Index Fungorum LSID server
Roger Hyam
roger at TDWG.ORG
Mon Apr 24 16:42:09 CEST 2006
This is great stuff.
The vocabulary URIs are temporary but we are working on a central system
for resolvable ones just now. We need a space for these as well as
schemaLocations and various other things.
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.
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.
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.
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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>
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>
> Landcare Research
> http://www.landcareresearch.co.nz
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
--
-------------------------------------
Roger Hyam
Technical Architect
Taxonomic Databases Working Group
-------------------------------------
http://www.tdwg.org
roger at tdwg.org
+44 1578 722782
-------------------------------------
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This is great stuff.<br>
<br>
The vocabulary URIs are temporary but we are working on a central
system for resolvable ones just now. We need a space for these as well
as schemaLocations and various other things.<br>
<br>
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.<br>
<br>
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 ( <a class="moz-txt-link-freetext" href="http://swdev.nokia.com/uriqa/CBD.html">http://swdev.nokia.com/uriqa/CBD.html</a>) 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.<br>
<br>
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.<br>
<br>
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.<br>
<br>
Well done for another LSID authority Kevin.<br>
<br>
All the best,<br>
<br>
Roger<br>
<br>
<br>
<br>
Kevin Richards wrote:
<blockquote cite="mids44aa6d1.027 at smtp.landcareresearch.co.nz"
type="cite">
<pre wrap="">Thanks for those comments Rod.
As you have seen this is an initial attempt.
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">The syntax
<TaxonNames:hasBasionym>
<rdf:Description
rdf:about="urn:lsid:indexfungorum.org:Names:148860" />
</TaxonNames:hasBasionym>
strikes me as odd.
</pre>
</blockquote>
</blockquote>
<pre wrap=""><!---->
This is due to an accidental omission of the RDF entity type of the
basionym object. Will fix this.
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">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" />
</pre>
</blockquote>
</blockquote>
<pre wrap=""><!---->
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'.
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">The attribute
TaxonNames:nomenclaturalCode=<a class="moz-txt-link-rfc2396E" href="http://tdwg.org/2006/03/12/TaxonNames/NomenclaturalCode/#botanical">"http://tdwg.org/2006/03/12/TaxonNames/
NomenclaturalCode/#botanical"</a> of the tag <TaxonNames:TaxonName> is
problematic. Firstly, I don't know why this is an attribute rather
</pre>
</blockquote>
</blockquote>
<pre wrap=""><!---->than
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">just another tag,
</pre>
</blockquote>
</blockquote>
<pre wrap=""><!---->
Due to my lack of understanding of RDF and when to use attributes as
opposed to tags - I was blindly following an example.
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">and the URI
<a class="moz-txt-link-freetext" href="http://tdwg.org/2006/03/12/TaxonNames/NomenclaturalCode/#botanical">http://tdwg.org/2006/03/12/TaxonNames/NomenclaturalCode/#botanical</a>
returns a 404. If this is just a made up URI then this is bad --
</pre>
</blockquote>
</blockquote>
<pre wrap=""><!---->EVERY
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">URI in an RDF document must be real -- unlike XML schema where any
</pre>
</blockquote>
</blockquote>
<pre wrap=""><!---->old
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">rubbish can be used.
</pre>
</blockquote>
</blockquote>
<pre wrap=""><!---->
Also due to the prototyping stage of this 'project'. Will be fixed by
online TDWG ontologies at some stage I assume?
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap=""> <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
</pre>
</blockquote>
</blockquote>
<pre wrap=""><!---->this
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">is in principle a bad thing(TM)
</pre>
</blockquote>
</blockquote>
<pre wrap=""><!---->
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
WARNING: This email and any attachments may be confidential and/or
privileged. They are intended for the addressee only and are not to be read,
used, copied or disseminated by anyone receiving them in error. If you are
not the intended recipient, please notify the sender by return email and
delete this message and any attachments.
The views expressed in this email are those of the sender and do not
necessarily reflect the official views of Landcare Research.
Landcare Research
<a class="moz-txt-link-freetext" href="http://www.landcareresearch.co.nz">http://www.landcareresearch.co.nz</a>
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
</pre>
</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
-------------------------------------
Roger Hyam
Technical Architect
Taxonomic Databases Working Group
-------------------------------------
<a class="moz-txt-link-freetext" href="http://www.tdwg.org">http://www.tdwg.org</a>
<a class="moz-txt-link-abbreviated" href="mailto:roger at tdwg.org">roger at tdwg.org</a>
+44 1578 722782
-------------------------------------
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