[Taxacom] Periodical and book list
Roger Hyam
roger at hyam.net
Mon Jan 22 14:46:03 CST 2007
I replied to Bob's message and forgot to cc the list. Here is a very
slightly altered version of it which kind of addresses Rod's points
as well.
I think an open access reference manager system is a good idea. I
spent some time talking about this with people and consider the first
step would be to get something going for the top level references.
The granularity debate usually follows the line of wanting GUIDs for
articles and then GUIDs for pages (that have been digitized) and how
about GUIDs for paragraphs. Nomenclaturists will often raise the fact
that they need a GUID to point to the paragraph containing the
protolog or other nomenclatural event when there are several on a
page. Or there may be a series of 5 papers that need to be referred
to as a whole such as a monograph published over several years etc. etc.
My thinking is that this is a little like issuing GUIDs for
geographical objects. Firstly we need a general coordinates system to
refer to a place in bibliographic space like a long lat. We can do
this with journal id + volume + part + page. We may then need GUIDs
for named locations within this bibliographic space (most typically
articles). They are parallel systems. The former is easier to set up
and the latter can always be resolved to it. In fact better than in
the geospatial world because the locations are absolute. The
geographic location of Paris is debatable but the location of the
page span of an article is more solid (though I am sure there are
some which are debatable).
So it is the difference between building a coordinate system and
building a gazetteer. I think we should probably build the coordinate
system slightly ahead of the gazetteer simply because it is easier
and enables us to normalize the journals that occur in the gazetteer.
If I resolve a GUID to a protolog I will expect the resulting
metadata to tell me unambiguously where I can find the thing. If I
resolve a whole bunch of GUIDs to protologs I would like my computer
to be able to relate them in some way. Tell me that one resides
inside another or two are adjacent for example. None of this can be
done without a standardized list of journals or standard titles. Much
of it can be done only by standardizing the journals and not
bothering with anything else.
So what we need is a Bibliographic Positioning System (BPS instead of
GPS?) that enables the building of a gazetteer (biblio-names instead
of geo-names?).
Both systems would, of course, map all the different identifiers to
each other. An LSID might return the DOI, ISBN or ISSN and any other
common catalogue number that is available. One could then follow the
DOI to a PDF of a recent document that is only available under
subscription. Also the whole thing would mesh beautifully with the
Biodiversity Heritage Library so another link might take you to a
page image of an out of copyright work and another to a marked up
version of the text.
Lets do it!
Roger :)
On 22 Jan 2007, at 19:55, Roderic Page wrote:
> I think this is a good idea (although I still think if we were
> truly serious we'd look at serving DOIs, they will be picked up by
> publishers, LSIDs probably won't be), but that's another issue.
>
> The complication here is deciding whether two references are the
> same or not. In other words, if say I merge ant literature from two
> different sources (such as FORMIS and Hymenoptera Name Server), can
> I avoid giving two different identifiers for the same reference? We
> would need reasonable means of deciding whether two alternative
> ways of writing the same reference (or variations on journal names,
> or author names) were just that, alternatives.
>
> I also think for this project to be actually useful, it should
> provide a web service where somebody could see whether a given
> paper exists in the database (i.e., has a GUID). OpenURL provides
> an obvious model for a query interface, namely a URL with a
> standard list of parameters. This is how I discover whether ant
> papers already have a DOI (see http://semant.blogspot.com/
> 2006_08_01_semant_archive.html).
>
> So, what I propose is this:
>
> 1. A database of taxonomic literature is created, seed with files
> from anybody willing to contribute.
>
> 2. For all references in that database, existing GUIDs are searched
> for (e.g., DOIs and Handles)
>
> 3. A OpenURL service is created whereby a user can submit
> bibliographic details and the service returns a match (with some
> indication of how good the match is), and a GUID (either existing
> DOI, or whatever type of GUID the database supports.
>
> This would require some work on recognising matching references
> (see http://del.icio.us/rdmpage/bibliographic-references for some
> pointers).
>
> I always thought this would be the quickest, easiest way of
> providing a useful service and demonstrating the utility of GUIDs
> and metadata to the broader community.
