VSM
Translating any knowledge into a computable form, made easy.
Here we collect all information about VSM:
-
Intros:
-
How VSM works:
-
‘Intuitive Representation of Computable Knowledge’
(Preprint, 2020)
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.
-
Many explained VSM examples
(using an earlier vsm-box prototype).
-
Animated demo/intro, see below.
-
Demos:
-
Code:
-
vsm-box :
the user interface of VSM
(as a <vsm-box> HTML-element)
(GitHub)
-
vsm
organization on GitHub : VSM's core enabling modules. See their Readme:
-
Code-use demo,
see below.
-
Use in other projects:
-
UniBioDicts organization:
A collection of modules for Unified access to Biological
Dictionary data, served from disparate terminology providers.
(For use in VSM-boxes).
-
causalBuilder:
A web app that generates VSM-templates that follow the
MI2CAST
standard,
for molecular biologists who are creating structured knowledge about
causal molecular interactions.
(Uses VSM-box).
-
SciCura:
-
SciCura v1, see demo section
(← select a template at the top left there);
used for a collaborative curation project at NTNU university.
-
SciCura v1 to v2:
draft description.
-
Connection to other technologies:
-
VSM to RDF:
translation of VSM-sentences to RDF
(draft, work in progress).
-
E.g. output to the
PSI-MITAB2.8
format
(via causalBuilder).
-
Funding:
Dr. Steven V. has no salary and has to work for free (since Dec 2019) (and 2011–2016).
Funding agencies have delayed VSM and all it enables, far too long now.
I need your direct support. Please use my
Patreon,
Paypal,
GitHub Sponsors if you can.
Overview and examples: how to create and read computable knowledge in a vsm-box.
It is easy to use a vsm-box in your project.
For example: paste this in a file called 'test.html', and open it in your browser:
<!doctype html>
<html>
<head>
<!-- 1) Load the vsm-box module, and a vsm-dictionary to provide terms+identifiers. -->
<script src="https://unpkg.com/vsm-box@^1.0.0/dist/vsm-box.standalone.min.js"></script>
<script src="https://unpkg.com/vsm-dictionary-local@^2.6.0/dist/vsm-dictionary-local.min.js"></script>
</head>
<body>
<!-- 2) Place a vsm-box element on the web page. -->
<vsm-box id=vsmbox autofocus=true></vsm-box>
<br> <textarea id=textarea readonly rows=31 cols=45></textarea> <!-- (Textfield to show vsm-box data). -->
</body>
<script>
// 3) Connect the vsm-box to a vsm-dictionary. Here we make one that provides demo-data.
// Or we could use online vocabulary data, like with vsm-dictionary-bioportal etc.
vsmbox.vsmDictionary = new VsmDictionaryLocal({
refTerms: ['it'],
dictData: [
{ id: 'http://dem.o/A', name: 'Demo dictionary A',
entries: [
{ id: 'http://dem.o/A/A:01', terms: [{ str: 'Jo' }, { str: 'Joanna' }] }, // Synonyms.
{ id: 'http://dem.o/A/A:02', terms: [{ str: 'eats' }], descr: 'an eating activity' }
]
}
]
});
// 4) Optional: Fill the vsm-box with a VSM-template. Uncomment this to do so:
/*vsmbox.initialValue = {
terms: [ { placeholder: 'name' }, { str: 'eats', classID: 'http://dem.o/A/A:02', instID: null }, {} ],
conns: [ { type: 'T', pos: [ 0, 1, 2 ] } ]
};*/
// 5) Receive vsm-box content updates. Here we show its data-content live in the textfield below it.
vsmbox.addEventListener('change', showData);
function showData(event) { textarea.value = JSON.stringify(event.detail[0], null, 2) }
showData({ detail: [vsmbox.initialValue || { terms: [], conns: [] }] });
</script>
</html>
