[DDI-users] Usage of DDI for biomedical research
I-Lin Kuo
ddi-users@icpsr.umich.edu
Thu, 31 Oct 2002 09:57:09 -0500
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>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/>http://www.swmed.edu/library/
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<br>
<blockquote type=cite class=cite 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 type=cite class=cite 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 type=cite class=cite 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>
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