[Tdwg-guid] Demise of Phyloinformatics journal
Scott Federhen, NCBI
federhen at ncbi.nlm.nih.gov
Wed Nov 29 17:48:47 CET 2006
Hi all:
We are grappling with the same kinds of issues
here at the NCBI (Library of Medicine) though our mandate
covers the NIH-funded biological literature (as opposed to the
NSF-funded literature) so our archive is weak on systematics and such.
PubMed Central (PMC) is a full-text literature archive, which has
backscanned complete runs of some participating journals, and is also
intended to include all papers published on NIH-funded research.
We have also developed a portable version of this system (pPMC)
which has been used to set up collaborating national archives
in other countries, e.g. UK-PMC.
I just wanted to mention it as a potential model, since it hadn't
come up in the discussion yet.
http://www.pubmedcentral.nih.gov/
http://www.ukpmc.org/
Cheers,
:Scott federhen at ncbi.nlm.nih.gov
GenBank Taxonomy & LinkOut
On Nov 29, 2006, at 4:26 AM, Robert Huber wrote:
> Dear all,
>
> The Phyloinformatics journal shows how easy social contracts can
> fail and formerly trusted archives just
> disappear...
> There are some initiatives which aim to provide standards for the
> preservation and archiving of digital contents.
> For example the OAIS reference model (http://public.ccsds.org/
> publications/archive/650x0b1.pdf) which aims
> to become ISO. Or here in germany the the DINI initiative (http://
> www.dini.de/) and the NESTOR project
> (http://www.langzeitarchivierung.de/index.php?newlang=eng).
> Both german initiatives aim to provide certificates for long term
> archives, I guess similar to the quality standard
> ISO 9001 .
>
> It would be very interesting to me if you knew similar initiatives
> from your countries?
>
> Today, it is impossible to estimate how good the ability of a
> content provider (including taxonomic databases)
> for real long term archiving really is . Certificates could help a
> lot I think, especially if they would require a
> 'fall back strategy' of the candidate archive. Such a strategy
> could simple be to nominate a partner archive
> which would store the content on their servers in case of emergency
> (and resolve the LSIDs in our case).
>
> best regards, Robert
>
> -----Ursprüngliche Nachricht-----
> Von: tdwg-guid-bounces at mailman.nhm.ku.edu [mailto:tdwg-guid-
> bounces at mailman.nhm.ku.edu]Im Auftrag von P. Bryan Heidorn
> Gesendet: Dienstag, 28. November 2006 23:14
> An: Richard Pyle
> Cc: tdwg-guid at mailman.nhm.ku.edu
> Betreff: Re: [Tdwg-guid] Demise of Phyloinformatics journal
>
> It is important to inform the Library of Congress and other
> entities about the special needs of the taxonomic community so
> that they can put the appropriate mechanisms into place. The
> library community solution including, academic libraries, LC and
> its counterparts in other countries do make a fairly survivable
> system that might indeed survive some major upheavals. The
> biodiversity community need not go it alone. It is better to share
> the deeper pockets of nuclear physics, astronomy, and medicine.
> We have unique needs but we can rely on subsystems put into place
> for these other sciences.
>
> Also, currently, going digital does not mean not using paper. For
> the near future it would be good to have a few paper copies of
> important documents along with the digital copy. Also, if we have
> digital copy, at any point in the future, assuming we still have
> trees to make paper, we can decide to abandon the digital systems
> and print out what we want. It is not an either/or decision not and
> will not be in the future either.
