Index Fungorum LSID server

Roderic Page at BIO.GLA.AC.UK
Mon Apr 24 21:17:35 CEST 2006

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 ( 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

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  
( If we don't make our stuff  
findable, we are wasting our time.


>  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="" />
>>>>      </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 has a
>>>> complementary tag such as
>>>>      <TaxonNames:isBasionymOf rdf:resource =
>>>> " 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="
>>>> 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
>>>> returns a 404. If this is just a made up URI then this is bad --
>>>> 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
> -------------------------------------
>  roger at
>  +44 1578 722782
> -------------------------------------
Professor Roderic D. M. Page
Editor, Systematic Biology
Graham Kerr Building
University of Glasgow
Glasgow G12 8QP
United Kingdom

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