[Taxacom] RSS feeds for new (or newly digitised) names
Roderic Page
r.page at bio.gla.ac.uk
Fri May 8 06:26:22 CDT 2009
Dear Wolfgang,
On 8 May 2009, at 11:23, faunaplan at aol.com wrote:
>
> Wouldn't the task of creating better access to biodiversity
> information be much easier if we had the following work steps:
>
> - a master index of all publications with DOIs and - on my wishlist
> - also with human-readable unique handles (e.g., 'Smith, A. & Jones,
> B. 1900a').
A master index would be great, but human readable handles such as
'Smith A & Jones B, 1900a' would be a mistake, unless they were
supported as search terms, not as identifiers. Identifiers need to be
simple things that people can't muck with (i.e., there should be only
one way to write them). I think there's a lot of confusion between
having a useful identifier and having a service to return identifiers.
Using 'Smith A & Jones B, 1900a' as an identifier is problematic, but
having a service that lists possible matches to 'Smith A & Jones B,
1900a' would be very useful.
As a discipline we still handle literature as if it didn't exist
digitally (and the good news is a lot more is online than many realise)
>
>
> - a master index of all available nomina, urgently needed to work
> through the fast growing mess of misspellings, phantom names, and
> homonymies.
uBio made major progress towards this. It's incomplete (and not being
updated, which is a major problem)
>
>
> - default classifications (checklists) where we could resolve the
> subjective synonymy of nomina (tags) at least for the purposes of
> achieving overview.
Again, uBio went some way to this. Perhaps we need a service that
takes a name and returns a list along the lines of:
ITIS accepts this name
NCBI thinks it's a synonym
WoRMs accepts it
etc
>
>
> - a "catalogue"-style index of the applied accepted nomenclature as
> it is found in the publications. There is a long tradition of
> printed catalogues doing exactly this: the cataloguer selected his
> own set of accepted taxonomic names (or relying on a default
> classification) and from that point creating a view on previous
> publications with citation of the applied names in each publication.
> View without having a clear point of view =chaos.
>
>
> In my opinion, the "crisis in taxonomy" feeling among biodiversity
> informaticians is mainly caused by an unclear distinction between
> nomenclature as an instrument (tag system) and the applied
> nomenclature (application of names as tags for taxonomic concepts.
> Isn't it a bit like the difference between software and the
> application of software?).
> Here is a typical example why we should make the distinction: a name
> as a tag is principally unambiguous because it is fixed to a unique
> type specimen (or can be restricted20to that), - however, the
> original first application of this name to a taxonomic concept can
> indeed be ambiguous! (talking about zoological names in
> particular, ... botany has some fundamental differences which are
> not applicable to zoological nomenclature).
I agree that names are basically tags that we apply to information,
and then we make some judgement about whether things with the same tag
are, in fact, the same thing.
>
>
> Currently we only have fragments of the above infrastructural
> elements. There is
> - no master index of publications. Still it's extremely time-
> consuming to find individual works contained in the legacy
> literature digitized on biodiversitylibrary.org etc.
Yep. BHL is making a lot of progress, but finding stuff in BHL is hard
work as they don't support article-level searching (although they are
working on this). I think one issue is there are several perspectives
on literature:
- nomenclators, for whom the individual page is the unit of interest
- librarians, who have sometimes bizarre notions of what is useful
metadata about a publication (rooted in physical objects)
- publishers, for whom the modern unit is the (digitised) article
These combine to create a mess.
>
> - by far no complete index of names (zoology= lion's share!)
> available as tags for taxonomic concepts. So far, ZooBank is just
> collecting applied nomenclature but does not focus on the available
> name strings (tags).
> - only a few taxonomic checklists fit-for-use as a standard basis...
So, the real task here is to figure out how we make progress. There
are lots of people working in this area, but I think there are
obstacles, much of it rooted in the lack of access to data, and the
lack of tools to fix the obvious errors.
If we dumped everything we had into a wiki, and let the community
clean/annotate/fix/add to it, I think we'd resolve a lot of these
issues...
Regards
Rod
>
>
> Cheers,
> Wolfgang
> -------------------------------------
>
> Wolfgang Lorenz, Tutzing, Germany
>
>
>
>
>
>
>
>
>
> -----Ursprüngliche Mitteilung-----
> Von: Roderic Page <r.page at bio.gla.ac.uk>
> An: Taxacom <taxacom at mailman.nhm.ku.edu>
> Verschickt: Do., 7. Mai. 2009, 14:04
> Thema: [Taxacom] RSS feeds for new (or newly digitised) names
>
>
>
>
>
>
>
>
>
>
> Dear All,
>
> I've been exploring the idea of a service that integrates RSS feeds
> containing information on biodiversity (broadly defined). A bit like
> uBio's RSS ( http://www.ubio.org/index.php?pagename=ubioRSS ) but with
> additional types of information. In order to make tis happen I need to
> create feeds for databases that don't have them, and some of these may
> be useful beyond my own muckin
> g around with data integration.
>
> You can see the list of feeds at http://biogid.info/rss
>
> At present they include a ZooBank feed (listing latest items added
> there) and feeds for each plant family in IPNI (listing plant names
> added in the last 30 days) You can view the feeds in a feed reader, or
> in most modern web browsers. Where possible I include links to digital
> literature (e.g., through DOIs), but this is not easy (see my
> obligatory rant http://iphylo.blogspot.com/2009/05/nomenclators-digitised-literature-fail.html
>
> ).
>
> I hope to add some more feeds in the coming weeks.
>
> Regards
>
> Rod
>
>
>
> ---------------------------------------------------------
> Roderic Page
> Professor of Taxonomy
> DEEB, FBLS
> Graham Kerr Building
> University of Glasgow
> Glasgow G12 8QQ, UK
>
> Email: r.page at bio.gla.ac.uk
> Tel: +44 141 330 4778
> Fax: +44 141 330 2792
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> Blog: http://iphylo.blogspot.com
> Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
>
>
>
>
>
>
>
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---------------------------------------------------------
Roderic Page
Professor of Taxonomy
DEEB, FBLS
Graham Kerr Building
University of Glasgow
Glasgow G12 8QQ, UK
Email: r.page at bio.gla.ac.uk
Tel: +44 141 330 4778
Fax: +44 141 330 2792
AIM: rodpage1962 at aim.com
Facebook: http://www.facebook.com/profile.php?id=1112517192
Twitter: http://twitter.com/rdmpage
Blog: http://iphylo.blogspot.com
Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
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