nickynicolson

from sklearn.metrics import confusion_matrix
import pandas as pd

def cm2df(cm, labels):
    df = pd.DataFrame()
    # rows
    for i, row_label in enumerate(labels):
        rowdata={}
        # columns
        for j, col_label in enumerate(labels): 

nickynicolson

<?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 -->

nickynicolson

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:

nickynicolson

nickynicolson

This graph gist demonstrates use of Jaccard calculation to determine similarity between two sets of nodes

nickynicolson

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

nickynicolson

// 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

nickynicolson

= 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

nickynicolson

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'