[Syrphidae] FW: FW: genera gender list and database storage

[Francis Gilbert]

-----Original Message-----
From: Bastiaan [mailto:bastiaan at wakkie.org] 
Sent: 06 January 2021 11:47
To: dyanega at gmail.com
Cc: Hoverfly discussion list <syrphidae at lists.nottingham.ac.uk>
Subject: Re: [Syrphidae] FW: genera gender list and database storage

Hi all,

Thank you very much all for your comments especially to Douglas for your 
extensive explanation of the ICZN Code and how other communities are 
dealing with it! I must admit I had to read the extensive explanation a 
couple of times to get a grasp of it though, but that's just me as I am 
more a visual person. I have to admit a list maintained by the community 
conform the Code is the ultimate goal for everyone here I presume.

As the groundbreaking work (in process) of Chris Thompson (the authors 
of both the ICZN Code and Systema Dipterorum (SD) and still the single 
maintainer of the Syrphid part) it is the best source available. All 
other websites (gbif etc.) use this as basis. I am not looking at 
replacing SD nor I feel qualified to do so but in order to serve a world 
list on syrphidae.com I am in need of a smooth way to link to SD which 
is very complex task in its current state.

The problem I am facing with SD is that record ID's are not consistent 
over updates. So basically I can only rely on text without ID's that 
link to a not always consistent (sometimes with not yet published rank 
changes) Valid names are without a record IDs, authors nor years and 
missing citations of any rank changes. This all makes it on my side very 
prone to a lot of interpretation errors.

What I have done so far:

1) Added a fixed UUID (Universally unique identifier) to all names I 
found in the copy of SD in December 2019. (Chis if you like to have 
those please let me know)
2) Linked programmatically all valid names, misspellings etc. to the 
correct UUID. This needs a lot of ironing to get this smooth though.
3) Linked the Family till Sub specific name hierarchy together to form 
one big tree.
4) Linked synonyms etc to the current accepted names

Most hours (and luckily these days I have some left) are spend on fixing 
errors in the parent-child and hierarchy relationships due unclear links 
within SD. The database contain roughly around 13000+ records and is 
basically Chris's work in SD combined with the phylogeny (also work in 
progress) spreadsheet found online + my own additions of some missing 
parts (All send to Chris btw).

About phylogeny is using PhyloCode (http://phylonames.org/) not a good 
idea?

Currently I am not yet able to compile the full hierarchical checklist 
from the family till subspecies level due to the errors mentioned above 
and difficulty linking species with gender variations back to their 
original name, hence my question to the community if there was a easy 
way to do this. I understand now it became even more tedious work but 
hey... it needs to be done at one point as I have 1000's of photos 
waiting to be connected to these UUID's for the new syrphidae.com and 
8Gb of literature (not publicly available for obvious reasons)

Help on administrating this on syrphidae.com would be greatly 
appreciated of course and I can provide the community access to it but 
before doing so I need first cutting some rough edges and make it dummy 
proof (no offense intended) as for now pure (recursive) SQL knowledge is 
needed to compile them. I have not yet made a web (form) based 
interaction with the database but if the community likes to participate 
I am happy to create that on syrphidae.com.

My dream is to eventually have a driving community (yes you!) running 
syrphidae.com in all its assets.

Let me know if there is interest in moving this forward ... quicker (as 
I am moving this way)

