Lots of small changes

blast/maketree.php

@@ -36,6 +36,7 @@
 $nexus .="begin paup;\n";
 $nexus .="   [root trees at midpoint]\n";
 $nexus .="   set rootmethod=midpoint;\n";
+$nexus .="   set outroot=monophyl;\n";
 $nexus .="   [construct tree using neighbour-joining]\n";
 $nexus .="   nj;\n";
 $nexus .="   [ensure branch lengths are output as substituions per nucleotide]\n";

course/projects/index.html

@@ -63,14 +63,28 @@ <h4>Reconciling taxonomic names</h4>
 <h4>Name changes and obsolete labels</h4>
 <p>How fast do taxonomic names change? What are the implications of this for people using these names? For example, for a public museum such as the Hunterian Zoology museum, how many names for the animals exhibited have changed since the labels were printed?</p>
 
+<h4>Linking bird names to literature</h4>
+<p>Avibase has a copy of Peter's checklist of birds of the world as an Excel spreadsheet, see
+<a href="http://avibase.bsc-eoc.org/peterschecklist.jsp">The Peters' Check-list of the Birds of the World Database</a> (local copy <a href="PETERS_DATABASE_version_1.xlsx">here</a>). 
+Can you parse the text and locate the references online?</p>
+
 <h3>Mapping</h3>
 
 <h4>Where are new species being found?</h4>
-<p>Find a list of recently described species (for example, follow a journal like <a href="https://twitter.com/zootaxa">Zootaxa</a> on Twitter, or <a href="https://species.wikimedia.org/wiki/Category:New_species_2014">Wikispecies</a>, and locate as many on a map. Comapare this to the distribution of protected area on <a href="http://protectedplanet.net">http://protectedplanet.net</a>.</p>
+<p>Find a list of recently described species (for example, follow a journal like <a href="https://twitter.com/zootaxa">Zootaxa</a> on Twitter, or <a href="https://species.wikimedia.org/wiki/Category:New_species_2014">Wikispecies</a>, and locate as many on a map. Compare this to the distribution of protected area on <a href="http://protectedplanet.net">http://protectedplanet.net</a>.</p>
 
 <h4>Extracting geographic data from papers</h4>
 <p>A lot of geographic information is locked up in scientific papers. Can you write a regular expression to extract latitude and longitudes from a paper? Can you add this information to Google Earth?</p>
 
+<h3>Conservation</h3>
+
+<h4>How useful is GBIF for conservation?</h4>
+<p>Take a number of species on the <a href="http://www.iucnredlist.org">IUCN Red List</a> and find them in <a href="http://www.gbif.org">GBIF</a>. Is there sufficient information in GBIF for you to assess the status of those species? You could investigate the use of <a href="http://geocat.kew.org">GeoCAT</a> using GBIF data. See also <a href="http://www.iucnredlistassessments.org">IUCN Red List assessments</a></p>
+
+<h3>Ecological associations</h3>
+
+<h4>Add data to Global Biotic Interactions (GloBI)</h4>
+<p>Find a data set for ecological interactions (e.g., host and parasites) and add it to <a href="http://www.globalbioticinteractions.org/">Global Biotic Interactions (GloBI)</a>.</p>
 
 <div id="disqus_thread"></div>
 <script type="text/javascript">

services/reconciliation_api.php

@@ -115,7 +115,7 @@ function StoreHit($query_key, $hit)
 
 	//----------------------------------------------------------------------------------------------
 	// Handle an individual query
-	function OneQuery($query_key, $text, $limit = 1)
+	function OneQuery($query_key, $text, $limit = 1, $properties = null)
 	{
 
 	}
@@ -140,7 +140,13 @@ function Query($queries, $callback)
 			}				
 			$this->result->${query_key}->result = array();
 
-			$this->OneQuery($query_key, $text, $limit);
+			$properties = null;
+			if (isset($query->properties))
+			{
+				$properties = $query->properties;
+			}
+
+			$this->OneQuery($query_key, $text, $limit, $properties);
 
 			if (count($this->result->${query_key}->result) == 0)
 			{
@@ -150,7 +156,9 @@ function Query($queries, $callback)
 
 		}
 
-		if (0)
+		// sort ?
+		
+		if (1)
 		{
 			file_put_contents('tmp/r.txt', "Return: \n" . print_r($this->result, true), FILE_APPEND);
 		}			

services/reconciliation_envo.php

@@ -72,7 +72,7 @@ function QueryInitialise()
 
