[Taxacom] ITS, Species 2000,[Scanned]

Mary Barkworth Mary at biology.usu.edu
Sun May 27 08:34:59 CDT 2007


Rod and others:
 
If we need GUIDs (and I agree that we do), could we not come up with a
way of assigning them that is logical - then we get moving.  If some yet
to be determined world body then decides other numbers are needed - that
body could link through the taxonomist ids.  I do not know who first
came up with Index Herbariorum, the reference that provides a "GUID" for
herbaria, but it is incredibly useful and probably did not require a big
organization to get started. So how to do this?
 
The only route that I can see is a multi-part number. Currently, many
books and journals have an isbn or issn number. For books, starts with
that, then beginning page number then end page number. Preface material
with negatives? 0-19-515208/0219-0202 is the treatment of Hemerocallis
in FNA26. The slash separates the book isbn from the page numbers.  I
allowed 4 digits for the page numbers.  Journal numbers would have to
allow for volume and issue numbers (and the option of issue numbers
being absent).
 
Some current books/journals do not have isbn/issn numbers - and it
probably costs money to have one.  If we found out how such numbers are
constructed, we could come up with a similar system and preface it with
a P (Provisional) or T (taxonomists' number).  Alternatively, for
journals use some widely accepted (if there is such a thing)
abbreviation as the standard journal name. For botanists there is BPH
(Botanico Periodicum Huntianum) as a system - but its volumes are not
available on line - the data could be made available on line - TROPICOS
and IPNI must have tables that are, in essence, this kind of resource.
So long as one does not copy but merely uses the data, it is not - as I
understand it, violation of copyright. There might be a more appropriate
resource - and you folks working with other organisms need to start
developing something equivalent to BPH. 
 
Past literature: Develop rules, for converting titles to numbers (or use
letters - unless there is some reason that GUIDS cannot contain
characters), then go with the page number bit.
 
OK - this is very simplistic - even I can see problems with it - but we
could get started.   
 
Next step, for those so inclined, or interested, start making
uncopyrighted resources available using the taxonomists guids. Here I
would urge those who have rather good resources for names (MO and IPNI
get my nod for vascular plants and bryophytes), please devise a way so
that taxonomists around the world can contribute to building up the
resource.  For instance, my dearly beloveds are stipoid grasses. There
are many others with a deep affection for this group.  If we, between
us, made available the basic literature - it would help others and start
building a resource. Obviously, people are doing it for themselves, most
are wanting to share what they do - but we keep being told it is
impossible because there is so much ground work to be done.  The result
is paralysis - or waiting for huge global projects.  Let's start
building wooden bridges, using wheelbarrows, but with an awareness that
eventually they will be replaced by bridges of steel, concrete - or
whatever wonderful materials go into today's amazing bridges.  
 
Mary
 
 
 
 
 
 
 

________________________________

From: taxacom-bounces at mailman.nhm.ku.edu on behalf of Roderic Page
Sent: Sun 5/27/2007 3:29 AM
To: Paul Kirk
Cc: TAXACOM
Subject: Re: [Taxacom] ITS, Species 2000,[Scanned]



There are two issues here, the first is having global identifiers 
(GUIDs) for literature, the second is accessing that literature.

GUIDS give us some useful things:

1. If we have the same GUID we are talking about the same thing

- this is a step forward compared to trying to figure out if two 
bibliographic citations (written in different formats) are, in fact, 
the same. This is a major issue for databases -- if they store GUIDs 
for references they become much more interoperable.

2. Given a GUID I can get metadata abut a reference

- CrossRef provides a tool for harvesting metadata about a DOI, which 
makes assembling bibliographies easier


In my view these are important. By having GUIDs it means you and I 
can work independently (say, by assembling links between names and 
literature, then combine and merge that information simply by 
combining and merging GUIDs. This makes working in a distributed 
fashion possible.

And it also means that I can't wait for these GUIDs. They underpin 
everything that I need to do (and, I suggest, much of what 
biodiversity informatics aspires to create).

Regarding access, that is a completely separate issue (and even in my 
ivory tower I don't have full access to everything in JSTOR). 
However, I suggest that knowing that an electronic copy of the work 
is available is at least a small step. BHL will not help matters 
much, unless it goes after post 1923 stuff. I also think what 
organisations like BHL, GBIF and EoL should think about is targeting 
the huge amount of small museum and society literature that could be 
digitised. Some of these journals (such as Psyche http://
psyche.entclub.org/ or the Raffles Bulletin of Zoology) are online, 
but many aren't. I suspect there is much of value to be had in this 
material.