>
> On Nov 28, 2006, at 1:40 PM, Richard Pyle wrote:
>
>>
>> I certainly agree with Dave that the technology exists, and I
>> agree with
>> Roger that we seem to be on the right path. My comment about it
>> being "a
>> much bigger issue than our community is able to solve" was more
>> along the
>> lines of ensuring persistence for centuries or millenia. The
>> Library of
>> Congress was appropriated $100 million to deal with this issue
>> (http://www.digitalpreservation.gov/about/index.html), which is a
>> just a bit
>> more than we have access to. The real problem, of course, is that
>> because
>> digital media have existed for only a few decades, we don't have an
>> established track record to say, with adequate confidence, that we
>> "know"
>> how to preserve digital data for centuries or millenia (in the way
>> that some
>> paper-based media have survived for such periods of time). This
>> is why the
>> system along the lines of what we're discussing can only really be
>> thought
>> of as a "pilot project".
>>
>> The fact of the matter is, we don't really need to have confidence
>> that our
>> system is good enough to perservere for centuries. We only have
>> to be
>> confident that it will perservere until technology establishes a
>> system that
>> *will* survive for centuries. If we're lucky, that probably will
>> happen
>> within the next few decades.
>>
>> So...to echo Roger, "the sun is shining and I feel we are heading
>> in the
>> right direction" -- Rumsfeldisms notwithstanding.
>>
>> Aloha,
>> Rich
>>
>> Richard L. Pyle, PhD
>> Database Coordinator for Natural Sciences
>> and Associate Zoologist in Ichthyology
>> Department of Natural Sciences, Bishop Museum
>> 1525 Bernice St., Honolulu, HI 96817
>> Ph: (808)848-4115, Fax: (808)847-8252
>> email: deepreef at bishopmuseum.org
>> http://hbs.bishopmuseum.org/staff/pylerichard.html
>>
>>
>>
>>> -----Original Message-----
>>> From: Dave Vieglais [mailto:vieglais at ku.edu]
>>> Sent: Monday, November 27, 2006 5:08 PM
>>> To: Richard Pyle
>>> Cc: "'\"Döring, Markus\"'"; tdwg-guid at mailman.nhm.ku.edu
>>> Subject: Re: [Tdwg-guid] Demise of Phyloinformatics journal
>>>
>>> I think such a system is quite well within the grasp of this
>>> community- even without any particularly novel new
>>> developments. We have a system for unique IDs (LSIDs) which
>>> can be assigned to each document (actually each combination
>>> of object + metadata). Assuming the documents are stored in
>>> an environment exposed by a protocol such as OAI (Open
>>> Archives Initiative), a harvester could easily retrieve
>>> copies of documents (actually any objects with IDs).
>>> There's nothing to stop the harvester cache being exposed by
>>> the same protocol. With a group of these harvester + OAI
>>> servers, and no limits on subscriptions then each harvester
>>> would have a copy of everything, probably an undesirable outcome.
>>>
>>> Harvester reach could be restricted by queries such as "all
>>> objects of type document" or "all objects published before
>>> 1999" or any other query supported by the metadata. Or,
>>> given the availability of one or more indexers, which index
>>> all the available OAI services, a query such as "all objects
>>> for which there are only 9 copies" could be executed. The
>>> result would be a list of LSIDs that need to be retrieved by
>>> the cache. Of course there will be time lags between index
>>> and harvester states, so there will likely end up being more
>>> than 10 copies of objects per cache, but is that really a problem?
>>>
>>> All the pieces necessary for building such a system already
>>> exist in the WASABI framework - LSID assignment, OAI server,
>>> OAI harvester, indexer, cache.
>>> The only real modification is to adapt the WASABI server to
>>> store objects along with their metadata, but this was kind of
>>> planned to support media objects. I don't mean to preach
>>> WASABIsh here, such a topic has been on my mind for a while
>>> (actually distributed object storage, not just documents).
>>> TAPIR and other protocols would probably work just fine as
>>> well with some modifications.
>>>
>>> It seems pretty simple, but perhaps I'm missing some important
>>> pieces?
>>>
>>>
>>> cheers,
>>> Dave V.
>>>
>>> Richard Pyle said the following on 28-11-2006 09:05:
>>>> Great article, Markus! Very similar to what I had in mind.
