On Jun 20, 2011, at 7:47 PM, Andrea Splendiani wrote: > Let's be precise. > I think everybody here would agree that to have opaque unique identifier is a > sensible policy for individuals more often than not. > To keep the analogy with relational databases, the issue is not whether ID > should be opaque or not, but whether Table and Column names should be opaque > or not.
+1 very well put. > Thinking about ontology terms, there are good reasons for which these should > be "codes", rather than definitions in a word (that is, to at least avoid the > temptations). Whether they 'should' be codes, is in the tradeoff area. I > guess it depends on domains. It makes sense for OBO, less for DBPedia. > What I was originally finding a bit too much is that 'everything' should > necessarily have an opaque id. We can live with rdf:type, perhaps obo:partOf > and so on... > > ciao, > Andrea > > > > > Il giorno 20/giu/2011, alle ore 23.38, Michel_Dumontier ha scritto: > >> It’s exactly the same reason why we have tables with incremental primary >> keys or have social security numbers for people and ISBN’s for books. The >> identifier is meant to identify one thing, and should not clash with other >> things having similar or exact names. What that thing is, is up to you. But >> you don’t need a fancy algorithm to generate them so that you ensure >> uniqueness. In creating RDF data (for Bio2RDF), we’re often put in the >> position of having to create unique identifiers (so as to avoid unreliable >> blank nodes), and we sometimes have no other alternative but to hash 3-8 >> values to get that (and to ensure we’ll generate the same identifier in the >> future). Having a guaranteed primary key is definitely good for change >> management. >> >> However, if you’re quite sure that your system will never generate the same >> identifier (EVER EVER EVER) for another entity, then go ahead and use labels >> in your URIs. But if you expect some churn in the meantime (as will happen >> with domain ontologies – see ‘Protein’ for BioPAX as an example), then you >> may want to investigate a more principled approach. There are many cases in >> SIO where I changed the label – to be more accurate wrt to the definition or >> just to conform to a new label syntax. Had I linked the label to the >> identifier, this would cause some cognitive dissonance, and be a pain for >> users to update. >> >> m. >> >> From: public-semweb-lifesci-requ...@w3.org >> [mailto:public-semweb-lifesci-requ...@w3.org] On Behalf Of Sivaram Arabandi, >> MD >> Sent: Monday, June 20, 2011 3:56 PM >> To: Chime Ogbuji >> Cc: Andrea Splendiani; Vagnoni,Matthew M; James Malone; HCLS >> Subject: Re: My task from last week: Semantic free identifiers >> >> I couldn't "agree" more with Andrea and Chime on this one. And would like to >> see some good reason(s) for us to continue to be burdened by them. >> The standard answer - 'tooling can help in managing the readability aspects' >> has been heard several times, and yet everyone seems to pass around 'raw RDF >> or SPARQL snippets with readable URIs' - for sure these will be absolutely >> unreadable if we were to use totally opaque identifiers. >> >> I recently had a discussion on this topic with Michel (during Semtech) and >> this exact line of thinking that Mark alluded to in his email came up: >> "though I guess, for them, "partOf" *is* opaque... so...?? >> Perhaps that argument is somewhat spurious??" >> >> --Sivaram >> ____________________________ >> Sivaram Arabandi, MD, MS >> Ph: 216.374.2883 >> >> http://ontolog.cim3.net/cgi-bin/wiki.pl?SivaramArabandi >> http://www..linkedin.com/pub/sivaram-arabandi/1/9ab/92a >> >> >> >> On Jun 20, 2011, at 3:34 PM, Chime Ogbuji wrote: >> >> >> On Monday, June 20, 2011 at 3:08 PM, Andrea Splendiani wrote: >> >> Hi, >> sorry to jump on this thread like this... >> >> To be honest, I'm kind of concerned by the insistence on semantic-opaque >> identifiers. >> I am as well and I have been for some time. >> I understand the reason for them, >> >> Actually, I would be interested in hearing the reason for them enumerated, >> because I have had a hard time imagining what could possibly offset the >> (significant) impact on readability that it has on biomedical ontologies. >> The barrier is already high for non-logicians and non-semantic web >> aficionados to use biomedical ontologies. Why set it any higher? >> >> -- Chime >> >> >> No virus found in this message. >> Checked by AVG - www.avg.com >> Version: 10.0.1382 / Virus Database: 1513/3715 - Release Date: 06/20/11 >> > > Andrea Splendiani > Senior Bioinformatics Scientist > Centre for Mathematical and Computational Biology > +44(0)1582 763133 ext 2004 > andrea.splendi...@bbsrc.ac.uk > > >
