- From: Andrea Splendiani <andrea.splendiani@bbsrc.ac.uk>
- Date: Tue, 21 Jun 2011 19:41:12 +0000
- To: James Malone <malone@ebi.ac.uk>
- Cc: "andrea splendiani (RRes-Roth)" <andrea.splendiani@rothamsted.ac.uk>, Helena Deus <helenadeus@gmail.com>, Matt Vagnoni <matthew.vagnoni@uth.tmc.edu>, Michel_Dumontier <michel_dumontier@carleton.ca>, "Sivaram Arabandi, MD" <sivaram.arabandi@gmail.com>, "M. Scott Marshall" <mscottmarshall@gmail.com>, Chime Ogbuji <chimezie@gmail.com>, "MMVagnoni@mdanderson.org" <mmvagnoni@mdanderson.org>, HCLS <public-semweb-lifesci@w3.org>, Jonathan Rees <jar@creativecommons.org>
Skipping the line of reasoning that leads to these conclusions... I think one of the main point is the role of the 'web'. Whether we are talking about terminologies encoded in OWL/RDF, or about a distributed web-based information space. I bet we could make a test and see the correlation between who prefers opaque vs transparent ids, and who prefers OWL-apis vs Jena. In my opinion, it is desirable to have opaque identifiers for large medical terminologies. But transparent? identifiers work better for relations and for tight dictionaries (e.g.: DC). It doesn't really change that much if you use tools or not at the end (at least for me). ciao, Andrea Il giorno 21/giu/2011, alle ore 20.13, James Malone ha scritto: > So.. a long but useful discussion. That will teach me to open my big mouth :) > > Is this fair as the PRIMARY reasons for this difference in opinions: > > 1. Having semantic information such as a label in a URI makes it easier > to, at a glance, grasp some sort of meaning of a class/predicate and makes > SPARQLing and looking at RDF easier. > > 2. NOT having semantic information in a URI ensures class definitions need > to be looked up before they can be used, hence, reducing ambiguity and > that it potentially improves maintainability. > > Can 1 be resolved by tooling? Seems to me 2 is happening already and will > grow as practice in a lot of the bio-ontology community. If there is a > lack of tooling surely this group should be looking at doing something > about that - funding, lobbying.. > > James > > > > > >> Hi, >> >> I think there is some confusion going on on the subject. >> >> We need to name things in an unique way. In many cases codes are just the >> best option. No wonder we all have tax-codes and the like, it's easier >> than >> to try to find a unique name based on some attributes. >> >> The case of terminologies is an interesting case, as we need to name >> terms. >> There is a temptation to use the 'face value' of the term as a name, as >> opposed to a code. The former is clearly opening the doors for >> ambiguities, >> in this context. >> >> Beside terminologies, there are many other cases where you name thing: >> >> rdf:type >> >> owl:Class >> >> Is there a need for these to be semantically opaque ? I don't think so, >> they >> are good for mnemonics and the formal meaning is clearly defined >> elsewhere. >> >> The original thread didn't start from somebody questioning GO terms... but >> the need to replace 'partOf' with a code. >> >> To tell a funny story... I have an (unrelated) homonymous in my home town >> (which is a bit weird given the size of the town and the frequency of my >> last name). Given the identifier clash... I ended up receiving funny >> things, >> like love letters or urgent calls from unknowns... (not sure I missed some >> as well...). >> Now, when i went to register a website, which one would be better: >> mydomain/AndreaSplendiani >> mydomain/001 >> >> I cannot really see any reason for the latter, and several reasons against >> it. >> Does mydomain/001 protects friend and lovers of my homonymous from >> confusion >> ? Most likely not. >> >> ciao, >> Andrea >> >> >> Il giorno 21/giu/2011, alle ore 18.46, Helena Deus ha scritto: >> >>> Other standards (outside of semantic web) saw the need to rely on >>> numeric >> identifiers, even if that created a burden for their users >>> e.g. in SNOMED Lung = T-28000 >>> >>> Of course it is a pain to query SNOMED with "all the diseases that >>> affect >> T-28000". >>> But the fact is that despite the inconvenience of having to fetch that >> identifier prior to the query, SNOMED is widely used. >>> >>> What is so special about semantic web identifiers that they don't need >>> to >> follow the same path? >> >> Andrea Splendiani >> Senior Bioinformatics Scientist >> Centre for Mathematical and Computational Biology >> +44(0)1582 763133 ext 2004 >> andrea.splendiani@bbsrc.ac.uk >> >> >> >> >> > > > -- > European Bioinformatics Institute, > Wellcome Trust Genome Campus, > Hinxton, > Cambridge, CB10 1SD, > United Kingdom > Tel: + 44 (0) 1223 494 676 > Fax: + 44 (0) 1223 492 468 > Andrea Splendiani Senior Bioinformatics Scientist Centre for Mathematical and Computational Biology +44(0)1582 763133 ext 2004 andrea.splendiani@bbsrc.ac.uk
Received on Tuesday, 21 June 2011 19:42:02 UTC