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update doe build script

This commit is contained in:
Steve Baskauf 2021-09-05 19:53:57 -04:00
parent 9eff3c452d
commit ec2745359e
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# Script to build Markdown pages that provide term metadata for simple vocabularies
# Steve Baskauf 2020-06-28 CC0
# This script merges static Markdown header and footer documents with term information tables (in Markdown) generated from data in the rs.tdwg.org repo from the TDWG Github site
# Note: this script calls a function from http_library.py, which requires importing the requests, csv, and json modules
import re
import requests # best library to manage HTTP transactions
import csv # library to read/write/parse CSV files
import json # library to convert JSON to Python data structures
import pandas as pd
# -----------------
# Configuration section
# -----------------
# !!!! Note !!!!
# This is an example of a simple vocabulary without categories. For a complex example
# with multiple namespaces and several categories, see build-page-categories.ipynb
# This is the base URL for raw files from the branch of the repo that has been pushed to GitHub. In this example,
# the branch is named "pathway"
githubBaseUri = 'https://raw.githubusercontent.com/tdwg/rs.tdwg.org/master/'
headerFileName = 'termlist-header.md'
footerFileName = 'termlist-footer.md'
outFileName = '../../docs/doe/index.md'
# This is a Python list of the database names of the term lists to be included in the document.
termLists = ['degreeOfEstablishment']
# NOTE! There may be problems unless every term list is of the same vocabulary type since the number of columns will differ
# However, there probably aren't any circumstances where mixed types will be used to generate the same page.
vocab_type = 2 # 1 is simple vocabulary, 2 is simple controlled vocabulary, 3 is c.v. with broader hierarchy
# Terms in large vocabularies like Darwin and Audubon Cores may be organized into categories using tdwgutility_organizedInClass
# If so, those categories can be used to group terms in the generated term list document.
organized_in_categories = False
# If organized in categories, the display_order list must contain the IRIs that are values of tdwgutility_organizedInClass
# If not organized into categories, the value is irrelevant. There just needs to be one item in the list.
display_order = ['']
display_label = ['Vocabulary'] # these are the section labels for the categories in the page
display_comments = [''] # these are the comments about the category to be appended following the section labels
display_id = ['Vocabulary'] # these are the fragment identifiers for the associated sections for the categories
# ---------------
# Function definitions
# ---------------
# replace URL with link
#
def createLinks(text):
def repl(match):
if match.group(1)[-1] == '.':
return '<a href="' + match.group(1)[:-1] + '">' + match.group(1)[:-1] + '</a>.'
return '<a href="' + match.group(1) + '">' + match.group(1) + '</a>'
pattern = '(https?://[^\s,;\)"]*)'
result = re.sub(pattern, repl, text)
return result
# 2021-08-06 Replace the createLinks() function with functions copied from the QRG build script written by S. Van Hoey
def convert_code(text_with_backticks):
"""Takes all back-quoted sections in a text field and converts it to
the html tagged version of code blocks <code>...</code>
"""
return re.sub(r'`([^`]*)`', r'<code>\1</code>', text_with_backticks)
def convert_link(text_with_urls):
"""Takes all links in a text field and converts it to the html tagged
version of the link
"""
def _handle_matched(inputstring):
"""quick hack version of url handling on the current prime versions data"""
url = inputstring.group()
return "<a href=\"{}\">{}</a>".format(url, url)
regx = "(http[s]?://[\w\d:#@%/;$()~_?\+-;=\\\.&]*)(?<![\)\.,])"
return re.sub(regx, _handle_matched, text_with_urls)
term_lists_info = []
frame = pd.read_csv(githubBaseUri + 'term-lists/term-lists.csv', na_filter=False)
for termList in termLists:
term_list_dict = {'list_iri': termList}
term_list_dict = {'database': termList}
for index,row in frame.iterrows():
if row['database'] == termList:
term_list_dict['pref_ns_prefix'] = row['vann_preferredNamespacePrefix']
term_list_dict['pref_ns_uri'] = row['vann_preferredNamespaceUri']
term_list_dict['list_iri'] = row['list']
term_lists_info.append(term_list_dict)
# Create column list
column_list = ['pref_ns_prefix', 'pref_ns_uri', 'term_localName', 'label', 'definition', 'usage', 'notes', 'term_modified', 'term_deprecated', 'type']
if vocab_type == 2:
column_list += ['controlled_value_string']
elif vocab_type == 3:
