Re: [Treebase-devel] [PhyloWS] query predicate vocabulary

[Arlin S. <ar...@um...>]

Are all those references to "identifer" (tree identifier,  matrix  
identifier) going to be anchored in some way by dcterms:identifier?    
And likewise with all those references to "title"?

Terms such as "study" appear in various ontologies (search http://bioportal.bioontology.org 
).

Arlin

On Oct 2, 2010, at 6:15 PM, Hilmar Lapp wrote:

> (Sorry for cross-posting - this does concern both treebase and phylows
> groups though)
>
> Rutger et al,
>
> I assume that the TreeBASE terms and predicate vocabulary terms
> spreadsheet [1] is the basis for the treebase.owl [2] ontology in the
> TreeBASE codebase? If so, I was happy to see the tb. prefix removed
> from the property labels in the OWL file. If not, what is the relation
> between the two? (BTW neither vocabulary artifact is linked from the
> TreeBASE API documentation [3] - shouldn't they, or at least one of
> them, possibly the OWL file?)
>
> One of the outcomes of the Phylogenetics Standards working meeting at
> the 2010 TDWG conference [4] is that we need to move forward on a
> standard PhyloWS query predicate vocabulary. Obviously, the one
> created for TreeBASE would be a template for that, and ultimately
> TreeBASE could import that vocabulary, and add its own custom
> predicates (similarly as it now imports Dublin Core and then adds its
> own predicates). I think this approach (standard ontology that
> individual data providers import into theirs and then add to) would
> also allow data providers to add annotations indicating which
> predicates they actually support.
>
> Are there concerns or considerations that could make this a bad idea?
>
> Assuming for a moment that it's not a bad idea, here are some initial
> thoughts I had when looking at the treebase.owl file as the presumed
> starting point.
> 1) The pattern for constructing the label uses a dot to delimit
> "words" (e.g., identifier.tree), whereas normally the pattern I've
> seen uses CamelCase (which would yield treeIdentifier). For the
> standard vocabulary I'd rather stick with common conventions, so what
> were the reasons or examples that motivated the dot pattern?
> 2) None of the properties seems to have a definition. I think in the
> standard one we should aim for all properties to have good
> definitions. Do others agree that this is worthwhile, or do you think
> this wouldn't gain anything. (There are initial definitions in the
> spreadsheet, for example.)
> 3) The spreadsheet has additional information that looks actually
> useful, such as the Xpath expression for NeXML. Wouldn't that be worth
> retaining to?
>
> Nico - I don't know whether you're subscribed to the phylows group -
> if not, you may want to if you want to stay in the loop on this.
>
> 	-hilmar
>
> [1] https://spreadsheets.google.com/pub?key=0Av8UW3JvZsgcckwtLU83cHloUjhGY25uRzUtb2ZBbHc&hl=en&single=true&gid=0&output=html
> [2] http://treebase.svn.sourceforge.net/viewvc/treebase/trunk/treebase-core/src/main/resources/treebase.owl
> [3] https://sourceforge.net/apps/mediawiki/treebase/index.php? 
> title=API
> [4] http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/WorkingMeeting2010#Further_develop_thePhyloreferenc
> -- 
> ===========================================================
> : Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
> ===========================================================
>
>
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-------
Arlin Stoltzfus (ar...@um...)
Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST
IBBR, 9600 Gudelsky Drive, Rockville, MD
tel: 240 314 6208; web: www.molevol.org