>>> I've never
>>>> visited BitTorrent, but I gather that its structure and
>>> function are
>>>> not altogether different from the original Napster. Your
>>> description
>>>> of a system that monitors available copies of any digital
>>> document and
>>>> automatically ensures that a minimum number of copies are extant is
>>>> *exactly* what I was thinking. In my view, there wouldn't
>>> be only one
>>>> "hall monitor" server, but dozens or hundreds (likely
>>> correlated with
>>>> major institutions or hard-core individuals with ample
>>> available storage space).
>>>> And I would probably draw the line for minimum number of copies at
>>>> closer to 100 or so, and also include algorithms to ensure they are
>>>> adequately distributed on geographic scales. Obviously,
>>> GUIDs would be
>>>> a critical component of such a system.
>>>>
>>>> It's a much bigger issue than our community is able to
>>> solve, I think
>>>> -- but certainly we could implement some pilot projects along
>>>> these
>>>> lines for our own data needs, to see how such a system
>>> might work within our context.
>>>>
>>>> Aloha,
>>>> Rich
>>>>
>>>>> -----Original Message-----
>>>>> From: tdwg-guid-bounces at mailman.nhm.ku.edu
>>>>> [mailto:tdwg-guid-bounces at mailman.nhm.ku.edu] On Behalf Of
>>> "Döring,
>>>>> Markus"
>>>>> Sent: Monday, November 27, 2006 5:56 AM
>>>>> To: tdwg-guid at mailman.nhm.ku.edu
>>>>> Subject: Re: [Tdwg-guid] Demise of Phyloinformatics journal
>>>>>
>>>>> Richards post and Napster keyword reminded me of a vague
>>> idea I had
>>>>> for some time to use P2P networks like bittorrent as an persitent
>>>>> storage space. You can read about it a bit more closely here:
>>>>>
>>>>> http://www.pywrapper.com/markus/blog/2006/using-bittorrent-as-
>>>>> a-persistent-storage-space/
>>>>>
>>>>> Don't take it as a real proposal, but I like the general
>>> idea if it.
>>>>> It might even have been done already within the GRID
>>> community. But
>>>>> it conveys the original internet idea of distributing
>>> resources and
>>>>> minimizing impact if a nodes gets lost.
>>>>>
>>>>> A quite nice discussion by the way.
>>>>> Markus
>>>>> --
>>>>> Markus Döring
>>>>> Botanic Garden and Botanical Museum Berlin Dahlem, Dept. of
>>>>> Biodiversity Informatics Königin-Luise-Str. 6-8, D-14191 Berlin
>>>>> Phone: +49 30 83850-284
>>>>> Email: m.doering at bgbm.org
>>>>> URL: http://www.bgbm.org/BioDivInf/
>>>>>
>>>>>
>>>>>> -----Original Message-----
>>>>>> From: tdwg-guid-bounces at mailman.nhm.ku.edu
>>>>>> [mailto:tdwg-guid-bounces at mailman.nhm.ku.edu] On Behalf
>>> Of Richard
>>>>>> Pyle
>>>>>> Sent: Sonntag, 26. November 2006 20:42
>>>>>> To: 'P. Bryan Heidorn'; tdwg-guid at mailman.nhm.ku.edu; 'Taxacom'
>>>>>> Subject: Re: [Tdwg-guid] Demise of Phyloinformatics journal
>>>>>>
>>>>>>
>>>>>>
>>>>>> I only just now read Bryan Heidorn's excellent post on this topic
>>>>>> (below). One thing I would add is that the nature of the
>>>>> internet and
>>>>>> electronic information allow us opportunities to ensure
>>>>> permanence and
>>>>>> access that were either impossible, or prohibitively
>>>>> expensive even a
>>>>>> decade ago. Imagine, for example, an internet protocol
>>>>> that allowed
>>>>>> both institutions and individuals to "plug in" and expose their
>>>>>> digitial catalogs of stored electronic publications (and other
>>>>>> resources) such that the whereabouts of literally thousands
>>>>> of copies
>>>>>> of every electronic publication could be known to anyone.
