[tcs-lc] where to go now..

[Paul Kirk]

After this email from Jessie what follows might be seen as not focussed on what we are trying to achieve in 10 days. However, the weekend is coming up so some of us may have time to quickly read whats below and give a few simple comments (like which starship did you fly in on?). So here goes...

I'm still unclear, as I suppose I always have been, as to what the end use applications of TCS will help us do because unless we have some fairly clear idea we will end up with schema for a camel when the end user wants a horse.

So, since Gregor mentioned real fungi a couple of days ago I'll continue with a few hypothetical end user needs, in this case comparing real data from two national checklists to determine if they are using the same concepts.

For some time I've been working with the British Lichen Society on the Checklist of Lichens of the British Isles. Now some of the lichens are fairly ancient, they are good indicator so they also appeal to people outside taxonomy. Recently I've been doing some work with the Checklist of Australian Lichens.

So, here is my first example of what I imagine end users might want to do (text in square brackets is mine as are the 'soon to be real' LSIDs):

British Isles Checklist (extract) 
GENUS Acarospora {GUID:DOF28} [27 species + 52 synonyms/misapplications - only 12 listed]
SPECIES 1 - Acarospora admissa (Nyl.) Kullh. {urn:lsid:indexfungorum.org:names:375465} - syn. Lecanora admissa Nyl. {urn:lsid:indexfungorum.org:names:387547}
SPECIES 2 - Acarospora badiofusca (Nyl.) Th. Fr. {urn:lsid:indexfungorum.org:names:375487} - syn. Lecanora badiofusca Nyl. {urn:lsid:indexfungorum.org:names:387712}; Acarospora admissa sensu auct. brit. p.p. {urn:lsid:indexfungorum.org:names:448861}
SPECIES 3 - Acarospora cervina A. Massal. {urn:lsid:indexfungorum.org:names:375509}
SPECIES 4 - Acarospora fuscata (Nyl.) Arnold {urn:lsid:indexfungorum.org:names:375564} - syn. Lecanora badia var. fuscata Nyl. {urn:lsid:indexfungorum.org:names:463134}; Acarospora peliscypha sensu auct. brit. {urn:lsid:indexfungorum.org:names:448863}
SPECIES 5 - Acarospora heppii (Nägeli) Nägeli {urn:lsid:indexfungorum.org:names:375580} - syn. Myriospora heppii Nägeli {urn:lsid:indexfungorum.org:names:395801}
SPECIES 6 - Acarospora peliscypha Th. Fr. {urn:lsid:indexfungorum.org:names:375664}
SPECIES 7 - Acarospora sinopica (Wahlenb.) Körb. urn:lsid:indexfungorum.org:names:375718} - syn. Endocarpon sinopicum Wahlenb. {urn:lsid:indexfungorum.org:names:384768}
SPECIES 8 - Acarospora smaragdula (Wahlenb.) A. Massal. {urn:lsid:indexfungorum.org:names:375720} - syn. Endocarpon smaragdulum Wahlenb. {urn:lsid:indexfungorum.org:names:384769}; Acarospora murina Sandst. {urn:lsid:indexfungorum.org:names:375637}; Acarospora amphibola Wedd. {urn:lsid:indexfungorum.org:names:375477}; Acarospora scyphulifera Vain. {urn:lsid:indexfungorum.org:names:375713}; Acarospora scabrida sensu auct. brit. {urn:lsid:indexfungorum.org:names:452057}
SPECIES 9 - Acarospora subrufula (Nyl.) H. Olivier {urn:lsid:indexfungorum.org:names:375736} - syn. Lecanora subrufula Nyl. {urn:lsid:indexfungorum.org:names:389382}
SPECIES 10 - Acarospora umbilicata Bagl. {urn:lsid:indexfungorum.org:names:375763} - syn. Acarospora umbilicata f. congredians H. Magn. {urn:lsid:indexfungorum.org:names:452075}
SPECIES 11 - Acarospora veronensis A. Massal. {urn:lsid:indexfungorum.org:names: 375771}
SPECIES 12 - Acarospora verruciformis H. Magn. {urn:lsid:indexfungorum.org:names:375772}

