[Taxacom] iSpecies with Wikipedia

Roderic Page r.page at bio.gla.ac.uk
Tue Mar 25 16:29:20 CDT 2008

Dear Andy,

Thanks for the comments, most appreciated. My responses are inserted  

On 25 Mar 2008, at 18:46, Andy Mabbett wrote:

> I think that's an excellent move; though there are some bugs; and some
> potential features you might add.
> For instance, it works for both "Pica pica" and "magpie", and for  
> "Tyto
> alba", but not "barn owl".

Although I might not explicitly state it, I only ever intended  
iSpecies to hand bionomial names. It can return results for common  
names, but this more accidental than anything else. In the same way,  
I don't check whether the search string is actually a scientific  
name. I could do this via uBio, althouh it doesn't have all names (yet).

> In another case, searching for just "pica" returns:
>         Pica can refer to:
>                 * Pica (unit of measure), in typesetting and document
>                 layout
>                 * Pica (disorder), abnormal appetite for earth and  
> other
>                 non-foods
>                 * Pica (genus), a genus of magpie
>                 * Pica Press, a publishing imprint
>                 [...]
> Likewise, the result for "Hobby" is not appropriate. Perhaps it  
> would be
> a good idea if you tested for the presence of a taxobox, and, if  
> none is
> present, dropped the inclusion, or searched further using some form of
> heuristic?

I'll take a look at handling the disambiguation pages (which is what  
you get for "Pica"). This is likely to be a pain. It's unlikely to be  
a big issue for binomial names (unless Wikipedia has some bionomial  

> The GBIF map for "pica pica" shows all but one example as being in  
> South
> America (the other is in Africa - possibly a wrongly-signed  
> longitude?).

No idea, iSpecies simply displays what GBIF has. Some locality  
records are clearly false (marine organisms on land, and visa versa)  
and at some point somebody will hopefully do something about these  
(see http://iphylo.blogspot.com/2007/11/gbif-data-evaluation.html ).

> You don't yet mention Wikipedia on your "how it works" page.

True, this was done in a hour or so before going in to work (i.e.,  
not polished).

> The image searches for a genus (e.g. "Pica") or common name (e.g.
> "Hobby") are often mostly or all false-positives. You might like to  
> add
> a Flickr image search, too. There are several ways in which you  
> could do
> this, including searches for plain text search, tags or machine-tags
> (e.g. "taxonomy:genus=Pica", "taxonomy:binomial=Alcedo_atthis"). The
> latter would limit false positives. I'm happy to advise further if
> required, though I note we discussed machine tags in early February  
> this
> year.
> You could also search for images on Bioimages:
>         <http://www.bioimages.org.uk/>
> which uses Google for as a search engine; for example::
>         <http://tinyurl.com/34ue8k>

As above, I only ever intended iSpecies to search for bionomials.

I may add Flickr, but not Bioimages. I need APIs, and Bioimages  
doesn't have one, which is why I use Yahoo image search. IMHO this is  
the big obstacle to mashing up data -- the lack of web services.

> Other possible links would be to the relevant entry on The National
> Biodiversity Network's Species Dictionary:
>         <http://nbn.nhm.ac.uk/nhm/>
> and WikiSpecies:
>         <http://species.wikimedia.org/>

Wikispecies is almost useless, and I don't want to make "blind  
links". The links iSpecies does report are from NCBI's LinkOut  
service, so there's a good chance they exist and are relevant.

> The long list of links above the map needs to be marked up as a list,
> and presented as with bullets or similar. Likewise, the list of  
> articles
> from Google.

I've finally gotten around to making the NCBI Linkout links a list,  
but I won't do this for the literature just yet (I've got other  
things to do there first).

> Please use a DOCTYPE declaration (preferable HTML 4.01 STRICT), and
> validate your HTML - watch out especially for unescaped ampersands.

Validating Javascript-laden HTML is no fun, and not a priority right  

> It would also be sensible to use more human-friendly URLs (which could
> also then be used for tags); so that, for example:
>   http://darwin.zoology.gla.ac.uk/~rpage/ispecies/pica+pica
> would do what is currently done by:
>   http://darwin.zoology.gla.ac.uk/~rpage/ispecies/?q=pica 
> +pica&submit=Go

Good idea, I'll look at adding this.

> I've mentioned the species microformat previously; it would be
> appreciated if you could also use that in your pages. Again, I'm happy
> to advise further.

Not yet convinced these are useful. I'm experimenting with hCard and  
other formats in another context, but without applications that make  
use of them there's not much point.



> -- 
> Andy Mabbett
> _______________________________________________
> Taxacom mailing list
> Taxacom at mailman.nhm.ku.edu
> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom

Professor Roderic D. M. Page
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