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## gbif.asc

      
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                GenBank and GBIF
              
          
Cluster multiple occurrence records in GBIF


In this example we have the same sequence GQ247641 in two sequence datasets
("European Molecular Biology Laboratory Australian Mirror" and
"Geographically tagged INSDC sequences"), and also the voucher specimen ("AM W.35546.001" or "AMS:W.35546")
also occurs in GBIF (provided by "Australian Museum provider for OZCAM"). Linking the two sequence
occurrences is trivial, we just link by the accession "GQ247641". Linking the sequence to the museum
specimen requires matching the slightly different strings "AM W.35546.001" and "AMS:W.35546".


The graph links three records in GBIf that all refer to the same thing.


## cltools.sh
#!/bin/sh

##
# Install autoconf, automake and libtool smoothly on Mac OS X.
# Newer versions of these libraries are available and may work better on OS X
#
# This script is originally from http://jsdelfino.blogspot.com.au/2012/08/autoconf-and-automake-on-mac-os-x.html
#

export build=~/devtools # or wherever you'd like to build

## jsonld.sh

curl -XDELETE 'localhost:9200/jsonld'

curl -XPOST 'localhost:9200/jsonld'

curl -XPUT 'localhost:9200/jsonld/doc/1' -d '
{
  "@context":
  {
    "dc": "http://purl.org/dc/elements/1.1/",

## index.html
<!DOCTYPE html>
<html>

  <head>
    <meta http-equiv="content-type" content="text/html; charset=utf-8" />
    <title>GBIF and Google Maps</title>

    <style type="text/css">
      body {
        margin: 0;

## Multiple identifiers
== Handling multiple identifiers

Many objects of interest will have multiple identifiers, and each identifier may have different, complementary data associated with it.

One approach is to treat each identifier as a node, and link it to node for the corresponding object (essentially the object is treated as a bnode). We therefore refer to an object as "the object identifier by <identifier>". If we have correctly associated multiple identifiers with the same object, then we can link the two objects together.

When we have a link to create to another object, we use MERGE (id)-[]-(object) to ensure that id-object exists, then we link to it. In the example below we have a work with DOI 10.3897/phytokeys.44.7993, which cites PMID 21653447. First we create the work with DOI 10.3897/phytokeys.44.7993.

//hide
//setup

## query.txt
The Mediawiki API can be used to find qhat wikipedia pages link to BioStor, e.g.:

https://en.wikipedia.org/w/api.php?action=query&list=exturlusage&euquery=biostor.org&eulimit=20

See https://www.mediawiki.org/wiki/API:Lists/All#Exturlusage for details.

## Cricula.nexus
#NEXUS

Begin trees;  [Treefile saved Thu Aug 20 21:42:14 2015]
[!
>Data file = /Users/rpage/Sites/geojson-phylogeny-demo/bold-api/service/tmp/SAUPA642-10/SAUPA642-10.nex
>Neighbor-joining search settings:
>  Ties (if encountered) will be broken systematically
>  Distance measure = uncorrected ("p")
>  (Tree is unrooted)
]

## Cricula.geojson

      
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                Cricula barcode map
              
          
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## index.html
<!DOCTYPE html>
<html>
<head>
    <title>GBIF search</title>
    <meta charset="utf-8" />
    <link
        rel="stylesheet"
        href="http://cdn.leafletjs.com/leaflet-0.7/leaflet.css"
    />
    <link

## geojson-conversion.sh
# Bulk convert shapefiles to geojson using ogr2ogr
# For more information, see http://ben.balter.com/2013/06/26/how-to-convert-shapefiles-to-geojson-for-use-on-github/

# Note: Assumes you're in a folder with one or more zip files containing shape files
# and Outputs as geojson with the crs:84 SRS (for use on GitHub or elsewhere)

#geojson conversion
function shp2geojson() {
  ogr2ogr -f GeoJSON -t_srs crs:84 "$1.geojson" "$1.shp"
}
	#!/bin/sh

	##
	# Install autoconf, automake and libtool smoothly on Mac OS X.
	# Newer versions of these libraries are available and may work better on OS X
	#
	# This script is originally from http://jsdelfino.blogspot.com.au/2012/08/autoconf-and-automake-on-mac-os-x.html
	#

	export build=~/devtools # or wherever you'd like to build

	curl -XDELETE 'localhost:9200/jsonld'

	curl -XPOST 'localhost:9200/jsonld'

	curl -XPUT 'localhost:9200/jsonld/doc/1' -d '
	{
	"@context":
	{
	"dc": "http://purl.org/dc/elements/1.1/",
	<!DOCTYPE html>
	<html>

	<head>
	<meta http-equiv="content-type" content="text/html; charset=utf-8" />
	<title>GBIF and Google Maps</title>

	<style type="text/css">
	body {
	margin: 0;
	== Handling multiple identifiers

	Many objects of interest will have multiple identifiers, and each identifier may have different, complementary data associated with it.

	One approach is to treat each identifier as a node, and link it to node for the corresponding object (essentially the object is treated as a bnode). We therefore refer to an object as "the object identifier by <identifier>". If we have correctly associated multiple identifiers with the same object, then we can link the two objects together.

	When we have a link to create to another object, we use MERGE (id)-[]-(object) to ensure that id-object exists, then we link to it. In the example below we have a work with DOI 10.3897/phytokeys.44.7993, which cites PMID 21653447. First we create the work with DOI 10.3897/phytokeys.44.7993.

	//hide
	//setup
	The Mediawiki API can be used to find qhat wikipedia pages link to BioStor, e.g.:

	https://en.wikipedia.org/w/api.php?action=query&list=exturlusage&euquery=biostor.org&eulimit=20

	See https://www.mediawiki.org/wiki/API:Lists/All#Exturlusage for details.
	#NEXUS

	Begin trees; [Treefile saved Thu Aug 20 21:42:14 2015]
	[!
	>Data file = /Users/rpage/Sites/geojson-phylogeny-demo/bold-api/service/tmp/SAUPA642-10/SAUPA642-10.nex
	>Neighbor-joining search settings:
	> Ties (if encountered) will be broken systematically
	> Distance measure = uncorrected ("p")
	> (Tree is unrooted)
	]
	# Bulk convert shapefiles to geojson using ogr2ogr
	# For more information, see http://ben.balter.com/2013/06/26/how-to-convert-shapefiles-to-geojson-for-use-on-github/

	# Note: Assumes you're in a folder with one or more zip files containing shape files
	# and Outputs as geojson with the crs:84 SRS (for use on GitHub or elsewhere)

	#geojson conversion
	function shp2geojson() {
	ogr2ogr -f GeoJSON -t_srs crs:84 "$1.geojson" "$1.shp"
	}