- From: Marijke Keet <keet@inf.unibz.it>
- Date: Mon, 16 Jul 2007 16:45:19 +0200
- To: Eric Neumann <eneumann@teranode.com>
- CC: public-semweb-lifesci <public-semweb-lifesci@w3.org>
Eric Neumann ha scritto: > Alan, > > the life science community has for years applied an implicit > transitivity to records of things, so that when many say: > > "http://purl.uniprot.org/uniprot/P12345 is expressed only in species > homo sapien" > > they usually imply that "the protein referenced by > datarecord:http://purl.uniprot.org/uniprot/P12345 is expressed only in > species homo sapien" > > I am not arguing for or against this "short-cut", but it is what it > is, and certainly can be handled adding certain logic rules to dealing > with datarecords and their content. shortcuts can be fine as long as people are aware of it what exactly the shortcut stands for. Eric's email from earlier this morning stated that there is no difference, which is different from agreeing on a shortcut. that aside, even the extended version contains several shortcuts and implicit information. - by the maths foundation of databases, "datarecord:http://purl.uniprot.org/uniprot/P12345" refers to an instance. - by the remainder of the sentence above mentioning "homo sapiens", this refers to a type (leaving out discussion about the ontological status of "species), suggesting thereby that "the protein" is not a particular protein, but protein at the class/universal level. - then, to make the natural language sentence a coherent piece, "datarecord:http://purl.uniprot.org/uniprot/P12345" should contain data at the type-level, which is does - what the user finds out upon manual inspection. now, I easily can come up with another natural language rendering and 'implicit transitivity': "the protein referenced by datarecord:http://purl.uniprot.org/uniprot/P12345 is expressed only in Joe Soap", which changes the meaning entirely, in that there is some particular protein expresses in some individual. in my computer scientist mode, neither do I want to manually browse to the URL and read the record nor do NLP on any part-of-speech that contains "http://purl.uniprot.org/uniprot/P12345" to figure this out. Whatever the identifier system (Scott Marshall has a nice list of requirements & points in today's emails on the topic), the vagaries of above-suggested 'implicit transitivity' would need to be spelled out explicitly so that any other software wanting to use the ID system can recognise the records for what they (are supposed to) represent. best regards, marijke > > Consider that it may be impossible to change the non-software part of > the LS community on how they think about records vs. conceptual > entities that exist in the real-world (non-IR). > > Eric > > > On Jul 16, 2007, at 12:45 AM, Alan Ruttenberg wrote: > >> >> On Jul 15, 2007, at 1:53 PM, Eric Jain wrote: >> >>>> Yes, but what sorts of statements can be made using >>>> http://purl.uniprot.org/uniprot/P12345 as the subject? Because it >>>> can mean any of the below, even the protein class itself, how can a >>>> *semantic web* statement be made using it? >>> >>> http://purl.uniprot.org/uniprot/P12345 is meant to be used for >>> anything that isn't tied to a specific representation, hoped that >>> would be clear? >> >> There are proteins, and there are records about proteins. Records >> come in different formats. If I make a statement using this url, is >> is about the record? or the protein? How should the agent come to know? >> >> -Alan >> >> >> > > > Eric Neumann, PhD > Senior Strategist, Teranode Corporation > W3C co-chair Healthcare and Life Sciences Interest Group > MIT Fellow, Science Commons > +1 781 856 9132 > >
Received on Monday, 16 July 2007 14:45:30 UTC