 	//----------------------------------------------------------------------------------------------
 	// Handle an individual query
-	function OneQuery($query_key, $text, $limit = 5)
+	function OneQuery($query_key, $text, $limit = 5, $properties = null)
 	{
 		$param = array(
 			'partialName' => $text, 

services/reconciliation_eol.php

@@ -49,7 +49,7 @@ function Types()
 
 	//----------------------------------------------------------------------------------------------
 	// Handle an individual query
-	function OneQuery($query_key, $text, $limit = 1)
+	function OneQuery($query_key, $text, $limit = 1, $properties = null)
 	{
 		$url = 'http://eol.org/api/search/1.0/' . rawurlencode($text) . '.json';
 

services/reconciliation_gbif.php

@@ -46,7 +46,7 @@ function Types()
 
 	//----------------------------------------------------------------------------------------------
 	// Handle an individual query
-	function OneQuery($query_key, $text, $limit = 1)
+	function OneQuery($query_key, $text, $limit = 1, $properties = null)
 	{
 		$url = 'http://data.gbif.org/ws/rest/taxon/list?scientificname=' . urlencode($text) . '&dataresourcekey=1';
 

services/reconciliation_gbif_dataset.php

@@ -0,0 +1,108 @@
+<?php
+
+// GBIF dataset (with publisher UUID as ID property to narrow search)
+
+require_once (dirname(__FILE__) . '/reconciliation_api.php');
+
+
+//--------------------------------------------------------------------------------------------------
+class GBIFDatasetService extends ReconciliationService
+{
+	//----------------------------------------------------------------------------------------------
+	function __construct()
+	{
+		$this->name 			= 'GBIF Dataset';
+
+		$this->identifierSpace 	= 'http://www.gbif.org/';
+
+		$this->schemaSpace 		= 'http://rdf.freebase.com/ns/type.object.id';
+
+		$this->Types();
+
+		$view_url = 'http://www.gbif.org/dataset/{{id}}';
+
+		$preview_url = '';	
+		$width = 430;
+		$height = 300;
+
+		if ($view_url != '')
+		{
+			$this->View($view_url);
+		}
+		if ($preview_url != '')
+		{
+			$this->Preview($preview_url, $width, $height);
+		}
+	}
+
+	//----------------------------------------------------------------------------------------------
+	function Types()
+	{
+		$type = new stdclass;
+		$type->id = '/common/topic';
+		$type->name = 'Freebase topic';
+		$this->defaultTypes[] = $type;
+	} 	
+
+	//----------------------------------------------------------------------------------------------
+	// Handle an individual query
+	function OneQuery($query_key, $text, $limit = 1, $properties = null)
+	{
+		$url = '';
+		if ($properties)
+		{
+			file_put_contents(dirname(__FILE__) . '/tmp/prop.txt', json_encode($properties), FILE_APPEND);
+
+			if ($properties[0]->pid == '/type/object/id')
+			{
+				// find datasets for this organisation
+				$url .= 'http://api.gbif.org/v1/organization/' . $properties[0]->v . '/publishedDataset';
+			}
+			else
+			{
+				// crude search
+				$url = 'http://api.gbif.org/v1/dataset?q=' . urlencode($text);
+			}
+
+
+		}
+		else
+		{
+			// crude search
+			$url = 'http://api.gbif.org/v1/dataset?q=' . urlencode($text);
+		}
+
+		file_put_contents(dirname(__FILE__) . '/tmp/url.txt', $url . "\n", FILE_APPEND);
+
+		$json = get($url);
+
+		if ($json != '')
+		{
+			$obj = json_decode($json);
+
+			foreach ($obj->results as $result)
+			{
+				$hit = new stdclass;
+				$hit->id 	= $result->key;
+				$hit->name 	= $result->title;
+				similar_text($text, $hit->name, $hit->score);
+				$hit->match = ($hit->score == 1);
+				$this->StoreHit($query_key, $hit);
+			}
+		}
+
+	}
+
+
+}
+
+$service = new GBIFDatasetService();
+
+if (1)
+{
+	file_put_contents(dirname(__FILE__) . '/tmp/publisher.txt', $_REQUEST['queries'], FILE_APPEND);
+}
+
+$service->Call($_REQUEST);
+
+?>