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[tillea@rki.de: Re: Debtags for medical issues]

Hello,

For the friends in debtags-devel:

I'm forwarding here an interesting thread from debian-med, where they
explore using Debtags.

The main issue is where to put the medical tags, especially, if I
understood correctly, when 'medicine' can be under 'biology' sometimes,
or sometimes 'biology' can be under 'medicine', depending on the
contexts.

My proposed solution would be (as you can imagine) having a separate
'medicine' facet (and in the future a 'genetics' facet, if there is
enough software and someone is willing to maintain it), and let them
nest where suitable according to the tagsets of packages.

If instead we choose to put them into a hierarchy, I'm open to
suggestions on how to do it, because I can't decide.

The only non-controversial item here is the
works-with::image:raster:dicom : when used on his images side it can go
there, or we can have another dicom tag where more appropriate to
symbolise using it for managing patient data.


For everyone:

I'm cc-ing both list to try to have a cross-discussion; if this is not
wanted, please let me know.


Ciao,

Enrico

--
GPG key: 1024D/797EBFAB 2000-12-05 Enrico Zini <enrico@debian.org>
--- Begin Message --- 
On Tue, 26 Jul 2005, Thijs Kinkhorst wrote:


You're probably aware of the Debtags effort, and if not, please see
here: [1] [2]. I think tags are an excellent way to link "our" packages.

Definitely.  I'm in great favour of that and I'll update the CDD documentation
regarding debtags as soon as possible.


I was a bit surprised that no tags for medical applications exist yet,
when I was tagging[3] the ctn package there was no way to indicate it
was Medical Imaging related or even Medical in general.

Some example tags I could imagine:

field::medicine
field::medicine::imaging
field::medicine::dental

I append some more:

 field::medicine::biology  (or should wie use field::medicine::microbiology
 field::medicine::genetics
 field::medicine::devel
 field::medicine::doc
 field::medicine::pharmacy
 field::medicine::physics


But also a tag like:

works-with::dicom

Definitely.


Can we put such a list of tags together and how do we arrange to get it
into the tag collection?

Unfortunately I missed the chance at DebConf to sit down with Enrico to
sort this out.  Enrico, is it OK if we CC you in this thread?

Thanks for your effort (and thanks for hosting mein Utrecht as well - as
you see, I'm back now ;-) )

          Andreas.

--
http://fam-tille.de

--- End Message ---
--- Begin Message --- 
On Wed, Jul 27, 2005 at 09:08:52AM +0200, Andreas Tille wrote:

> >I was a bit surprised that no tags for medical applications exist yet,
> >when I was tagging[3] the ctn package there was no way to indicate it
> >was Medical Imaging related or even Medical in general.
> >Some example tags I could imagine:
> >field::medicine
> >field::medicine::imaging
> >field::medicine::dental
> I append some more:
>  field::medicine::biology  (or should wie use field::medicine::microbiology
>  field::medicine::genetics
>  field::medicine::devel
>  field::medicine::doc
>  field::medicine::pharmacy
>  field::medicine::physics

Sounds great to me.  Could you please also provide a short description
and one or two example packages for each of these tags?

> >But also a tag like:
> >works-with::dicom
> Definitely.

I definitely need a description for this one as well :)  What is dicom
precisely?  If dicom is a raster image format used in medicine, how
about works-with::image:raster:dicom ?


> >Can we put such a list of tags together and how do we arrange to get it
> >into the tag collection?
> Unfortunately I missed the chance at DebConf to sit down with Enrico to
> sort this out.  Enrico, is it OK if we CC you in this thread?

Sure, and thanks for having done it.


Ciao,

Enrico

--
GPG key: 1024D/797EBFAB 2000-12-05 Enrico Zini <enrico@debian.org>

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--- Begin Message --- 
On Wed, 27 Jul 2005, Enrico Zini wrote:


field::medicine

  Description: Anything what is gathered in the Debian-Med project.
  Example packages: All packages named "med-*" and their dependencies and
       which have no more detailed tagging in the following list (for instance
       med-tools and their dependencies because this is kind of "all the rest")


field::medicine::imaging

  Description: Packaged that deal with medical imaging like Dicom viewers etc.
  Example packages: med-imaging and its dependencies


field::medicine::dental

  Description: Dental practice management
  Example: med-dent and odnotolinux (its only dependency)


 field::medicine::biology  (or should wie use field::medicine::microbiology
 field::medicine::genetics

Meta-question to the list: Should we split up these two dependencies?
Currently we have med-bio (only a single package) What do you think?


 field::medicine::devel

  Description: Libraries which help in development of medical applications
  Example: med-bio-dev and med-iamging-dev and its dependencies


 field::medicine::doc

  Description: Packages that provide useful information about free medical software
  Example: med-doc and dependencies (Uhmm, I have to do something about this
           it is quite outdated! :-()


 field::medicine::pharmacy

  Description: Packages which are useful for pharmacy
  Example: med-pharmacy and its dependencies


 field::medicine::physics

  Description: Packages useful for medical physics
  Eaxample: med-physics and dependencies.


