Comments for Robert Stevens' Blog

Comment on Which is used most for biomedical ontologies: OBO Format or OWL? by Robert Stevens

Robert Stevens — Thu, 16 May 2013 12:50:21 +0000

I toyed with the idea about puttitng in this point about hybrid modes of work – and, yes, it does sort of make the distinction in the original sentence irelevant these days. I don’t know how much the data would be different in 2010, when the paper was written, but I suspect we’d not see a tremendous difference (I may take a look to see if the data is available).

the next sentence I may look at is along the lines of “recent years have seen an increase in the numbers of biomedical ontologies”.
this

Comment on Which is used most for biomedical ontologies: OBO Format or OWL? by David OS

David OS — Thu, 16 May 2013 11:56:37 +0000

But if OBO is just an eccentric dialect of OWL with reduced expressiveness, is this distinction meaningful?

I consider Drosophila anatomy [1], development [1] and phenotype [2] ontologies to be OWL ontologies whose master version lives in OBO for a mixture of pragmatic and legacy reasons. Conversion is under continuous integration and they are constantly tested using OWL reasoners and browsed and queried in OWL during the dev process. One of the major uses of the anatomy ontology is for live DL queries via elk on VFB.

Much of this also applies to GO.

[1] https://sourceforge.net/p/fbbtdv
[2] https://sourceforge.net/p/fbcv

Comment on Ontologies are not the only fruit by Why use an ontology? | Ontogenesis

Why use an ontology? | Ontogenesis — Mon, 18 Mar 2013 21:45:04 +0000

[...] of statement in an ontology]; from this we can say that “ontologies are not the only fruit. That is, to capture sufficient knowledge about a domain for computational and information sharing [...]

Comment on An Update to the Amino Acids Ontology by rmrmg

rmrmg — Tue, 05 Feb 2013 18:03:28 +0000

I have tried to perform some simple reasoning (in DL Query in Protege editor), e.g.:
“AminoAcid and (hasSize some Large) and (hasPolarity some Polar) and (hasHydrophobicity some Hydrophilic) and (hasCharge some Positive)”
result is quite strange:
subClasses: Histidine, LargePositiveAliphaticAminoAcid

Is there any possibility to obtain only aminoacid (not aminoAcid group)?

Comment on Why the Pizza Ontology Tutorial? by An Exercise in Irrelevance » Blog Archive » Disjoints in Clojure-owl

An Exercise in Irrelevance » Blog Archive » Disjoints in Clojure-owl — Fri, 11 Jan 2013 15:06:14 +0000

[...] from Manchester syntax. I will explain this using examples, perhaps inevitably, based around pizza (http://robertdavidstevens.wordpress.com/2010/01/22/why-the-pizza-ontology-tutorial/), which I have started to develop using [...]

Comment on Why the Pizza Ontology Tutorial? by An Exercise in Irrelevance » Blog Archive » Clojure OWL 0.2

An Exercise in Irrelevance » Blog Archive » Clojure OWL 0.2 — Mon, 03 Dec 2012 16:24:58 +0000

[...] this in my version of the Pizza ontology which seemed as good a demonstrator to start with as any (http://robertdavidstevens.wordpress.com/2010/01/22/why-the-pizza-ontology-tutorial/); this also contains some custom “one-off” patterns, for building “named” [...]

Comment on Easing the pain of ontology building with Populous by MRR

MRR — Mon, 19 Nov 2012 07:49:11 +0000

Thanks for the answer. This still feels a bit dangerous to me, but we might give it a try.

Comment on Easing the pain of ontology building with Populous by Robert Stevens

Robert Stevens — Thu, 15 Nov 2012 09:29:53 +0000

we mostly put in gene identifiers (such as Entrez id) and it’s thus usually not a problem. Also, ontology id are usually put into cells for describing entities and Populous renders the label, so Excel doesn’t change the label either. Finally, I turn auto-change off in Excel.

Comment on Easing the pain of ontology building with Populous by MRR

MRR — Wed, 14 Nov 2012 08:23:32 +0000

Interesting. How do you deal with the tendency of MS Excel to modify short terms such as gene names?
http://nsaunders.wordpress.com/2012/10/22/gene-name-errors-and-excel-lessons-not-learned/

Comment on A Kidney and Urinary Pathway Knowledgebase by Easing the pain of ontology building with Populous « Robert Stevens' Blog

Easing the pain of ontology building with Populous « Robert Stevens' Blog — Tue, 13 Nov 2012 20:46:22 +0000

[...] used Populous in the construction of the KUPKB. We needed to extend the Kidney and Urinary Pathway Ontology (KUPO) to include more kidney cells [...]