[Taxacom] taxonomic names databases

[Tony Rees]

Thinking a step further (again, possibly only talking to myself here
:) ), even some of the above "cross linking" between datasets could
potentially be outsourced, further spreading that load - at least some
of the building blocks are there (but not the IRMNG <> ION mapping
anywhere else at this time, so far as I can see).

For example, IRMNG data dumps are already used (as one component) in
"taxonomic backbone" building exercise by GBIF, Open Tree of Life,
Encyclopedia of Life, Atlas of Living Australia and possibly others,
and this process will/should be refreshed with new releases of IRMNG
and other data sources. To do this, such "name aggregators" will
already be comparing names and identifiers from IRMNG to those from
other sources and most likely, keeping whatever mappings they make
"somewhere", maybe even exposing them, as here for the previously used
example (species name in Diptera):

Open Tree: https://tree.opentreeoflife.org/opentree/argus/ottol@4474544/Aagaardia-protensa
GBIF: http://www.gbif.org/species/1446570
(the relevant page on EOL does not appear to have mapped the IRMNG
entry, but no matter).

Now, so far as I know there is not a publicly advertised way to search
Open Tree, GBIF or EOL by IRMNG ID, but from purely a technical
viewpoint, there is no reason why there could not be. For example
taking the Open Tree page, that then already maps IRMNG: 10561410 to
both OTT: 4474544 and GBIF: 1446570, and the GBIF page maps the IRMNG
entry to the same one in GBIF (1446570) and also to 4 other data
databases ("checklists" in GBIF speak) plus whatever occurrence data
GBIF may hold.

The upshot of the above is that if one could search the above systems
by IRMNG identifier, with certain caveats (such as the relevant cross
mapping being correctly done) IRMNG what not need to know what
identifiers Open Tree, GBIF etc. were using for the same names (these
could be retrieved on the fly or even not needed) and in addition,
could leverage whatever additional links such systems have already
made.

For example, in my previous post I said it would be nice for a user
(human or machine) to be able to go from fungal records in IRMNG to
the relevant entry in Index (or Species) Fungorum, which might for
example contain the original literature for a particular taxon name
and save IRMNG the task of compiling that. It turns out that this
should already be possible : for example the Open Tree page for the
fungus Amanita caesarea already lists the following:

Reference taxonomy:
OTT: 769441

Source taxonomy:
Index Fungorum: 208468
NCBI: 67695
GBIF: 5452695
GBIF: 5240269
IRMNG: 10381934

This means they have already cross mapped IRMNG: 10381934 to Index
Fungorum: 208468, saving me the trouble, and there *should* be a way
to provide users with a route to go from the (presently bare bones)
IRMNG page here:
http://www.irmng.org/aphia.php?p=taxdetails&id=10381934 to the
equivalent in IF:
http://www.indexfungorum.org/Names/namesrecord.asp?RecordID=208468

Which contains the original publication information "Citations in
published lists or literature: Saccardo's Syll. fung. V: 8; XII: 905;
XIX: 44" as well as the magic additional link "Page Image for
Protologue:" which points here:
http://www.librifungorum.org/Image.asp?ItemID=82&ImageFileName=0252b.jpg

Now that's looking like a win (thanks, Paul and the Open Tree folk in
this instance).

Comments, anyone?

Regards - Tony


-- 
Tony Rees, New South Wales, Australia
https://about.me/TonyRees