Sounds great to me.  Could you please also provide a short description
and one or two example packages for each of these tags?

Please speak up if the things I mentioned above are a little bit to simple.


works-with::dicom

Could the imaging people please be a little bit more verbose here?


I definitely need a description for this one as well :)  What is dicom
precisely?  If dicom is a raster image format used in medicine, how
about works-with::image:raster:dicom ?


Kind regards

        Andreas.

--
http://fam-tille.de

--- End Message ---
--- Begin Message --- 
On Wed, July 27, 2005 11:17, Andreas Tille wrote:
>>  field::medicine::biology  (or should wie use
>> field::medicine::microbiology
>>  field::medicine::genetics
> Meta-question to the list: Should we split up these two dependencies?
> Currently we have med-bio (only a single package) What do you think?

Yes, it makes sense to split these up. A large chunk of the packages
currently under med-bio are genetics-related (sequencing, linkage). So a
tag of field::medicine:genetics would be in order. For any remaining
packages you could use the :biology alternative.


regards,
Thijs

--- End Message ---
--- Begin Message --- 
On Wed, July 27, 2005 10:27, Enrico Zini wrote:
>> >works-with::dicom

> I definitely need a description for this one as well :)  What is dicom
> precisely?  If dicom is a raster image format used in medicine, how
> about works-with::image:raster:dicom ?

A description could be "DICOM (Digital Imaging and Communications in
Medicine) is a standardized format for the exchange of medical images." So
you could indeed rename it as works-with::image:raster:dicom.

If you'd be strict, the DICOM format allows for more than just images,
such as patient data. But the image is the most important part, so it
might be best to put it under image:raster.

This is just one tag I came up with while looking at my own packages. It
would be good if other maintainers from Debian-Med would check their
packages, add existing tags and report here the tags that they would like
to have added but didn't exist yet.


regards,
Thijs

--- End Message ---
--- Begin Message --- 
Enrico Zini wrote:

>On Wed, Jul 27, 2005 at 09:08:52AM +0200, Andreas Tille wrote:
>  
>
>>>I was a bit surprised that no tags for medical applications exist yet,
>>>when I was tagging[3] the ctn package there was no way to indicate it
>>>was Medical Imaging related or even Medical in general.
>>>Some example tags I could imagine:
>>>field::medicine
>>>field::medicine::imaging
>>>field::medicine::dental
>>>      
>>>
>>I append some more:
>> field::medicine::biology  (or should wie use field::medicine::microbiology
>>    
>>
There may be problem here. In Andreas' CDD bioinformatics is a subfield
of biology/microbiology. That is fine, so it is all within medicine. The
problem is the distinction between medically motivated activities and
other that are mere of an organisational necessity or biological. Some
bioinformatics reserach is actually done in medical informatics, other
from within genetics laboratories, and yet others from clinical research
institutes. It is a very thin line here. I am not certain if this
distinction should be made on a higher level. And should it be
field::medicine::biology or rather field::biology::medicine? The latter
would make no sense in the way the CDD is currently been set up.

A field::bioinformatics I would not mind to see, a subfield
field::medicine::bioinformatics, either as an alternative to
medicine::biology, would also make sense to me and would cater more
easily to adapt that to the evolving ontologies of bioinformatics tools
and services within the MyGrid.org.uk and BioMoby.org communities. I do
not think that Debian should address this alone. It would help the
Debian distribution to share such software specification with the
respective communities. Andreas, please consider to mention the tags in
Utrecht, as it is a real hot topic, indeed!!

>> field::medicine::genetics
>>    
>>
Programs designed to aid the analysis of biological processes with data
provided through genetic labs
    r-cran-qtl - linkage analysis for polygenic diseases
ok, it would also get a tag for bioinformatics.