>>>>> The system I
>>>>>> envision is somewhat of a cross between existing protocols for
>>>>>> interlibrary loan, and the original Napster. Certainly all
>>>>> sorts of
>>>>>> copyright issues need to be sorted out, but these are short-term
>>>>>> problems (less than a century), compared to the long-term
>>>>>> (multi-millenia?) issue of information persistence. The point is,
>>>>>> knowing the whereabaouts of extant copies of digital documents,
>>>>>> coupled with the amazing ease and low cost of duplication
>>>>> and global
>>>>>> dissemination (not to mention plummeting costs of
>>>>> electronic storage
>>>>>> media), would virtually guarantee the long-term persistence
>>>>> of digital
>>>>>> information.
>>>>>>
>>>>>> Any system is, of course, vulnerable to the collapse (or major
>>>>>> perturbation) of human civilization. And the electronic
>>> translator
>>>>>> problem I alluded to in an earlier post cannot be
>>> ignored. But to
>>>>>> pretend that the potential doesn't exist or shouldn't be actively
>>>>>> pursued is pure folly, in my opinion.
>>>>>>
>>>>>> Aloha,
>>>>>> Rich
>>>>>>
>>>>>> Richard L. Pyle, PhD
>>>>>> Database Coordinator for Natural Sciences
>>>>>> and Associate Zoologist in Ichthyology Department of Natural
>>>>>> Sciences, Bishop Museum
>>>>>> 1525 Bernice St., Honolulu, HI 96817
>>>>>> Ph: (808)848-4115, Fax: (808)847-8252
>>>>>> email: deepreef at bishopmuseum.org
>>>>>> http://hbs.bishopmuseum.org/staff/pylerichard.html
>>>>>>
>>>>>>
>>>>>>
>>>>>>> -----Original Message-----
>>>>>>> From: tdwg-guid-bounces at mailman.nhm.ku.edu
>>>>>>> [mailto:tdwg-guid-bounces at mailman.nhm.ku.edu] On Behalf Of P.
>>>>>>> Bryan Heidorn
>>>>>>> Sent: Friday, November 24, 2006 8:22 AM
>>>>>>> To: tdwg-guid at mailman.nhm.ku.edu; Taxacom
>>>>>>> Subject: Re: [Tdwg-guid] Demise of Phyloinformatics journal
>>>>>>>
>>>>>>> The problem and solution has less to do with the Internet
>>>>> and more
>>>>>>> to do with institutional longevity.
>>>>>>> The permanence of paper has less to do with acid free
>>>>> paper and more
>>>>>>> to do with the relative permanence of the institutions
>>> that house
>>>>>>> them. Most paper documents over a hundred years old have
>>>>> been lost
>>>>>>> forever because there were no permanent institutions to
>>> hold them
>>>>>>> until the advent of public and academic libraries. Papers in
>>>>>>> individual scientists collections are discarded when they
>>>>> die. War
>>>>>>> and economic upheavals left paper in rain and fire. It is
>>>>> foolhardy
>>>>>>> to assume that what is on paper is safe.
>>>>>>>
>>>>>>> We know that dissemination of information in electronic
>>>>> form is must
>>>>>>> more economical than paper dissemination. The issue is
>>>>> development
>>>>>>> of proper institutions with adequate stable funding to
>>>>> develop and
>>>>>>> maintain copies into "perpetuity".
>>>>>>> Commercial publishers, are clearly not the answer for
>>>>> preservation.
>>>>>>> Corporations and publishers go out of business all the
>>>>> time. It is
>>>>>>> only because libraries kept paper copies that we still have a
>>>>>>> record.
