text-annotator

text-annotator

A JavaScript library for annotating plain text in the HTML
The annotation process is:

1. Search: Search for a piece of plain text in the HTML; if finding it, store its location identified by an index and then return the index for later annotation
2. Annotate: Annotate the found text given its index
   It can be seen that in order to annotate a piece of text, two steps, search and annotate, are taken. The idea of decomposing the annotation process into the two steps is to allow more flexibility, e.g., the user can search for all pieces of text first, and then annotate (some of) them later when required (e.g., when clicking a button). There is also a function combining the two steps, as can be seen in the An example of the usage section.
   text-annotator can be used in the browser or the Node.js server.

Import

install it via npm

npm install --save text-annotator

import TextAnnotator from 'text-annotator'

include it into the head tag

<script src="public/js/text-annotator.min.js"></script>

An example of the usage

// below is the HTML
/*
<div id="content">
  <p><b>Europe PMC</b> is an <i>open science platform</i> that enables access to a worldwide collection of life science publications and preprints from trusted sources around the globe.</p>
  <p>Europe PMC is <i>developed by <b>EMBL-EBI</b></i>. It is a partner of <b>PubMed Central</b> and a repository of choice for many international science funders.</p>
</div>
*/

// create an instance of TextAnnotator
// content is the HTML string within which a piece of text can be annotated
var annotator = new TextAnnotator({content: document.getElementById('content').innerHTML})

// search for 'EMBL-EBI' in the HTML
// if found, store the location of 'EMBL-EBI' and then return the index; otherwise return -1
var highlightIndex = annotator.search('EMBL-EBI')
// highlightIndex = 0

// annotate 'EMBL-EBI' in the HTML
if (highlightIndex !== -1) {
  document.getElementById('content').innerHTML = annotator.highlight(highlightIndex)
  // <span id="highlight-0" class="highlight"> is used to annotate 'EMBL-EBI', see below
/*
<div id="content">
  <p><b>Europe PMC</b> is an <i>open science platform</i> that enables access to a worldwide collection of life science publications and preprints from trusted sources around the globe.</p>
  <p>Europe PMC is <i>developed by <span id="highlight-0" class="highlight"><b>EMBL-EBI</b></span></i>. It is a partner of <b>PubMed Central</b> and a repository of choice for many international science funders.</p>
</div>
*/
}

// search for all occurances of 'Europe PMC' in the HTML
var highlightIndexes = annotator.searchAll('Europe PMC')
// highlightIndexes = [1, 2]

// annotate all the found occurances of 'Europe PMC' given their indexes
if (highlightIndexes.length) {
  document.getElementById('content').innerHTML = annotator.highlightAll(highlightIndexes)
  // <span id="highlight-1" class="highlight"> and <span id="highlight-2" class="highlight"> are used to annotate 'Europe PMC', see below
/*
<div id="content">
  <p><span id="highlight-1" class="highlight"><b>Europe PMC</b><span> is an <i>open science platform</i> that enables access to a worldwide collection of life science publications and preprints from trusted sources around the globe.</p>
  <p><span id="highlight-2" class="highlight">Europe PMC</span> is <i>developed by <span id="highlight-0" class="highlight"><b>EMBL-EBI</b></span></i>. It is a partner of <b>PubMed Central</b> and a repository of choice for many international science funders.</p>
</div>
*/
}

// search for and then annotate 'a partner of PubMed Central'
document.getElementById('content').innerHTML = annotator.searchAndHighlight('a partner of PubMed Central').content
// searchAndHighlight returns { content, highlightIndex }
// <span id="highlight-3" class="highlight"> is used to annotate 'a partner of PubMed Central', see below
/*
<div id="content">
  <p><span id="highlight-1" class="highlight"><b>Europe PMC</b><span> is an <i>open science platform</i> that enables access to a worldwide collection of life science publications and preprints from trusted sources around the globe.</p>
  <p><span id="highlight-2" class="highlight">Europe PMC</span> is <i>developed by <span id="highlight-0" class="highlight"><b>EMBL-EBI</b></span></i>. It is <span id="highlight-3" class="highlight">a partner of <b>PubMed Central</b></span> and a repository of choice for many international science funders.</p>
</div>
*/