column_list += ['controlled_value_string', 'skos_broader']
if organized_in_categories:
column_list.append('tdwgutility_organizedInClass')
column_list.append('version_iri')
# Create list of lists metadata table
table_list = []
for term_list in term_lists_info:
# retrieve versions metadata for term list
versions_url = githubBaseUri + term_list['database'] + '-versions/' + term_list['database'] + '-versions.csv'
versions_df = pd.read_csv(versions_url, na_filter=False)
# retrieve current term metadata for term list
data_url = githubBaseUri + term_list['database'] + '/' + term_list['database'] + '.csv'
frame = pd.read_csv(data_url, na_filter=False)
for index,row in frame.iterrows():
row_list = [term_list['pref_ns_prefix'], term_list['pref_ns_uri'], row['term_localName'], row['label'], row['definition'], row['usage'], row['notes'], row['term_modified'], row['term_deprecated'], row['type']]
if vocab_type == 2:
row_list += [row['controlled_value_string']]
elif vocab_type == 3:
if row['skos_broader'] =='':
row_list += [row['controlled_value_string'], '']
else:
row_list += [row['controlled_value_string'], term_list['pref_ns_prefix'] + ':' + row['skos_broader']]
if organized_in_categories:
row_list.append(row['tdwgutility_organizedInClass'])
# Borrowed terms really don't have implemented versions. They may be lacking values for version_status.
# In their case, their version IRI will be omitted.
found = False
for vindex, vrow in versions_df.iterrows():
if vrow['term_localName']==row['term_localName'] and vrow['version_status']=='recommended':
found = True
version_iri = vrow['version']
# NOTE: the current hack for non-TDWG terms without a version is to append # to the end of the term IRI
if version_iri[len(version_iri)-1] == '#':
version_iri = ''
if not found:
version_iri = ''
row_list.append(version_iri)
table_list.append(row_list)
# Turn list of lists into dataframe
terms_df = pd.DataFrame(table_list, columns = column_list)
terms_sorted_by_label = terms_df.sort_values(by='label')
terms_sorted_by_localname = terms_df.sort_values(by='term_localName')
terms_sorted_by_label
# generate the index of terms grouped by category and sorted alphabetically by lowercase term local name
text = '### 3.1 Index By Term Name\n\n'
text += '(See also [3.2 Index By Label](#32-index-by-label))\n\n'
for category in range(0,len(display_order)):
text += '**' + display_label[category] + '**\n'
text += '\n'
if organized_in_categories:
filtered_table = terms_sorted_by_localname[terms_sorted_by_localname['tdwgutility_organizedInClass']==display_order[category]]
filtered_table.reset_index(drop=True, inplace=True)
else:
filtered_table = terms_sorted_by_localname
filtered_table.reset_index(drop=True, inplace=True)
for row_index,row in filtered_table.iterrows():
curie = row['pref_ns_prefix'] + ":" + row['term_localName']
curie_anchor = curie.replace(':','_')
text += '[' + curie + '](#' + curie_anchor + ')'
if row_index < len(filtered_table) - 1:
text += ' |'
text += '\n'
text += '\n'
index_by_name = text
text = '\n\n'
# Comment out the following two lines if there is no index by local names
#text = '### 3.2 Index By Label\n\n'
#text += '(See also [3.1 Index By Term Name](#31-index-by-term-name))\n\n'
for category in range(0,len(display_order)):
if organized_in_categories:
text += '**' + display_label[category] + '**\n'
text += '\n'
filtered_table = terms_sorted_by_label[terms_sorted_by_label['tdwgutility_organizedInClass']==display_order[category]]
filtered_table.reset_index(drop=True, inplace=True)
else:
filtered_table = terms_sorted_by_label
filtered_table.reset_index(drop=True, inplace=True)
for row_index,row in filtered_table.iterrows():
if row_index == 0 or (row_index != 0 and row['label'] != filtered_table.iloc[row_index - 1].loc['label']): # this is a hack to prevent duplicate labels
curie_anchor = row['pref_ns_prefix'] + "_" + row['term_localName']
text += '[' + row['label'] + '](#' + curie_anchor + ')'
if row_index < len(filtered_table) - 2 or (row_index == len(filtered_table) - 2 and row['label'] != filtered_table.iloc[row_index + 1].loc['label']):
text += ' |'
text += '\n'
text += '\n'
index_by_label = text
decisions_df = pd.read_csv('https://raw.githubusercontent.com/tdwg/rs.tdwg.org/master/decisions/decisions-links.csv', na_filter=False)
# generate a table for each term, with terms grouped by category
# generate the Markdown for the terms table
text = '## 4 Vocabulary\n'
for category in range(0,len(display_order)):
if organized_in_categories:
text += '### 4.' + str(category + 1) + ' ' + display_label[category] + '\n'
text += '\n'
text += display_comments[category] # insert the comments for the category, if any.
