[tcs-lc] where to go now..

[Kennedy, Jessie]

Paul wrote:

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?
 If they have the same GUID then they should be the same. So should they have the same GUID if they have different species included? well if well if you base your concept equivalence on included species then yes they are different and should have different GUIDs. Does the mongraph of Acarospora include all of these species? if so we don't have a problem and all we are doing is sub-setting the genus Acarospora to give those found in each country.

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?). 

yes - or as I say the same GUID should imply that and as long as neither checklists include any specie snot in the monograph everything is hunky dory.

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. 

but I guess a computer doesn't know that... now I'm sure we could develop software that helped you enter concepts form a monograph so that you could put in the AccordingTo details i.e.publication and author first and it automatically put these details into each concept for you when you created them and generated you a GUID. Thereafter if anyone referred to the GUID then that's the concept they mean. 

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. 

here I guess again because of the equivalence test you've given we would have to conclude they are different. BUT if you knew better you could create a relationship assertion that says that they are congruent then our equivalence algorithm could put your decision above that of the inclusion list. OR we could ensure that say the SPECIES 11 and SPECIES 8 (maybe in the next revisions of the Australian and British Isles checklists) , say in their definition that they are indeed congruent to the one in the Monograph. Clearly equivalence algorithms would need to consider prioritisation of decision making and this might need to have some user control (for certain users anyway.)

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). 

Here I think you are correct because what has happened is that the concept has changed - to include specimens  that are bigger than you first said they could be. So I'd expect you to revise your definition of Acarospora smaragdula 

 to include the new character circumscription but for you to say that you think your revised one is congruent to your first one. Then it's clear.

 
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 you got it right I answered before I read that.... but it's not to get the schemas to work - it's just to make what you've so clearly explained there for everyone and even a computer to understand so that it might make it easier for the poor Aussies (excuse me...) or whomever to know what's going on when you're really then only that knows.

So you are correct in all of your statements but all of them can be dealt with and dealing with them will become simpler and simpler over time as we sort all these discrepancies out. Rather than avoiding the issue and always being unsure and having to trace down a human expert to answer every question we might ever have. So you guys can then get on and deal with the x% of the world we don't know anything about yet :-)

Jessie 

and no the exams aren't written yet - I couldn't resist hits Paul - thanks....


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