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EMuUsers Administrator
Posts:41
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| 21-04-2005 12:49 AM |
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I'm curious how other institutions handle certain situations involving
changes in accepted taxonomy. For example, suppose you have 100 records in
the Catalog module identified as scientific name A. They each have a single
link to name A in the Taxonomy module. Now suppose name A is determined to
be a synonym of name B. Presumably you would represent this in EMu by
making name A a synonym of name B in the Taxonomy module. This would
(obviously) not update the name (A) in the Catalog Summary Data for those
100 records.
Now suppose you acquire a new collection containing 50 specimens of this
taxon. When you catalog these in EMu, presumably you will use the currently
accepted scientific name B. The previous 100 records will thus have a
different name in their summary data than the 50 new specimens.
Does anyone handle this situation differently, say by changing the link to
Taxonomy for the original 100 records, or by adding a new link to name B to
those 100?
If not, how do you handle querying for specimens of this taxon? It seems
you'd have to query through the Taxonomy module for "B and any synonyms of
B" in order to get all records IDed as B or as A.
And how does this affect querying through the public web interface?
Thanks!
Tom Trombone
Thomas J. Trombone
Data Manager
Division of Vertebrate Zoology - Ornithology
American Museum of Natural History |
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EMuUsers Administrator
Posts:41
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| 21-04-2005 3:36 AM |
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Tom et al.,
I suggest the way to handle this is the same way to handle labels: - in
the taxonomy module, you synonymized name A with B as suggested - all of
your specimens will then receive an annotation label with the new name B
- in your catalogue, you add the new name B as additional identification
for each of those collections, and click this name as Filed Under: Yes;
you then have an identification history of which the most actual name is
the displayed name (depending on how you set your identification table)
- if you get new collections, they will be labelled and databased with
name B only I guess there should be some automatism involved here; for
example, select all catalogue records with name A; add name B as
additional identification for each record (kind of a global replace of
an empty field with a name). I don't know whether this is possible in
EMu but it should be. Robert
-- Robert Luecking
Department of Botany
The Field Museum of Natural History |
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EMuUsers Administrator
Posts:41
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| 21-04-2005 10:18 AM |
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Dear Everyone,
We essentially follow what has already been stated. However, we do not automatically relabel the collections previously catalogued under name A as name B. The collections are checked to make sure that the identification as name A was actually correct in the first place before the new name B is applied. Once this process is complete, then the name of each of the database records is corrected, either to the new name B or to some other identification. This process is the slowest part of our curation process and is the point that tends to fail. Irrespective of the weakness of the current system, global changes are regarded as too problematic. Of course, partial taxon concept changes can only be re-identified by looking at each collection sepearately. However, it would be nice if EMu would give the option of returning the records identified by one name, plus all the synonym names. Unfortunately, this is not possible, at least, not with our version of EMu. For web delivery, in our!
plant information service - PlantNET (http://plantnet.rbgsyd.nsw.gov.au/), a user can search via a synonym or by the accepted name.
Cheers
Barry |
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EMuUsers Administrator
Posts:41
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| 21-04-2005 11:13 AM |
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Hi there,
I also essentially follow what Robert said below, but try to get around
Barry's problem of identification accuracy by adding a qualifier to the
records of specimens which have not been reidentified (I don't have the
resources to confirm identifications for all updates). The qualifier is:
"junior synonym update - specimen not re-examined" and it currently goes
into the identification notes field.
I agree with Barry that it would be nice for Emu to have the option of
returning records identified by one name, plus all the synonym names -
especially as our types are catalogued by the name under which they were
described. The only way to currently return all synonyms is to ensure
that the the accepted name and the synonyms are included in the
identification histories of relevant records.
Cheers,
Di
Dianne J Bray
Collection Manager, Fishes, Reptiles and Amphibians
Sciences Department, Museum Victoria |
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EMuUsers Administrator
Posts:41
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| 21-04-2005 11:52 AM |
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Hi again,
I have been thinking about my problem with EMu returning all associated names and, of course, there is a solution - I just did not think of it when I last wrote. One should go to the taxonomy record and recover all the names and then include these in the catalogue search.