filtered_table = terms_sorted_by_localname[terms_sorted_by_localname['tdwgutility_organizedInClass']==display_order[category]]
filtered_table.reset_index(drop=True, inplace=True)
else:
filtered_table = terms_sorted_by_localname
filtered_table.reset_index(drop=True, inplace=True)
for row_index,row in filtered_table.iterrows():
text += '<table>\n'
curie = row['pref_ns_prefix'] + ":" + row['term_localName']
curieAnchor = curie.replace(':','_')
text += '\t<thead>\n'
text += '\t\t<tr>\n'
text += '\t\t\t<th colspan="2"><a id="' + curieAnchor + '"></a>Term Name ' + curie + '</th>\n'
text += '\t\t</tr>\n'
text += '\t</thead>\n'
text += '\t<tbody>\n'
text += '\t\t<tr>\n'
text += '\t\t\t<td>Term IRI</td>\n'
uri = row['pref_ns_uri'] + row['term_localName']
text += '\t\t\t<td><a href="' + uri + '">' + uri + '</a></td>\n'
text += '\t\t</tr>\n'
text += '\t\t<tr>\n'
text += '\t\t\t<td>Modified</td>\n'
text += '\t\t\t<td>' + row['term_modified'] + '</td>\n'
text += '\t\t</tr>\n'
if row['version_iri'] != '':
text += '\t\t<tr>\n'
text += '\t\t\t<td>Term version IRI</td>\n'
text += '\t\t\t<td><a href="' + row['version_iri'] + '">' + row['version_iri'] + '</a></td>\n'
text += '\t\t</tr>\n'
text += '\t\t<tr>\n'
text += '\t\t\t<td>Label</td>\n'
text += '\t\t\t<td>' + row['label'] + '</td>\n'
text += '\t\t</tr>\n'
if row['term_deprecated'] != '':
text += '\t\t<tr>\n'
text += '\t\t\t<td></td>\n'
text += '\t\t\t<td><strong>This term is deprecated and should no longer be used.</strong></td>\n'
text += '\t\t</tr>\n'
text += '\t\t<tr>\n'
text += '\t\t\t<td>Definition</td>\n'
text += '\t\t\t<td>' + row['definition'] + '</td>\n'
text += '\t\t</tr>\n'
if row['usage'] != '':
text += '\t\t<tr>\n'
text += '\t\t\t<td>Usage</td>\n'
text += '\t\t\t<td>' + convert_link(convert_code(row['usage'])) + '</td>\n'
text += '\t\t</tr>\n'
if row['notes'] != '':
text += '\t\t<tr>\n'
text += '\t\t\t<td>Notes</td>\n'
text += '\t\t\t<td>' + convert_link(convert_code(row['notes'])) + '</td>\n'
text += '\t\t</tr>\n'
if (vocab_type == 2 or vocab_type == 3) and row['controlled_value_string'] != '': # controlled vocabulary
text += '\t\t<tr>\n'
text += '\t\t\t<td>Controlled value</td>\n'
text += '\t\t\t<td>' + row['controlled_value_string'] + '</td>\n'
text += '\t\t</tr>\n'
if vocab_type == 3 and row['skos_broader'] != '': # controlled vocabulary with skos:broader relationships
text += '\t\t<tr>\n'
text += '\t\t\t<td>Has broader concept</td>\n'
curieAnchor = row['skos_broader'].replace(':','_')
text += '\t\t\t<td><a href="#' + curieAnchor + '">' + row['skos_broader'] + '</a></td>\n'
text += '\t\t</tr>\n'
text += '\t\t<tr>\n'
text += '\t\t\t<td>Type</td>\n'
if row['type'] == 'http://www.w3.org/1999/02/22-rdf-syntax-ns#Property':
text += '\t\t\t<td>Property</td>\n'
elif row['type'] == 'http://www.w3.org/2000/01/rdf-schema#Class':
text += '\t\t\t<td>Class</td>\n'
elif row['type'] == 'http://www.w3.org/2004/02/skos/core#Concept':
text += '\t\t\t<td>Concept</td>\n'
else:
text += '\t\t\t<td>' + row['type'] + '</td>\n' # this should rarely happen
text += '\t\t</tr>\n'
# Look up decisions related to this term
for drow_index,drow in decisions_df.iterrows():
if drow['linked_affected_resource'] == uri:
text += '\t\t<tr>\n'
text += '\t\t\t<td>Executive Committee decision</td>\n'
