-
Notifications
You must be signed in to change notification settings - Fork 2
Expand file tree
/
Copy pathindex.html
More file actions
520 lines (494 loc) · 19.9 KB
/
index.html
File metadata and controls
520 lines (494 loc) · 19.9 KB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head>
<!-- updated 2016-01-25 -->
<!-- site meta data -->
<meta http-equiv="content-type" content="text/html; charset=utf-8" />
<meta name="description" content="NeXML is a file format for encoding phyloinformatic data using XML." />
<meta name="keywords" content="NeXML, XML, NEXUS, phyloinformatics, phylogenetics, phylogenies, trees, dna, rna, nucleotide, standard, continuous, amino, acid, matrix, tree, network, data" />
<meta name="author" content="Rutger Vos" />
<meta name="robots" content="index,follow" />
<meta name="verify-v1" content="mYceuNu58e0c0TNJ/gJ2NO63bxeH1nu28sZ2rtzcLoM=" />
<title>NeXML - phylogenetic data as xml</title>
<link rel="stylesheet" href="/css/style.css" type="text/css" />
<link rel="stylesheet" href="/css/schema.css" type="text/css" />
<script type="text/javascript" src="/js/functions.js"></script>
<script type="text/javascript" src="/js/schema.js"></script>
<link rel="shortcut icon" href="/img/favicon.ico" />
</head>
<body>
<!-- This heading is only here for text browsers without css -->
<h1 class="hide">NeXML - phylogenetic data as xml</h1>
<div id="thetop">
<a id="top" name="top"></a>
<p class="hide">
Skip to:
<a href="#sitemenu" accesskey="2">Site menu</a> |
<a href="#maincontent" accesskey="3">Main content</a>
</p>
</div>
<div id="container">
<div id="main">
<!-- main banner in the top-left -->
<div id="logo">
<h1>
[<a href="/" accesskey="4">NeXML</a>]
</h1><span id="tagline">Rich phyloinformatic data</span>
</div>
<!-- site blurb in the top-middle -->
<div id="intro">
<h2>
<a id="maincontent" name="maincontent"></a>
The future data exchange standard is here!
</h2>
<p>
NeXML is an exchange standard for representing
phyloinformatic data — inspired by the commonly used
NEXUS format, but more robust and easier to process.
</p>
</div>
<div class="clear"></div>
<!-- validate form -->
<div id="validateDiv">
<form
action="/phylows/validator"
enctype="multipart/form-data"
method="post"
id="validateForm">
<fieldset id="validateFieldset">
<legend class="hide">Process nexml data</legend>
<select id="validateSelect">
<option value="/phylows/validator">validate</option>
<option value="/phylows/nex2xml">nexus -> nexml</option>
<option value="/phylows/newick2xml">newick -> nexml</option>
<option value="/phylows/xml2json">nexml -> json</option>
<option value="/phylows/xml2rdf">nexml -> rdf</option>
</select>
<input type="file" name="file" id="validateUpload"/>
<input type="button" onclick="submitForm()" id="validateSubmit" value="Submit"/>
</fieldset>
</form>
</div>
<!-- main heading of this page -->
<h3 class="headerstyle">Overview</h3>
<!-- http://www.nexml.org/ -->
<div style="padding-bottom:1em;margin-top: 1em; margin-left: 10px;color: #888888">
<small></small>
</div>
<!-- TITLE: NeXML - phylogenetic data as xml -->
<!-- HEADING: Overview -->
<p>
The <a rel="nofollow" href="http://www.citeulike.org/user/rvosa/article/2011773">
NEXUS flat file format</a> is a commonly used syntax for
phylogenetic data. Unfortunately, over time, non-compliant NEXUS implementations
have overloaded the standard - which has caused various
<a rel="nofollow" href="https://www.nescent.org/wg_evoinfo/NEXUS_Problems">
problems</a>. Meanwhile, mature technologies around the
<a rel="nofollow" href="http://www.w3.org/XML/">XML</a> standard have
emerged. These technologies have the potential to greatly
simplify and improve robustness in the processing of rich phylogenetic
data. This website is the home for the community-driven NeXML project, which
seeks to leverage XML technologies in the development of a data standard
that translates NEXUS concepts into a syntax that is more easily validated
and processed. This approach promises several advantages:
</p>
<ul>
<li class="rss">
<strong>Syntax validation</strong> — some of the issues hampering
interoperability are caused by the fact that no formal
specification exists for NEXUS and other flat files, and no unambiguous way
to validate them. Using <a rel="nofollow" href="http://www.w3.org/XML/Schema">
XML Schema</a> we have defined a versioned grammar against which
data files can be validated syntactically. In addition, this website has a validation
service (the orange box in the center of every page) that also checks the semantics
of uploaded NeXML files beyond ways that can be expressed in XSD schema language.
