RDF query and inference in a distributed environm ent

Patricia Mergen p_mergen at YAHOO.COM
Wed Jan 4 08:16:56 CET 2006

Dear Colleagues

  Yes I agree with Chuck that we have to be carefull here.

  For example providers have agreed to make their data public by  providing it to GBIF, but are not aware what this really implies. Most  of our providers are for example very pleased to have now their  georeferenced data so easy and nice in google earth others are not  because of the lack of precision or the fact that apparently some  center of areas are shown fasely as too precise sampling points.

  The same reactions of lost of control or "where does my data show up  and how" will certainly come with mirrors, caching or "central" GUID  attributions.  Before suggesting anything official as a GUID and  GUID system,  I agree with Chuck that  we should  be  aware  of  political  implications and  maybe  misinterpretation of our purely technical purposes.  I guess there  will  be some "legal" documents  needed to   negociate  and  agree  in advance  in form maybe as  an extension to GBIF data users and providers agreements ?


Chuck Miller <Chuck.Miller at MOBOT.ORG> wrote:                  v\:* {behavior:url(#default#VML);} o\:* {behavior:url(#default#VML);} w\:* {behavior:url(#default#VML);} .shape {behavior:url(#default#VML);}                    st1\:*{behavior:url(#default#ieooui) }                    Querying a central database is certainly  technically easier and more responsive than distributed data. Mirroring servers  is mature technology.  And, disk drives get cheaper every day.

    But, in addition to the social, technical  and financial factors that limit the ability to implement distributed caches or  full mirrors there is also the political factor, which GBIF has spent great  effort successfully addressing.  As a global entity, GBIF cannot exist  without the political support from its members that leads in turn to financial  support.  Most of the members of GBIF are sovereign nations who seek to  preserve and protect their country&#8217;s assets.  Some protect more than  others.

    To cache or mirror data in multiple  locations, the dilemma lies in the simplest question: &#8220;Where is my data?&#8221;   A cache or mirror from a technologist&#8217;s perspective is just a  technical trick, identical to the original, dependent upon the master version,  no big deal.  But, simplistically, the data may be actually located in  another country, no matter how it got there, and some politicians could  misconstrue the whole thing, if not properly negotiated and agreed upon in  advance.  In my experience, negotiating such agreements is more work than  the technical development.

    I think the distributed nature of DiGIR  was critical to selling it at the start of GBIF.  The original design assured  providers that their source data would &#8220;stay&#8221; in their country and  not be wholesale copied somewhere else.  It&#8217;s hard to say what the political  effect of creating mirrors would be.

    Chuck Miller
    Missouri Botanical Garden


    From: Patricia Mergen  [mailto:p_mergen at YAHOO.COM]
  Sent: Wednesday, January 04, 2006  5:38 AM
  Subject: Re: [TDWG-GUID] RDF query  and inference in a distributed environment

        Dear Rich

  Richard Pyle  <deepreef at BISHOPMUSEUM.ORG> wrote:
    Hi Patricia,

  Many thanks for the feedback (and thanks also to Bob -- who I neglected to
  thank in my previous post).

  What do you reckon would be the limiting social and financial factors for
  full mirrors? In social terms, if I'm going to expose my data to the world
  anyway (e.g., via DiGIR), then I don't see why I would be socially reluctant
  to allow others to mirror the data (provided robust syncronization protocols
  are in place -- see my previous response to Bob; and provided data
  "ownership" credentials are embedded within the core metadata).

       I agree with you about the logic in this. However  accoding to my daily experience with potential dataproviders there is a lot of  teaching and conviencing needed to make this logic accepted that this does not  result in the loss of control over own data. I agree that to be conviencing a  robust syncronization is needed.