Cheers
Barry |
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EMuUsers Administrator
Posts:41
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| 22-04-2005 5:36 AM |
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Thanks for your responses!
I understand what Barry means about global changes being problematic, but in
a very large collection I'd think the alternative - changing potentially
thousands of records by hand - may not be feasible.
Like Diane, we won't have the resources to confirm IDs on all our specimens
before updating their taxonomy in EMu. I like the idea of using comments to
indicate new names due to taxonomic revisions, but it has seemed to me that
it would be cleaner (and more normalized) to restrict such revisions to the
Taxonomy module and add new name links to the Catalog record only when the
determination actually changes. But we'd presumably still need a way to get
the currently accepted name into the Catalog record.
Of course synonyms can be recovered by sub-querying through Taxonomy first
(as Barry pointed out). Does anyone's public web interface do this? Or
does everyone have the public query directly on Catalog for searches by
taxon name?
Cheers,
Tom |
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EMuUsers Administrator
Posts:41
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| 22-04-2005 6:36 AM |
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Tom - FMNH has a Taxonomy query, independent of the specimen data.
See http://emuweb.fieldmuseum.org/botany/taxonomic.php
Keep in mind we are only Botany so far.
Regards,
Joanna |
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EMuUsers Administrator
Posts:41
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| 22-04-2005 7:05 AM |
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Re-reading what I wrote, I think I was unclear. I was wondering if anyone has the public query for specimen data from the Catalog module by first going through the Taxonomy module, to catch any records IDed as synonyms of the taxon requested. (So a person would query over the web for your holdings of specimens of taxonomic name X, and the query would first look in Taxonomy to see what synonyms are associated with that name (say, Y and Z), and then look for specimens in Catalog IDed as any of those names – X, Y, or Z.) This way records from Catalog that had not yet been updated would be returned, as long as the synonym links already existed in Taxonomy. If I understand correctly FMNH allows querying for specimen data on Catalog, or querying for purely taxonomic data on Taxonomy, but doesn’t link them anyhow.
Cheers,
Tom |
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EMuUsers Administrator
Posts:41
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| 22-04-2005 5:01 PM |
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Hello Tom,
The KE EMu Mapper currently does exactly this. Unfortunately the data
returned can be a little confusing, while being strictly correct. If you
ask for taxon X, you may end up getting back taxa Y and Z (as you
suggest). The issue is that it takes a specialist in that area to
recognise that in fact X, Y and Z are really the same thing. When the
results are mapped it gets worse since each of X, Y and Z are mapped
using different colours (as they are different taxonomy records). So
while it is possible to do what you request, I suppose I am just
flagging that it may be hard to explain to people the results that are
displayed.
Regards
bern. |
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EMuUsers Administrator
Posts:41
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| 14-06-2005 1:10 AM |
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I wish someone from KE would chime in on this thread.
At CMA we do not have taxonomy but we do have what I think is a similar problem when a Party has been known by various names over its history and each iteration is entered in emu as a separate Party, linked to the other iterations as synonyms.
I thought that when searching for any one of these names in the Catalogue, you would get records associated with any one of the synonymous parties. I thought that was the whole point of synonyms. But obviously I've not actually tested this.
One way to accomplish the same outcome, I think, would be to exploit the Also Search function in the registry. I think if you did an Also Search registry entry for that module (Parties for us, Taxonomy for you) whereby the Summary Data field will also search on the Synonym field, then when you enter a name in the catalogue query form, thereby launching a search in the linked module's Summary Data field, it would also return any matches in the Synonym field.
I would have tested this theory but am home today with a sick daughter. If someone tries, would you let me know if it works?
Will
William Real
Director of Technology Initiatives
Carnegie Museum of Art |
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