Australian Checklist (extract)
GENUS Acarospora A.Massal.; Acarosporaceae {GUID:DOF28} [all 12 species listed]
SPECIES 1 - Acarospora cervina A.Massal., Ric. Auton. Lich. Crost.: 28 (1852) {urn:lsid:indexfungorum.org:names:375509}
SPECIES 2 - Acarospora citrina (Taylor) Zahlbr. ex Rech., Denkschr. Kaiserl. Akad. Wiss. Wien, Math.-Naturwiss. Kl. 88: 28 (1911) {urn:lsid:indexfungorum.org:names:375518} - syn. Urceolaria citrina Taylor, London J. Bot. 6: 158 (1847) {urn:lsid:indexfungorum.org:names:408206}; A. wilsonii H.Magn., Monogr. Acarospora: 71 (1929) {urn:lsid:indexfungorum.org:names:375778}
SPECIES 3 - Acarospora fuscata (Nyl.) Arnold, Verh. K.K. Zool.-Bot. Ges. Wien 22: 279 (1872) {urn:lsid:indexfungorum.org:names:375564}
SPECIES 4 - Acarospora fuscorufa F.Wilson ex H.Magn., Bih. Kongl. Svenska Vetensk.-Akad. Handl. 7: 309 (1929) {urn:lsid:indexfungorum.org:names:375566}
SPECIES 5 - Acarospora macrocarpa H.Magn., Göteborgs Kungl. Vetensk. Samhälles Handl., Math. Naturvensk. Skr., Ser. B, 6: 25 (1956) {urn:lsid:indexfungorum.org:names:363868}
SPECIES 6 - Acarospora negligens H.Magn., Bih. Kongl. Svenska Vetensk.-Akad. Handl. 7: 58 (1929) {urn:lsid:indexfungorum.org:names:375639}
SPECIES 7 - Acarospora nodulosa (Dufour) Hue, Nouv. Arch. Mus. Hist. Nat., sér. 5, 1: 160 (1909) {urn:lsid:indexfungorum.org:names:375646} - syn. Placodium ferdinandii Müll.Arg., Flora 64: 508 (1881) {urn:lsid:indexfungorum.org:names:401113}; A. ferdinandii (Müll.Arg.) Hue, Nouv. Arch. Mus. Hist. Nat., sér. 5, 1: 160 (1909) {urn:lsid:indexfungorum.org:names:375557}
SPECIES 8 - Acarospora novae-hollandiae H.Magn., Bih. Kongl. Svenska Vetensk.-Akad. Handl. 7: 89 (1929) {urn:lsid:indexfungorum.org:names:375648}
SPECIES 9 - Acarospora reagens Zahlbr., Bih. Kongl. Svenska Vetensk.-Akad. Handl. 13: 162 (1902) {urn:lsid:indexfungorum.org:names:375686}
SPECIES 10 - Acarospora sinopica (Wahlenb.) Körb., Parerga Lichenol.: 57 (1859) {urn:lsid:indexfungorum.org:names:375718}
SPECIES 11 - Acarospora smaragdula (Wahlenb.) A.Massal., Ric. Auton. Lich. Crost.: 29 (1852) {urn:lsid:indexfungorum.org:names:375720}
SPECIES 12 - Acarospora tasmanica Räsänen, Ann. Bot. Soc. Zool.-Bot. Fenn. "Vanamo" 21: 5 (1946) {urn:lsid:indexfungorum.org:names:363907}

First question: are the generic concepts the same in both checklists? Here the only conclusion we can come to whatever tools we develop to analize TCS documents containing these data is that they are different concepts due to different included species. Or am I missing something like these are inappropriate datasets to answer the question?

This would be the wrong conclusion so whats wrong?

Both checklists should have Acarospora sensu Kirk 1980 (A monograph of Acarospora) as an 'atribute' of the genus then the included species become irrelevant (yes?).

So, the TCS requires the dwindling number of taxonomists to take more time in what they are doing to include something they would probably say is 'stating the bleedin obvious' - there is only one monograph of Acarospora and everyone and his dog use it.

So to the next example:

British Isles Checklist
SPECIES 8 - Acarospora smaragdula (Wahlenb.) A. Massal. - syn. Endocarpon smaragdulum Wahlenb .; Acarospora murina Sandst.; Acarospora amphibola Wedd.; Acarospora scyphulifera Vain.; Acarospora scabrida sensu auct. brit.