</li>
<li class="rss">
<strong>Semantic annotation</strong> — an issue in current file
formats is that their semantics are not well-defined. For example, what does
it mean to use an ambiguity code in a matrix? Is it uncertainty or polymorphism?
With the wider <a rel="nofollow" href="https://www.nescent.org/wg_evoinfo/">
EvoInfo working group</a> we are developing an <a href="http://www.evolutionaryontology.org">
ontology</a> on which we are mapping NeXML schema types so that the semantics
of data files become well-defined. In addition, NeXML has a facility for
annotating fundamental phylogenetic data objects (such as trees, character
state matrices and taxa) with ontology predicates and objects using
<a href="http://www.w3.org/TR/xhtml-rdfa-primer/">RDFa</a>.
</li>
<li class="rss">
<strong>Web services</strong> — a number of different
technologies (such as <a rel="nofollow" href="http://www.xmlrpc.com/">XML-RPC</a>,
<a rel="nofollow" href="http://en.wikipedia.org/wiki/Representational_State_Transfer">REST</a>
and <a rel="nofollow" href="http://www.w3.org/TR/soap/">SOAP</a>) have
emerged allowing disparate, xml-based services to be glued together
over the internet. For example, the
<a href="http://evoinfo.nescent.org/PhyloWS" rel="nofollow">PhyloWS</a>
initiative seeks to develop conventions for RESTful phylogenetic web
services for which NeXML is one of the preferred response formats.
</li>
<!--li class="rss">
<strong>Native XML databases</strong> — relational
databases are based on a fixed schema. For phylogenetic
data this poses problems, because the field of phyloinformatics
moves very rapidly: new metrics and analysis types are
published constantly.
<a rel="nofollow" href="http://xmldb-org.sourceforge.net/">XML databases</a>
are freed from this constraint, simplifying storage of
unusual data types.
</li-->
</ul>
<p>
Because of the advantages of NeXML over current standards, developers of phylogenetic
software have come together as part of the <a href="http://www.nescent.org">
NESCent</a> working group for <a href="https://www.nescent.org/wg_evoinfo">
evolutionary informatics</a> to develop this
<a href="https://github.com/nexml/nexml/wiki/NeXML-Manual">
new data exchange standard</a> based on XML technologies.
</p>
<p>
<strong>We have recently published a description of NeXML in <em>Systematic
Biology</em>. If you use NeXML in your research, please consider citing
<a href="http://dx.doi.org/10.1093/sysbio/sys025">doi:10.1093/sysbio/sys025</a></strong>
</p>
<p class="internallink">
[ <a href="#top">Back to top</a> ]
</p>
<h3 class="headerstyle">
What are we doing about it?
</h3>
<p>
NeXML development is being undertaken along a number of tracks:
</p>
<ul>
<li class="rss">
In the first place, there's an XML schema. This
schema (currently designated as namespace http://www.nexml.org/2009)
is explained on our
<a href="https://github.com/nexml/nexml/wiki/NeXML-Manual">wiki</a> and
<a href="/doc/schema-1">formally documented</a>; the latest version is available from
<a href="https://github.com/nexml/nexml/tree/master/xsd">git</a>.
