[Taxacom] Species Pages - where are the online descriptions?

Mon Feb 2 17:57:07 CST 2009

Yes, having some standard vocabulary and constructs would be very  
helpful, and as you suggest an initial step is to use well defined and  
described identifiers for the various terms, much as has been done  
with the Dublin Core.  Similarly, drawing terms from well defined  
schemas and vocabularies such as OBOE, Darwin Core, EML, and so forth  
goes a long way towards providing semantically interoperable content  
on these types of pages.  So yes, gathering together a few of the  
commonly used and/or well defined schemas and term sets will be very  
helpful to those of us interested in presenting information that can  
be reused and machine interpreted fairly easily.

Unfortunately, the page you mentioned has some problems being parsed  
as RDFa.  Perhaps try something like, for example:

<td class="ordername"><a href="/Archaeognatha/">Archaeognatha</a></td>

changes to:

<td class="ordername"><a href="/Archaeognatha/"  
property="dwc:Order">Archaeognatha</a></td>

and add xmlns:dwc="http://rs.tdwg.org/dwc/terms/" to the list of  
namespaces.

This wouldn't do anything more than indicate that the string  
"Archaeognatha" is a taxonomic order, but it does at least add some  
semantic meaning to the term that can be determined with fairly simple  
processing.

On Feb 2, 2009, at 16:42 , Peter DeVries wrote:

> Thanks Dave,
>
> I have been working a little with RDFa, but I had some problems with  
> getting my rails created pages to validate.
>
> Eventually I would like to refactor these so they work correctly  
> with RDFa.
>
> In the meantime, it would be useful to have some standard vocabulary  
> that we can all agree on to tie the RDF or RDFa information
> together.
>
> Here is a page of mine in RDFa, but it would be nice to have it  
> marked up in a standard but more useful vocabulary.
>
>  http://insects.entomology.wisc.edu/
>
> Thanks!
>
> - Pete
>
>
> On Mon, Feb 2, 2009 at 4:26 PM, Dave Vieglais <vieglais at ku.edu> wrote:
> Hi Peter,
> This is pretty much in line with my suggestion yesterday of using  
> RDFa in existing pages to provide some semantic tagging of content.   
> The advantage of RDFa over plain RDF is that the pages require  
> little change (they are still valid HTML) yet can be easily parsed  
> as RDF.  RDFa is described at http://www.w3.org/TR/xhtml-rdfa- 
> primer/ and a couple of very simple examples of relevance are  
> available at http://code.google.com/p/darwincore/wiki/Example_RDFa.
>
> regards,
>  Dave V.
>
>
> On Feb 2, 2009, at 15:56 , Peter DeVries wrote:
>
> Hi Roger,
> I thought that this might also be a good opportunity to suggest that  
> we work
> out a standard RDF markup
> that describes species and family information that exists on web  
> pages.
>
> I was thinking something that tied a page to a specific taxon concept.
>
> For instance, this page
>
> http://eco.bcb.iastate.edu/mosquito/browse_species2.php?spcID=364
>
> Has information about this species concept
>
> http://species.geospecies.org/spec_concept_uuid/84b8badd-b899-40ea-8f89-f39f3048c270/
>
>
> Which is also known by this species concept (your uri)
>
> http://tdwg....
>
> You would also need the backward link so.
>
> This species concept http://tdwg....
>
> has a web page about it at
> http://eco.bcb.iastate.edu/mosquito/browse_species2.php?spcID=364
>
> If there was some standard markup these could be loaded into a  
> knowledge
> base and queried.
>
> I was thinking of doing something like this since I am starting to  
> get too
> many pages for species and I don't
> want to keep adding additional fields to my species, family, and order
> database tables.
>
> It would make more sense to have some common ontology that we could  
> all
> use.
>
> I was thinking of modeling these species pages as subclasses of
> foaf:Document here are some examples
>
> speciesWikipediaPage
> speciesEOLPage
> speciesIowaMosquitoesPage
>
> You can see this in the lastest GeoSpecies Ontology
>
> http://rdf.geospecies.org/ont/gsontology.owl
>
> To avoid problems and recognize subtle difference in species  
> concepts it
> might need to have support for more
> than one species concept. Most of these pages probably apply to  
> several
> variations of what is a species, but
> it make some sense to allow the concept authors some discretion as to
> whether a page about African Aedes vexans
> pertains to a species concept about North American Aedes vexans.
>
> What do you think?
>
> - Pete
>
> On Sun, Feb 1, 2009 at 4:58 AM, Roger Hyam <rogerhyam at mac.com> wrote:
>
> Hi,
>
> I am looking for websites that have good "Species Pages". By species
> page I mean (and this is my definition) a page that contains a
> description of the species and not a page that simply lists the
> nomenclature associated with the acceptance of a name. You could send
> the URL of a species page to a student who didn't know what the
> organism was and they could use it to confirm the identity of a
> specimen.
>
> An example of what I think of as a species page is  the Fishbase page
> for Gadus morhua (Atlantic Cod):
> http://www.fishbase.org/Summary/SpeciesSummary.php?id=69
> There is a lot of information on this page and a description of the
> organism can be gleaned from it.
>
> This FloraBase page is another example:
> http://florabase.calm.wa.gov.au/browse/profile/26
> Very brief but attempts to define the taxon.
>
> Wikipedia has a good page for cod but there isn't a good taxon
> description so it is a borderline species page
> http://en.wikipedia.org/wiki/Gadus_morhua
>
> Catalogue of Life has a goal of producing a page for every species and
> it aims to do this by combining pre-existing data I believe but I
> wonder where this data is.
> Their page on badger comes from Arkive (http://www.arkive.org/) which
> is an imaging database http://eol.org/pages/328046 and their page on
> cod comes from Fishbase http://eol.org/pages/206692
>
> Pages I don't consider Species Pages are:
>
> Catalogue of Life has a page that comes from Fishbase but that chucks
> out the "useful" information and only maintains the nomenclature.
> http://www.catalogueoflife.org/show_species_details.php?record_id=5347829
>
> The ITIS page is similar to the CoL page
>
> http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=164712
>
> Likewise Fauna Europaea page for Meles meles (Badger) lacks a
> description because it is a nomenclatural database.
> http://www.faunaeur.org/full_results.php?id=305312
>
> I'd like to build a list of sites offering "real" species page
> information - with descriptions. At the moment it seems like the major
> source of these pages are electronic versions of the literature. We
> have good descriptions in sources like eFloras.org
> http://www.efloras.org/florataxon.aspx?flora_id=5&taxon_id=242417133
> and I hope BHL will be a source. This is a shame as these pages
> typically lack large numbers of images and the possibility of
> including other media.
>
> I'd be grateful for any suggestions of sites that contain species
> pages (as per my definition).
>
> Many thanks,
>
> Roger
>
> BTW: I'd rather use the term "Taxon Page" as these things could apply
> at any rank but there seems to be a consensus to call them Species
> Pages no matter what rank they apply to and people are typically
> interested in species.
>
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>
>
> -- 
> ---------------------------------------------------------------
> Pete DeVries
> Department of Entomology
> University of Wisconsin - Madison
> 445 Russell Laboratories
> 1630 Linden Drive
> Madison, WI 53706
> ------------------------------------------------------------
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>
>
> -- 
> ---------------------------------------------------------------
> Pete DeVries
> Department of Entomology
> University of Wisconsin - Madison
> 445 Russell Laboratories
> 1630 Linden Drive
> Madison, WI 53706
> ------------------------------------------------------------