text += '\t\t\t<td><a href="http://rs.tdwg.org/decisions/' + drow['decision_localName'] + '">http://rs.tdwg.org/decisions/' + drow['decision_localName'] + '</a></td>\n'
text += '\t\t</tr>\n'
text += '\t</tbody>\n'
text += '</table>\n'
text += '\n'
text += '\n'
term_table = text
text = index_by_label + term_table
# read in header and footer, merge with terms table, and output
headerObject = open(headerFileName, 'rt', encoding='utf-8')
header = headerObject.read()
headerObject.close()
footerObject = open(footerFileName, 'rt', encoding='utf-8')
footer = footerObject.read()
footerObject.close()
output = header + text + footer
outputObject = open(outFileName, 'wt', encoding='utf-8')
outputObject.write(output)
outputObject.close()
print('done')

92
docs/doe/index.md
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@ -120,11 +120,11 @@ Due to the requirements of [Section 1.4.3 of the Darwin Core RDF Guide](http://r
</tr>
<tr>
<td>Modified</td>
<td>2020-10-13</td>
<td>2021-09-01</td>
</tr>
<tr>
<td>Term version IRI</td>
<td><a href="http://rs.tdwg.org/dwcdoe/values/version/d001-2020-10-13">http://rs.tdwg.org/dwcdoe/values/version/d001-2020-10-13</a></td>
<td><a href="http://rs.tdwg.org/dwcdoe/values/version/d001-2021-09-01">http://rs.tdwg.org/dwcdoe/values/version/d001-2021-09-01</a></td>
</tr>
<tr>
<td>Label</td>
@ -132,11 +132,11 @@ Due to the requirements of [Section 1.4.3 of the Darwin Core RDF Guide](http://r
</tr>
<tr>
<td>Definition</td>
<td>Not transported beyond limits of native range</td>
<td>Not transported beyond limits of native range.</td>
</tr>
<tr>
<td>Notes</td>
<td>Considered native and naturally occuring. See also Blackburn et al. 2011 <a href="https://doi.org/10.1016/j.tree.2011.03.023">https://doi.org/10.1016/j.tree.2011.03.023</a> category A</td>
<td>Considered native and naturally occurring. See also "category A" in Blackburn et al. 2011. <a href="https://doi.org/10.1016/j.tree.2011.03.023">https://doi.org/10.1016/j.tree.2011.03.023</a></td>
</tr>
<tr>
<td>Controlled value</td>
@ -166,11 +166,11 @@ Due to the requirements of [Section 1.4.3 of the Darwin Core RDF Guide](http://r
</tr>
<tr>
<td>Modified</td>
<td>2020-10-13</td>
<td>2021-09-01</td>
</tr>
<tr>
<td>Term version IRI</td>
<td><a href="http://rs.tdwg.org/dwcdoe/values/version/d002-2020-10-13">http://rs.tdwg.org/dwcdoe/values/version/d002-2020-10-13</a></td>
<td><a href="http://rs.tdwg.org/dwcdoe/values/version/d002-2021-09-01">http://rs.tdwg.org/dwcdoe/values/version/d002-2021-09-01</a></td>
</tr>
<tr>
<td>Label</td>
@ -178,15 +178,15 @@ Due to the requirements of [Section 1.4.3 of the Darwin Core RDF Guide](http://r
</tr>
<tr>
<td>Definition</td>
<td>Individuals in captivity or quarantine (i.e. individuals provided with conditions suitable for them, but explicit measures of containment are in place)</td>
<td>Individuals in captivity or quarantine (i.e., individuals provided with conditions suitable for them, but explicit measures of containment are in place).</td>
</tr>
<tr>
<td>Usage</td>
<td>Only for cases where specific actions have been taken place to prevent escape of individuals or propagules</td>
<td>Only for cases where specific actions have been taken place to prevent escape of individuals or propagules.</td>
</tr>
<tr>
<td>Notes</td>
<td>See also Blackburn et al. 2011 <a href="https://doi.org/10.1016/j.tree.2011.03.023">https://doi.org/10.1016/j.tree.2011.03.023</a> category B1</td>