Cheers,
Bastiaan

Francis Gilbert schreef op 04-01-2021 20:42:
> FROM: Douglas Yanega [mailto:dyanega at gmail.com]
> SENT: 04 January 2021 19:20
> TO: syrphidae at lists.nottingham.ac.uk
> SUBJECT: Re: [Syrphidae] genera gender list and database storage
> 
> On 1/1/21 5:59 AM, Bastiaan wrote:
> 
>> Hi all,
>> 
>> Happy new year (for whom it may concern ;-)
>> 
>> A new years question:
>> 
>> I am looking for a list of all genera with there gender. Or is there
>> a general rule I can interpret it from the genus name?
>> 
>> I like to keep only protonym (original combination) intact plus the
>> + specific name without the gender part in the database so I never
>> have to change it again. Then I will link them to their current
>> accepted parent. Based of the parent 'genus' name gender I can
>> create the current accepted name.
>> 
>> I guess from what I understood so far is that the subgenus name does
>> not effect the specific name? Like in Leucozona laternaria?
>> 
>> As example where the specific_name changes:
>> 
>> Musca fasciolata  --> Chrysotoxum fasciolatum
>> Musca laternarius --> Leucozona (Ischyrosyrphus) laternaria
>> 
>> In Systema Dipterorum for example all of the four above mentioned
>> names are stored. (and this on their turn slipped down into
>> different websites gbif inaturalist etc.)
> 
> As a Commissioner of the ICZN, I can perhaps offer some help here:
> 
> (1) If you do not have a hard copy of the Code - and even if you DO -
> the most up-to-date version is the online version, accessible here:
> 
> https://www.iczn.org/the-code/the-international-code-of-zoological-nomenclature/the-code-online/
> 
> 
> PLEASE NOTE: the online version incorporates a small number of
> significant changes that have occurred since the last hard copy
> version printed in 1999, so it is generally recommended to refer to
> the online version.
> 
> (2) The nomenclatural gender of a genus is often, but not always,
> easily inferred. Sometimes, upon investigation, it proves to be in
> direct conflict with prevailing practice. The rules governing the
> methodology for determining the gender of a genus are given in Article
> 30. Note in particular the exceptions in Art. 30.1.4, some of which
> are arbitrary, and not strictly in keeping with grammar (e.g., how to
> treat names ending in "-odes").
> 
> (3) The nomenclatural status of a species epithet is governed by
> Article 31, and may be rather difficult to establish with certainty;
> taxonomists COMMONLY make errors. A case in point is the name you
> refer to above: "laternarius" is not an adjective, it is a noun.
> Therefore, the correct formation under the ICZN is "Leucozona
> laternarius"; this is true, and must be adhered to, regardless of
> prevailing usage by dipterists. Technically speaking, under the Code,
> variant spellings that are VARIANT ONLY IN THE SENSE OF GENDER are NOT
> different spellings. In other words, if people are presently using
> "Leucozona laternaria" the change to "Leucozona laternarius" is NOT a
> change in spelling; it does not require any annotation, it does not
> have any authorship, and (perhaps most importantly) the spelling
> "laternaria" CANNOT be maintained by invoking any Code provisions that
> preserve incorrect spellings in prevailing usage - because
> "laternaria" is the SAME NAME as "laternarius", and not an incorrect
> spelling as the Code defines it. If one were, say, "laternarius" and
> the original publication turned out to be "lanternarius", then those
> WOULD be variant spellings, and prevailing usage could be invoked.
> 
> (4) At present, there are errors and omissions in all of the print and
> online resources that offer lists or catalogs of names (for all
> organisms, not just syrphids). The number of errors in the genders of
> genera represent a trivially tiny proportion, mostly names that are
> neuter but ending in "-a" (e.g. all names ending in "-gramma" or
> "-soma"). However, the number of errors where taxonomists have treated
> epithets that are nouns as adjectives (or the converse) are a SMALL
> BUT SIGNIFICANT proportion. As such, if you want to compile an
> ACCURATE list, it will require some effort on your part to find and
> correct the existing errors in the available resources.
> 
> (5) The primary source of contentious cases among species epithets are
> names that have the potential to be either a noun or an adjective:
> under Art. 31.2.2, you MUST consult the original description to see if
> the author provided explicit evidence that such a name was intended to
> be an adjective, and if there is no such evidence, all such names MUST
> be treated under the Code as nouns. In some cases, this can be easily
> checked, especially if the name is Latin in origin and well-known to
> exist as both noun and adjective, such as "pumilus" (see
> https://en.wiktionary.org/wiki/pumilus). In some such cases,
> taxonomists ignore the Code, and this could create problems (e.g., no
> one EVER treats the epithet "alba" as a noun, even though this is a
> genuine Latin usage: https://en.wiktionary.org/wiki/alba#Latin). Yet
> other cases, ESPECIALLY those involving words from Greek that have
> been Latinized, can be incredibly confusing and contentious. For
> example, the term "cephala" is a Latinized Greek noun, and words
> ending in "-cephala" can be considered noun phrases, but could also be
> argued to be adjectival under some conditions. There is no universal
> agreement on this, most particularly because the Latinization of Greek
> is not a traditional practice except by taxonomists; we cannot consult
> non-taxonomic sources for an objective assessment, and taxonomists
> cannot come to a consensus. To continue the example, some taxonomists
