extending PhyloXML
vincent B
we are currently considering using PhyloXML to encode transfer events
in reconciled gene trees. For each transfer, we need to describe
several data and sub-data such as species tree branch origin, species
tree branch arrival, confidence, min date, max date, a reference of
block event, etc. We also need to encode additional information for
duplications and losses, but I'll come to it later. Let's already
consider transfers.
The current PhyloXML format does not seem to allow this, that is to
have elements we need here (though it has an element for
duplications). We first thought to use the property element, but here
again we are stopped as it cannot be of complex type, hence we cannot
define elements inside the property element in an XML document that
would use it, moreover it cannot have more than the small number of
attributes that is declared for it.
We tried to play a little bit with it though, but were unsuccessful in
making Archeopteryx reading a file that was completed to contain the
example property that is given on the PhyloXML web pages:
<property datatype="xsd:integer" ref="NOAA:depth" applies_to="clade"
unit="METRIC:m"> 200 </property>
We then said, "well we will then define an extension of PhyloXML by
using the import possibility in xml schema definitions, exploiting the
extensibility of the XML language" (as advertized on the PhyloXML web
page). But then what about current tools?
Q1 - how well do existing PhyloXML tools (Archeopteryx
Hypertree, ....) handle this property element?
Q2 - how well do this tool react to elements not defined in the
Phyloxml xsd
Q3 - which of these tools would be able to read an xml file that would
refer to an XML schema that would be an extension of the current
PhyloXML schema?
Q4 - does anyone have an example of schema extending the current
PhyloXML format?
Best regards.
Christian Zmasek
Thank you for these interesting questions.
>Dear all,>we are currently considering using PhyloXML to encode transfer events>in reconciled gene trees. For each transfer, we need to describe>several data and sub-data such as species tree branch origin, species>tree branch arrival, confidence, min date, max date, a reference of>block event, etc. We also need to encode additional information for>duplications and losses, but I'll come to it later. Let's already>consider transfers.
>The current PhyloXML format does not seem to allow this, that is to>have elements we need here (though it has an element for>duplications). We first thought to use the property element, but here>again we are stopped as it cannot be of complex type, hence we cannot>define elements inside the property element in an XML document that>would use it, moreover it cannot have more than the small number of>attributes that is declared for it.
>We tried to play a little bit with it though, but were unsuccessful in>making Archeopteryx reading a file that was completed to contain the>example property that is given on the PhyloXML web pages:><property datatype="xsd:integer" ref="NOAA:depth" applies_to="clade">unit="METRIC:m"> 200 </property>
Which version of Archeopteryx did you use?And what happened when you
tried to read these example files (i.e. did you get an error message
or was Aptx unable to to display these property values)?
The reason why I am asking is because the newest version (ie the one
you can download under "Development Snapshot") should definitely be
able to read ALL the example files.This newest version is also able
to display the property values (although only as text and somewhat
ugly at that -- I plan to upload a newer version by tomorrow).
>We then said, "well we will then define an extension of PhyloXML by>using the import possibility in xml schema definitions, exploiting the>extensibility of the XML language" (as advertized on the PhyloXML web>page). But then what about current tools?
>Q1 - how well do existing PhyloXML tools (Archeopteryx>Hypertree, ....) handle this property element?
A1: Aptx has to be able to handle the property elements -- if not,
please let me know. The display of these values might only be in
textual form, though.
>Q2 - how well do this tool react to elements not defined in the>Phyloxml xsd
A2: Aptx should ignore these (i.e. no error messages but also no
display).If not, please let me know.(an example this is the alignment
in the example files)
>Q3 - which of these tools would be able to read an xml file that would>refer to an XML schema that would be an extension of the current>PhyloXML schema?
A3: I don't know the answer to this question.
>Q4 - does anyone have an example of schema extending the current>PhyloXML format?
A4: I don't know the answer to this question.
Sincerely,
Christian