<td>See also "category B1" in Blackburn et al. 2011. <a href="https://doi.org/10.1016/j.tree.2011.03.023">https://doi.org/10.1016/j.tree.2011.03.023</a></td>
</tr>
<tr>
<td>Controlled value</td>
@ -216,11 +216,11 @@ Due to the requirements of [Section 1.4.3 of the Darwin Core RDF Guide](http://r
</tr>
<tr>
<td>Modified</td>
<td>2020-10-13</td>
<td>2021-09-01</td>
</tr>
<tr>
<td>Term version IRI</td>
<td><a href="http://rs.tdwg.org/dwcdoe/values/version/d003-2020-10-13">http://rs.tdwg.org/dwcdoe/values/version/d003-2020-10-13</a></td>
<td><a href="http://rs.tdwg.org/dwcdoe/values/version/d003-2021-09-01">http://rs.tdwg.org/dwcdoe/values/version/d003-2021-09-01</a></td>
</tr>
<tr>
<td>Label</td>
@ -228,11 +228,11 @@ Due to the requirements of [Section 1.4.3 of the Darwin Core RDF Guide](http://r
</tr>
<tr>
<td>Definition</td>
<td>Individuals in cultivation (i.e. individuals provided with conditions suitable for them, but explicit measures to prevent dispersal are limited at best)</td>
<td>Individuals in cultivation (i.e., individuals provided with conditions suitable for them, but explicit measures to prevent dispersal are limited at best).</td>
</tr>
<tr>
<td>Notes</td>
<td>Examples include gardens, parks and farms. See also Blackburn et al. 2011 <a href="https://doi.org/10.1016/j.tree.2011.03.023">https://doi.org/10.1016/j.tree.2011.03.023</a> category B2</td>
<td>Examples include gardens, parks and farms. See also "category B2" in Blackburn et al. 2011. <a href="https://doi.org/10.1016/j.tree.2011.03.023">https://doi.org/10.1016/j.tree.2011.03.023</a></td>
</tr>
<tr>
<td>Controlled value</td>
@ -262,11 +262,11 @@ Due to the requirements of [Section 1.4.3 of the Darwin Core RDF Guide](http://r
</tr>
<tr>
<td>Modified</td>
<td>2020-10-13</td>
<td>2021-09-01</td>
</tr>
<tr>
<td>Term version IRI</td>
<td><a href="http://rs.tdwg.org/dwcdoe/values/version/d004-2020-10-13">http://rs.tdwg.org/dwcdoe/values/version/d004-2020-10-13</a></td>
<td><a href="http://rs.tdwg.org/dwcdoe/values/version/d004-2021-09-01">http://rs.tdwg.org/dwcdoe/values/version/d004-2021-09-01</a></td>
</tr>
<tr>
<td>Label</td>
@ -274,11 +274,11 @@ Due to the requirements of [Section 1.4.3 of the Darwin Core RDF Guide](http://r
</tr>
<tr>
<td>Definition</td>
<td>Individuals directly released into novel environment</td>
<td>Individuals directly released into novel environment.</td>
</tr>
<tr>
<td>Notes</td>
<td>For example, fish stocked for angling, birds for hunting. See also Blackburn et al. 2011 <a href="https://doi.org/10.1016/j.tree.2011.03.023">https://doi.org/10.1016/j.tree.2011.03.023</a> category B3</td>
<td>For example, fish stocked for angling, birds for hunting. See also "category B3" in Blackburn et al. 2011. <a href="https://doi.org/10.1016/j.tree.2011.03.023">https://doi.org/10.1016/j.tree.2011.03.023</a></td>
</tr>
<tr>
<td>Controlled value</td>
@ -308,11 +308,11 @@ Due to the requirements of [Section 1.4.3 of the Darwin Core RDF Guide](http://r
</tr>
<tr>
<td>Modified</td>
<td>2020-10-13</td>
<td>2021-09-01</td>
</tr>
<tr>
<td>Term version IRI</td>
<td><a href="http://rs.tdwg.org/dwcdoe/values/version/d005-2020-10-13">http://rs.tdwg.org/dwcdoe/values/version/d005-2020-10-13</a></td>
