple DAS server may<br />
be implemented as a set of XML files hosted by a standard web server<br />
while more complex servers with search support may be implemented as<br />
CGI scripts or through embedded web server extensions. The URLs do<br />
not need to define a hierarchical structure nor even be on the same<br />
machine. Compare this to the DAS1 specification where some URLs were<br />
constructed by direct string modification of other URLs.<br />
<br />
==Details==<br />
<br />
A sources request is a request for information about the data sets<br />
available from a DAS server. This may be a list of all data sources,<br />
a list of all versions of a given data source, or information about a<br />
specific version. All three are done by fetching a sources document<br />
given a URL. The returned format is identical for all three cases,<br />
except that some portions will require one element instead a list of<br />
zero or more elements.<br />
<br />
The sources request does not use query parameters. A future version<br />
of DAS/2 may add optional query parameters to the sources request, but for now <br />
servers should respond with an HTTP error code 400 "Bad<br />
Request" if any query parameters are included.<br />
<br />
===Example response document===<br />
<br />
''[Do we need this example in addition to the above?]''<br />
<br />
The response document looks like the following:<br />
<br />
<P>Response:</P><br />
<pre class="speclist">Content-Type: application/x-das-sources+xml<br />
<br />
&lt;?xml version="1.0" encoding="UTF-8"?&gt;<br />
&lt;SOURCES<br />
xmlns="http://biodas.org/documents/das2"<br />
xml:base="http://dev.wormbase.org/das/genome/"&gt;<br />
<br />
&lt;MAINTAINER<br />
name="Yoyodyne DNA Systems"<br />
email="yoyodyna@example.com"<br />
href="http://www.example.com/" /&gt;<br />
<br />
&lt;SOURCE uri="volvox" title="Volvox Database"<br />
doc_href="http://www.example.org/volvox_db.pdf"&gt;<br />
<br />
&lt;VERSION uri="volvox/build_1" title="Build 1, October 2002"<br />
writeable="no" created="2002-10-15" modified="2002-10-25T09:56:23"&gt;<br />
<br />
&lt;MAINTAINER<br />
name="Volvox helpdesk"<br />
email="volvox-help@example.com" /&gt;<br />
&lt;COORDINATES uri="http://ncbi.nlm.nih.gov/das-genomes/human-35"<br />
taxid="3066" source="chromosome" authority="NCBI" version="35" /&gt;<br />
<br />
&lt;COORDINATES uri="http://embl.ebi.ac.uk/genome/volvox-clone"<br />
taxid="2034" source="clone" authority="EMBL" /&gt;<br />
<br />
&lt;CAPABILITY type="segments" query_uri="volvox/1/segments"&gt;<br />
&lt;FORMAT name="fasta"/&gt;<br />
&lt;FORMAT name="raw"/&gt;<br />
&lt;/CAPABILITY&gt;<br />
&lt;CAPABILITY type="types" query_uri="volvox/1/types"&gt;<br />
&lt;FORMAT name="das2xml" /&gt;<br />
&lt;/CAPABILITY&gt;<br />
&lt;CAPABILITY type="features" query_uri="volvox/1/features"&gt;<br />
&lt;FORMAT name="das2xml" /&gt;<br />
&lt;/CAPABILITY&gt;<br />
&lt;CAPABILITY type="locks" query_uri="volvox/1/locks" /&gt;<br />
<br />
&lt;/VERSION&gt;<br />
&lt;/SOURCE&gt;<br />
&lt;/SOURCES&gt;<br />
</pre><br />
<br />
===SOURCES element===<br />
<br />
The root element is named SOURCES. The MAINTAINER element is<br />
optional. A server should provide at least one of the 'name', 'email'<br />
or 'href' attributes. The 'name' is short human-readable text, the<br />
'email' is an email address and the 'href' is a URL meant for a human<br />
using a web browser. The MAINTAINER element under the SOURCES element<br />
designates the maintainer for the server, which may be different than<br />
the maintainer for the data sources.<br />
<br />
The SOURCES element has zero or more <a href="#link_element">LINK<br />
elements</a> linking the sources document to some other document.<br />
<br />
The SOURCES element has zero or more SOURCE elements. The 'uri'<br />
attribute is a URI and must be a unique identifier within a SOURCES<br />
document. It should be fetchable and if fetchable it must respond<br />
with a sources document describing the given data source. The 'title'<br />
is a short label describing the source to people. The optional<br />
'description' contains up to a paragraph of text (no HTML markup) with<br />
more details about the data source. The optional 'doc_href' is a URL<br />
for a web browser to display human-readable documentation.<br />
<br />
===MAINTAINER element===<br />
<br />
A SOURCES element may have an optional MAINTAINER element. The syntax<br />
is the same as the one at the SOURCES level. If present it contains<br />
the contact information for the maintainer of the given data source.<br />
If not present clients may use the SOURCES MAINTAINER as the SOURCE<br />
MAINTAINER.<br />
<br />
===VERSION element===<br />
<br />
A data source may have multiple VERSION elements. The definition of<br />
what constitutes a new version is left to the data provider. VERSION<br />
elements should be listed in creation time order, with the oldest<br />
versions first. The 'uri' attribute is a URI and must be a unique<br />
identifier within the data source. It should be fetchable and if<br />
fetchable it must respond with a source document describing only the<br />
specific versioned data source. The 'title' is a short label<br />
describing the version to people. The optional description contains<br />
up to a paragraph of text (no HTML markup) with more details about the<br />
version. The optional 'doc_href' is a URL for a web browser to<br />
display human-readable documentation.<br />
<br />