>>>>>>>
>>>>>>> Digital preservation and access problems exist for all
>>>>> sciences and
>>>>>>> government documents so there is no need to the biodiversity
>>>>>>> community to go it alone on this. We are just in the
>>> beginning of
>>>>>>> the digital publishing history and have not yet
>>>>> established adequate
>>>>>>> preservation mechanisms within libraries to handle data
>>> curation,
>>>>>>> preservation and access in all the situations where it is
>>>>> necessary.
>>>>>>> There are projects underway world wide to address this issue.
>>>>>>> In the United States the Library of Congress The
>>> National Digital
>>>>>>> Information Infrastructure and Preservation Program http://
>>>>>>> www.digitalpreservation.gov/ is one example. The U.S.
>>>>>>> Government agency the Institute of Museum and Library Services
>>>>>>> (IMLS) http:// www.imls.gov/ began grant programs to train
>>>>>>> librarians and museum curators in digital librarianship and most
>>>>>>> recently in digital data curation
>>>>>>> http://www.imls.gov/applicants/grants/
>>>>>>> 21centuryLibrarian.shtm is addressing the education issues.
>>>>>>> The University of North Carolina
>>>>>> http://www.ils.unc.edu/digccurr2007/
>>>>>>> papers.html and the University of Illinois
>>>>> http://sci.lis.uiuc.edu/
>>>>>>> DCEP/ have begun working on best practices and education.
>>>>> This week
>>>>>>> say the successful Data Curation Conference (DCC) in Glasgow,
>>>>>>> Scotland http://www.dcc.ac.uk/events/dcc-2006/. DCC will
>>>>> be running
>>>>>>> "Long-term Curation and Preservation of Journals"
>>>>>>> 31 January 2007. (as an aside, at DCC conference I saw
>>>>> results of a
>>>>>>> survey in "Attitudes and aspirations in a diverse world:
>>>>> the Project
>>>>>>> StORe perspective on scientific repositories" Graham Pryor,
>>>>>>> University of Edinburgh http://www.dcc.ac.uk/events/dcc-2006/
>>>>>>> programme/presentations/g-pryor.ppt that more scientists trusted
>>>>>>> publishers to save their digital documents than their home
>>>>>>> institutions and libraries! It is clear that scientists are
>>>>>>> generally not trained in economics and that the information
>>>>>>> technology management of many institutions must be abysmal!
>>>>>>>
>>>>>>> We need something like to 5 institution rule for distribution to
>>>>>>> apply for digital documents. Digital documents need to be
>>>>> replicated
>>>>>>> as well for both access and preservation.
>>>>>>> Institutions like the Internet Archive help with some of
>>>>> the current
>>>>>>> problems.
>>>>>>> Institutional Repositories (IR) are another. Many
>>>>> universities and
>>>>>>> libraries world wide are beginning these. It is authors'
>>>>>>> responsibility to deposit their publications in these
>>>>> institutions
>>>>>>> and to support their creation. JSTOR and other institutions also
>>>>>>> exist. They all have their weaknesses and additional research,
>>>>>>> development and funding is needed to adequately address
>>>>> the issues.
>>>>>>> Also, all journals need to be managed using good data curation
>>>>>>> principles but al too often the publishers in spite of best
>>>>>>> intentions are not educated in such issues.
>>>>>>>
>>>>>>> Digital publishing of taxonomic literature are not the
>>>>> full answer
>>>>>>> for current poor dissemination of taxonomic literature.
>>>>> The deposit
>>>>>>> of a published name in five institutions is a
>>>>> preservation rule, not
>>>>>>> a dissemination rule. We hurt science and human health
>>>>> is we do not
>>>>>>> at the same time address the information access issue.
>>>>> We need to
>>>>>>> aspire to better dissemination and preservation. Electronic
>>>>>>> publishing will help but only if appropriate institutions
>>>>> in place.
>>>>>>> On the smaller issue, DOIs for publications, electronic
>>>>> or paper is
>>>>>>> a no-brainer. URLs were never designed to be permanent.
>>> URLs were
>>>>>>> designed to be reused and be flexible.