> will consider the endings "-cephala", "-cephalus", and "-cephalum" to
> all be adjectival, always. Other taxonomists will treat "-cephala" as
> a noun, but "-cephalus" and "-cephalum" as adjectival. Other
> taxonomists will look at the prefix, and if the prefix is LATIN, then
> "-cephala", "-cephalus", and "-cephalum" are nouns, but if the prefix
> is GREEK, then "-cephala", "-cephalus", and "-cephalum" are adjectival
> (e.g., "caeruleocephalus" is a noun but "cyanocephalus" is an
> adjective). Still other taxonomists, such as myself, TRYING TO FOLLOW
> THE CODE, will use the evidence of disagreement to claim that such
> names MIGHT be either nouns or adjectives, _depending on who you ask_,
> and therefore choose to apply Article 31.2.2 to ANY such word; under
> this interpretation they can only be adjectival if the original
> description explicitly stated that the name was adjectival; otherwise,
> they are all nouns by default. I will point out, with some regret,
> that consensus does not even exist among the Commissioners as to how
> and when 31.2.2 should be applied.
> 
> (6) I would encourage people who are concerned with the potential for
> grammatical confusion to destabilize the spelling of names to consider
> the following points: (A) there is a precedent, implemented by John
> Oswald at TAMU, to make available an exhaustive online catalog of
> names in which every single genus has its gender established following
> the Code, and in which all of the species epithets are stated to be
> either declinable (adjectival) or not, and showing the different
> correct gender-matching spellings whenever the name is declinable. He
> has done this for the entire superorder Neuropterida, singlehandedly,
> demonstrating the feasibility of providing a definitive resource:
> https://lacewing.tamu.edu/SpeciesCatalog/Main (B) there is a mechanism
> presently embedded in the Code under Article 79 called the "List of
> Available Names" (a.k.a. LAN), by which a group of taxonomic experts
> can establish their OWN determination of the parameters of all names
> for their taxonomic group, EVEN IF that determination may in some
> cases conflict with the Code (as embodied in Art. 79.4.1: "A name
> occurring in an adopted Part of the_ List of Available Names in
> Zoology_ is deemed be an available name and to have the spelling,
> date, and authorship recorded in the _List_ (DESPITE ANY EVIDENCE TO
> THE CONTRARY)."). The point is that if the Syrphid community wants to
> have their own catalog, adhering to existing practice (not necessarily
> always adhering to the Code), there IS a mechanism available to
> accomplish this. (C) taken together, you have two basic options: if
> you follow Oswald's example, you can create and maintain an online
> resource that people studying syrphids can use, and if EVERYONE uses
> this source and ONLY this source, then even if it is not
> Code-compliant, at least the usage of names will be consistent. You
> can do this immediately, with no involvement from outside your
> community. You would not be the first or even second community
> adopting a practice that allows for stabilization of names but does
> not follow the Code. If you follow the LAN model, you can create a
> similar resource, but one that is BY DEFINITION Code-compliant; the
> drawback is that it will take an absolute minimum of 5 years for the
> full external review process once the proposed List has been submitted
> to the Commission for consideration. I have personally made a similar
> recommendation to the lepidopterist community (who presently reject
> gender agreement in violation of the Code, but who, if they formalized
> it under a LAN, would have the Commission's formal support to continue
> this practice), and also to the herpetologist community (who presently
> suffer from a prolific self-publishing amateur whose works are
> technically Code-compliant but are being boycotted by the professional
> community, in violation of the Code, though if they implement a LAN
> they can render all his names permanently unavailable with the
> Commission's formal support).
> 
> (7) As a final aside I will note that as an entomology collection
> manager (with some 4 million specimens) I maintain a personal
> authority file of valid insect names, as part of our asset management.
> I have 210,254 species names presently recorded, and have personally
> screened 158,112 of these to determine which ones are definitively
> declinable (70,781), which ones are definitively not (77,368), and
> which ones will require examination of the original description under
> Art. 31.2.2 (9,963). It's tedious, but not impossible. Note that the
> proportion of names REQUIRING examination of the original description
> is only 6% of the total. If I am correct that there are fewer than
> 7000 valid syrphid species names, you can expect only ~500 names that
> will need scrutiny, the vast majority of which should prove to be
> indeclinable because the original description gives no etymology at
> all. The remaining ~6500 can be screened within a week, IF THERE IS AN
> EXISTING COMPILED LIST OF VALID NAMES. If you would be willing to
> trust my assessments, I would be willing to help with this, I have
> lots of practice. ;-)
> 
> Sincerely,
> 
> --
> 
> Doug Yanega      Dept. of Entomology       Entomology Research Museum
> 
> Univ. of California, Riverside, CA 92521-0314     skype: dyanega
> 
> phone: (951) 827-4315 (disclaimer: opinions are mine, not UCR's)
> 
>              https://faculty.ucr.edu/~heraty/yanega.html
> 
>   "There are some enterprises in which a careful disorderliness
> 
>         is the true method" - Herman Melville, Moby Dick, Chap. 82
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