rdmpage’s gists

rdmpage / _q5fYmzIRsaO1zdwL9Ja5A.json

Last active August 29, 2015 10:15

API call to get hypothesis.is annotation https://hypothes.is/a/_q5fYmzIRsaO1zdwL9Ja5A

	{
	"updated": "2015-08-28T23:58:18.165753+00:00",
	"target": [
	{
	"source": "http://www.gbif.org/occurrence/912442645",
	"selector": [
	{
	"conformsTo": "https://tools.ietf.org/html/rfc3236",
	"type": "FragmentSelector",
	"value": "occurrence"

rdmpage / Taxa with same basionym

Last active August 29, 2015 14:27

	== Taxonomy tester - taxa with same basionym

	This test asks whether there are multiple taxa with the same basionym. Logically this should not occur.

	This example uses the legume genrra Poissonia and Coursetia.


	//hide
	//setup
	//output

rdmpage / Anachronistic species and genus names

Last active August 29, 2015 14:26

	== Taxonomy tester - anachronistic species and genus names

	This test compares the dates of species names and the genus name. If a name is a new combination then the author name is enclosed in parentheses. If a species is placed in a genus that was published after the species was described, then logically the name is a new combination. However in some cases GBIF has species names which violate this rule.

	This example uses the butterfly genus Heliopyrgus

	//hide
	//setup
	//output
	[source,cypher]

rdmpage / Subspecies

Last active August 29, 2015 14:26

	== Taxonomy tester - species and subspecies with same name

	This test compares the epithets of species and subspecies in the same genus. If a subspecies with a given epithet exists in a genus, there should not be another species (other than the species to which subspecies belongs if it is the nominate subspecies).

	This example uses the butterfly genus Heliopyrgus

	//hide
	//setup
	//output
	[source,cypher]

rdmpage / Generic names don't match

Last active August 29, 2015 14:26

	== Taxonomy tester - genus names should match species name

	This test compares the generic name of a species with that of the genus it is placed in. These should be the same, but often aren't, signalling a problem, such as a homonym, synonym, or spelling mistake.

	This example uses the butterfly genus Forsterinaria Gray, 1973, see http://bionames.org/search/Forsterinaria, which is a replacement name for the genus Haywardina Forster, 1964, see http://biostor.org/reference/77525. GBIF has Forsterinaria http://bionames.org/taxa/gbif/3257628 but the species names are labelled with Haywardina (which it also has in its classification, http://www.gbif.org/species/1894033 ).

	//hide
	//setup
	//output
	[source,cypher]

rdmpage / gist:a91e351279438d2ec1e6

Last active August 29, 2015 14:26

	== Taxonomy tester - same species name in different genera

	This gist loads a graph of the GBIF classification for bats of the family Molossidae, and tests for possible duplicated species. It is essentially a Neo4J version of the "papaya plot" http://iphylo.blogspot.co.uk/2013/08/cluster-maps-papaya-plots-and-trouble.html

	Note that this is a very simple test, we should also test for subspecies names as well, and standardise epithets to avoid missing matches due to differing gender of genus names.

	//hide
	//setup
	//output
	[source,cypher]

rdmpage / simple.sql

Created May 18, 2015 10:37

Simple ION dump

	SELECT
	IFNULL(id, ""),
	IFNULL(cluster_id, ""),
	IFNULL(nameComplete, ""),
	IFNULL(taxonAuthor, ""),
	IFNULL(`group`, ""),
	IFNULL(publication, "")
	INTO OUTFILE "/tmp/markus.tsv"
	FIELDS TERMINATED BY "\t" ENCLOSED BY "" ESCAPED BY ""
	LINES TERMINATED BY "\n"

rdmpage / bold.txt

Created March 25, 2015 10:55

BOLD phylogeny from API

	BOLD has a (hidden) API to retrieve a Newick tree for a BIN. For example on the page http://www.boldsystems.org/index.php/Public_BarcodeCluster?clusteruri=BOLD:AAD8242 we see an SVG tree. Under the hood this is called by: http://www.boldsystems.org/index.php/Public_Ajax_BINTree?clusterguid=BOLD:AAD8242&clusteruri=BOLD:AAD8242&clustername=BIN38242&clusterid=1738567

	It's not clear where the "clusterid" comes from, but without it the API call fails.

rdmpage / traits.html

Last active August 29, 2015 14:17

CouchDB-like view of EOL Trait data

	<html>
	<head>
	<title>CouchDB-like view of EOL Trait data</title>
	<meta charset="UTF-8"/>
	<script src="https://ajax.googleapis.com/ajax/libs/jquery/1.11.2/jquery.min.js"></script>
	</head>
	<body>
	<h1>CouchDB-like view of EOL Trait data</h1>
	<p>API call like this: http://eol.org/api/traits/26374</p>
	<div id="output"></div>

rdmpage / 576129791759384576.json

Created March 18, 2015 13:19

Tweet from web client, includes geocoding, retrieved from https://api.twitter.com/1.1/statuses/show.json?id=576129791759384576

	{
	"created_at": "Thu Mar 12 21:17:00 +0000 2015",
	"id": 576129791759384600,
	"id_str": "576129791759384576",
	"text": "#myGBIF (via web client)",
	"source": "<a href=\"http://twitter.com\" rel=\"nofollow\">Twitter Web Client</a>",
	"truncated": false,
	"in_reply_to_status_id": null,
	"in_reply_to_status_id_str": null,
	"in_reply_to_user_id": null,

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