<td><a href="http://rs.tdwg.org/dwcdoe/values/version/d005-2021-09-01">http://rs.tdwg.org/dwcdoe/values/version/d005-2021-09-01</a></td>
</tr>
<tr>
<td>Label</td>
@ -320,11 +320,11 @@ Due to the requirements of [Section 1.4.3 of the Darwin Core RDF Guide](http://r
</tr>
<tr>
<td>Definition</td>
<td>Individuals released outside of captivity or cultivation in a location, but incapable of surviving for a significant period</td>
<td>Individuals released outside of captivity or cultivation in a location, but incapable of surviving for a significant period.</td>
</tr>
<tr>
<td>Notes</td>
<td>Such as frost tender plants sown or planted in a cold climate. See also Blackburn et al. 2011 <a href="https://doi.org/10.1016/j.tree.2011.03.023">https://doi.org/10.1016/j.tree.2011.03.023</a> category C0</td>
<td>For example, frost-tender plants sown or planted in a cold climate. See also "category C0" in Blackburn et al. 2011. <a href="https://doi.org/10.1016/j.tree.2011.03.023">https://doi.org/10.1016/j.tree.2011.03.023</a></td>
</tr>
<tr>
<td>Controlled value</td>
@ -354,11 +354,11 @@ Due to the requirements of [Section 1.4.3 of the Darwin Core RDF Guide](http://r
</tr>
<tr>
<td>Modified</td>
<td>2020-10-13</td>
<td>2021-09-01</td>
</tr>
<tr>
<td>Term version IRI</td>
<td><a href="http://rs.tdwg.org/dwcdoe/values/version/d006-2020-10-13">http://rs.tdwg.org/dwcdoe/values/version/d006-2020-10-13</a></td>
<td><a href="http://rs.tdwg.org/dwcdoe/values/version/d006-2021-09-01">http://rs.tdwg.org/dwcdoe/values/version/d006-2021-09-01</a></td>
</tr>
<tr>
<td>Label</td>
@ -366,11 +366,11 @@ Due to the requirements of [Section 1.4.3 of the Darwin Core RDF Guide](http://r
</tr>
<tr>
<td>Definition</td>
<td>Individuals surviving outside of captivity or cultivation in a location, no reproduction</td>
<td>Individuals surviving outside of captivity or cultivation in a location with no reproduction.</td>
</tr>
<tr>
<td>Notes</td>
<td>Trees planted in the wild for forestry or ornament may come under this category. See also Blackburn et al. 2011 <a href="https://doi.org/10.1016/j.tree.2011.03.023">https://doi.org/10.1016/j.tree.2011.03.023</a> category C1</td>
<td>Trees planted in the wild for forestry or ornament may come under this category. See also "category C1" in Blackburn et al. 2011. <a href="https://doi.org/10.1016/j.tree.2011.03.023">https://doi.org/10.1016/j.tree.2011.03.023</a></td>
</tr>
<tr>
<td>Controlled value</td>
@ -400,11 +400,11 @@ Due to the requirements of [Section 1.4.3 of the Darwin Core RDF Guide](http://r
</tr>
<tr>
<td>Modified</td>
<td>2020-10-13</td>
<td>2021-09-01</td>
</tr>
<tr>
<td>Term version IRI</td>
<td><a href="http://rs.tdwg.org/dwcdoe/values/version/d007-2020-10-13">http://rs.tdwg.org/dwcdoe/values/version/d007-2020-10-13</a></td>
<td><a href="http://rs.tdwg.org/dwcdoe/values/version/d007-2021-09-01">http://rs.tdwg.org/dwcdoe/values/version/d007-2021-09-01</a></td>
</tr>
<tr>
<td>Label</td>
@ -412,11 +412,11 @@ Due to the requirements of [Section 1.4.3 of the Darwin Core RDF Guide](http://r
</tr>
<tr>
<td>Definition</td>
<td>Individuals surviving outside of captivity or cultivation in a location, reproduction is occurring, but population not self-sustaining</td>
<td>Individuals surviving outside of captivity or cultivation in a location. Reproduction is occurring, but population not self-sustaining.</td>
