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Topic: BLS Lichen Species Dictionary (2)

Unfortunately, the new lichen dictionary seems to have got itself into a bit of a tangle with species aggregates and species names with s. lat. and s. str. taxa. The new names work fine on importing new data, but our existing records are still attached to taxon names that no longer appear in the taxon dictionary, and so can't be selected either from the dictionary or in the report wizard.

Anyone holding copies of the BLS datasets or using the BLS dictionary will have this problem, and the NBN Gateway may be affected as well (it is always down when I try to use it so I wouldn't know). So far we have found 41 taxa and over 100,000 records that are affected in our database, so we need an automated solution to this.

There are five batch updates that redetermine taxa, but of course none of them can be used because they all require you to select the old and new taxa from the dictionary, and our old taxa are not showing in the new dictionary. Presumably we will have to write our own batch update to do this, using the TLIkeys. Does anyone already have a program to do this?

Janet


The list of taxa (so far) follows:

Aspicilia cinerea s. lat.
Aspicilia cinerea s. str.
Caloplaca citrina s. lat.
Caloplaca citrina s. lat.
Caloplaca citrina s. str.
Caloplaca ferruginea s. lat.
Caloplaca ferruginea s. str.
Caloplaca herbidella s. lat.
Caloplaca herbidella s. str.
Caloplaca holocarpa s. lat.
Caloplaca holocarpa s. str.
Cetrelia olivetorum s. lat.
Cetrelia olivetorum s. str.
Cladonia chlorophaea s. lat.
Cladonia chlorophaea s. str.
Cladonia coccifera s. lat.
Cladonia coccifera s. str.
Cladonia squamosa s. lat.
Degelia plumbea s. lat.
Degelia plumbea s. str.
Hypotrachyna revoluta s. lat.
Hypotrachyna revoluta s. str.
Lecania erysibe s. lat.
Lecania erysibe s. str.
Lecidea fuscoatra s. lat.
Lecidea fuscoatra s. str.
Lecidea lactea s. lat.
Lecidea lactea s. str.
Lepraria incana s. lat.
Lepraria incana s. str.
Micarea prasina s. lat.
Micarea prasina s. str.
Ochrolechia turneri s. lat.
Ochrolechia turneri s.str.
Peltigera neckeri
Polyblastia inumbrata agg.
Pseudocyphellaria thouarsii s. lat.
Punctelia subrudecta s. lat.
Punctelia subrudecta s. str.
Xanthoria candelaria s. lat.
Xanthoria candelaria s.str.

Janet Simkin
British Lichen Society

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Re: BLS Lichen Species Dictionary (2)

Janet

We need to dig a bit deeper into this.  Taxon_List_Item key, shouldn't disappear so I assume that they have become synonyms of a new or previously existing taxa.  I will check a few out.

Mike Weideli

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Re: BLS Lichen Species Dictionary (2)

For the ones I have checked it does look like the old names (taxon list_item_keys) have become synonyms of the new names. NameServer seesm to relect this, so the Gateway will be Ok as it doesn't use Taxon_List_Item_Keys.  Also if you report on the new name you will get all the old names as well providing Option 'Tranlate to full term' is set to true in Tools/Options.  Most users will not be affected, because, they will have this option set to true.

However, I am not sure the dictionary is correct in that  I think that although NameServer is dealing with these taxa as synonyms, they are not being treated as synonyms within the British Isles List of Lichens and Lichenicolous Fungi. I think they were set up as synonyms with the list, than they would appear even with the 'Translate' to full term option turned off.  Chris needs to look at this before you start changing keys. However, if it is necessary, I think it should  be possible to identify all the cases and make the change with a few quries.

Mike Weideli

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Re: BLS Lichen Species Dictionary (2)

I have switched Translate to full term on but it hasn't made any difference, the existing records for those taxa still can't be accessed through the taxon dictionary or the report wizard.

Janet

Janet Simkin
British Lichen Society

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Re: BLS Lichen Species Dictionary (2)

I wouldn't expect them to show up in the lists, because they are no longer valid taxa, just synonyms. What it would expect is that if you report on the new name you get  both old and new taxa. This isn't going to help you because you will get two lines for what is the same species. I would think you would be best redeterming the entries and I will help with this. Most general users will be reporting using the recommended name and will not be affected.