</li>
<li class="rss">
Secondly, the community is implementing NeXML read and/or write abilities in a
number of software applications:<br/>
<table id="implementations">
<tr>
<td>
<img alt="rOpenSci" src="/img/rOpenSci.png"/>
</td>
<td>
Carl Boettiger and Scott Chamberlain have developed an
<a
href="https://github.com/ropensci/RNeXML">excellent NeXML
library for R</a> for
<a
href="http://ropensci.org/">rOpenSci</a>.
</td>
</tr>
<tr>
<td>
<img alt="TreeBASE" src="/img/treebase.jpg"/>
</td>
<td>
<a href="http://www.treebase.org">
TreeBASE</a> supports serialization to NeXML.<br/>
</td>
</tr>
<tr>
<td>
<img alt="Mesquite" src="/img/mesquite.gif"/>
</td>
<td>
The <a href="http://mesquiteproject.org">Mesquite</a> project
supports <a href="https://github.com/nexml/nexml.java">reading
and writing</a> of NeXML. Wayne Maddison and Peter Midford
helped start an implementation for this that is currently being
maintained by Rutger Vos.<br/>
</td>
</tr>
<tr>
<td>
<img alt="DAMBE" src="/img/dambe.gif"/>
</td>
<td>
Xuhua Xia's <a href="http://dambe.bio.uottawa.ca/dambe.asp">DAMBE</a>
version 5.2.31 for Windows Vista/7 reads and writes NeXML
data.<br/>
</td>
</tr>
<tr>
<td>
<img alt="PhenoScape" src="/img/phenoscape_logo.jpg"/>
</td>
<td>
The <a href="http://www.phenoscape.org">PhenoScape</a>
project uses NeXML to annotate complex morphological character
states with ontology terms in its
<a href="http://phenoscape.org/wiki/Phenex">Phenex editor</a>.<br/>
</td>
</tr>
<!--tr>
<td>
<img alt="R" src="/img/Rlogo.jpg"/>
</td>
<td>
The <a href="https://r-forge.r-project.org/projects/phylobase/">
phylobase</a> package for <a rel="nofollow" href="http://www.r-project.org/">
R</a> reads and writes tree descriptions, with character matrices under way.
This implementation is being developed by Aaron Mackey.<br/>
</td>
</tr-->
<tr>
<td>
<img alt="DendroPy" src="/img/dendropy1.png"/>
</td>
<td>
Jeet Sukumaran has implemented NeXML I/O for python in the
<a href="https://dendropy.org/">DendroPy</a> package.
