[Taxacom] IRMNG is moving...

Geoffrey Read gread at actrix.gen.nz
Wed Jul 20 21:18:51 CDT 2016


Hi Tony,

Thanks for the comprehensive response (and for the reminder about Rod's
version of NomZoo).  We can discuss the WoRMS presentation issues
elsewhere (I do think initial search results should display a short
hierarchy), but just wondering what you or WoRMS can do to continue your
homonym lists, which presumably took quite a bit of work to make, and
might be unique?

http://www.cmar.csiro.au/datacentre/irmng/homonyms.htm

Geoff

On Thu, July 21, 2016 9:10 am, Tony Rees wrote:
> Hello Geoff, and nice to hear from you (although despite being nearly (!)
> neighbours, we have not met...)
>
> I agree that "classic" IRMNG has/had some neat features, indeed I put them
> in because that was what I wanted to see myself in a search result as a
> client of my own system, so to speak. Having said that, there are some
> other nice features in the VLIZ search and display software which I never
> put into my version, that include simultaneous search across all ranks,
> search of the literature, separation of accepted names from synonyms, a
> searchable taxon tree, a set of web services for remote searching by other
> applications, that I have not had to build, and extend the functionality
> in
> those areas. Plus the key aspects including homonym/same name display
> across all kingdoms are supported, e.g. search for genus = "Ceratium"
> gives
> the following:
>
> (from
> http://www.irmng.org/aphia.php?p=taxlist&tName=Ceratium&rComp=%3D&tRank=180&action=search
> )
> ---------------
> Search for '*Ceratium*' returned 6 matching records. Click on one of the
> taxon names listed below to check the details. [new search
> <http://www.irmng.org/aphia.php?p=search>] [direct link
> <http://www.irmng.org/aphia.php?p=taxlist>]
>
> *Ceratium* Schrank, 1793
> <http://www.irmng.org/aphia.php?p=taxdetails&id=1273897>
> *Ceratium* Gistl, 1848
> <http://www.irmng.org/aphia.php?p=taxdetails&id=1274070>
> *Ceratium* Thienemann, 1828
> <http://www.irmng.org/aphia.php?p=taxdetails&id=1274013> accepted as
> *Phycita* Curtis, 1828
> <http://www.irmng.org/aphia.php?p=taxdetails&id=1325008>
> *Ceratium* Blume, 1825
> <http://www.irmng.org/aphia.php?p=taxdetails&id=1274128> accepted as
> *Eria* J.
> Lindley, 1825 <http://www.irmng.org/aphia.php?p=taxdetails&id=1352801>
> *Ceratium* Agassiz, 1846
> <http://www.irmng.org/aphia.php?p=taxdetails&id=1274194> accepted as
> *Keratella* Bory de St. Vincent, 1827
> <http://www.irmng.org/aphia.php?p=taxdetails&id=1350212>
> *Ceratium* J.B. Albertini & L.D. Schweinitz, 1805
> <http://www.irmng.org/aphia.php?p=taxdetails&id=1273955> accepted as
> *Ceratiomyxa* J. Schröter in Engler & Prantl, 1889
> <http://www.irmng.org/aphia.php?p=taxdetails&id=1072848>
>
> ---------------
> Also the fuzzy matching is there, but only if a submitted spelling is not
> found, example:
>
> Search for '*Ceratius*' returned 0 matching records,
> but 77 *fuzzy*, matching records. Click on one of the taxon names listed
> below to check the details. [new search
> <http://www.irmng.org/aphia.php?p=search>] [direct link
> <http://www.irmng.org/aphia.php?p=taxlist>]
>
> *Ceracis* Mellié, 1849
> <http://www.irmng.org/aphia.php?p=taxdetails&id=1300176>
> *Cerais* Van der Wulp, 1881
> <http://www.irmng.org/aphia.php?p=taxdetails&id=1294709>
> *Cerallus* Jacquelin du Val, 1859
> <http://www.irmng.org/aphia.php?p=taxdetails&id=1389602>
> *Ceramis* Gerstaecker, 1858
> <http://www.irmng.org/aphia.php?p=taxdetails&id=1447898> accepted as
> *Hylaia* Guérin-Ménéville, 1857
> <http://www.irmng.org/aphia.php?p=taxdetails&id=1424224>
> *Ceramium* A.W. Roth, 1797
> <http://www.irmng.org/aphia.php?p=taxdetails&id=1268868>
> *Ceramium* Blume, 1827
> <http://www.irmng.org/aphia.php?p=taxdetails&id=1268939> accepted as
> *Thottea* Rottboell, 1783
> <http://www.irmng.org/aphia.php?p=taxdetails&id=1354867>
> *Ceramium* Wiggers, 1780
> <http://www.irmng.org/aphia.php?p=taxdetails&id=1469377>
> *Ceramius* Latreille, 1810
> <http://www.irmng.org/aphia.php?p=taxdetails&id=1440314>
> *Ceramus* Rafinesque, 1815
> <http://www.irmng.org/aphia.php?p=taxdetails&id=1422472> (nomen nudum)
> *Ceranicus* <http://www.irmng.org/aphia.php?p=taxdetails&id=1284748>
> *Ceranigus* Hoffmann, 1968
> <http://www.irmng.org/aphia.php?p=taxdetails&id=1460126> accepted as
> *Curanigus* Faust, 1898
> <http://www.irmng.org/aphia.php?p=taxdetails&id=1412046>
> *Ceranisus* Walker, 1842
> <http://www.irmng.org/aphia.php?p=taxdetails&id=1400284>
> *Ceranthus* Schreber, 1789
> <http://www.irmng.org/aphia.php?p=taxdetails&id=1323050> accepted as
> *Chionanthus* Linnaeus, 1753
> <http://www.irmng.org/aphia.php?p=taxdetails&id=1295541>
> *Ceranthus* Linnaeus, 1758
> <http://www.irmng.org/aphia.php?p=taxdetails&id=1323089>
> *Cerapus* Say, 1817
> <http://www.irmng.org/aphia.php?p=taxdetails&id=1379223>
> *Cerastis* Ochsenheimer, 1816
> <http://www.irmng.org/aphia.php?p=taxdetails&id=1299104>
> *Cerastis* Kolbe, 1883
> <http://www.irmng.org/aphia.php?p=taxdetails&id=1299135> accepted as
