New tags for biology and medicine.

Benjamin Mesing bensmail at
Tue Sep 4 10:10:30 UTC 2007


I believe it is past time to react to this proposal, we don't want to be
seen as some kind of black hole, everything that goes in never comes
out. And since I have some spare time at hand, I will make a start.
Generally speaking the proposed tags are relativly detailed. I believe
this level of detail is required only by biologists or people in the
medical field. Thus we need to decide, if those details should become
part of the main vocabulary database. Another way would be to provide
them in a different vocabulary/tag database - debtags supports multiple
of those.

Below you can find my thoughts towards the proposal under the assumption
that the tags should become part of the main database.

Index: debian-packages
--- debian-packages     (révision 2253)
+++ debian-packages     (copie de travail)
@@ -559,6 +559,18 @@
+Tag: field::biology:bioinformatics
+Description: Bioinformatics
+ Sequence analysis software.
+Tag: field::biology:molecular
+Description: Molecular biology
+ Software useful to molecular cloning and related wet biology.
+Tag: field::biology:structural
+Description: Structural biology
+ Software useful to model tridimentional structures.

This is probably a reasonable distinction, though we have to decide if
we want such a fine-grained separation of the "field" facet. We would
also end up with needing the same level of detail for electronics,
chemistry, physics,...

+Tag: field::medicine
+Description: Medicine

I believe that one is agreed upon.

+Tag: field::medicine:imaging
+Description: Medical Imaging

Same as for the ::biology:* tags

+Tag: made-of::algorithm:dynamic-programming
+Description: Dynamic programming
+Tag: made-of::algorithm:hashing
+Description: Hashing
+Tag: made-of::algorithm:hidden-markov-model
+Description: Hiden Markov Model (HMM)
+Tag: made-of::algorithm:neural-network
+Description: Neural Network

Can you please give an example of such a package? I have no idea how a
package made of an algorithm looks like.

+Tag: works-with::sequence
+Description: Sequence
+ The program manipulates data made of a sequence of elements from a
finite set.

Somehow this is different to the current tags in works-with, but I
believe it could fit in. E.g. sorting applications could also fit in

+Tag: works-with::sequence:nuceleic
+Description: Nucleic acids
+ Sequence of nucleic acids: DNA, RNA but also non-natural nucleic acids
such as PNA or LNA.
+Tag: works-with::sequence:peptidic
+Description: Proteins
+ Sequence of aminoacids: peptides and proteins.

Quite detailed, though otherwise, people proably won't pick
works-with::sequence if searching for algorithms working on a DNA.

+Tag: works-with-format::plaintext:aln
+Description: Clustal/ALN
+ Used in multiple alignment of biological sequences.
+Tag: works-with-format::plaintext:fasta
+Description: Fasta/Pearson
+ Very popular format for biological sequencs.
+Tag: works-with-format::plaintext:nexus
+Description: Nexus
+ Popular format for phylogenetic trees.

I am not sure it is a good idea to put those beneath "plaintext". There
are the two cases: 
     1. Someone searching for a tool for editing plaintext would end up
        with the special purpose plaintext:aln editors, which IMO is
     2. Someone searching for a special purpose plaintext:aln editor
        could deduce from the tag name, that he could also use
        plaintext, and if he knows that ALN is a plaintext format he
        could navigate there smoothly (which assumes that the tags are
        displayed in a hierarchical manner).

So the formats could as well be top level. Though this would mean
cluttering the works-with-format facet. Could there be a
works-with-format::special-purpose:* group?
Do we need a way to express releationships beween tags like: show
works-with-format::plaintext:aln only if field::biology or
field::medicine is selected? Or do we want to cover this by requiring
sophisticated UIs, which detect this in an automatic fashion.

+Tag: suite::emboss
+Description: EMBOSS
+ Software and data related to the European Molecular Biology Open
Software Suite.

Sounds good to me.

+Tag: use::analysis
+Description: Analysis
+ Software for turning data into knowledge.

+Tag: use::comparison
+Description: Comparison
+ To find what relates or differs in two or more objects.


+Tag: use::comparison:alignment
+Description: Alignment
+ To identify similarities in two objects by maximising the overlap of
identical parts.
+Tag: use::comparison:phylogeny
+Description: Phylogenetic analysis
+ To infer lineage relationships.

Those seems to be covered by use analysis to me.

Thanks Charles for brining the topic up again.

Regards Ben

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