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<body>
<div class="div-intro">
<h1>VSM<span>(Visual Syntax Method)</span></h1>
<div class="h1-sub">
Representing any knowledge in a computable form, made easy.
</div>
<div class="h1-sub2"><p>
VSM enables people to put knowledge in a computable form, ‘like they think’.
<br>• VSM’s <b>semantic model</b> reflects how knowledge is represented in the human mind;
<br>• and its <b>user interface</b> enables one to read & enter knowledge in that intuitive form.
</p><p>
VSM is thus a <b>human-centered</b> method for creating
<b>context-rich</b>, <b>multi-topic</b>, <b>computable knowledge</b> – and
a gateway to any other format and to computation.
</p><p>
VSM’s elegant knowledge representation may also
serve as a practical basis in the design of <b>semantic machine learning</b>.
</p></div>
<div class="h1-sub3">
Here we collect all information on VSM:
</div>
<ul class="main-list">
<li>
<b>Intros</b>:
<ul class="intros">
<li>
‘<a href="https://vsm.github.io/vsm-pages/intro"
>How to easily plant complex ideas into computers</a>’
<span class="info push">(Long blog, 2018)</span>
<li>
‘<a href="https://www.dropbox.com/s/52itmb000wsrneo/A_bold_vision_for_computable_scientific_knowledge_Vercruysse_S_2019_Blog.pdf?dl=0"
>A bold vision for computable scientific knowledge</a>’
<span class="info push">(Short blog, 2019)
<span class="orig-link">[<a class="orig-link"
href="https://www.ntnutechzone.no/en/2019/06/a-bold-vision-for-computable-scientific-knowledge">orig link</a>]</span>
</span>
</ul>
<li>
<b>How VSM works</b>:
<ul class="how-vsm-works">
<li>
<b>‘<a href="https://www.preprints.org/manuscript/202007.0486"
>Intuitive Representation of Computable Knowledge</a>’</b>
<span class="info push">(Main Paper — Preprint, 2020)</span>
<div class="li-footer paper">
Paper :
<span>
<!--todo
<a href="javascript:void(0);" onclick="show_hide_abstract(this, 'vsm-paper')">Show abstract</a></span>
-->
<a href="https://www.preprints.org/manuscript/202007.0486">Abstract</a></span>
<span>
<a href="https://www.preprints.org/manuscript/202007.0486/v2/download">Main PDF</a></span>
<span>
In detail: <a href="https://www.preprints.org/manuscript/202007.0486/v2/download/supplementary">Supplementary PDF</a></span>
<span class="outreach">
<span>
Share:
<a target="_blank" href="mailto:?subject=From%20Preprints:%20Intuitive%20Representation%20of%20Computable%20Knowledge&body=https://www.preprints.org/manuscript/202007.0486/v2%20%0D%0A%0D%0AFrom%20Preprints:%20Intuitive%20Representation%20of%20Computable%20Knowledge:%0D%0A%0D%0AScientific%20progress%20is%20increasingly%20dependent%20on%20knowledge%20in%20computation-ready%20forms.%20In%20the%20life%20sciences%2C%20among%20others%2C%20many%20scientists%20therefore%20extract%20and%20structure%20knowledge%20from%20the%20literature.%20In%20a%20process%20called%20manual%20curation%2C%20they%20enter%20knowledge%20into%20spreadsheets%2C%20or%20into%20databases%20where%20it%20serves%20their%20and%20many%20others%27%20research.%20Valuable%20as%20these%20curation%20efforts%20are%2C%20the%20range%20and%20detail%20of%20what%20can%20practically%20be%20captured%20and%20shared%20remains%20limited%2C%20because%20of%20the%20constraints%20of%20current%20curation%20tools.%20Many%20important%20contextual%20aspects%20of%20observations%20described%20in%20literature%20simply%20do%20not%20fit%20in%20the%20form%20defined%20by%20these%20tools%2C%20and%20thus%20cannot%20be%20captured.%20Here%20we%20present%20the%20design%20of%20an%20easy-to-use%2C%20general-purpose%20method%20and%20interface%2C%20that%20enables%20the%20precise%20semantic%20capture%20of%20virtually%20unlimited%20types%20of%20information%20and%20details%2C%20using%20only%20a%20minimal%20set%20of%20building%20blocks.%20Scientists%20from%20any%20discipline%20can%20use%20this%20to%20convert%20any%20complex%20knowledge%20into%20a%20form%20that%20is%20easily%20readable%20and%20meaningful%20for%20both%20humans%20and%20computers.%20The%20method%20VSM%20forms%20a%20universal%20and%20high-level%20language%20for%20encoding%20ideas%2C%20and%20for%20interacting%20with%20digital%20knowledge.">
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<span>
<a href="https://www.preprints.org/manuscript/202007.0486">Cite</a>
</span>
</span>
</div>
<div class="paper-abstract" id="abstract-vsm-paper">
Scientific progress is increasingly dependent on knowledge in computation-ready
forms. In the life sciences, among others, many scientists therefore extract and
structure knowledge from the literature. In a process called manual curation,
they enter knowledge into spreadsheets, or into databases where it serves their
and many others' research. Valuable as these curation efforts are, the range and
detail of what can practically be captured and shared remains limited, because
of the constraints of current curation tools. Many important contextual aspects
of observations described in literature simply do not fit in the form defined by
these tools, and thus cannot be captured. Here we present the design of an easy-
to-use, general-purpose method and interface, that enables the precise semantic
capture of virtually unlimited types of information and details, using only a
minimal set of building blocks. Scientists from any discipline can use this to
convert any complex knowledge into a form that is easily readable and meaningful
for both humans and computers. The method VSM forms a universal and high-level
language for encoding ideas, and for interacting with digital knowledge.
