Which DebTag for Debian-Med ?

[Steffen Moeller]

Hi Charles, Thijs, Andreas and the rest,

On Monday 08 January 2007 10:41, Thijs Kinkhorst wrote:
> Hi Charles and the rest,
> On Mon, 2007-01-08 at 17:46 +0900, Charles Plessy wrote:
> > +
> > +Tag: suite::debian-med::bio
> > +Description: med-bio
> > + This package is installed, recommended or suggested by the med-bio
> > metapackage.
[...]

> I do not think that "suite" is the right choice, tagging with "field" is
> much more useful; as you can see, under "field" are such fields as
> astronomy, biology and chemistry already available. Adding
> "field::medicine" would be useful to me, and to put subclasses of
> medicine below it:

If I'd have a veto then I would use it against a very early suggestion of 
field::medicine::bio(logy).

> examples:
>
> 	field::medicine:pharmacy
fine
> 	field::medicine:imaging
I do not like this one as imaging is a technology rather than a subfield like 
vets or pharmacy. Radiologists, dermatologists and many other disciplines 
have tons of images. But admittedly I do not see a way around it, really, as 
we are all used to talk about "medical imaging" as a field.
> 	field::medicine:practice
fine, I would not mind "information systems" instead of practice, though.
> 	field::medicine:veterinary
fine

For fields::biology I see be the subfields

fields::biology::sequence
fields::biology::sequence::dna
fields::biology::sequence::rna
fields::biology::sequence::protein
fields::biology::structure
fields::biology::interaction
fields::biology::genomics
fields::biology::proteomics
fields::biology::metabolomics

I would like to combine these tags with something like

::search (ok, I just found use::searching, this will do)
::alignment (how about use::comparison and use::comparison::alignment, then?)

Suggestions?

Molecular pathways I see within ::interaction. Gene regulation depends, most 
likely it would be genomics. Charles?

> But well, I leave the final decision to the debtags developers, since
> they are most known with the design of the tags database. But please,
> whatever it is, decide on it somewhere soon so we can start :)

There is more to it. E.g. I am missing something like 

use::analysis

. First I though about "use::research", but then thought that this is 
nonsense. The existing use::checking would come later once one has a 
hypothesis generated,

Then there is at least for my qtdmm package

use::measuring
hardware::input::dmm for Digital Multi Meter
works-with::device

missing. Measuring semantically goes next to the existing use::monitor but at 
least to me means something different. Or is it use::scanning in terms of 
data sampling?

Ah, right and on formats. The following come to mind:
works-with-format::biology::fasta
works-with-format::biology::aln
works-with-format::biology::pdb
works-with-format::biology::embl (EMBL-format works both for protein and 
nucleotide sequences)
works-with-format::biology::...

And something else I missed, particularly for the emerging workflow utilities:

scope::utility:wrappable, in the sense that other applications use that 
wrapped utility. Though there may be a more professional way to express this.

I was removed the debtags developers list, presumably because of being too 
busy to contribute. I apologize and would not mind too be added back in as 
smoe-guest. If allowed I volunteer to add (and describe) the in the following 
undisputed terms to svn this week.

Best regards

Steffen
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