>  
>
>>>But also a tag like:
>>>works-with::dicom
>>>      
>>>
>>Definitely.
>>    
>>
>I definitely need a description for this one as well :)  What is dicom
>precisely?  If dicom is a raster image format used in medicine, how
>about works-with::image:raster:dicom ?
>  
>
Dicom comprises standards for the exchange of medical data between
machines. Raster, yes, also.

Many greetings

Steffen

--- End Message ---
--- Begin Message --- 
On Wed, Jul 27, 2005 at 11:26:06AM +0200, Steffen Moeller wrote:

> distinction should be made on a higher level. And should it be
> field::medicine::biology or rather field::biology::medicine? The latter
> would make no sense in the way the CDD is currently been set up.

This is difficult and interesting: anyone minds if I forward the whole
thread to debtags-devel@lists.alioth.debian.org?

Also, it would be interesting to Cc the thread there as well.


Ciao,

Enrico

--
GPG key: 1024D/797EBFAB 2000-12-05 Enrico Zini <enrico@debian.org>

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--- End Message ---
--- Begin Message --- 
Enrico Zini wrote:

>On Wed, Jul 27, 2005 at 11:26:06AM +0200, Steffen Moeller wrote:
>  
>
>>distinction should be made on a higher level. And should it be
>>field::medicine::biology or rather field::biology::medicine? The latter
>>would make no sense in the way the CDD is currently been set up.
>>    
>>
>This is difficult and interesting: anyone minds if I forward the whole
>thread to debtags-devel@lists.alioth.debian.org?
>  
>
It is a perfect topic for an everlasting flame bait. Please spread it.

I think we can well decide if a single package has something to do with
genetics or bioinformatics or with physics, though we cannot decide,
from the user's perspective, how one domain is related to the other.
Such relationships are however determined by the tools suggesting,
recommending or extending each other. Again, these links will be
bidirectinal no matter what fields:: are being scetched.

Hence, the specialisation of the fields:: classification we should
strive to make irrelevant, creating tools the present the world to the
user as he is likely to perceive it, with dynamic interdependencies on
the basis of the tools that are installed already. Like, a matrix of
all-against-all in terms of debian/control-based interpackage links and
order the tools or the fields 2 or 3dimensionally after principal
component analysis. Sounds like an interesting and fairly quick research
project to me.

Many greetings

Steffen

--- End Message ---
--- Begin Message --- 
On Wed, 27 Jul 2005, Steffen Moeller wrote:


There may be problem here. In Andreas' CDD bioinformatics is a subfield
of biology/microbiology. That is fine, so it is all within medicine. The
problem is the distinction between medically motivated activities and
other that are mere of an organisational necessity or biological. Some
bioinformatics reserach is actually done in medical informatics, other
from within genetics laboratories, and yet others from clinical research
institutes. It is a very thin line here. I am not certain if this
distinction should be made on a higher level. And should it be
field::medicine::biology or rather field::biology::medicine? The latter
would make no sense in the way the CDD is currently been set up.

Well, DebTags are currently not really related to a CDD.  So it can also be
vice-versa as you suggested.  It is a question which should be discussed
at the DebTags list as Enrico suggested.  IMHO the tagging just depends
from your point of view.  If we talk about Books we have to decide in which
shelf (Biology or Medicine) we have to put the book.  But if we talk about
a software package I see no problem in tagging it for both categories.
The sense behind DebTags is that user should find a piece of software.
To let all users find the packages of their interest, they need both fields.
(I hope that I understood the tagging principle right.)


A field::bioinformatics I would not mind to see, a subfield
field::medicine::bioinformatics, either as an alternative to
medicine::biology, would also make sense to me and would cater more
easily to adapt that to the evolving ontologies of bioinformatics tools
and services within the MyGrid.org.uk and BioMoby.org communities. I do
not think that Debian should address this alone. It would help the
Debian distribution to share such software specification with the
respective communities. Andreas, please consider to mention the tags in
Utrecht, as it is a real hot topic, indeed!!

You noticed that I'm *back* from Utricht, right. ;-)
I wanted to give you a quick report, but I had some time constraints ...


Programs designed to aid the analysis of biological processes with data
provided through genetic labs
   r-cran-qtl - linkage analysis for polygenic diseases
ok, it would also get a tag for bioinformatics.
...
Dicom comprises standards for the exchange of medical data between
machines. Raster, yes, also.

So now we dive into some field of library science ...

Kind regards

        Andreas.

--
http://fam-tille.de

--- End Message ---

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