[DDI-users] Usage of DDI for biomedical research
Karen Harker
ddi-users@icpsr.umich.edu
Fri, 01 Nov 2002 11:25:17 -0600
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Thank you all for your input. I've been reading and saving these emails
to digest them later. It may be a while before we can actually start
planning such a project, but I hope to bring this infofrmation with me
when we do.
Thanks, again.
Karen R. Harker, MLS
UT Southwestern Medical Library
5323 Harry Hines Blvd.
Dallas, TX 75390-9049
214-648-1698
http://www.swmed.edu/library/
>>> ikuo@icpsr.umich.edu 10/31/02 8:57:09 AM >>>
The DDI is the closest I've been able to find, but I am not sure of
its viability to describe the kind of research being conducted here. For
instance, I imagine there will be a need to include the species of
subjects (i.e. humans, drosophila, mouse, etc.), as well as some
extension for microbiological information (i.e. use of microarrays,
types of proteins, etc.).
The species of the subject for the entire study can be placed in the
<subject> tag under <stdyinfo>
<stdyinfo>
<subject>drosophila</subject>
</stdyinfo>
or, as someone suggested, in the <universe> tag under <var> or
<varGrp>
I would probably use <universe> under <varGrp>
Is anybody aware of an application of DDI to biological or biomedical
research?
Thank you very much for your assistance.
Before you apply the DDI to bio research, you should be aware of a few
of its shortcomings:
A) DDI is heavy. There are a lot more tags and attributes in
DDI than you are probably ever going to use.
B) Despite attempts at making the language neutral, the DDI tag
names and attribute names and tag structure still have a bias towards
social science survey data. The unfamiliar terminology will make it
uncomfortable for bio researchers to work with.
C) The current implementation of the DDI is not extensible. You
cannot add your own tags and attributes to the DDI to adapt it for
biological or biomedical research.
What are the advantages of using DDI?
1) DDI is already designed. You don't have to come up with your
own tagging system
2) DDI is a standard
3) There are already a number of (free) tools available to work
with DDI, such as www.nesstar.org NESSTAR PUBLISHER and NESSTAR
EXPLORER. It is likely that more tools will be developed as DDI becomes
more widely adopted.
If I were doing this project, I'd construct a lean XML schema using
bio-science vocabulary but with a structure based on DDI. Then, if I
wanted to use DDI tools like NESSTAR's, I would write an XSLT style
sheet used to convert the bio-science lean XML schema into DDI. In order
make the writing of the XSLT style sheet straightforward, in the design
of the bio-science XML I would keep the structure of the DDI but just
excise all the unnecessary tags and attributes, change some tag and
attribute names to something more appropriate to bio-science, and add
just a limited number of extension tags.
Karen R. Harker, MLS
UT Southwestern Medical Library
5323 Harry Hines Blvd.
Dallas, TX 75390-9049
214-648-1698
http://www.swmed.edu/library/
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<DIV><FONT size=2></FONT>Thank you all for your input. I've been reading and
saving these emails to digest them later. It may be a while before we can
actually start planning such a project, but I hope to bring this infofrmation
with me when we do.</DIV>
<DIV> </DIV>
<DIV>Thanks, again.</DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV>Karen R. Harker, MLS<BR>UT Southwestern Medical Library<BR>5323 Harry Hines
Blvd.<BR>Dallas, TX 75390-9049<BR>214-648-1698<BR><A
href="http://www.swmed.edu/library/">http://www.swmed.edu/library/</A><BR><BR>>>>
ikuo@icpsr.umich.edu 10/31/02 8:57:09 AM >>><BR><BR></DIV>
<BLOCKQUOTE class=cite cite="" type="cite"><FONT size=2>The DDI is the closest
I've been able to find, but I am not sure of its viability to describe
the kind of research being conducted here. For instance, I imagine there will
be a need to include the species of subjects (i.e. humans, drosophila, mouse,
etc.), as well as some extension for microbiological information (i.e. use of
microarrays, types of proteins, etc.). </FONT></BLOCKQUOTE><BR>The species
of the subject for the entire study can be placed in the <subject> tag
under
<stdyinfo><BR><BR><stdyinfo><BR><X-TAB> </X-TAB><subject>drosophila</subject><BR></stdyinfo><BR><BR>or,
as someone suggested, in the <universe> tag under <var> or
<varGrp><BR><BR>I would probably use <universe> under
<varGrp><BR><BR>
<BLOCKQUOTE class=cite cite="" type="cite"><FONT size=2>Is anybody aware of an
application of DDI to biological or biomedical research?
</FONT><BR> <BR><FONT size=2>Thank you very much for your
assistance.</FONT></BLOCKQUOTE><BR>Before you apply the DDI to bio research, you
should be aware of a few of its
shortcomings:<BR><X-TAB> </X-TAB>A)
DDI is heavy. There are a lot more tags and attributes in DDI than you are
probably ever going to
use.<BR><X-TAB> </X-TAB>B)
Despite attempts at making the language neutral, the DDI tag names and attribute
names and tag structure still have a bias towards social science survey data.
The unfamiliar terminology will make it uncomfortable for bio researchers to
work with.<BR><X-TAB> </X-TAB>C)
The current implementation of the DDI is not extensible. You cannot add your own
tags and attributes to the DDI to adapt it for biological or biomedical
research.<BR><BR>What are the advantages of using
DDI?<BR><X-TAB> </X-TAB>1) DDI is
already designed. You don't have to come up with your own tagging
system<BR><X-TAB> </X-TAB>2) DDI
is a
standard<BR><X-TAB> </X-TAB>3)
There are already a number of (free) tools available to work with DDI, such as
<A href="http://www.nesstar.org/" eudora="autourl">www.nesstar.org</A> NESSTAR
PUBLISHER and NESSTAR EXPLORER. It is likely that more tools will be developed
as DDI becomes more widely adopted.<BR><BR>If I were doing this project, I'd
construct a lean XML schema using bio-science vocabulary but with a structure
based on DDI. Then, if I wanted to use DDI tools like NESSTAR's, I would
write an XSLT style sheet used to convert the bio-science lean XML schema into
DDI. In order make the writing of the XSLT style sheet straightforward, in the
design of the bio-science XML I would keep the structure of the DDI but just
excise all the unnecessary tags and attributes, change some tag and attribute
names to something more appropriate to bio-science, and add just a limited
number of extension tags.<BR>
<BLOCKQUOTE class=cite cite="" type="cite"><BR>Karen R. Harker, MLS<BR>UT
Southwestern Medical Library<BR>5323 Harry Hines Blvd.<BR>Dallas, TX
75390-9049<BR>214-648-1698<BR><A
href="http://www.swmed.edu/library/">http://www.swmed.edu/library/</A></BLOCKQUOTE><BR></BODY></HTML>
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