</div>
<li>
<span class="demo-note"><a href="#vsm-intro-interface"
><b>GIF animation</b></a>:
entering knowledge into computable statements</span>
<span class="info">(vsm-box interface).</span>
<li>
<a href="https://www.youtube.com/watch?v=0kHWBZIL04E"><b>Video animation</b></a>:
converting text to VSM, automatically
<span class="info">(ongoing research).</span>
<!--
<li>
Many explained <a href="https://vsm.github.io/vsm-pages/examples">VSM examples</a>.
<span class="info">(with an earlier vsm-box prototype).</span>
-->
<!--
<li>
<span class="info">
(earlier versions on the VSM-pages:
<a href="https://vsm.github.io/vsm-pages/vsm">how VSM works</a>,
<a href="https://vsm.github.io/vsm-pages/summary">summary</a>,
<a href="https://vsm.github.io/vsm-pages/discussion">discussion</a>)
</span>
-->
</ul>
<li>
<b>Demos</b>:
<ul class="demos">
<li>
Live  <a href="demo"><b>Demo</b></a> 
of the ‘<span class="code-text">vsm-box</span>’ user interface,  which supports the VSM model.
<br>
+ examples, JSON editor, RDF/SVG export.
<li>
Many <a href="https://vsm.github.io/vsm-pages/examples">editable, explained examples</a>.
<li>
Customizable templates for knowledge entry:  see <a href="#causalBuilder">causalBuilder</a>, below.
</ul>
<li>
<b>Code</b>:
<ul class="code">
<li>
<b><a href="https://github.com/vsm/vsm-box">vsm-box</a></b>:
the user interface of VSM
<span class="info">(as a <vsm-box> HTML-element)</span>
<span class="info">(GitHub)</span>
<!-- <span class="info">(open-source)</span> -->
<div class="li-footer paper">
<span>
Paper :
<a href="https://www.preprints.org/manuscript/202007.0557">Abstract</a></span>
<span>
<a href="https://www.preprints.org/manuscript/202007.0557/v1/download">PDF</a></span>
<span class="outreach">
<span>
Share:
<a target="_blank" href="mailto:?subject=From Preprints: VSM-box: General-purpose Interface for Biocuration and Knowledge Representation&body=https://www.preprints.org/manuscript/202007.0557/v1 %0D%0A%0D%0AFrom Preprints: VSM-box: General-purpose Interface for Biocuration and Knowledge Representation:%0D%0A%0D%0AVSM is a recently introduced method for entering and displaying any type of knowledge, in a form that is both semantically precise for computation and intuitive for human understanding. VSM is the combination of a new semantic model, and the design for a dedicated user interface to support it. Here we present the implementation of this user interface, as a sophisticated HTML-element, <vsm-box>, that can be embedded in any web-based curation app. We show how developers can use it for biocuration projects, customize it to particular end-user needs, and contribute to its growth. Vsm-box is open-source at https://github.com/vsm/vsm-box under the AGPL license, as a JavaScript (ES6) Vue.js web-component that runs in all modern web browsers. It is the capstone of the VSM organization at https://github.com/vsm that groups its supporting modules. Extensive supplementary material on VSM and vsm-box is available at https://vsm.github.io.">
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<span>
<a href="https://www.preprints.org/manuscript/202007.0557">Cite</a>
</span>
</span>
</div>
<div class="li-footer paper">
<span>
Poster:
<a href="https://doi.org/10.5281/zenodo.4265420">View poster</a>
</span>
</div>
<li>
<span class="demo-note"><a href="#vsm-intro-code">Code example</a>:
how to put a vsm-box on a web page.</span>
<li>
<a href="https://github.com/vsm">VSM GitHub-organization</a>:
the core modules enabling VSM. Their Readmes:
<div class="li-footer modules"