Mike Weideli

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Re: BLS Lichen Species Dictionary (2)

"What it would expect is that if you report on the new name you get  both old and new taxa" - that's what we expected as well, but it is not happening. The old records are not appearing in reports.

It sounds like redetermination is the only option, so I'll have to check through the whole database now to see if any other species are affected. Only 2600 species names to check.....

Janet

Janet Simkin
British Lichen Society

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Re: BLS Lichen Species Dictionary (2)

Hi everyone

I'm not sure whether this is perhaps an issue to do with the new checklist or just the way that Recorder reports on the records it holds? When we worked on the list I think everyone agreed that what we have in the checklist and in the wider database itself represented the correct taxonomy but is this issue a quirk with the standard Recorder reports? Would it have helped if we had included more of the old synonyms in the new checklist?

As always I'm happy to help, if I can. :)

Best wishes,
Chris R.

Chris Raper, Manager of the UK Species Inventory, Angela Marmont Centre for UK Biodiversity,
Natural History Museum, Cromwell Road, London, SW7 5BD.  (tel: 020 7942 5894)
also Tachinid Recording Scheme (http://tachinidae.org.uk/)

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Re: BLS Lichen Species Dictionary (2)

Hi Mike

Is the problem that the report is only bringing out records for names that are in the current version of the checklist? Synonyms that were not listed in the new checklist obviously still exist in previous versions (no TLIK would have been deleted) and in the Nameserver where all synonyms are resolved into their recommended names. As I remember there were quite a lot of changes in authority spelling so unwanted or confusing synonyms were taken out of the checklist itself.

Best wishes,
Chris R.

Chris Raper, Manager of the UK Species Inventory, Angela Marmont Centre for UK Biodiversity,
Natural History Museum, Cromwell Road, London, SW7 5BD.  (tel: 020 7942 5894)
also Tachinid Recording Scheme (http://tachinidae.org.uk/)

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Re: BLS Lichen Species Dictionary (2)

I think I undertsand why Janet has a  problem.  I think Janet has just been using just the Lichen list  and the preferred name for reporting, however, this doesn't work once the synonyms aren't represented in the list.  Janet has avoided the use of recommended names derived from nameserver, because up to now these have come from the Fungi list. Among other things this would mean the sort orders would be derived from the  Fungi list and not from the Lichen Society list. Changing the Lichen list to a preferred list and giving it priority over the Fungi list for the Lichen will partly solve the problem, but it would mean Janet changing her reporting to use the recommended names instead of the preferred names.   Taking everything into consideration I would think that redetermining the taxa would be the best solution. I will do what I can to help with this.

Mike Weideli

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Re: BLS Lichen Species Dictionary (2)

Thanks Mike ... as you say, it's a fearfully complex situation and, although the checklist isn't incorrect, you have to be so careful when reporting to make sure there are no underlying dependencies and assumptions being made that you are unaware of. :)

Chris Raper, Manager of the UK Species Inventory, Angela Marmont Centre for UK Biodiversity,
Natural History Museum, Cromwell Road, London, SW7 5BD.  (tel: 020 7942 5894)
also Tachinid Recording Scheme (http://tachinidae.org.uk/)

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Re: BLS Lichen Species Dictionary (2)

I have been looking into this some more and can confirm that the old data is being picked up correctly as a synonym for the new name for many taxa, but not for all. The problems are mostly to do with species aggregates, sensu latos and sensu strictos, none of which are picking up their synonyms correctly. There seem to be a few other oddities as well but I'll report back on them when I get to the end of the list. It's a long list so that will take a while.

When we redetermine these can we do it by adding a new determination rather than amending the existing one, so that we have a dated audit trail?

Janet

Janet Simkin
British Lichen Society

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Re: BLS Lichen Species Dictionary (2)

Once we have a list I will do a batch update, which will create the new preferred determinations, leaving the original determination as non-preferred.

Mike Weideli