  As for financial, I prefaced my original post with the observation of ever
  decreasing $/GB for storage space. I suspect that, before TDWG nails down
  the GUID protocols, entry-level web servers (of the sort that even the most
  modest DiGIR provider would need to establish) will come with nearly a TB of
  disk storage space by default. Perhaps the cost of bandwidth will be a
  limiting factor? Or maybe DB software capable of managing such large

       I agree that for machines and storage it is not that  expensive. I was     more referring to the human ressources  needed to manage the     mirror. Smaller institutions do not  have necessary the funds or cannot justify to their hierachy that staff is  devoting time to maintain a full miror containing mainly "references"  to information coming from other institutions, but it is easier to justify the  time spent to contribute to the whole with the part concerning directly the  institution ...

  As for IPR -- well, ultimately that applies mostly to specimens. And again,
  assuming that "ownership" metadata remains intact, I see no basis for
  increased apprehension about allowing mirrored copies of data records (as
  GBIF already does, for example) over and above exposing them in the first

  Yes I agree with you here too, but as said before this need teaching and  convincing ...

  Personally, I don't think the social, legal, or financial barriers are
  significantly greater for a mass-mirror paradigm than they are for
  distributed complementary data sets. I suspect the major barriers will be
  more technical (i.e., those aforementioned "robust syncronization

  Yes I agree with you that robust syncronization will be needed but as my IT  colleague always remind me, I guess we must not forget that setting up an IT  infrastructure is most of the time 10 % technical issues to be solved and 90%  of the time solving "human problems and barriers" to make it work and  accepted ...



  -----Original Message-----
  From: Taxonomic Databases Working Group GUID Project
  [mailto:TDWG-GUID at LISTSERV.NHM.KU.EDU]On Behalf Of Patricia Mergen
  Sent: Tuesday, January 03, 2006 10:31 PM
  Subject: Re: RDF query and inference in a distributed environment

  Dear Richard

  I agree with you that several mirror copies will and are needed, preferably
  well spread geographically as back-ups. This is exactely the approach of
  GBIF, as they are now in the process to mirror their services.

  However as highlighted by Bob Morris their is are social, but also financial
  barriers to have all contributing institutions run a "full" mirror.  In order
  to insure the participation of all those who are willing to, I believe that
  a distributed system where each provider can participate with his part
  should be kept. Those who have the ressources could of course set up full
  mirrors if this match their needs and if this is allowed by the providers
  (there are also IPRs issues which may be raise here by some institutions).


  Richard Pyle wrote:
  > Long term what I think might happen is that users have their own triple
  > stores, and as they do queries the results get added to their own
  > triple store and they can make inferences locally that they are
  > interested in. MIT's Piggy bank project
  > (http://simile.mit.edu/piggy-bank/) is an example of this sort of
  > approach.

  With hard drive sizes spiraling skyward, and $/GB ($/TB) spiraling
  downward.... I'm wondering whether or not the "distributed" system  that
  serves us best might be "distributeded mirror copies", rather than
  distributed complementary data. I've been pushing this approach for
  taxonomic data for a while, but perhaps it would be useful for other shared
  data as well (geographic localities, people/agents, publications/references,
  etc.) Even for specimen data -- where "ownership" is unambiguous --  it
  seems that as long as the ownership is clearly embedded in the core
  metadata, there are more fundamental advantages in storing and serving data
  from multiple data resources, rather than serving it from only one single
  data resource.

  One way to look at it would be "robust caching", with automated  update
  capabilities. The main benefits would be:

  1) Large-scale distributed backup of the world's biodata (ensuring
  perpetuity across a changing technological landscape);
  2) Performance and reliability enhancement for local data authority needs;
  4) Essentially 100% data availability (like DNS), regardless of which
  servers are up or down at any given moment;
  3) Maximization of distributed work/effort for data "maintenance and

  The point is, the technology discussions would focus less on issues of
  distributed queries, and more on issues of replication/synchronization and
  data edit authorization protocols.

  Perhaps this would be reaching too far, too soon. But on the other han d, I
  don't see why implementing a "distributed mirror" system would be any  more
  technically, financially, or socially challenging than implementing a
  distributed query system for distributed data.


  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

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