[Taxacom] taxonomic names databases

Richard Pyle deepreef at bishopmuseum.org
Thu Sep 1 13:00:13 CDT 2016


Hi All,

On the pure mechanics of identifier cross-linking, I draw your attention to:

http://bioguid.org/about

I've put development of this service on hold while we build new server infrastructure at Bishop Museum, but further development will be included as part of a Global Names grant proposal we will be submitting shortly.

On the names cross-walking, I agree with Paul that GNI is the logical set of services and tools that would best be used for building the identifier cross-links among scientific names (and will be especially so if we get this next round of funding).  Both GNI and BioGUID (as well as GNUB) are part of the growing family of "Global Names" indexes and services.

Aloha,
Rich


> -----Original Message-----
> From: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of
> Paul Kirk
> Sent: Thursday, September 1, 2016 12:22 AM
> To: Tony Rees; godfoder
> Cc: taxacom
> Subject: Re: [Taxacom] taxonomic names databases
> 
> My opinion, as always ...
> 
> 
> The logical place to provide this cross walking is the GNI. It's goal is to index all
> names (just the 'names', nothing more, nothing less) whether they are fungi
> sensu stricto (names for taxa in kingdom Fungi), fungi sensu lato (chromistan
> analogues and protozoan analogues traditionally studied by mycologists), fungal
> interlopers (Rozellomycota/Cryptomycota and microsporidia) or non-marine
> species of fungi 'accumulated' by the Interim Register of Marine and Non-marine
> Genera. The GNI is domain neutral and thus cannot be accused of 'stepping on
> other peoples toes'. Lets not all of us do everything :-)
> 
> 
> Paul
> 
> ________________________________
> From: Taxacom <taxacom-bounces at mailman.nhm.ku.edu> on behalf of Tony
> Rees <tonyrees49 at gmail.com>
> Sent: 01 September 2016 11:04
> To: godfoder
> Cc: taxacom
> Subject: Re: [Taxacom] taxonomic names databases
> 
> Hi Alex,
> 
> As I think I showed in my example, it should be possible one day for IRMNG to
> provide a cross walk directly to (say) Index Fungorum for the fungi utilizing cross
> mapping already in place e.g. at the Open Tree Taxonomy (should they agree to
> support such a mediating service). Also since IRMNG IDs are already in GBIF,
> provide the same facility to link to relevant GBIF pages with the additional
> information you describe. The components are already in place, just needs a few
> cross-walking services to be created by the relevant intermediate parties, and a
> little extra coding at the IRMNG end...
> 
> The future is not far away, maybe.
> 
> Regards - Tony
> 
> Tony Rees, New South Wales, Australia
> https://about.me/TonyRees
> 
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> 7.jpg?w=1200&h=140&q=80&dpr=1&auto=format&fit=max&crop=faces]<htt
> ps://about.me/TonyRees>
> 
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> about.me
> View Tony Rees on about.me, your personal page with a purpose. Tony Rees
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> 
> 
> 
> 
> On 1 September 2016 at 06:47, godfoder <godfoder at acis.ufl.edu> wrote:
> 
> > This is a great example of identifier cross linking in action and
> > working pretty well. I think that, even if you disagree with GBIF's
> > choices in constructing the backbone, that this level of cross linking
> > among disparate taxonomies is incredibly valuable. It would be great
> > if we could search every database for any identifier of our choosing
> > and expect a result such as your proposed searching of GBIF and OTT
> > based on IRMNG IDs. I think GBIF is working to enable that at least to
> > some extent, although the API call I expected to do this did not work:
> > http://api.gbif.org/v1/species
> > ?datasetKey=0938172b-2086-439c-a1dd-
> c21cb0109ed5&sourceid=10561410 .
> > For now though, we're still a ways away from that goal.
> >
> > Although this is liable to get my head bitten off, I think that this
> > cross linking makes GBIF's taxon identifiers much more valuable than
> > IRMNG's even if they are potentially less correct (hang on, don't
> > lynch me just yet) scientifically. The (oversimplified) theory behind
> > Google's famous page rank algorithm is that a node on a graph can be
> > ranked based on the number of inbound and outbound links. This turns
> > out to be a fantastic basis for ranking the relevance of a huge amount of
> different types of information.
> > GBIF has done the work to build out the outbound links from their
> > taxonomic identifiers, as well as building a whole internal link
> > network between taxonomy and occurrence data. For projects with
> > limited resources looking to inter-relate data this means that whether
> > you're a data aggregator, species modeling project , working on a
> > competing backbone, or focused on a specific taxonomic niche knowing
> > the GBIF taxonIDs of your subjects is very useful.
> >
> > This doesn't mean I think that other taxonomies and projects should
> > abandon their own identifiers, quite to the contrary. I think that
> > local identifiers often capture a level of specificity that is
> > virtually impossible to represent in aggregated data sets. What I do
> > think, is that projects like IRMNG who are looking to capture value
> > for themselves, should actively seek out and integrate these high
> > value identifiers into their own databases. If both Index Fungorum and
> > IRMNG did this, it would be possible to link the two databases based
> > on their shared knowledge of GBIF IDs. It would also make it much
> > easier in the future to do a cross walk between the two database to
> > directly incorporate each-others identifiers since you could start from that
> shared knowledge.
> >
> > - Alex
> >
> >
> > On 08/31/2016 03:18 PM, Tony Rees wrote:
> >
> >> 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
> >>
> >>
> >>
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