Australian Checklist
SPECIES 11 - Acarospora smaragdula (Wahlenb.) A.Massal., Ric. Auton. Lich. Crost.: 29 (1852)

Are the species concepts the same in both checklists? Again the only conclusion we can come to is that they are different. But again this would be wrong 'cause only synonyms used in the country are included, not the full global synonymy - if the checklists included the full global synonymy things would be OK but thats not how most checklists I have used are compiled.

final example (hypothetical):

Kirk worked in the UK and contributed to the checklist before his monograph, and the first three of these four specimens were cited in that work; they are also cited in the checklist. [A, B, C are characters, numbers are values]

British Isles Checklist
Acarospora smaragdula
specimen i - 1904; A1; B2; C3
specimen ii - 1975; A2; B3; C4
specimen iii - 1976; A2; B2; C3
specimen iv - 1986; A1; B2; C3

Australian Checklist
Acarospora smaragdula
specimen i - 1981; A3; B4; C6
specimen ii - 1982; A4; B4; C7

Now we have real biometric data so are the species concepts the same in both checklists? Again the only conclusion we can come to is that they are different 'cause the specimens cited are different and the biometric data have non-overlapping values. This again would be wrong, the species concepts are the same.  Before the Kirk monograph the poor aussies were unable to identify any species of Acarospora and now they find they have 12. Kirk examined the aussie material but its obviously not in his monograph and this fact was not included in the dataset because the examination didn't change the identification (most collections do not annotate specimen labels 'examined by: date'). The biometric data from the two sources do not overlap 'cause the aussie specimens are bigger (warmer climate).

So, in order for the TCS to work here it requires some concurrent input from a taxonomist (Kirk; an edition 2 of a subset of the monograph if you will). At this point I see a cunning plan in the best blackadder tradition. If the scheming schemers can convince politicians that their schemas are the best thing since sliced bread, in a bioinformatics sense, and are essential to understand biodiversity and prevent it's loss, then a proportion of the vast wads they get to develop their schemas could pay for some more taxonomist to make their schemas work, hoorah!


OK, somewhat light hearted but am I being unfair? And if so, why?

Am I barking up the wrong tree (polite) or barking mad?

Is Schema a plural word? is there a singular? Schemum? :o)

p.s. Kirk in this story is hypothetical


-----Original Message-----
From: Kennedy, Jessie
To: tcs-lc at ecoinformatics.org
Sent: 10/03/05 14:15
Subject: RE: [tcs-lc] where to go now..

The date I will have to announce the TCS is March 20th....

Jessie

>-----Original Message-----
>From: tcs-lc-admin at ecoinformatics.org
>[mailto:tcs-lc-admin at ecoinformatics.org]On Behalf Of Roger Hyam
>Sent: 10 March 2005 14:15
>To: tcs-lc at ecoinformatics.org
>Subject: Re: [tcs-lc] where to go now..
>
>
>Hi Jessie
>
>Could you put some firm dates on those day counts. I am using 
>my fingers 
>and a wall planner here but some one else may be doing the 
>same and not 
>coming up with the same dates.
>
>Thanks,
>
>Roger
>
>Kennedy, Jessie wrote:
>
>>Dear list
>>
>>You may or may not be aware of the rules for putting forward 
>standards for TDWG but the bottom line is that a standard must 
>be given to the exec to be made open for discussion at TDWG 60 
>days prior to the meeting. We complied with this last year for 
>TCS and had a discussion and agree to make some changes.
>>the next stage is to put the standard forward to TDWG for 
>voting - this version has to be publicised 180 days before the 
>next meeting.
>>I had hoped we would be reaching consensus but to be honest 
>can't tell if we're getting nearer or further to consensus. I 
>really don't know where to go from here.....so need your help! 
>>
>>As chair of the Names/Concepts subgroup of TDWG I will put 
>forward the TCS in time that it might be voted on at TDWG - 
>knowing that although it has to be out for discussion 180 days 
>in advance we can make some changes in the interim period.
>>
>>But I don't know what to do yet about the name element in TCS. 
>>
>>As I've said before I thought LC was replacing the name 
>element for TCS but I think what is being proposed for LC is 
>very different to what Walter intended by the name element in 
>ABCD. TCS was designed with this type of name element in mind 
>but we tried to show how nomenclaturalists could use the TCS 
>for their purposes. Just like we tried to show how others 
>could use it for their purposes. 
>>
>>I think I would be very happy to at least get agreement on a 
>type at the level that was there and what Walter needs 
>independent of what the nomenclaturalists need in terms of 
>relationships, types etc.
>>Then if the nomenclaturalists don't think they can represent 
>their information in TCS maybe they should put together an 
>alternative schema for discussion this year at TDWG - is this 
>a sensible way to go ahead?
>>
>>Jessie
>>This message is intended for the addressee(s) only and should 
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>>  
>>
>
>-- 
>
>==============================================
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