Index Fungorum LSID server

Roger Hyam roger at TDWG.ORG
Tue Apr 25 09:35:49 CEST 2006


 Hi Rod,

(Here I have switched from using reciprocal - which is confusing to
using the OWL terminology)

I think my point is where do we draw the line in developing workable
ontologies. What rules do we have as to formally defined relationships?
Some properties should have inverseOf
(http://www.w3.org/TR/2004/REC-owl-guide-20040210/#inverseOf) properties
and some properties should not - but how do we decide which is which?

Unless we have rules to apply then every time we want to create a new
relationship the community will split over whether the inverseOf
property should be defined or not.

Any suggestions as to what the rules should be?

Cheers,

Roger


Roderic Page wrote:
> On 24 Apr 2006, at 16:42, Roger Hyam wrote:
>
>>
>>  The isBasionymOf property is an interesting one. This does not exist
>> in the current vocabulary because it is based on the schema version
>> of TCS. The thinking in TCS went that a name that is a basionym does
>> not 'know' that it is a basionym and therefore it would be wrong to
>> model this as a property of the object. There are many places where
>> this might be an issue. Does a specimen know that it is the type of a
>> name? Without the name it isn't a type.
>
> What about the relationship? From my perspective, it's useful to know
> that the original name for Eutypella ventricosa is Valsa ventricosa,
> and this is what I model using the predicate "hasBasionym". So it's a
> relationship, not a property of an object.
>
>>
>>  If you called an LSID for a specimen would you expect to be told
>> that the specimen was the type of a name?  If we use Concise Bounded
>> Descriptions ( http://swdev.nokia.com/uriqa/CBD.html) then we won't
>> know unless there is a triple with a subject of the specimen and an
>> object of the name (i.e. we have an isTypeSpecimenOf property or
>> similar). But logically where does this stop? We can't add reciprocal
>> properties to the object definition for everything that anyone may
>> say of it. If I define a taxon with a list of specimens I wouldn't
>> expect all the specimens to have reciprocal includedInTaxonConcept
>> links back to my object. It would be impossible in an open system
>> where some one else may own the record.
>
> No, we don't want reciprocal record for everything, but there are
> cases where it is useful, especially WITHIN a single source. For
> example, if I have access to all of IndexFungorum then I can run a
> query that discovers all the names for which Valsa ventricosa is the
> basionym. But if I don't have a copy of IndexFungorum, and I'm relying
> on the metadata attached to a LSID, then if the metadata for Valsa
> ventricosa has "isBasionnymOf" tags connecting it to all names for
> which it is a basionym, I can discover those names. More importantly,
> I can infer whether two names are synonyms (e.g., if two names share
> Valsa ventricosa as a basionym, then those names are synonyms).
> Without this, I'm stuck. I think what we need to consider is whether
> two names that are synonyms (or whatever relationship we are
> interested in) are "reachable", that is given the metadata for the
> names we can go from name A to B and visa versa. This is related to
> the concept of a "scutter" :
>
> "a scutter is simply a computer program that loads, parses, interprets
> and acts upon the contents of a Web of interconnected RDF/XML
> documents. In this sense it is just a Semantic Web variant on the old
> theme of distributed Web indexing, sometimes called a 'harvester',
> 'spider', or 'robot'. The links between RDF documents are usually, but
> not necessarily, expressed using RDF's 'rdfs:seeAlso' property." (see
> http://rdfweb.org/topic/Scutter)
>
> So, I think we gain a lot of power if our metadata is sufficiently
> linked to support a scutter. For example, given metadata for a PubMed
> publication, we could get to sequences, via that to taxa (including
> names in numerous databases via LinkOut), to specimens, and so on, all
> via metadata. Indeed, one could let a scutter loose and aggregate data
> a la Google -- who needs GBIF anyway ;-).
>
> In fact, this would be a cool challenge. Start a scutter and see what
> can be retrieved.
>
>>
>>  I am thinking aloud here but we have to be very careful in adding
>> things to vocabularies - even when they seem really useful.
>> Ultimately if a client wants to know everything about a object that a
>> data source has it will have to ask the "Give me all the things that
>> refer to X" question. Either that or we have to guarantee that all
>> links are always reciprocal - which we can't.
>
