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<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<html lang="en"><head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8"><title>Phylotastic web services</title>
<link rel="stylesheet" type="text/css" href="css/phylotastic.css"><!-- Date: 2012-06-08 --></head><body>
<div class="wrapper clearfix">
<div class="header"><a href="./index.html"><img src="images/Phylotastic_logo.png"></a></div>
<div class="maincol">
<br>
<img src="images/services_black.png">
<p>The Phylotastic project has created many web-services. Below are services that make up the phylotastic ecology of web services. You can find more information on these services in our <a href="https://github.com/phylotastic/phylo_webservices.git" target="_top">Github repository.</a> </p>
<ul class="demolist">
<li><a href="https://github.com/phylotastic/phylo_services_docs/blob/master/ServiceDescription/PhyloServicesDescription.md#web-service-1" target="_blank">Find Scientific Names on webpages</a>
<p> A service for finding scientific names on web pages using <a href="http://gnrd.globalnames.org" target="_top">Global Names Recognition and Discovery</a>. </p>
<p>Usage details are in this <a href="https://github.com/phylotastic/phylo_services_docs/blob/master/ServiceDescription/PhyloServicesDescription.md#web-service-1" target="_blank">Documentation</a> </p>
<li><a href="https://github.com/phylotastic/phylo_services_docs/blob/master/ServiceDescription/PhyloServicesDescription.md#web-service-2" target="_blank">Find Scientific Names on free-form text </a>
<p> A service for finding scientific names on free-form text using <a href="http://gnrd.globalnames.org" target="_top">Global Names Recognition and Discovery</a>. </p>
<p>Usage details are in this <a href="https://github.com/phylotastic/phylo_services_docs/blob/master/ServiceDescription/PhyloServicesDescription.md#web-service-2" target="_blank">Documentation</a> </p>
<li><a href="https://github.com/phylotastic/phylo_services_docs/blob/master/ServiceDescription/PhyloServicesDescription.md#web-service-3" target="_blank">Resolve Scientific Names with OpenTree</a>
<p> A service for taxonomic name resolution of scientific names using <a href="https://github.com/OpenTreeOfLife/opentree/wiki/Open-Tree-of-Life-APIs#tnrs" target="_top">OpenTreeOfLife</a>. </p>
<p>Usage details are in this <a href="https://github.com/phylotastic/phylo_services_docs/blob/master/ServiceDescription/PhyloServicesDescription.md#web-service-3" target="_blank">Documentation</a> </p>
<li><a href="https://github.com/phylotastic/phylo_services_docs/blob/master/ServiceDescription/PhyloServicesDescription.md#web-service-4" target="_blank">Resolve Scientific Names with GNR</a>
<p> A service for taxonomic name resolution of scientific names using <a href="http://resolver.globalnames.org" target="_top">Global Names Resolver</a>. </p>
<p>Usage details are in this <a href="https://github.com/phylotastic/phylo_services_docs/blob/master/ServiceDescription/PhyloServicesDescription.md#web-service-4" target="_blank">Documentation</a> </p>
<li><a href="https://github.com/phylotastic/phylo_services_docs/blob/master/ServiceDescription/PhyloServicesDescription.md#web-service-5" target="_blank">Get Phylogenetic trees</a>
<p> A service for getting Phylogenetic Trees from <a href="https://github.com/OpenTreeOfLife/opentree/wiki/Open-Tree-of-Life-APIs#taxonomy" target="_top">OpenTreeOfLife</a>. </p>
<p>Usage details are in this <a href="https://github.com/phylotastic/phylo_services_docs/blob/master/ServiceDescription/PhyloServicesDescription.md#web-service-5" target="_blank">Documentation</a> </p>
<li><a href="https://github.com/phylotastic/phylo_services_docs/blob/master/ServiceDescription/PhyloServicesDescription.md#web-service-6" target="_blank">Get Species from a Taxon</a>
<p> A service for getting all Species that belong to a particular Taxon using <a href="https://github.com/OpenTreeOfLife/opentree/wiki/Open-Tree-of-Life-APIs#taxonomy" target="_top">OpenTreeOfLife</a>. </p>