There are many DendroPy
<a href="https://github.com/nexml/nexml/wiki/NeXML-Manual">code samples</a>
for dealing with NeXML data in the wiki manual.<br/>
</td>
</tr>
<tr>
<td>
<img alt="BioPerl" src="/img/BioPerlLogo.png"/>
</td>
<td>
Chase Miller has implemented
<a href="http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/NexmlIO.html">Bio::NexmlIO</a> for
<a href="http://www.bioperl.org">BioPerl</a>, which under
the hood reuse Rutger Vos's
<a href="http://search.cpan.org/dist/Bio-Phylo/">Bio::Phylo</a>
parser libraries.<br/>
</td>
</tr>
<tr>
<td>
<img alt="BioRuby" src="/img/bioruby-gem.png"/>
</td>
<td>
Anurag Priyam and Rutger Vos have developed a
<a href="http://rubygems.org/gems/bio-nexml">NeXML I/O plugin</a>
for the
<a href="http://www.bioruby.org">
BioRuby</a> open source bioinformatics library for Ruby.<br/>
</td>
</tr>
<tr>
<td>
<img alt="ETE" src="/img/ete_logo.png"/>
</td>
<td>
Jaime Huerta-Cepas' team is working on NeXML I/O for the
<a href="http://etetoolkit.org">
ETE</a> Python environment for tree exploration.<br/>
</td>
</tr>
<tr>
<td>
<img alt="mx" src="/img/mx_icon.png"/>
</td>
<td>
Matt Yoder has implemented NeXML serialization for the
<a href="http://mx.phenomix.org/index.php/Main_Page">
mx</a> collaborative web-based content management system for evolutionary
systematists.<br/>
</td>
</tr>
<tr>
<td>
<img alt="PhyloBox" src="/img/phylobox.jpg"/>
</td>
<td>
Andrew Hill has added NeXML support to
<a href="http://phylobox.appspot.com/">
PhyloBox</a>.<br/>
</td>
</tr>
<tr>
<td>
<img alt="jsPhyloSVG" src="/img/jsphylosvg.png"/>
</td>
<td>
Sam Smits has made it so that the
<a href="http://www.jsphylosvg.com">
jsPhyloSVG</a> tree visualization widget can now show NeXML trees.<br/>
</td>
</tr>
<tr>
<td>
<img alt="NamesOnNodes" src="/img/namesonnodes.png"/>
</td>
<td>
Mike Keesey has added NeXML support to <a href="http://namesonnodes.org/">Names On Nodes</a>,
a web application that automatically applies biological nomenclature to datasets.
</td>
</tr>
<tr>
<td>
<img alt="DendroScope" src="/img/dendroscope.jpg"/>
</td>
<td>
Daniel Huson's <a href="http://ab.inf.uni-tuebingen.de/software/dendroscope/">DendroScope</a>
development team has adopted NeXML as its primary file format for storing visualization (styling)
metadata. However, at present, its implementation is <strong>not</strong> fully
compliant so should not be taken as a template to generate NeXML output.
</td>
</tr>
<tr>
<td>
<img alt="phyloGeoRef" src="/img/phylogeoref.jpg"/>
</td>
<td>
For the 2011 Google Summer of Code, Apurv Verma has added
NeXML reading capability to
<a href="https://github.com/kdiverson/phyloGeoRef">phyloGeoRef</a>.<br/>
</td>
</tr>
<tr>
<td>
<img alt="HIVQuery" src="/img/hivq.jpg"/>
</td>
<td>
Mark Jensen has implemented NeXML compatability for the
<a href="http://fortinbras.us/">HIVQuery</a> web
application.<br/>
</td>
</tr>
</table>
</li>
<li class="rss">
Third, we're crossreferencing the NeXML schema with the
<a rel="nofollow" href="http://www.evolutionaryontology.org">Character Data Analysis Ontology</a>
which is being developed by other members of the EvoInfo working group.
</li>
</ul>
<p class="internallink">
[ <a href="#top">Back to top</a> ]
</p>
<h3 class="headerstyle">
Get involved!
</h3>
<p>
If you are interested in being involved in the NeXML project
in any way, please do! Here are some ways to get involved:
</p>
<ul>
<li class="rss">
<strong>Get informed</strong> — information about the NeXML
project is distributed over the <a href="https://github.com/nexml/nexml/wiki/NeXML-Manual">manual</a>
(for an overview of vision, plans, implementation),
<a href="/doc/schema-1">documentation</a>
(for formal description of the schema) and the
<a href="https://lists.sourceforge.net/lists/listinfo/nexml-discuss">mailing list</a>
(for immediate plans and discussion).
</li>
<li class="rss">
<strong>Try it out</strong> — the download section of the
website has nightly builds of bindings for various languages.
Take these for a spin!
</li>
<li class="rss">
<strong>Contribute</strong> — if you are a programmer interested
in extending NeXML support, please contact us through the mailing
list to get commit support for the subversion repository.
