[Taxacom] Periodical and book list
Roderic Page
r.page at bio.gla.ac.uk
Tue Jan 23 05:31:51 CST 2007
I'm not sure I follow this analogy. Surely the relationship between
bibliographic items is a part-whole relationship? An article is part
of an issue, which is part of a journal? A paragraph is part of an
article. The notion of a rather BPS seems a distraction, especially
as bibliographic locations are localised within a publication (unlike
geospatial co-ordinates, which are, literally, global). Perhaps I'm
missing something?
Regarding discovering part-whole relationships, these can be easily
specified by Dublin Core, and indeed providers such as Ingenta
already use this, such as
<meta name="DCTERMS.isPartOf" scheme="URI" content="urn:ISSN:
1063-5157"/>
embedded in the HTML here: http://www.ingentaconnect.com/content/
tandf/usyb/2006/00000055/00000003/art00002
I also think we can simply issue GUIDs for whatever we want, when we
want them, at whatever level is appropriate.
One topic we haven't pursued is creating identifiers. Perhaps Serial
Item and Contribution Identifiers (SICIs) would be useful. They are
used by JSTOR, for example, and are a NISO standard (http://
www.niso.org/standards/standard_detail.cfm?std_id=530). See http://
www.ukoln.ac.uk/bib-man/factfile/standard-numbers/sici/ for a brief
introduction. They might be a useful way to assign identifiers that
could reused in some sense. Put another way, somebody with a list of
references could generate identifiers that somebody else would make
use of, independently of getting the GUID resolution infrastructure
up and running.
I note that BioOne's DOI's are constructed from SICI, for example
doi:10.1206/0003-0082(2006)502[0001:NSAFRS]2.0.CO;2
which is the DOI for
PRENDINI L (2006) New South African Flat Rock Scorpions (Liochelidae:
Hadogenes). American Museum Novitates: Vol. 3502, No. 1 pp. 1–32
0003-0082 is the ISSN for American Museum Novitates
2006 is the date (it can be month and day as well)
502 is the issue number (curiously truncated in this example
0001 is the starting page
NSAFRS is an abbreviation of the title
the rest are codes and checksums. SICI's can incorporate other
information as well.
Regards
Rod
On 22 Jan 2007, at 20:46, Roger Hyam wrote:
>
> 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
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
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>>>> 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
>>
>>
>>
>
----------------------------------------
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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