Nicky Nicolson nickynicolson

## name-reconciliation-python.ipynb

      
              1 file
            
          
              0 forks
            
          
              0 comments
            
          
              2 stars
            
          
                nickynicolson
                / name-reconciliation-python.ipynb
            
            
              Last active
              February 12, 2016 16:25
            
              
                Name reconciliation in Python
              
          
      Sorry, something went wrong. Reload?
      Sorry, we cannot display this file.
      Sorry, this file is invalid so it cannot be displayed.
      
          Viewer requires iframe.
      
    
## IFTTT-Zotero-to-Trello-recipe.md

      
              1 file
            
          
              0 forks
            
          
              3 comments
            
          
              8 stars
            
          
                nickynicolson
                / IFTTT-Zotero-to-Trello-recipe.md
            
            
              Last active
              November 17, 2020 22:43
            
          
    Automating reading list management

What I'm using:


Zotero: In browser integration mean that its a single click to save citation information (and a full-text PDF if available)
...but I'm using  Trello to stay on top of tasks, and my "to-read" list needs to have a presence in my "to-do" list, as Trello gives a better single view of my work than zotero.
What I'd like:

Cards for new "to-read" articles in Trello, automatically - without cut + paste.

  
## neo4j-jaccard.adoc

      
              1 file
            
          
              0 forks
            
          
              0 comments
            
          
              0 stars
            
          
                nickynicolson
                / neo4j-jaccard.adoc
            
            
              Last active
              August 29, 2015 14:27
            
          
This graph gist demonstrates use of Jaccard calculation to determine similarity between two sets of nodes


## 0_reuse_code.js
// Use Gists to store code you would like to remember later on
console.log(window); // log the "window" object to the console

## gbseq2tsv.xsl
<?xml version="1.0" encoding="UTF-8"?>
<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform">
<xsl:output method="text" indent="yes" encoding="UTF-8"/>
<xsl:variable name="delimiter" select="'&#09;'"/>
<xsl:variable name="newline" select="'&#10;'"/>

<xsl:template match="/">
	<!-- header line -->
	<xsl:value-of select="concat('primary_accession',$delimiter,'date_created',$delimiter,'date_last_amended', $delimiter, 'definition', $delimiter, 'title', $delimiter, 'reference', $delimiter, 'doi', $delimiter, 'specimen_voucher', $delimiter, 'bio_material', $delimiter, 'organism', $newline)"/>
	<!-- data -->

## cypher-meta-graph-w-counts
// Create meta-graph with orphan counts
MATCH (n)
/* ugly string replace to convert collection of labels to colon delimited string */
WITH replace(replace(replace(replace(str(labels(n)),'[',''),']',''),'"',''),',',':') AS l, count(distinct n) AS c
MERGE (mn:Meta_Node {name:l,count:c})
WITH mn
MATCH (a)-[r]->(b)
WITH replace(replace(replace(replace(str(labels(a)),'[',''),']',''),'"',''),',',':') AS a_labels
	, count(distinct a) AS from_count
	, type(r) AS rel_type

## OpenRefine-column-addition-OpenTree-TNRS-match_names
import urllib
import urllib2

try:
  # Base url for the TNRS match_names API
  url = 'http://api.opentreeoflife.org/v2/tnrs/match_names'
  # Encode data value to be looked up as an array of names:
  data = '{"names": ["'+value+'"]}'
  print "Looking up: " + data
  # Set HTTP headers:

## Taxonomic-mind-mapper
= The taxonomic mind-mapper
Nicky Nicolson, Peter Hovenkamp
:neo4j-version: 2.1.0
:author: Nicky Nicolson
:twitter: nickynicolson

== Domain
We investigate the use of the scheme in: https://docs.google.com/document/d/1FIxNrrGrIZs0l4QJEdGfctXbYVL4cQhKspmMEHmKAGg/edit with a use case in the taxonomy of Diplazium tomentosum (https://docs.google.com/document/d/1vni44RBwGNZ7iRCFf243NtcD-7xwjHrDeAPehato7KY/edit?usp=sharing)

== Data model

## Taxonomic-mind-mapper
Peter investigates the taxonomy of Diplazium tomentosum.

//console

He starts with one of the types from the Leiden herbarium (http://plants.jstor.org/specimen/l0051073):

[source,cypher]
----
CREATE (s:Specimen{id:"L0051073"
    ,jstorUrl:'http://plants.jstor.org/specimen/l0051073'
	// Use Gists to store code you would like to remember later on
	console.log(window); // log the "window" object to the console
	<?xml version="1.0" encoding="UTF-8"?>
	<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform">
	<xsl:output method="text" indent="yes" encoding="UTF-8"/>
	<xsl:variable name="delimiter" select="' '"/>
	<xsl:variable name="newline" select="' '"/>

	<xsl:template match="/">
	<!-- header line -->
	<xsl:value-of select="concat('primary_accession',$delimiter,'date_created',$delimiter,'date_last_amended', $delimiter, 'definition', $delimiter, 'title', $delimiter, 'reference', $delimiter, 'doi', $delimiter, 'specimen_voucher', $delimiter, 'bio_material', $delimiter, 'organism', $newline)"/>
	<!-- data -->
	// Create meta-graph with orphan counts
	MATCH (n)
	/* ugly string replace to convert collection of labels to colon delimited string */
	WITH replace(replace(replace(replace(str(labels(n)),'[',''),']',''),'"',''),',',':') AS l, count(distinct n) AS c
	MERGE (mn:Meta_Node {name:l,count:c})
	WITH mn
	MATCH (a)-[r]->(b)
	WITH replace(replace(replace(replace(str(labels(a)),'[',''),']',''),'"',''),',',':') AS a_labels
	, count(distinct a) AS from_count
	, type(r) AS rel_type
	import urllib
	import urllib2

	try:
	# Base url for the TNRS match_names API
	url = 'http://api.opentreeoflife.org/v2/tnrs/match_names'
	# Encode data value to be looked up as an array of names:
	data = '{"names": ["'+value+'"]}'
	print "Looking up: " + data
	# Set HTTP headers:
	= The taxonomic mind-mapper
	Nicky Nicolson, Peter Hovenkamp
	:neo4j-version: 2.1.0
	:author: Nicky Nicolson
	:twitter: nickynicolson

	== Domain
	We investigate the use of the scheme in: https://docs.google.com/document/d/1FIxNrrGrIZs0l4QJEdGfctXbYVL4cQhKspmMEHmKAGg/edit with a use case in the taxonomy of Diplazium tomentosum (https://docs.google.com/document/d/1vni44RBwGNZ7iRCFf243NtcD-7xwjHrDeAPehato7KY/edit?usp=sharing)

	== Data model
	Peter investigates the taxonomy of Diplazium tomentosum.

	//console

	He starts with one of the types from the Leiden herbarium (http://plants.jstor.org/specimen/l0051073):

	[source,cypher]
	----
	CREATE (s:Specimen{id:"L0051073"
	,jstorUrl:'http://plants.jstor.org/specimen/l0051073'