><span><a href="https://github.com/vsm/vsm-box">vsm-box</a></span
><span><a href="https://github.com/vsm/vsm-dictionary">vsm-dictionary</a></span
><span><a href="https://github.com/vsm/vsm-dictionary-local">-local</a></span
><span class="smaller"><a href="https://github.com/vsm/vsm-dictionary-remote-demo">-remote-demo</a></span
><span><a href="https://github.com/vsm/vsm-dictionary-cacher">-cacher</a></span
><span><a href="https://github.com/vsm/vsm-dictionary-combiner">-combiner</a></span
><span><a href="https://github.com/vsm/vsm-autocomplete">vsm‑autocomplete</a></span
><span class="smaller"><a href="https://github.com/vsm/vsm-json-pretty">vsm-json-pretty</a></span
><span class="smaller"><a href="https://github.com/vsm/string-style-html">string-style-html</a></span
><span class="_smaller"><a href="https://github.com/vsm/demo">vsm-box demo + toolkit</a></span
><span><a href="https://github.com/vsm/vsm-to-rdf">vsm‑to‑rdf</a></span
><span><a href="https://github.com/vsm/vsm-template-generator">(vsm‑template‑generator)</a></span
><span><a href="https://github.com/vsm/nlp-to-vsm">nlp‑to‑vsm</a></span
>
<!--
<span class="info"><br><a href="https://github.com/stcruy/to-exponential">to-exponential</a></span
><span class="info"><a href="https://github.com/stcruy/building-a-reusable-vue-web-component">building-a-…component</a></span>
-->
</div>
</ul>
<li>
<b>Use in other projects</b>:
<ul class="projs">
<li>
<b><a name="causalBuilder" href="https://mi2cast.github.io/causalBuilder">causalBuilder</a></b>:<br>
A web app that generates VSM-templates that follow the
<a href="https://doi.org/10.1093/bioinformatics/btaa622">MI2CAST</a>
standard,
for molecular biologists who are creating structured knowledge about
causal molecular interactions.
<span class="info">(Uses VSM-box).</span>
<div class="li-footer paper">
<span>
Paper :
<a href="https://doi.org/10.1093/database/baaa107">Abstract</a></span>
<span>
<a href="https://academic.oup.com/database/article-pdf/doi/10.1093/database/baaa107/36422627/baaa107.pdf">PDF</a></span>
<span class="outreach">
<span>
<a href="https://academic.oup.com/database/article/doi/10.1093/database/baaa107/6129748">Cite</a>
</span>
</span>
</div>
<li>
<b>NLP to VSM</b>:
<span class="info">(as part of
<a href="https://blah7.linkedannotation.org">BLAH7</a> hackathon</a>):</span>
<ul class="proj-sublist">
<li>
<a href="https://github.com/vsm/nlp-to-vsm">nlp-to-vsm</a> repo:
‘From natural language to VSM semantic structures’.
<li>
<a href="https://vsm.github.io/nlp-to-vsm">live demo</a> page
<span class="info">(pilot study experiment).</span>
</ul>
<li>
<b><a href="https://github.com/UniBioDicts">UniBioDicts</a></b> organization:<br>
A set of modules that give Unified access to Biological Dictionary data,
served from different terminology providers' APIs.
<span class="info">(For use in VSM-boxes).</span>
<div class="li-footer paper">
<span>
Paper :
<a href="https://doi.org/10.1093/bioinformatics/btaa1065">Abstract</a></span>
<span>
<a href="https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaa1065/35314132/btaa1065.pdf">PDF</a></span>
<span class="outreach">
<span>
<a href="https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa1065/6050700">Cite</a>
</span>
</span>
</div>
<li>
<b>SciCura</b>:
<ul class="proj-sublist">
<li>
SciCura v1, see <a href="http://demo.scicura.org">demo section</a>
<span class="info">(← select a template at the top left there);</span>
<br>used for a collaborative curation project at NTNU university.
</span>
<li>
<a href="https://vsm.github.io/vsm-pages/scicura">SciCura v1 to v2</a>:
draft description.
