{ "version": "https://jsonfeed.org/version/1.1", "title": "chem-bla-ics", "description": "Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.", "home_page_url": "https://chem-bla-ics.linkedchemistry.info/", "feed_url": "https://chem-bla-ics.linkedchemistry.info/2015/09/27/coding-owl-ontology-in-html5-and-rdfa.json", "icon": "https://chem-bla-ics.linkedchemistry.info/assets/images/chem-bla-ics_logo.png", "language": "en", "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286", "_orcid": "0000-0001-7542-0286" } ], "items": [ { "id": "https://doi.org/10.59350/4k55a-8c261", "url": "https://chem-bla-ics.linkedchemistry.info/2015/09/27/coding-owl-ontology-in-html5-and-rdfa.html", "title": "Coding an OWL ontology in HTML5 and RDFa", "content_html": "

\nThere are many fancy tools to edit ontologies. I like simple editors, like nano. And like any hacker, I can hack\nOWL ontologies in nano. The hacking implies OWL was never meant to be hacked on a simple text editor;\nI am not sure that is really true. Anyways, HTML5 and RDFa will do fine, and\nhere is a brief write up. This post will not cover the basics of RDFa and does assume you already know how triples work. If not, read this\nRDFa primer first.

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The BridgeDb DataSource Ontology

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This example uses the BridgeDb DataSource Ontology, created by BridgeDb developers from Manchester University (Christian,\nStian, and Alasdair). The ontology covers describing data sources of identifiers, a technology outlined in the BridgeDb paper by Martijn (see below)\nas well as terms from the Open PHACTS Dataset Descriptions for the Open Pharmacological Space\nby Alasdair et al.

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Because I needed to put this online for Open PHACTS (BTW,\nthe project won a big award!)\nand our previous solution did not work well enough anymore. You may also see the HTML of the result first. You may also want to verify it really is\nHTML: here is the HTML5 validation report.\nAlso, you may be interested in what the ontology in RDF looks like: here is\nthe extracted RDF for the ontology.\nNow follow the HTML+RDFa snippets. First, the ontology details (actually, I have it split up):

\n\n
<div about=\"http://vocabularies.bridgedb.org/ops#\"\n     typeof=\"owl:Ontology\">\n  <h1>The <span property=\"rdfs:label\">BridgeDb DataSource Ontology</span>\n    (version <span property=\"owl:versionInfo\">2.1.0</span>)</h1>\n  <p>\n    This page describes the BridgeDb ontology. Make sure to visit our\n    <a property=\"rdfs:seeAlso\" href=\"http://www.bridgedb.org/\">homepage</a> too!\n  </p>\n</div>\n<p about=\"http://vocabularies.bridgedb.org/ops#\">\n  The OWL ontology can be extracted\n  <a property=\"owl:versionIRI\"\n     href=\"http://www.w3.org/2012/pyRdfa/extract?uri=http://vocabularies.bridgedb.org/ops#\">here</a>.\n  The Open PHACTS specification on\n  <a property=\"rdf:seeAlso\"\n    href=\"http://www.openphacts.org/specs/2013/WD-datadesc-20130912/#bridgedb\"\n  >Dataset Descriptions</a> is also useful.\n</p>\n
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This is the last time I show the custom color coding, but for a first time it is useful. In red are basically the predicates, where @about\nindicates a new resource is started, @typeof defines the rdf:type, and @property indicates all other predicates. The blue and\ngreen blobs are literals and object resources, respectively. If you work this out, you get this OWL code (more or less):

\n\n
bridgedb: a owl:Ontology;\n  rdfs:label \"BridgeDb DataSource Ontology\"@en;\n  rdf:seeAlso\n    <http://www.openphacts.org/specs/2013/WD-datadesc-20130912/#bridgedb>;\n  rdfs:seeAlso <http://www.bridgedb.org/>;\n  owl:versionIRI\n    <http://www.w3.org/2012/pyRdfa/extract?uri=http://vocabularies.bridgedb.org/ops#>;\n  owl:versionInfo \"2.1.0\"@en .\n
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An OWL class

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Defining OWL classes are using the same approach: define the resource it is @about, define the @typeOf and giving is properties.\nBTW, note that I added a @id so that ontology terms can be looked up using the HTML # functionality. For example:

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<div id=\"DataSource\"\n  about=\"http://vocabularies.bridgedb.org/ops#DataSource\"\n  typeof=\"owl:Class\">\n  <h3 property=\"rdfs:label\">Data Source</h3>\n  <p property=\"dc:description\">A resource that defines\n    identifiers for some biological entity, like a gene,\n    protein, or metabolite.</p>\n</div>\n
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An OWL object property

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Defining an OWL data property is pretty much the same, but note that we can arbitrary add additional things, making use of <span>,\n<div>, and <p> elements. The following example also defines the rdfs:domain and rdfs:range:

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<div id=\"aboutOrganism\"\n  about=\"http://vocabularies.bridgedb.org/ops#aboutOrganism\"\n  typeof=\"owl:ObjectProperty\">\n  <h3 property=\"rdfs:label\">About Organism</h3>\n  <p><span property=\"dc:description\">Organism for all entities\n    with identifiers from this datasource.</span>\n    This property has\n    <a property=\"rdfs:domain\"\n      href=\"http://vocabularies.bridgedb.org/ops#DataSource\">DataSource</a>\n    as domain and\n    <a property=\"rdfs:range\"\n      href=\"http://vocabularies.bridgedb.org/ops#Organism\">Organism</a>\n    as range.</p>\n</div>\n
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So, now anyone can host an OWL ontology with dereferencable terms: to remove confusion, I have used the full URLs of the terms in @about attributes.

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References

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van Iersel, M. P., Pico, A. R., Kelder, T., Gao, J., Ho, I., Hanspers, K., Conklin, B. R., & Evelo, C. T. (2010). The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services. BMC Bioinformatics, 11(1). https://doi.org/10.1186/1471-2105-11-5 CrossRef Scholia
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", "summary": "There are many fancy tools to edit ontologies. I like simple editors, like nano. And like any hacker, I can hack OWL ontologies in nano. The hacking implies OWL was never meant to be hacked on a simple text editor; I am not sure that is really true. Anyways, HTML5 and RDFa will do fine, and here is a brief write up. This post will not cover the basics of RDFa and does assume you already know how triples work. If not, read this RDFa primer first.", "image": "https://chem-bla-ics.linkedchemistry.info/assets/images/bdbOnto.png", "date_published": "2015-09-27T00:00:00+00:00", "date_modified": "2015-09-27T00:00:00+00:00", "tags": ["ontology","bridgedb","web","rdf","owl","rdfa"], "_references": [ { "url": "https://doi.org/10.1186/1471-2105-11-5", "doi": "10.1186/1471-2105-11-5" } ], "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ] } ] }