>
> Regards
>
> Rod
>
>
>
> On 22 Jan 2007, at 03:21, Robert K. Peet wrote:
>
>>
>> Hi Roger,
>>
>> What we really need is a set of GUIDs for individual references,
>> not just
>> journals/books. At present we have a set of DOI's used by Crossref,
>> endnote-based standards imbedded in EML and VegBank, a simple stub
>> in TCS
>> (for lack of a standard) and ABCD, and any number of standards if
>> you look
>> around. The only way to be able to communciate efficiently is
>> with some
>> GUID system for individual references. My take on the GUID
>> meeting last
>> February at NESCent is that we as a community have pretty much
>> converged
>> on LSIDs, and you seemed to agree. Why don't we just establish an
>> LSID-based reference repository and let folks start contributing
>> their
>> critical references? I would be happy to submit a few thousand,
>> were you
>> to set it up :-) .
>>
>> Cheers,
>> Bob
>>
>>
>> =====================================================================
>> =
>> Robert K. Peet, Professor & Chair Phone: 919-962-6942
>> Curriculum in Ecology, CB#3275 Fax: 919-962-6930
>> University of North Carolina Cell: 919-368-4971
>> Chapel Hill, NC 27599-3275 USA Email: peet at unc.edu
>> http://www.unc.edu/depts/ecology/
>> http://www.bio.unc.edu/faculty/peet/
>>
>> =====================================================================
>> =
>>
>>
>> On Wed, 17 Jan 2007, Roger Hyam wrote:
>>
>>> I am interested in conducting a social experiment.
>>>
>>> It would be very useful when combining taxonomic data from multiple
>>> databases if there were globally unique identifiers for major
>>> taxonomic publications (periodicals/serials and books). One could
>>> then supplement a reference citation like
>>>
>>> Edinb.J. Bot. 47(2): 89-200 (1990)
>>>
>>> with an LSID and/or a URL that will tell the user that
>>>
>>> Edinb. J. Bot. is the Edinburgh Journal of Botany published by HMSO
>>> in Edinburgh. It may also give other alias' it is known by and a
>>> note
>>> might say that it is a continuation of Notes from the Royal Botanic
>>> Garden Edinburgh.
>>>
>>> It would enable the user to merge the data with people who have used
>>> other abbreviations for the same publication title - possibly
>>> without
>>> human interaction.
>>>
>>> Lookup services could be created that went from abbreviation to full
>>> journal title.
>>>
>>> The trouble is that the major lists of publications (e.g. BPH, TL2
>>> etc) are either:
>>>
>>> - are not available electronically.
>>> - are available on a subscription basis.
>>> - are hopelessly out of date.
>>> - can not be added to instantly (if the one you want to use isn't
>>> cited).
>>> - are not freely distributable (i.e. you can't download the whole
>>> lot and use them as a lookup table in your database or re-distribute
>>> them as part of a product or archive them to keep you data safe)
>>>
>>> I am thinking that this is an ideal test case to see if the
>>> 'community' could build a freely distributable list that helps us
>>> all. The list would:
>>>
>>> - only include 'top level' publications i.e. periodicals, books,
>>> multi volume works. It is assumed that it is relatively easy to
>>> unambiguously identify a location within such publications via
>>> volume, part, and page/plate numbers.
>>> - contain a simple set of fields for each publication.
>>> - would be entirely freely distributable. i.e. a complete copy could
>>> be downloaded under a LGPL or creative commons type license.
>>> - contributors would be acknowledged in a contributors list, but
>>> nothing more.
>>> - users could comment on entries and submit new entries in real
>>> time.
>>> - would be a key into/integrate with current and future digitization
>>> efforts.
>>>
>>> I have three questions:
>>>
>>> 1) Has it already been done?
>>>
>>> 2) If this system were available now and populated with the majority
>>> of publications would you use it? Would it be useful?
>>>
>>> 3) Do you (or some one you know) have a database containing details
>>> of titles of periodicals or books that you could export data from as
>>> a contribution to seed the list? If so how many records would there
>>> be and what subject areas (within biodiversity studies) would they
>>> cover?
>>>
>>> You can mail me off list if you don't want to commit to anything in
>>> front of everyone.
>>>
>>> This is still a thought experiment at the moment. I'll mail a high
>>> level summary of replies I get back to the list.
>>>
>>> All the best,
>>>
>>> Roger Hyam
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Taxacom mailing list
>>> Taxacom at mailman.nhm.ku.edu
>>> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>>>
>>
>>
>> ====================================================================
>> Robert K. Peet, Professor Phone: 919-962-6942
>> Department of Biology, CB#3280 Fax: 919-962-6930
>> University of North Carolina Cell: 919-368-4971
>> Chapel Hill, NC 27599-3280 USA Email: peet at unc.edu
>> http://www.bio.unc.edu/faculty/peet/
>>
>> ====================================================================
>>
>> _______________________________________________
>> 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
>
>
>
More information about the Taxacom
mailing list