Regards

Rod







On 27 May 2007, at 09:58, Paul Kirk wrote:

> ITIS might have 8% of publication references which will link to 
> DOIs but what use are these links if the full text is sat behind 
> pay-to-view resources like JSTOR ... fine in the ivory towers of 
> Glasgow which presumably has a subscription but about as useful as 
> an inflatable dartboard to many who use the CoL in most of the rest 
> of the world who, like me, would find such a situation rather 
> frustrating. Far better to wait until these references are free 
> (BHL ... please lets have resolvable URL to the page images OUTSIDE 
> the human interface) than spend time building these links to 
> inaccessible resources.
>
> Paul
>
> p.s. Index Fungorum has about 12000 (4% of names) linked to page 
> images (in a open archive) where original descriptions of names can 
> be read and about 40% to the entry in the various printed indexes 
> (50% of these with the original description and other data).
>
> From: taxacom-bounces at mailman.nhm.ku.edu on behalf of Roderic Page
> Sent: Sun 27/05/2007 08:59
> To: TAXACOM
> Subject: Re: [Taxacom] ITS, Species 2000,[Scanned]
>
> Mary Barkworth wrote
>
> > We do ourselves a disservice by presenting opinions as facts. I also
> > dislike the idea that we are, de facto, being told that there is a
> > body
> > that will make the taxonomic decisions for the world.  At least 
> state
> > real sources for a taxonomic judgement, which I hope are published
> > treatments, not the faceless ITIS - which Outlook keeps wanting to
> > make
> > "IT IS" ;-).
>
> I agree, and have grumbled about how the Catalogue of Life handles
> literature (http://iphylo.blogspot.com/2007/05/catalogue-of-life-
> openurl-and-taxonomic.html) -- basically they've rendered the
> available literature links nearly useless. Databases such as CoL and
> ITIS would be of greater value if they linked to original literature
> explicitly. AS an exercise I mapped publications in ITIS to DOIs, and
> around 8% can be linked to DOIs (the full list is here: http://
> linnaeus.zoology.gla.ac.uk/~rpage/itis/ ). I suspect a lot more names
> in ITIS could be linked to original sources.
>
> Rich Pyle wrote:
>
> >
> > Wouldn't if be cool if all of these datasets were interconnected in
> > a way
> > that not only allowed the algorithmic analysis I described in my
> > previous
> > post to alert these "meta-authorities" when one of their
> > declarations about
> > synonym or classification deviated substantially from the collective
> > literature, but also exposed the data in such a way that made it
> > very easy
> > for taxonomists to provide instant feedback?  I bet we could
> > develop such an
> > infrastructure -- it would probably take about ten years and cost
> > about $50
> > million; but DAMN it would make my job as taxonomist much easier!
> > We just
> > need to think of a catchy name, with a simple three-letter 
> acronym....
>
>
> I don't think this needs anything like $50 M. A simple start is to
> take uBio RSS feeds (http://www.ubio.org/index.php?pagename=ubioRSS),
> extract literature linked to names, and for each name in a database
> flag whether it has been mentioned. By itself this would be a start.
>
> I've always felt that one of the simplest things the taxonomic
> community could do would be to assemble a central bibliography of
> taxonomic works, each assigned a GUID (DOIs, Handles, or persistent
> URLs), and where ever possible linked to an electronic version of the
> paper. Sounds a monumental task, but I suspect it is easier than
> people might think.
>
> Regards
>
> Rod
>
>
>
> ----------------------------------------
> Professor Roderic D. M. Page
> Editor, Systematic Biology
> DEEB, IBLS
> Graham Kerr Building
> University of Glasgow
> Glasgow G12 8QP
> United Kingdom
>
> Phone: +44 141 330 4778
> Fax: +44 141 330 2792
> email: r.page at bio.gla.ac.uk
> web: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
> iChat: aim://rodpage1962
> reprints: http://taxonomy.zoology.gla.ac.uk/rod/pubs.html
>
> Subscribe to Systematic Biology through the Society of Systematic
> Biologists Website: http://systematicbiology.org
> Search for taxon names: http://darwin.zoology.gla.ac.uk/~rpage/portal/
> Find out what we know about a species: http://ispecies.org
> Rod's rants on phyloinformatics: http://iphylo.blogspot.com
> Rod's rants on ants: http://semant.blogspot.com
>
>
>
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----------------------------------------
Professor Roderic D. M. Page
Editor, Systematic Biology
DEEB, IBLS
Graham Kerr Building
University of Glasgow
Glasgow G12 8QP
United Kingdom

Phone: +44 141 330 4778
Fax: +44 141 330 2792
email: r.page at bio.gla.ac.uk
web: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
iChat: aim://rodpage1962
reprints: http://taxonomy.zoology.gla.ac.uk/rod/pubs.html

Subscribe to Systematic Biology through the Society of Systematic
Biologists Website: http://systematicbiology.org
Search for taxon names: http://darwin.zoology.gla.ac.uk/~rpage/portal/
Find out what we know about a species: http://ispecies.org
Rod's rants on phyloinformatics: http://iphylo.blogspot.com
Rod's rants on ants: http://semant.blogspot.com



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