// remove annotation 'EMBL-EBI' given its index
// the index is 0 as shown above
document.getElementById('content').innerHTML = annotator.unhighlight(highlightIndex)
// annotation <span id="highlight-0" class="highlight"> is removed, see below
/*
<div id="content">
  <p><span id="highlight-1" class="highlight"><b>Europe PMC</b><span> is an <i>open science platform</i> that enables access to a worldwide collection of life science publications and preprints from trusted sources around the globe.</p>
  <p><span id="highlight-2" class="highlight">Europe PMC</span> is <i>developed by <b>EMBL-EBI</b></i>. It is <span id="highlight-3" class="highlight">a partner of <b>PubMed Central</b></span> and a repository of choice for many international science funders.</p>
</div>
*/

// help annotate one occurance of 'science' - the one within 'international science funders', by providing the prefix and postfix of 'Europe PMC'
var highlightIndex = annotator.search('science', { prefix: 'international ', postfix: ' funders' })
if (highlightIndex !== -1) {
  document.getElementById('content').innerHTML = annotator.highlight(highlightIndex)
}
// <span id="highlight-4" class="highlight"> is used to annotate 'science' within 'international science funders', see below
/*
<div id="content">
  <p><span id="highlight-1" class="highlight"><b>Europe PMC</b><span> is an <i>open science platform</i> that enables access to a worldwide collection of life science publications and preprints from trusted sources around the globe.</p>
  <p><span id="highlight-2" class="highlight">Europe PMC</span> is <i>developed by <b>EMBL-EBI</b></i>. It is <span id="highlight-3" class="highlight">a partner of <b>PubMed Central</b></span> and a repository of choice for many international <span id="highlight-4" class="highlight">science</span> funders.</p>
</div>
*/

Constructor options

new TextAnnotator(options = {})

Prop	Type	Description
content	string	The HTML string within which a piece of text can be annotated.

Search APIs and options

search(str, options = {})

searchAll(str, options = {})

Prop	Type	Description
trim	boolean	Whether to trim the piece of text to be annotated. Default is true.
caseSensitive	boolean	Whether to consider case in search. Default is false.
prefix	string	A string BEFORE the piece of text to be annotated. Default is ''.
postfix	string	A string AFTER the piece of text to be annotated. Default is ''.

Annotate APIs and options

highlight(highlightIndex, options = {})

highlightAll(highlightIndexes, options = {})

unhighlight(highlightIndex, options = {})

Prop	Type	Description
highlightTagName	string	The name of the annotation tag. Default is span so that the tag is <span ...>.
highlightClass	string	The class name of the annotation tag. Default is highlight so that the tag is <span class="highlight" ...>.
highlightIdPattern	string	The ID pattern of the annotation tag. Default is highlight- so that the tag is <span id="highlight-[highlightIndex]" ...>.

searchAndHighlight API and options

searchAndHighlight(str, options), where options = { searchOptions, highlightOptions }, searchOptions and highlightOptions are described above in the Annotate options table.

Examples from Europe PMC

text-annotator has been widely used in Europe PMC, an open science platform that enables access to a worldwide collection of life science publications. Here is a list of examples:

1. Article title highlighting: https://europepmc.org/search?query=cancer
2. Snippets: https://europepmc.org/article/PPR/PPR158972 (Visit from https://europepmc.org/search?query=cancer)
3. SciLite: https://europepmc.org/article/PPR/PPR158972 (Click the Annotations link in the right panel)
4. Linkback: https://europepmc.org/article/PPR/PPR158972#europepmc-6e6312219dcad15c9a7dda8f71dce9af (In the popup shown in Example 3, click "Share" to get this linkback URL)

Contact

Zhan Huang