</ul>
</ul>
<li>
<b>Connection to other technologies</b>:
<ul class="other-tech">
<li>
<b><a href="https://github.com/vsm/vsm-to-rdf">VSM to RDF</a></b>:
translation of VSM-sentences to RDF
<span class="info">(draft, work in progress).</span>
<li>
E.g. output to the
<a href="https://doi.org/10.1093/bioinformatics/btz132">PSI-MITAB2.8</a>
format
<span class="info">(via causalBuilder).</span>
<li>
NLP to VSM: see above.
</ul>
<!--
<li>
<b><a href="https://vsm.github.io/vsm-pages/about">About</a></b>
-->
<!--
<li>
<b>Funding</b>:
<div class="funding">
<div style="margin: 0.3em 0 0 0.7em;">
<b>No Funding</b> currently. Therefore please:
</div>
<div style="margin: 0.4em 0 0 1.4em;">
<span class="smaller-arrow">►</span><b>In your next grant proposal:  allocate funds</b> for VSM and S.V.
</div>
<div style="margin: 0.3em 0 0 1.4em;">
<span class="smaller-arrow">►</span><b>Speak</b> about VSM:  make others aware of its value.
</div>
<div style="margin: 0.3em 0 0 1.4em;">
<span class="smaller-arrow">►</span>Donate: 
<a href="https://patreon.com/stevencruy">Patreon</a>,
<a href="https://paypal.me/stcruy">Paypal</a>,
<a href="https://github.com/sponsors/stcruy">GH Sponsors</a>.
</div>
<div style="margin: 0.35em 0 0.2em 1.4em;">
<span class="funding-more-link" href="javascript:void(0);" onclick="(() => {
document.getElementsByClassName('funding-more')[0].classList.toggle('hidden');
this.innerHTML = this.innerHTML == 'more' ? '▼' : 'more';
})()"
>more</span>
</div>
<div class="funding-more hidden" style="margin: 0.8em 0 0 0;">
<div style="margin: 1em 0 0 0;">
A <b>determination</b> to create something truly new
is often met with great uncertainty of making a living.
This is especially so in science, where
<a target="_blank" href="https://www.nature.com/news/young-talented-and-fed-up-scientists-tell-their-stories-1.20872">
brutal conditions for fundraising can leave little time to do actual research</a>.
</div>
<div style="margin: 0.5em 0 0 0;">
Despite this reality, 
<a target="_blank" href="https://orcid.org/0000-0002-3136-7353">Dr. Steven V.</a>
chose to do <b>the many years of deep work</b> it required
to develop a new way forward to handle complex, contextualized knowledge digitally.
Because computable knowledge plays a central role in systems biology, in science generally,
and in tomorrow’s AI.
And it must be made practical to use for everyone.
</div>
<div style="margin: 0.5em 0 0 0;">
His results are now receiving excellent feedback from peers, 
but it leaves him for large periods <b>without funding</b>: since Dec 2019, as in 2011–2016.
 He is now expected to write discouraging amounts of grant proposals—without salary—for <b>tiny</b> chances of funding,
instead of doing the real innovation work that he's actually good at.
</div>
<div style="margin: 0.5em 0 0 0;">
It is unfortunate that a modern society makes its dedicated scientists
waste so much of their talent on defending their own existence.
</div>
<div style="margin: 0.5em 0 0.75em 0;">
S.V. is <b>looking for a reliable, long-term funding solution</b>,
to keep contributing to solving the world's toughest problems
on a computational intelligence scale.  — 
Contact <a href="https://stcruy.com">me</a>.