</tr>
<tr>
<td>Notes</td>
<td>Offspring are produced, but these either do not survive or are fertile enough to maintain the population. See also Blackburn et al. 2011 <a href="https://doi.org/10.1016/j.tree.2011.03.023">https://doi.org/10.1016/j.tree.2011.03.023</a> category C2</td>
<td>Offspring are produced, but these either do not survive or are not fertile enough to maintain the population. See also "category C2" in Blackburn et al. 2011. <a href="https://doi.org/10.1016/j.tree.2011.03.023">https://doi.org/10.1016/j.tree.2011.03.023</a></td>
</tr>
<tr>
<td>Controlled value</td>
@ -446,11 +446,11 @@ Due to the requirements of [Section 1.4.3 of the Darwin Core RDF Guide](http://r
</tr>
<tr>
<td>Modified</td>
<td>2020-10-13</td>
<td>2021-09-01</td>
</tr>
<tr>
<td>Term version IRI</td>
<td><a href="http://rs.tdwg.org/dwcdoe/values/version/d008-2020-10-13">http://rs.tdwg.org/dwcdoe/values/version/d008-2020-10-13</a></td>
<td><a href="http://rs.tdwg.org/dwcdoe/values/version/d008-2021-09-01">http://rs.tdwg.org/dwcdoe/values/version/d008-2021-09-01</a></td>
</tr>
<tr>
<td>Label</td>
@ -458,11 +458,11 @@ Due to the requirements of [Section 1.4.3 of the Darwin Core RDF Guide](http://r
</tr>
<tr>
<td>Definition</td>
<td>Individuals surviving outside of captivity or cultivation in a location, reproduction occurring, and population self-sustaining</td>
<td>Individuals surviving outside of captivity or cultivation in a location. Reproduction occurring, and population self-sustaining.</td>
</tr>
<tr>
<td>Notes</td>
<td>The population is maintained by reproduction, but is not spreading. See also Blackburn et al. 2011 <a href="https://doi.org/10.1016/j.tree.2011.03.023">https://doi.org/10.1016/j.tree.2011.03.023</a> category C3</td>
<td>The population is maintained by reproduction, but is not spreading. See also "category C3" in Blackburn et al. 2011. <a href="https://doi.org/10.1016/j.tree.2011.03.023">https://doi.org/10.1016/j.tree.2011.03.023</a></td>
</tr>
<tr>
<td>Controlled value</td>
@ -492,11 +492,11 @@ Due to the requirements of [Section 1.4.3 of the Darwin Core RDF Guide](http://r
</tr>
<tr>
<td>Modified</td>
<td>2020-10-13</td>
<td>2021-09-01</td>
</tr>
<tr>
<td>Term version IRI</td>
<td><a href="http://rs.tdwg.org/dwcdoe/values/version/d009-2020-10-13">http://rs.tdwg.org/dwcdoe/values/version/d009-2020-10-13</a></td>
<td><a href="http://rs.tdwg.org/dwcdoe/values/version/d009-2021-09-01">http://rs.tdwg.org/dwcdoe/values/version/d009-2021-09-01</a></td>
</tr>
<tr>
<td>Label</td>
@ -504,11 +504,11 @@ Due to the requirements of [Section 1.4.3 of the Darwin Core RDF Guide](http://r
</tr>
<tr>
<td>Definition</td>
<td>Self-sustaining population outside of captivity or cultivation, with individuals surviving a significant distance from the original point of introduction</td>
<td>Self-sustaining population outside of captivity or cultivation, with individuals surviving a significant distance from the original point of introduction.</td>
</tr>
<tr>
<td>Notes</td>
<td>The population is maintained by reproduction and is spreading. See also Blackburn et al. 2011 <a href="https://doi.org/10.1016/j.tree.2011.03.023">https://doi.org/10.1016/j.tree.2011.03.023</a> category D1</td>
