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Re: New tags for biology and medicine.


I am writing to our list, so whoever is officially answering Benjamin might 
want to consider ...

On Wednesday 05 September 2007 19:20:58 Benjamin Mesing wrote:

> also be ok, since we wouldn't have anything to do with that ;-). We
> would like to put the following tags in the main hierarchy either way:
>       * field::medicine
>       * use::comparison (though Enrico warned about the name - we would
>         imagine a diff tool from that, but I think it is just fine to
>         use it with different interpretation)
I think the understanding of a diff tool is fine. It is a ranked diff, though.
>       * use::analysis
>       * field::medicine:imaging (I wouldn't want to place that into
>         biology:: and don't see the need for a med:: facet yet)
d'accord, I think.
> If there are no objections I will add those in roughly a week.
> And the following tags in the biology facet (note that I have adapted
> some of the tag names):
>       * ::bioinformatics, ::molecular-biology, ::structural-biology
>         (though those could go into field::biology if you rather see
>         that)
biology::structural-biology I would not mind to see instead as 
biology::molecular-biology:structural ... nice? not so? 

>       * ::format:aln, ::format:fasta, ::format:nexus (or would you
>         rather have aln-format, fasta-format,..?)
I prefer ::format:aln
>       * ::emboss
biology::emboss is strange, I think. Sadly, it addresses many fields that we 
have just split apart.

>       * ::nucleic-acids, ::peptides
I would them have underneath ::molecular-biology, I think.

>       * ::alignment-analysis, ::phylogeny-analysis (if you really think
>         this is neccessary)
This I would prefer as biology::analysis:alignment. 
biology::analysis:phylogeny, biology::analysis:interaction. 

We do not have databases in Debian much, yet. But where would they go? 
Is "analysis" possibly not the right term? Is "::investigation" better?

> Once this is agreed upon and the remaining questions are answered, I
> will add the biology facet.

> We are not sure about the ::algorithm:* thing. They are not biology
> specific so it would be odd to put them there.

> Besides, Enrico pointed 
> out, that nearly everything (at least the software) is made-of
> algorithms.
I can agree here, too.

> Additionally, to me the whole made-of facet does not seem 
> very concise anyways...
The motivation is to see SSAHA and from the tags learn: ah, this does 
nucleotide sequence comparisons and searches with some hashing. Blast 
probably uses some hashing somewhere, too, but dynamic programming is what is 
key to its functionality.




Dr. Steffen Möller
University of Lübeck
Institute for Neuro- and Bioinformatics
Ratzeburger Allee 160
23538 Lübeck
T: +49 451 500 5504
F: +49 451 500 5502

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