</li>
</ul>
<p class="internallink">
[ <a href="#top">Back to top</a> ]
</p>
<h3 class="headerstyle">
Acknowledgements
</h3>
<p>
The research leading to these results has received funding from the [European
Community's] Seventh Framework Programme ([FP7/2007-2013] under grant agreement
n° [237046].
</p>
<p class="internallink">
[ <a href="#top">Back to top</a> ]
</p>
<h3 class="headerstyle">
Suggested citation
</h3>
<p>
<strong>Rutger A. Vos, J. P. Balhoff, J. A. Caravas, M. T. Holder, H. Lapp, P. E.
Midford, A. Priyam, J. Sukumaran, X. Xia, and A. Stoltzfus</strong>. 2012. NeXML:
rich, extensible, and verifiable representation of comparative data and metadata.
<em>Systematic Biology</em> <strong>61</strong>(4): 675-689
[<a href="http://dx.doi.org/10.1093/sysbio/sys025">doi:10.1093/sysbio/sys025</a>]
</p>
<p class="internallink">
[ <a href="#top">Back to top</a> ]
</p>
</div>
<div id="sidebar">
<!-- top-right site navigation menu -->
<h2 class="quicklinks">
<a id="quicklinks" name="quicklinks"></a>Quick links:
</h2>
<a class="quicklink" href="https://github.com/nexml/nexml/wiki/NeXML-Manual">Manual</a>
<a class="quicklink" href="/doc/schema-1">Schema documentation</a>
<a class="quicklink" href="http://dx.doi.org/10.1093/sysbio/sys025">NeXML publication</a>
<a class="quicklink" href="https://github.com/nexml/nexml/tree/master/examples">Example files</a>
<a class="quicklink" href="http://www.slideshare.net/rvosa/nexml-11158998">Slide show</a>
<br />
<h2 class="sidelink menuheader">
<a name="sitemenu"></a>Libraries:
</h2>
<a class="sidelink" href="https://github.com/nexml/nexml.java">Java</a>
<span class="hide">|</span>
<a class="sidelink" href="http://www.dendropy.org/">Python</a>
<span class="hide">|</span>
<a class="sidelink" href="http://search.cpan.org/dist/Bio-Phylo/">Perl</a>
<span class="hide">|</span>
<a class="sidelink" href="https://github.com/nexml/nexml.cpp">C++</a>
<span class="hide">|</span>
<a class="sidelink" href="https://github.com/nexml/nexml.js">JavaScript</a>
<span class="hide">|</span>
<a class="sidelink" href="https://github.com/nexml/bio-nexml">Ruby</a>
<span class="hide">|</span>
<a class="hide" href="#top" accesskey="1">Top of page</a>
<!-- links at the bottom right -->
<h3>
External links
</h3>
<ul>
<li class="external">
<a href="https://github.com/nexml" rel="nofollow">nexml@github</a>
</li>
<li class="external">
<a href="https://github.com/nexml/nexml/wiki/NeXML-Manual">NeXML wiki</a>
</li>
<li class="external">
<a href="https://github.com/evoinfo/cdao" rel="nofollow">CDAO</a>
</li>
<li class="external">
<a href="http://evoinfo.nescent.org/PhyloWS" rel="nofollow">PhyloWS</a>
</li>
</ul>
</div>
<div class="clear">
</div>
</div>
<div id="footer">
<p>
Site implementation and technology:
© <a href="http://rutgervos.blogspot.com" class="credit">Rutger Vos</a>.
Site design: © <a href="http://andreasviklund.com/" class="credit">Andreas Viklund</a>
of <a href="http://jokkmokk.biz/" title="ITUS Jokkmokk">Jokkmokk</a>.
</p>
</div>
<!--
<script src="http://www.google-analytics.com/urchin.js" type="text/javascript">
</script>
<script type="text/javascript">
_uacct = "UA-3174308-1";
urchinTracker();
</script>
-->
</body>
</html>