> No, you don't have to guarantee links are reciprocal, but you do want
> some degree of reachability -- that I can get from one object to
> another. If we aggregate everything into one central repository (a la
> Google indexing the web) then this isn't an issue, but it is if we
> don't. I agree that for some things we don't want to have reciprocal
> links -- but I'd suggest we'd need to think seriously about supporting
> basic search. As you point out, we need  to support the "Give me all
> the things that refer to X" question.
>
> Ultimately, I think we can't ignore search, or perhaps more generally
> "finability" (which depends on things being linked). See the wonderful
> book "Ambient Findability" by Peter Morville
> (http://www.oreilly.com/catalog/ambient/). If we don't make our stuff
> findable, we are wasting our time.
>
> Rod
>
>>
>>  On the other hand things that are in people's data bases that are
>> easy to pass should perhaps be represented in an ontology - if they
>> are useful.
>>
>>  Well done for another LSID authority Kevin.
>>
>>  All the best,
>>
>>  Roger
>>
>>
>>
>>  Kevin Richards wrote:Thanks for those comments Rod.
>>> As you have seen this is an initial attempt.
>>>
>>>
>>>>> The syntax
>>>>>
>>>>>      <TaxonNames:hasBasionym>
>>>>>        <rdf:Description
>>>>> rdf:about="urn:lsid:indexfungorum.org:Names:148860" />
>>>>>      </TaxonNames:hasBasionym>
>>>>>
>>>>> strikes me as odd.
>>>>>
>>> This is due to an accidental omission of the RDF entity type of the
>>> basionym object.  Will fix this.
>>>
>>>
>>>>> I also suggest that urn:lsid:indexfungorum.org:Names:148860 has a
>>>>> complementary tag such as
>>>>>
>>>>>      <TaxonNames:isBasionymOf rdf:resource =
>>>>> "urn:lsid:indexfungorum.org:Names: 213649" />
>>>>>
>>> Godd idea.  The fields are based on the initial implementation of
>>> TCS-RDF that Roger completed, and as he said, it is not a complete
>>> schema at this stage.  BTW the reverse RDF pointers can be viewed using
>>> launchpad by going into the launchpad settings and turning on 'Show
>>> back
>>> links'.
>>>
>>>
>>>
>>>>> The attribute
>>>>> TaxonNames:nomenclaturalCode="http://tdwg.org/2006/03/12/TaxonNames/
>>>>> NomenclaturalCode/#botanical" of the tag <TaxonNames:TaxonName> is
>>>>> problematic. Firstly, I don't know why this is an attribute rather
>>>>>
>>> than
>>>
>>>>> just another tag,
>>>>>
>>> Due to my lack of understanding of RDF and when to use attributes as
>>> opposed to tags - I was blindly following an example.
>>>
>>>
>>>
>>>>> and the URI
>>>>> http://tdwg.org/2006/03/12/TaxonNames/NomenclaturalCode/#botanical
>>>>> returns a 404. If this is just a made up URI then this is bad --
>>>>>
>>> EVERY
>>>
>>>>> URI in an RDF document must be real -- unlike XML schema where any
>>>>>
>>> old
>>>
>>>>> rubbish can be used.
>>>>>
>>> Also due to the prototyping stage of this 'project'.  Will be fixed by
>>> online TDWG ontologies at some stage I assume?
>>>
>>>
>>>>>     <TaxonNames:publishedIn><i>Syll. fung.</i> (Abellini)
>>>>> <b>1</b>: 148 (1882) (1882)</TaxonNames:publishedIn>
>>>>> has formatting information (the <i></i> and <b></b> tags). I think
>>>>>
>>> this
>>>
>>>>> is in principle a bad thing(TM)
>>>>>
>>> We debated this a little and decided to leave the field text the
>>> same as
>>> has been returned by other services of IndexFungorum.  But you have a
>>> good point and it is something we will need to discuss further in
>>> future.
>>>
>>> Kevin
>>>
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>>>
>>
>>
>> --
>>
>> -------------------------------------
>>  Roger Hyam
>>  Technical Architect
>>  Taxonomic Databases Working Group
>> -------------------------------------
>>  http://www.tdwg.org
>>  roger at tdwg.org
>>  +44 1578 722782
>> -------------------------------------
>>
>>
> ----------------------------------------------------------------------------------------------------------------
>
> Professor Roderic D. M. Page
> Editor, Systematic Biology
> DEEB, IBLS
> Graham Kerr Building
> University of Glasgow
> Glasgow G12 8QP
> United Kingdom
>
> Phone:    +44 141 330 4778
> Fax:      +44 141 330 2792
> email:    r.page at bio.gla.ac.uk
> web:      http://taxonomy.zoology.gla.ac.uk/rod/rod.html
> reprints: http://taxonomy.zoology.gla.ac.uk/rod/pubs.html
>
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>
>
>
>
>
>
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--

-------------------------------------
 Roger Hyam
 Technical Architect
 Taxonomic Databases Working Group
-------------------------------------
 http://www.tdwg.org
 roger at tdwg.org
 +44 1578 722782
-------------------------------------




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