[Tdwg-guid] Demise of Phyloinformatics journal
Robert Huber
rhuber at wdc-mare.org
Wed Nov 29 10:26:13 CET 2006
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
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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
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