The optional 'created' and 'modified' attributes are ISO timestamps<br />
specifying when the version was first made available and most recently<br />
modified. <br />
<br />
Each VERSION element may contain an optional MAINTAINER element, which<br />
has the same syntax and meaning as the MAINTAINER element at the<br />
SOURCES and SOURCE level. It contains the contact information for the<br />
maintainer of the specific version of the data source, which may be<br />
different than the maintainer for the data source or for the server.<br />
If the VERSION MAINTAINER is not present, clients may use the SOURCE<br />
MAINTAINER instead for contact information and if that does not exist<br />
clients may use the SOURCES MAINTAINER.<br />
<br />
===COORDINATES element===<br />
<br />
The COORDINATES element characterizes a coordinate system used by the<br />
versioned source. Each COORDINATES has a 'uri' attribute which exactly<br />
identifies the coordinate system. If two annotation servers have a<br />
COORDINATES with the same uri then they annotatate the same system. <br />
Coordinate system URIs for human and many model organism genomes are <br />
currently listed at http://www.biodas.org/wiki/GlobalSeqIDs. This list <br />
will soon be incorporated into the Sanger DAS/2 registry.<br />
<br />
<!-- XXX<br />
Best way to incorporate into Sanger DAS/2 registry may be to <br />
have registry list a versioned source for each (with only a segments capability)??<br />
Could this be auto-generated from wiki'd listing??<br />
<br />
Currently for DAS1 the Sanger Institute maintains an HTML summary of coordinate system <br />
URIs at http://www.dasregistry.org/help_coordsys.jsp, <br />
but that doesn't have the URIs that are showing up for coordinates <br />
in the DAS/2 registry sources doc, for example: "http://das.sanger.ac.uk/dasregistry/coordsys/CS_SPICEDS5" <br />
for human NCBI assembly v35. ???<br />
]<br />
XXX --><br />
<br />
To help people select an appropriate coordinate system to use, the<br />
COORDINATES element contains a set of attributes with additional<br />
details. The 'authority' attribute is the name of the organization<br />
that determined the coordinate system. It is a name like 'NCBI',<br />
'EMBL', 'Ensembl', 'HUGO_ID', 'IPI' or 'UniProt'. The 'source'<br />
attribute refers to the physical dimension of the coordinate system.<br />
It is a name like 'Chromosome', 'Clone', 'Contig', 'Gene_ID',<br />
'NT_Contig', 'Protein Sequence', 'Protein Structure', or 'Scaffold'.<br />
The Sanger registry contains a full list of these restricted<br />
vocabulary terms.<br />
<br />
The optional 'version' contains the version name of the build upon<br />
which the coordinate system is based. The optional 'created'<br />
attribute is the ISO timestamp for the coordinate system and is used<br />
when sorting by time, as when identifying the most recent version.<br />
The optional 'taxid' attribute is the NCBI taxonomy id of the<br />
organism, as a number.<br />
<br />
The COORDINATES element may contain an optional 'test_range' attribute<br />
used to test that the server is operational. Experience with DAS1<br />
found that the web interface code often did not catch errors at the<br />
database interface layer and would return empty results instead of<br />
correctly reporting errors. The test_range attribute contains a<br />
<a href="#feature_filters">feature filter query string</a> which can<br />
be passed to the "feature" CAPABILITY query_uri. The response after<br />
doing that feature filter request must contain at least one feature<br />
and should contain no more than a modest number. <br />
<br />
A versioned source may have more than one COORDINATES element. For<br />
example, features may be given in both chromosome and contig space,<br />
or in human and mouse coordinates.<br />
<br />
===CAPABILITY element===<br />
<br />
The CAPABILITY elements describe what sort of queries a client may do<br />
with the versioned source data. The query is done through the URL<br />
listed in the 'query_uri' field. Different query URLs support<br />
different query interfaces. The specific interface is listed in the<br />
'type' field. The specification defines the following query URL types:<br />
<br />
<table border="1"><br />
<tr><br />
<th>'type' value</th><br />
<th>for information about</th><br />
</tr><br />
<tr><br />
<td>segments</td><br />
<td>description of the regions on which features are located</td><br />
</tr><br />
<tr><br />
<td>types</td><br />
<td>the feature types</td><br />
</tr><br />
<tr><br />
<td>features</td><br />
<td>the features</td><br />
</tr><br />
<tr><br />
<td>locks</td><br />
<td>the locks</td><br />
</tr><br />
<tr><br />
<td>writeback</td><br />
<td>writeback support</td><br />
</tr><br />
</table><br />
<br />
Relative 'query_uri's are resolved according to the current xml:base.<br />
<br />
A CAPABILITY has zero or more FORMAT elements, each with a 'name'<br />
attribute. These list the supported formats for the given capability.<br />
To get the document in a given format, use the format's name in the<br />
"format" parameter of the query.<br />
<br />
A CAPABILITY has zero or more SUPPORTS elements, each with a 'name'<br />
attribute. These list the available extensions supported by the<br />
given capability.<br />
<br />
The [[DAS/2/Spec/Get-Genome/Segments|segments]] portion of the specification describes in<br />
more detail how the FORMAT and SUPPORTS elements are used.</div>SteveC