[Bioperl-l] Companion planting

[Peter Cock]

Hello Gordon,

In terms of taxonomies, one widely used but general one is the
NCBI's - e.g.

https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=3884

I don't know enough about the plant side taxonomy to say if
this has the granularity you want for cultivated beans?

Peter

On Sat, Aug 17, 2019 at 11:56 PM Gordon Haverland
<ghaverla at materialisations.com> wrote:
>
> Greetings.
>
> I am trying to fuse some (4-6?) of the larger lists of companion (or
> anti-companion) plantings together.  I am not anything remotely like a
> biologist or geneticist (materials science is where I come from), but I
> am back on the family farm and it needs some rehab.
>
> I want to incorporate taxonomy in my companion data.  There is some
> data which definitively states that the presence of A helps B, that the
> presence of B helps A and that both A helps B and B helps A.  Some data
> notes the companionship, but doesn't point to the detail of it.  And
> some I don't understand.
>
> For example, Wikipedia seems to think that Repel and Distract are
> important, but I don't think a single example of Distract was given.
>
> The only taxonomy I have any familiarity with, is that presented by
> Wikipedia.  I have no idea if that is the best available.  And it
> some group updates some taxonomy by agreement or concensus, I suspect
> modifying anything based on Wikipedia could be problematic.  Perhaps
> the more formal taxonomy databases are better?
>
> And stuff about classifying plants bugs me.  How beans as a
> "species" (or group of species) can not be broken into subgroups; when
> in the companion data we see things like bean/pole Helps and
> bean/runner should be Avoided?
>
> Maybe it isn't a subspecies type thing, maybe it is more like the
> "Clade" data that Wikipedia presents?  Not that I understand Clade more
> than anything else.
>
> One place where the "plant" kingdom interacts with the "animal" kingdom
> is in the use of Trap plants.  A plant present because it will be
> damaged or killed by some "animal" pest, instead of the wanted plant.
>
>
> I have looked at some of the "man" pages at MetaCPAN on taxonomy; and I
> haven't a clue as to how I would either freeze a perl structure
> (DBM::Deep?) or use SQLite3 (or PostgreSQL) to save a local copy of
> data.
>
>
> Personally, I would like to find a trap crop for deer; but I suspect
> none exist.
>
>
> More data is always nice.  I think I have one more "biggish" source to
> digest, which is by some definition "big".  But all of the stuff I am
> looking at is "popular", which may be why the definitions of things
> change from source to source.  Are there better sources that are more
> rigorous?
>
> My thinking is that this data (what plants do I want or not want
> close to X) probably changes with climate, soil, and maybe other
> things.  I suspect there are also interactions between plants (A helps
> B if C is not present, ...).
>
>
> Oh well, I am going to go back to merging my data.  Perhaps someone
> with nothing to do, could humour a poor materials scientist turned
> farmer (permaculture)?  :-)
>
> Have a great day!
> Gord
>
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