{ "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/2007/12/10/tagging-thesauri-or-ontologies.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/smfvd-pdy70", "url": "https://chem-bla-ics.linkedchemistry.info/2007/12/10/tagging-thesauri-or-ontologies.html", "title": "Tagging, thesauri or ontologies?", "content_html": "

Controlled vocabularies, hierarchies, microformats, RDF. Nico Adams pointed me to\nthis excellent video:

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It’s a really nifty piece of work, which goes into the differences between thesauri, controlled vocabularies,\nand, as such, ontologies, and social tagging systems. Both have their virtues; it is fuzzy logic versus ODEs\nall over again. Whether one is better than the other only depends on the problem at hand. For example, can\nyou imagine social tagging in atom typing prior to performing force field calculations? Or, an 150-term\nontology to annotate the scientific content of your literature archive?

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More from where they come from…

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The video appears to be made by the Digital Etnography group, which\nhas made several more movies. Certainly something I’m going to\ncheck out over the winter holidays (I guess I am quite a bit more religious about ODOSOS than about gods).

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Nico wrote: As long as we appreciate that there may be more than one top node…. I am not entirely sure,\nbut if he refers the thesauri, which are, a particular form of ontologies, where basically the only relations\nthat can be found are is-a or is-parent-of, resulting in a hierarchy of controlled terminology with one\ntop node (such as the Gene Ontology). Ontologies can and should be much richer if we really want to take\nadvantage of our information technologies, just like we do with any graph mining. Why mould reality in a\ntight hierarchy?

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Chemical ontologies

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Peter has [not seen the movie yet] (https://blogs.ch.cam.ac.uk/pmr/2007/12/09/ontologies-in-physics-and-chemistry/),\nbut replied with a recent comment he had on CML:

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Ebs and Michael had reviewed CML and questioned why the key concepts were atoms, molecules, electron,\nsubstances, whereas they suggested it would have been better to start from reactions. I think that’s\na very clear difference in orientation between endurants and perdurants. Although chemists publish\nreactions, most of the emphasis is on (new) substances and their properties. CML is designed to map\ndirectly onto the way chemists seem to think - at least in their public communication - e.g. through\ndocuments. Of course we can also do reactions in CML, but even there the emphasis is often on the\ncomponents.

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The suggestion by Ebs and Michael is indeed quite surprising: ontologies tries to capture knowledge and expressed this an a small set of terms, each of which with an accurate and non-overlapping meaning (orthogonal, if you wish). Now, the terms carbon, nitrogen, oxygen, and the other 104 elements are quite accurate and rather different from each other, at least from a chemical point of view. Sure, bonding is more difficult, and let’s not start about aromaticity. But to question atoms, bonds or electrons as key concepts??

", "summary": "Controlled vocabularies, hierarchies, microformats, RDF. Nico Adams pointed me to this excellent video:", "date_published": "2007-12-10T00:00:00+00:00", "date_modified": "2025-04-12T00:00:00+00:00", "tags": ["ontology"], "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ] } ] }