<p>Usage details are in this <a href="https://github.com/phylotastic/phylo_services_docs/blob/master/ServiceDescription/PhyloServicesDescription.md#web-service-6" target="_blank">Documentation</a> </p>
<li><a href="https://github.com/phylotastic/phylo_services_docs/blob/master/ServiceDescription/PhyloServicesDescription.md#web-service-7" target="_blank">Get Species from a specific country</a>
<p> A service for getting all Species (from a Taxon) from a particular country using <a href="https://github.com/OpenTreeOfLife/opentree/wiki/Open-Tree-of-Life-APIs#taxonomy" target="_top">OpenTreeOfLife</a> and <a href="http://www.inaturalist.org/pages/api+reference#get-places" target="_top">iNaturalist</a>. </p>
<p>Usage details are in this <a href="https://github.com/phylotastic/phylo_services_docs/blob/master/ServiceDescription/PhyloServicesDescription.md#web-service-7" target="_blank">Documentation</a> </p>
<li><a href="https://github.com/phylotastic/phylo_services_docs/blob/master/ServiceDescription/PhyloServicesDescription.md#web-service-8" target="_blank">Get images from EOL</a>
<p> A service to get image urls of a species using <a href="http://eol.org/api" target="_top">EOL</a>. </p>
<p>Usage details are in this <a href="https://github.com/phylotastic/phylo_services_docs/blob/master/ServiceDescription/PhyloServicesDescription.md#web-service-8" target="_blank">Documentation</a> </p>
<li><a href="https://github.com/phylotastic/phylo_services_docs/blob/master/ServiceDescription/PhyloServicesDescription.md#web-service-9" target="_blank">Get Species that have genomes</a>
<p> A service to get subset of Species that belong to a particular Taxon and have genome sequence in <a href="http://www.ncbi.nlm.nih.gov/books/NBK25500/#chapter1.Finding_Related_Data_Through_En" target="_top">NCBI</a>. </p>
<p>Usage details are in this <a href="https://github.com/phylotastic/phylo_services_docs/blob/master/ServiceDescription/PhyloServicesDescription.md#web-service-9" target="_blank">Documentation</a> </p>
<li><a href="https://github.com/phylotastic/phylo_services_docs/blob/master/ServiceDescription/PhyloServicesDescription.md#web-service-10" target="_blank">Get information urls of a list of species</a>
<p> Get information urls of a list of species <a href="http://eol.org/api" target="_top">EOL</a>. </p>
<p>Usage details are in this <a href="https://github.com/phylotastic/phylo_services_docs/blob/master/ServiceDescription/PhyloServicesDescription.md#web-service-10" target="_blank">Documentation</a> </p>
<li><a href="https://github.com/phylotastic/phylo_services_docs/blob/master/ServiceDescription/PhyloServicesDescription.md#web-service-11" target="_blank">Get lists of species</a>
<p> A service to get lists of species that a user of phylotastic web application has published. </p>
<p>Usage details are in this <a href="https://github.com/phylotastic/phylo_services_docs/blob/master/ServiceDescription/PhyloServicesDescription.md#web-service-11" target="_blank">Documentation</a> </p>
<li><a href="https://github.com/phylotastic/phylo_services_docs/blob/master/ServiceDescription/PhyloServicesDescription.md#web-service-12" target="_blank">Post a new list of species</a>
<p> A service to insert a new list of species by a phylotastic web application user. </p>
<p>Usage details are in this <a href="https://github.com/phylotastic/phylo_services_docs/blob/master/ServiceDescription/PhyloServicesDescription.md#web-service-12" target="_blank">Documentation</a> </p>
<li><a href="https://github.com/phylotastic/phylo_services_docs/blob/master/ServiceDescription/PhyloServicesDescription.md#web-service-13" target="_blank">Replace species of an existing list</a>
<p> A service to replace the existing species objects with new species object of an existing list. </p>
<p>Usage details are in this <a href="https://github.com/phylotastic/phylo_services_docs/blob/master/ServiceDescription/PhyloServicesDescription.md#web-service-13" target="_blank">Documentation</a> </p>
<li><a href="https://github.com/phylotastic/phylo_services_docs/blob/master/ServiceDescription/PhyloServicesDescription.md#web-service-14" target="_blank">Remove an existing list</a>
