[Taxacom] ITS, Species 2000,[Scanned]

Roderic Page r.page at bio.gla.ac.uk
Sun May 27 13:52:16 CDT 2007


On 27 May 2007, at 14:34, Mary Barkworth wrote:

> 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).


For journal articles one obvious candidate is the SICI (see http:// 
del.icio.us/rdmpage/sici for some links). It is a multipart number  
along the lines you suggest, and is used already by JSTOR. At a  
minimum it comprises an ISSN, a date of publication, volume number,  
and a starting page. It can contain additional information if available.

An example SICI is: 0026-6493(1988)75:4<1180:CDVAPP>2.0.CO;2-V

which corresponds to this paper: http://links.jstor.org/sici? 
sici=0026-6493(1988)75:4<1180:CDVAPP>2.0.CO;2-V


The "CDVAPP" part is constructed from the title of the paper. Note  
that we don't need all the bibliographic information to construct a  
SICI, just the ISSN, year, volume, and starting page will work as well.

>
> 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.

As far as I can tell, it costs nothing to obtain an ISSN (see http:// 
www.bl.uk/services/bibliographic/issn.html for example). Each country  
has it's own agency for assign ISSNs. It seems that an obvious thing  
for BHL to do would be to get ISSNs assigned for all taxonomic  
journals that lack them, either by applying for one itself, of if the  
journal is still being published, contacting the publishers to  
encourage them to arrange for one.

I think ISSNs are much more powerful than lists of standard names for  
journals. For exmaple, there are services that can return journal  
details based on ISSNs.


>
> 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.

I'd suggest using SICIs.

There are also BICIs for book parts (i.e., chapters, see http:// 
del.icio.us/rdmpage/bici ).


>
> 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.


I share your feeling that paralysis is the usual response. What  
continually astounds me is how little people are aware of the  
groundwork that already exists. Most of the issues (GUIDs, generating  
identifiers, searching based on journal metadata) have already been  
solved, in some cases (SICIs, OpenURL) a decade ago.

I think one approach would be a tool rather like Scribd (http:// 
www.scribd.com/) where we could simply upload PDFs and some basic  
bibliographic metadata (enough to generate a SICI). This tool would  
also support searching for a reference based on metadata, which would  
in turn facilitate linking lists of references to digital copies.

Regards

Rod

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

----------------------------------------
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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