</div>
</div>
</div>
-->
</ul>
<br><br><hr><br>
<a name="vsm-intro-interface"></a>
<p>
Overview and examples:<br><b>How to create and read computable knowledge in a vsm-box.</b>
</p>
<br>
<br>
</div>
<div style="max-width: 530px">
<img src="https://raw.githubusercontent.com/vsm/vsm-box/master/imgs/vsm-box-example.gif"
style="max-width: 100%" alt="vsm-box example animation">
</div>
<br><br>
<div style="max-width: 880px">
<img src="https://raw.githubusercontent.com/vsm/vsm-box/c7cd1ec5/imgs/vsm-box-examples-1.png" style="max-width: 100%" alt="vsm-box examples part 1">
<img src="https://raw.githubusercontent.com/vsm/vsm-box/c7cd1ec5/imgs/sep-0.png" style="max-width: 100%" alt="sep">
<img src="https://raw.githubusercontent.com/vsm/vsm-box/c7cd1ec5/imgs/vsm-box-examples-2.png" style="max-width: 100%" alt="vsm-box examples part 2">
<img src="https://raw.githubusercontent.com/vsm/vsm-box/c7cd1ec5/imgs/sep-1.png" style="max-width: 100%" alt="sep">
<img src="https://raw.githubusercontent.com/vsm/vsm-box/c7cd1ec5/imgs/vsm-box-examples-3.png" style="max-width: 100%" alt="vsm-box examples part 3">
<img src="https://raw.githubusercontent.com/vsm/vsm-box/c7cd1ec5/imgs/sep-1.png" style="max-width: 100%" alt="sep">
<img src="https://raw.githubusercontent.com/vsm/vsm-box/c7cd1ec5/imgs/vsm-box-examples-4.png" style="max-width: 100%" alt="vsm-box examples part 4">
<img src="https://raw.githubusercontent.com/vsm/vsm-box/c7cd1ec5/imgs/sep-2.png" style="max-width: 100%" alt="sep">
<img src="https://raw.githubusercontent.com/vsm/vsm-box/c7cd1ec5/imgs/vsm-box-examples-5.png" style="max-width: 100%" alt="vsm-box examples part 5">
<img src="https://raw.githubusercontent.com/vsm/vsm-box/c7cd1ec5/imgs/sep-0.png" style="max-width: 100%" alt="sep">
<img src="https://raw.githubusercontent.com/vsm/vsm-box/c7cd1ec5/imgs/vsm-box-examples-6.png" style="max-width: 100%" alt="vsm-box examples part 6">
<img src="https://raw.githubusercontent.com/vsm/vsm-box/c7cd1ec5/imgs/sep-1.png" style="max-width: 100%" alt="sep">
<img src="https://raw.githubusercontent.com/vsm/vsm-box/c7cd1ec5/imgs/vsm-box-examples-7.png" style="max-width: 100%" alt="vsm-box examples part 7">
</div>
<div class="div600">
<br><br>
<br><hr><br>
<a name="vsm-intro-code"></a>
<p>
<b>It is easy to use a vsm-box in your project.</b>
<br>For example: paste this in a file called 'test.html', and open it in your browser:
</p>
<br>
<pre class="code-example">
<!doctype html>
<html>
<a><head></a>
<meta charset="utf-8">
<i><!-- 1) <u>Load</u> the vsm-box module, and a vsm-dictionary to provide terms+identifiers. --></i>
<b><script src="https://cdn.jsdelivr.net/npm/vsm-box@^1.0.0/dist/vsm-box.standalone.min.js"></script></b>
<b><script src="https://cdn.jsdelivr.net/npm/vsm-dictionary-local@^2.6.0/dist/vsm-dictionary-local.min.js"></script></b>
<a></head></a>
<a><body></a>
<i><!-- 2) <u>Place</u> a vsm-box element on the web page. --></i>
<b><vsm-box</b> id=vsmbox autofocus=true<b>></vsm-box></b>
<span style=font-size:0px;><br> </span><textarea id=textarea readonly rows=31 cols=45></textarea> <i><!-- (Textfield for showing vsm-box's data content). --></i>
<a></body></a>
<a><script></a>
<i>// 3) <u>Connect</u> the vsm-box to a vsm-dictionary (one or more) :</i>
<i>// - use online vocabulary data (via `vsm-dictionary-bioportal`, `vsm-dictionary-uniprot` etc.)</i>
<i>// - or <span style="font-style: italic;">here</span> we make one that provides demo-data:</i>
<b>vsmbox.vsmDictionary = new VsmDictionary</b>Local({
dictData: [ { id: 'http://dem.o/A',
name: 'Demo dictionary A',
entries: [ { id: 'http://dem.o/A/A:01', terms: [ { str: 'Jo' }, { str: 'Joanna' } ] }, <i>// Two synonyms.</i>
{ id: 'http://dem.o/A/A:02', terms: [ { str: 'eats' } ], descr: 'an eating activity' } ]
} ],
refTerms: ['it']
});
<i>// 4) Optional: <u>Fill</u> the vsm-box with a VSM-template. Uncomment this to do so:</i>
<i>/*</i><b>vsmbox.initialValue = </b>{
terms: [ { placeholder: 'name' }, { str: 'eats', classID: 'http://dem.o/A/A:02', instID: null }, {} ],
conns: [ { type: 'T', pos: [ 0, 1, 2 ] } ]
};<i>*/</i>
<i>// 5) <u>Listen</u> to vsm-box content updates. Here we show its data-content live in the textfield below it.</i>
<b>vsmbox.addEventListener('change'</b>, showData);
<a>function</a> showData(event) { textarea.value = JSON.stringify(event.detail[0], null, 2) }
showData({ detail: [vsmbox.initialValue || { terms: [], conns: [] }] }); <i>// Show initial content.</i>
<a></script></a>
</html></pre>
<br><br>
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</body>
</html>