FW: [tdwg] Drupal and biodiversity informatics
Richard Pyle
Hi All,
I'm sitting in Marseille airport, roughly 12% of the way through my 60-hour
journey home from TDWG. Today's email brought the following (see below).
Note particularly the comment handling bibliographic information. Is anyone
on this list also plugged into that community? It seems we ought to have
some cross-pollenation.
While I'm here, I'll provide a quick summary of (my perspective of) how we
concluded the lit group discussions at TDWG. After a slow(ish) start in the
first session trying to revisit what we had been working on for the past 4-5
years (most of which was mostly dormant), we quickly converged around the
idea of reviewing the EndNote "standard" for citation data exchange. As I
briefly explained in my earlier response to Rod Page's post, this is the
pre-existing standard that Chris (F.) felt came closest to meeting our
community's needs (I'll leave it to him to elaborate on this point, if
anyone would like such elaboration). Have a look at the DTD file that Chris
circulated to see the unmolested template.
We spent the rest of the sessions reviewing this document,
elemetn-by-element and attribute-by-attribute, looking to determine:
1) which elements/attribtues were not of relevance to our approach to
modelling citation metadata; and
2) what bits that we feel are important for biodiversity literature metadata
that were not adequately represented in the extisting DTD file.
Needless to say, we found examples of both. As to the former, if an element
was "mostly harmless" and *might* be of use in an exchange standard, we left
it in there. But if it represnted an ill-defined element that had the
potential for encouraging confusion (e.g., secondary/tertiary
titles/authors; various "custom" and "misc" elements; etc.), then we felt it
should not be included in "our" version of the standard.
As for the second, we did our best to conform as much as possible to the
existing EndNote pseudo-schema, and only add additional sub-elements and/or
attributes to allow more explicit parsing/characterizing information that we
felt was important for an exchange standard in our community. Our
belief/hope is that we will be able to easily transform "our" version into
standard EndNote format via XSLT; but someone knowledgable about such things
will need to drive that.
The general guideline we incorporated for deciding what our exchange
standard needed was to answer the question "is this piece of information
useful for disambiguating duplicates". For the most part, I *think* that's
what we all felt was the most important need, and (again, for the most
part), I think we're right. However, there was one aspect of this that I
realized only after leaving the conference, which I think we need to discuss
more (see next post from me).
As I understand it, the next step is that Anna & Chris (L.) will clean up
and/or merge the various documents & notes we generated during the session,
then post them to this group's "Files" section. I volunteered to then take
on the task of transforming those notes into some formal sort of draft of
what we felt the biodiversity literature standard should be. I will
probably start by simply laying out a vocabulary (of sorts), which we can
then transform into a more structured document (like an XML schema).
I hope that, throughout the coming weeks & months, we will have a very
useful and engaging discussion of how to balance the various specific needs
of our community with the (strong) desire not to reinvent any wheels (and to
maintain as much compatibility as possible with existing standards).
Aloha,
Rich
-----Original Message-----
From: tdwg-b...@lists.tdwg.org [mailto:tdwg-b...@lists.tdwg.org] On
Behalf Of Lisa Walley
Sent: Friday, November 13, 2009 1:34 PM
To: td...@lists.tdwg.org
Subject: [tdwg] Drupal and biodiversity informatics
There is a growing number of biodiversity Web applications being built using
the Drupal content management system (http://groups.drupal.org/node/30444
). The nature of Drupal's modular framework lends itself to collaborative
development. I would like to invite all interested in building or using
Drupal for managing biodiversity data to join the Drupal discussion group
Bioinformatics: http://groups.drupal.org/bioinformatics
.
Up and coming discussions are on improvements to handling bibliographic
information: http://groups.drupal.org/node/35334
If there proves to be enough interest then I hope we can pursue a 'common
data model' for biodiversity data in Drupal. Essentially building common
base content-types that follow the standards outlined by TDWG and compatible
with or possibly even make direct use of EDIT's CDM framework:
http://groups.drupal.org/node/35338
Please invite any interested colleagues to join the discussions.
Kind regards,
Lisa
Lisa Walley
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Dave Roberts
On 14 Nov 2009, at 05:24, Richard Pyle wrote:
> Hi All,
>
> I'm sitting in Marseille airport, roughly 12% of the way through my
> 60-hour
> journey home from TDWG. Today's email brought the following (see
> below).
> Note particularly the comment handling bibliographic information.
> Is anyone
> on this list also plugged into that community? It seems we ought to
> have
> some cross-pollenation.
yes, we've been active with Drupal's bibliography module and EDIT's
literature component, ViTaL, built a harvester that served an
integrated library. That part of ViTaL is currently dormant due to
staff changes.
We (the Scratchpad team) are also tightly linked to the OU group who
are working in this area. Of course, Chris (L) also has a foot in
both these camps.
The Drupal bibliography module has issues and we have not had the
resource to be able to contribute towards resolution. Hopefully we'll
get the ViBRANT grant we're now putting together and that will
increase the resources at our disposal.
Cheers, Dave
--
Dr D.McL. Roberts, Tel: +44 (0)20 7942 5086
Dept. Zoology, Fax: +44 (0)20 7942 5054
The Natural History Museum,
Cromwell Road,
London SW7 5BD
Great Britain Email: d...@nomencurator.org
Web page:
http://scratchpads.eu
http://www.nhm.ac.uk/research-curation/projects/euk-extreme/
--
"You can't just ask customers what they want and then try and give it
to them. By the time you get it built, they'll want something
new." [Steve Jobs, quoted in The Guardian, Technology Section, 25 June
09].
--
Richard Pyle
Thanks, Dave -- this is very helpful! I should have looked at the list of
group members before sending that, and I would have immediately answered my
own question. The important thing is to maintain harmony going forward
among the various efforts.
Aloha,
Rich