View 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
View 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/",
View 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
View 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.
View 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)
]
View Cricula.geojson
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View primers.txt
Reference COI is NC_003128 Buteo buteo COI
TZBRD035-15.COI-5P [648bp] ctgatctttggtgnatgagcaggcatagccggcacagcacttagcctactaatccgcgcagaactaggacagccaggaacactattgggagacgaccaaatctacaatgtaatcgtaacagcccacgctttcgtcataatcttcttcatagtcatacctattatgatcggaggcttcggaaactgactggttccactcataattggcgccccagacatagcattcccccgcataaataatatgagcttctgactcctcccaccttcttttctcctcctactagcctcctctacagtagaagccggggctggcactggatgaactgtttatccacccctagccggtaatcttgcccacgcgggcgcatcagtagacctggctattttttcccttcacttggcaggcgtgtcgtccatcttaggagctattaactttatcaccacaattattaacataaagccccctgcactatcacaatatcaaacacccctcttcgtatgatccgtcctcattactgctatcctcttactactatccctgccagtcctagccgccgggattacaatactcctcaccgatcgcaacctcaacactacattctttgaccctgcaggaggaggagacccaatcctgtatcaacacctattc
TZBRD019-15.COI-5P tcttcggcgcctgagctggtatagtcggcaccgccctcagcttactcatccgtgcagaactcggccaacccggcacactcctaggtgacgaccaaatttataacgtaatcgttaccgcacatgccttcgtaataatcttcttcatagttataccaatcatgatcggaggattcggaaactgacttgttccactcataattggcgctc
View 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
View 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"
}
View collection.json
{"collection":{"name":"Mesoplodon","description":"Mesoplodon species","collection_items":[{"collected_item_type":"TaxonConcept","collected_item_id":328563}]}}