> *Cerastipsocus* Kolbe, 1884
> <http://www.irmng.org/aphia.php?p=taxdetails&id=1195354>
> *Cerastium* Linnaeus, 1753
> ( <http://www.irmng.org/aphia.php?p=taxdetails&id=1273262>etc.)
>
> The two main differences between the result display for "old" and "new"
> IRMNG being that in the new results, near matches are suppressed when the
> input name correctly matches at least one name currently held, and the
> taxonomic position + publication details for a name are not in the results
> list but on the page for each name (we can maybe talk to VLIZ about
> promoting these features or making them options in the "advanced search",
> as and when they do their next priority assignment (I am also cc-ing to
> WoRMS/VLIZ for their interest).
>
> Stepping back a little, it is important to realize that IRMNG had a
> limited-to-zero long term future at CSIRO in the advent of my departure
> which happened in 2014: with the best will in the world, a freely
> distributed, global-coverage system such as IRMNG would never be core
> business for them in an increasingly "research business" environment, and
> also such systems need a local carer-and-feeder to remain alive and
> thriving, which function is no longer there, but is present in good
> measure
> at VLIZ - in fact their IT/data management team is second to none plus
> they
> already have a precedent for ongoing, distributed editorship as with WoRMS
> (and again, like all things, the data held for any name, and the remote
> edit interface can and no doubt will evolve further with time and
> expressed
> user needs).
>
> Also I realise that for the marine species component of IRMNG (at least
> the
> extant ones), IRMNG and WoRMS will now no longer look very different to
> the
> user which is a good thing, as WoRMS has saved the trouble of IRMNG having
> to research that data separately, and much of it can and is already being
> replicated across both systems (when IRMNG started in 2006, WoRMS did not
> exist and so IRMNG effectively was serving both purposes). Where IRMNG
> does
> not duplicate WoRMS are its extensive holdings of nonmarine and fossil
> names (at genus level in particular, but also 1 million + species names),
> all within the same system as the marine ones for cross-domain (and Code)
> name resolution and comparison as needed, for filtering by habitat and
> fossil status, and for generating a synoptic view of "all life" (e.g. by
> browsing the taxon tree or reporting statistics by taxonomic group) that
> WoRMS simply cannot produce.
>
> I think the main thing is that VLIZ has made an offer to take IRMNG
> onwards
> and upwards in a way that few others can do and for the sake of
> continuation of the IRMNG data content and services to users, that is by
> far the best way forward for it and for me (in that if I fall under a bus
> tomorrow, or suddenly lose my interest in taxonomy and biodiversity, the
> system will not be compromised), and also there are many synergies between
> IRMNG and WoRMS, and the other taxonomic databases managed at VLIZ, that
> offer benefits to multiple systems for the future. So allowing for the
> fact
> that aspects such as what is directly returned to a user after submitting
> a
> search, and/or the remote taxon name edit form, can all change in the
> future and be influenced by user feedback, I would say the future for
> IRMNG
> looks very good even if I and other users have to get used to editing and
> seeing my/our search results in a slightly different way than previously.
>
> For the record, the ex-Nomenclator Zoologicus content (which has been
> vetted in many cases and had some errors fixed, etc.) which is displayed
> for animal genus names in IRMNG is still there on every relevant "genus
> level" page; it is also mostly accessible (if the original uBio/MBL copy
> is
> offline as seems at present) via a copy put online via Rod Page, with
> additional document links he has created, at http://iphylo.org/~rpage/nz/
> .
>
> Further comment welcome of course,
>
> Best regards - Tony
>
>
> Tony Rees, New South Wales, Australia
> https://about.me/TonyRees
>
> On 20 July 2016 at 21:42, Geoff Read <gread at actrix.gen.nz> wrote:
>
>>
>> Hi Tony,
>>
>> IRMNG at WoRMS at present looks to me as just another context variant of
>> the WoRMS Aphia database (I'm a WoRMS editor). The search interface has
>> the same limited options basic to WoRMS.
>>
>> This seems a step back. Where is the functionality of the old IRMNG for
>> finding and displaying homonym info and near matches in spelling under
>> any
>> genus name as a unified display. This was the only aspect I used it for.
>> Particularly important now  as Nomenclator zoologicus online appears to
>> have died again.
>>
>> People can still look up any genus at
>> http://www.cmar.csiro.au/datacentre/irmng/ and see the BIG difference in
>> the two initial outputs.
>>
>> I wanted the Classic IRMNG continued.  Perhaps WoRMS should think about
>> putting similar extended info into their initial search-result pages.





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