>>>>>>> With DOIs we can place the same paper in multiple digital or
>>>>>>> physical locations and reliably find copies.
>>>>>>>
>>>>>>> Bryan Heidorn
>>>>>>> --
>>>>>>>
>>>>>
>>> --------------------------------------------------------------------
>>>>>>> P. Bryan Heidorn Graduate School of Library and
>>>>> Information
>>>>>>> Science
>>>>>>> pheidorn at uiuc.edu University of Illinois at
>>>>>>> Urbana-Champaign MC-493
>>>>>>> (V)217/ 244-7792 501 East Daniel St., Champaign, IL
>>>>>> 61820-6212
>>>>>>> (F)217/ 244-3302 https://netfiles.uiuc.edu/pheidorn/www
>>>>>>>
>>>>>>>
>>>>>>> On Nov 24, 2006, at 9:54 AM, Renato De Giovanni wrote:
>>>>>>>
>>>>>>>> Rod,
>>>>>>>>
>>>>>>>> Thanks for sharing with us the information. I already
>>>>>> imagined that
>>>>>>>> things like that could happen, but it's always better to
>>>>>>> argue having
>>>>>>>> real examples.
>>>>>>>>
>>>>>>>> Anyway, just in case someone reading the story decides to
>>>>>>> blame URLs,
>>>>>>>> I just wanted to say that in my opinion the main issue
>>>>>> here is not
>>>>>>>> the technology or the GUID format being used. It's the
>>>>>>> business model
>>>>>>>> and the management strategy.
>>>>>>>>
>>>>>>>> I can easily imagine similar things happening to DOIs,
>>>>>>> LSIDs or other
>>>>>>>> kinds of issued GUIDs if the institution(s) behind them simply
>>>>>>>> disappear.
>>>>>>>>
>>>>>>>> Best Regards,
>>>>>>>>
>>>>>>>> Renato
>>>>>>>> --
>>>>>>>> IT Researcher
>>>>>>>> CRIA - Reference Center on Environmental Information
>>>>>>>> http://www.cria.org.br/
>>>>>>>>
>>>>>>>> On 24 Nov 2006 at 13:37, Roderic Page wrote:
>>>>>>>>
>>>>>>>>> The Open Access web-only journal "Phyloinformatics"
>>>>>> seems to have
>>>>>>>>> disappeared, with the Internet address http://
>>>>>>>>> www.phyloinformatics.org now up for sale. This means the
>>>>>> articles
>>>>>>>>> have just disappeared!
>>>>>>>>>
>>>>>>>>> There weren't many papers published, but some were
>>>>>>> interesting and
>>>>>>>>> have
>>>>>>>>> been cited in the mainstream literature.
>>>>>>>>>
>>>>>>>>> This also illustrates the problems with linking to digital
>>>>>>> resources
>>>>>>>>> using URLs, as opposed to identifiers such as DOIs. With
>>>>>>> the loss of
>>>>>>>>> the domain name, this journal has effectively died.
>>>>>>>>>
>>>>>>>>> A sobering lesson...
>>>>>>>>>
>>>>>>>>> Regards
>>>>>>>>>
>>>>>>>>> Rod
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> TDWG-GUID mailing list
>>>>>>>> TDWG-GUID at mailman.nhm.ku.edu
>>>>>>>> http://mailman.nhm.ku.edu/mailman/listinfo/tdwg-guid
>>>>>>>
>>>>>>>
>>>>>>>
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>
> --
> --------------------------------------------------------------------
> P. Bryan Heidorn Graduate School of Library and Information
> Science
> pheidorn at uiuc.edu University of Illinois at Urbana-Champaign
> MC-493
> (V)217/ 244-7792 501 East Daniel St., Champaign, IL 61820-6212
> (F)217/ 244-3302 https://netfiles.uiuc.edu/pheidorn/www
> Online Calendar: http://tinyurl.com/6fd5q
> Visit the Biobrowser Web site at http://www.biobrowser.org
>
>
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