<p> A service to remove an existing list. </p>
<p>Usage details are in this <a href="https://github.com/phylotastic/phylo_services_docs/blob/master/ServiceDescription/PhyloServicesDescription.md#web-service-14" target="_blank">Documentation</a> </p>
<li><a href="https://github.com/phylotastic/phylo_services_docs/blob/master/ServiceDescription/PhyloServicesDescription.md#web-service-15" target="_blank">Update metadata of an existing list</a>
<p> A service to update properties (metadata) of an existing list </p>
<p>Usage details are in this <a href="https://github.com/phylotastic/phylo_services_docs/blob/master/ServiceDescription/PhyloServicesDescription.md#web-service-15" target="_blank">Documentation</a> </p>
<li><a href="https://github.com/phylotastic/phylo_services_docs/blob/master/ServiceDescription/PhyloServicesDescription.md#web-service-16" target="_blank">Compare Phylogenetic Trees</a>
<p> A service to compare two Phylogenetic Trees using <a href="http://dendropy.org/library/treecompare.html#module-dendropy.calculate.treecompare" target="_top">dendropy</a>. </p>
<p>Usage details are in this <a href="https://github.com/phylotastic/phylo_services_docs/blob/master/ServiceDescription/PhyloServicesDescription.md#web-service-16" target="_blank">Documentation</a> </p>
</ul>
<!-- <li><a href="http://datelife.org/cgi-bin/R/result?taxa=Rhinoceros_unicornis%2CEquus_caballus%2CMus_musculus&format=newickmed&partial=liberal&useembargoed=no&uncertainty=100" target="_top">DateLife example</a> <p>Clicking the link above executes the URL <code>http://datelife.org/cgi-bin/R/result?taxa=Rhinoceros_unicornis%2CEquus_caballus%2CMus_musculus&format=newickmed&partial=liberal&useembargoed=no&uncertainty=100</code>, which gives the result <code>((Rhinoceros_unicornis:55.8,Equus_caballus:55.8):40.3,Mus_musculus:96.1);</code>, indicating that Rhinoceros and Horse diverged 55.8 MYA.
</p>
</li>
<li><a href="http://phylotastic-wg.cs.nmsu.edu/script/phylotastic.cgi" target="_top">Pruner (MapReduce)</a>
<p>This service invokes a pruner using an URL API as follows: <code>
phylotastic.cgi?format=newick&tree=mammals&species=Homo_sapiens,Pan_troglodytes,Gorilla_gorilla</code> where </p><ul class="littleul">
<li>format is one of { Newick, NeXML, NEXUS, PhyloXML }
</li><li>tree is one of { mammals, fishes, angiosperms, phylomatic, tol }
</li><li>species is a comma-separated list of taxonomic identifiers
</li></ul>
</li>
<li><a href="http://api.phylotastic.org/tnrs" target="_top">TNRS meta-service</a>
<p>The
TNRS meta-service accepts a list of names, and returns a JSON document
(in progress: DwC-A) that, for each name, lists the matches from all of
the back-end TNRSs that it aggregates. A hypothetical intelligent
client would apply rules to decide which matches to use. </p>
</li>
<li><a href="http://phylodiversity.net/phylomatic" target="_top">Phylomatic URL API</a>
<p>Phylomatic has a new web service interface (click the link above for explanation) that accepts URLs like this: <code>http://phylodiversity.net/phylomatic/pm/phylomatic.cgi?format=xml&tree=annonaceae%2Fannona%2FAnnona_cherimola%0D%0Aannonaceae%2Fannona%2FAnnona_muricata</code>.
</p>
</li>
<li><a href="https://github.com/OpenTreeOfLife/opentree/wiki/Open-Tree-of-Life-APIs" target="_top">OpenTree Web-services API Docs</a>
<p>OpenTree has a number of powerful web services to do things like get studies (with trees), match taxon names, query the taxonomy, and get the "induced subtree" (in OT terminology) for a named set of species. The link above points to their web services description. Some examples are explained in Arlin's <a href="http://blog.opentreeoflife.org/2014/10/07/tree-for-all-hackathon-series-introduction/">blogs about the 2014 OpenTree hackathon</a>.
</p>
</li>
<li><a href="http://phylotastic.cs.nmsu.edu/PhylotasticTreeStore/phylows/" target="_top">TreeStore</a>
<p>The
page above provides links to several queries that will retrieve sample
trees from a treestore. The server uses web2py to provide access to
trees stored in a Virtuoso triplestore. </p>
</li>
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