<td>The population is maintained by reproduction and is spreading. See also "category D1" in Blackburn et al. 2011. <a href="https://doi.org/10.1016/j.tree.2011.03.023">https://doi.org/10.1016/j.tree.2011.03.023</a></td>
</tr>
<tr>
<td>Controlled value</td>
@ -538,11 +538,11 @@ Due to the requirements of [Section 1.4.3 of the Darwin Core RDF Guide](http://r
</tr>
<tr>
<td>Modified</td>
<td>2020-10-13</td>
<td>2021-09-01</td>
</tr>
<tr>
<td>Term version IRI</td>
<td><a href="http://rs.tdwg.org/dwcdoe/values/version/d010-2020-10-13">http://rs.tdwg.org/dwcdoe/values/version/d010-2020-10-13</a></td>
<td><a href="http://rs.tdwg.org/dwcdoe/values/version/d010-2021-09-01">http://rs.tdwg.org/dwcdoe/values/version/d010-2021-09-01</a></td>
</tr>
<tr>
<td>Label</td>
@ -550,11 +550,11 @@ Due to the requirements of [Section 1.4.3 of the Darwin Core RDF Guide](http://r
</tr>
<tr>
<td>Definition</td>
<td>Self-sustaining population outside of captivity or cultivation, with individuals surviving and reproducing a significant distance from the original point of introduction</td>
<td>Self-sustaining population outside of captivity or cultivation, with individuals surviving and reproducing a significant distance from the original point of introduction.</td>
</tr>
<tr>
<td>Notes</td>
<td>The population is maintained by reproduction, is spreading, and their progeny is also reproducing and spreading. See also Blackburn et al. 2011 <a href="https://doi.org/10.1016/j.tree.2011.03.023">https://doi.org/10.1016/j.tree.2011.03.023</a> category D2</td>
<td>The population is maintained by reproduction, is spreading, and its progeny are also reproducing and spreading. See also "category D2" in Blackburn et al. 2011. <a href="https://doi.org/10.1016/j.tree.2011.03.023">https://doi.org/10.1016/j.tree.2011.03.023</a></td>
</tr>
<tr>
<td>Controlled value</td>
@ -584,11 +584,11 @@ Due to the requirements of [Section 1.4.3 of the Darwin Core RDF Guide](http://r
</tr>
<tr>
<td>Modified</td>
<td>2020-10-13</td>
<td>2021-09-01</td>
</tr>
<tr>
<td>Term version IRI</td>
<td><a href="http://rs.tdwg.org/dwcdoe/values/version/d011-2020-10-13">http://rs.tdwg.org/dwcdoe/values/version/d011-2020-10-13</a></td>
<td><a href="http://rs.tdwg.org/dwcdoe/values/version/d011-2021-09-01">http://rs.tdwg.org/dwcdoe/values/version/d011-2021-09-01</a></td>
</tr>
<tr>
<td>Label</td>
@ -596,15 +596,15 @@ Due to the requirements of [Section 1.4.3 of the Darwin Core RDF Guide](http://r
</tr>
<tr>
<td>Definition</td>
<td>Fully invasive species, with individuals dispersing, surviving and reproducing at multiple sites across a greater or lesser spectrum of habitats and extent of occurrence</td>
<td>Fully invasive species, with individuals dispersing, surviving and reproducing at multiple sites across a spectrum of habitats and geographic range.</td>
</tr>
<tr>
<td>Usage</td>
<td>This term is only used for those invasives with the highest degree of encroachment</td>
<td>This term is only used for those invasives with the highest degree of encroachment.</td>
</tr>
<tr>
<td>Notes</td>
<td>See also Blackburn et al. 2011 <a href="https://doi.org/10.1016/j.tree.2011.03.023">https://doi.org/10.1016/j.tree.2011.03.023</a> category E</td>
<td>See also "category E" in Blackburn et al. 2011. <a href="https://doi.org/10.1016/j.tree.2011.03.023">https://doi.org/10.1016/j.tree.2011.03.023</a></td>
</tr>
<tr>
<td>Controlled value</td>