[eml-dev] EML question

[Margaret O'Brien]

Hi Gail -
Adding to what Callie told you, I have seen several ways to include 
taxonomic information in EML. By the way, the document that Callie 
referenced is not really precise in it's recommendations, partly because 
in 2004 there were not a large number of rich EML files to learn from. 
It is in need of an update, and somewhat specific to LTER needs, but if 
you are interested in seeing how one group uses EML, I can get a copy to 
you.

We often put taxonomic information in a data table as you have 
suggested. This is the simplest method when the list is long, or is 
already included in the table to be published. If a dataset is concerned 
with only a few species, then we include a taxonomicCoverage tree with 
all the ranks labled. The flexibility of EML means that you could 
include any (or all) ranks, or just the unique binomial. The entire 
binomial should be included as one string, according to the rules of 
binomial nomenclature. So this form is recommended:
<taxonomicClassification>
<taxonRankName>genus</taxonRankName>
<taxonRankValue>Macrocystis</taxonRankValue>
<taxonomicClassification>
<taxonRankName>species</taxonRankName>
<taxonRankValue>Macrocystis pyrifera</taxonRankValue>
</taxonomicClassification>
</taxonomicClassification>

but not
<taxonomicClassification>
<taxonRankName>genus</taxonRankName>
<taxonRankValue>Macrocystis</taxonRankValue>
<taxonomicClassification>
<taxonRankName>species</taxonRankName>
<taxonRankValue>pyrifera</taxonRankValue>
</taxonomicClassification>
</taxonomicClassification>

Ideally, it would be great to get all the taxonomic info into the 
metadata so that it can be effectively searched. This can be impractical 
though, and if many taxa are included, the metadata can be quite 
extensive. I have cc'd the EML development group with your question, in 
case any others want to chime in. Please let this group know of your 
experiences using EML -
Regards,
Margaret O'Brien

========================
Margaret O'Brien
Information Management
Santa Barbara Coastal LTER 
Marine Science Institute
University of California
Santa Barbara, CA  93106-6150

805-893-2071
mob at icess.ucsb.edu
http://sbc.lternet.edu
========================



Callie Bowdish wrote:
> Hi Gail,
>
> Here is a section out of the LTER emlbestpractices_oct2004.doc. I 
> think the phrase "organisms relevant to the study" and "broader 
> taxonomic searches" are helpful things to keep in mind when making 
> decisions on how much taxonomic information to include. It is also 
> considered important to include the Classification System or authority 
> that was used for naming when possible. Archived data is designed to 
> last for a long time so the ability to find something that may not 
> seem so important currently may in the future be valuable. It is also 
> a good reason to put some thought into including the Classification 
> System and choosing what taxon to include in the eml document.
>
> "<taxonomicCoverage> The <taxonomicCoverage> element (see Example 2.1) 
> should be used to document taxonomic information for all organisms 
> relevant to the study. Genus, species name binomial and common name 
> should always be included, but higher level taxa should also be 
> included whenever possible to support broader taxonomic searches. 
> Blocks of <taxonomicClassification> elements should be hierarchically 
> nested within a single <taxonomicCoverage> element as illustrated in 
> Example 2.1 rather than repeated at the same level. The 
> <generalTaxonomicCoverage> element should be included to describe the 
> general procedure of how the taxonomy was determined (keys used, 
> etc.), should include a general textual description of all flora/fauna 
> in the study (scope), as well as how finely grained the taxonomy is 
> broken down to – for example “family” or “genus and species.”
>
> Note that elements within common <taxonRankName> entries can be 
> combined in the hierarchy to create a taxonomic “tree” (not 
> illustrated), but this practice may impede combining and re-using 
> <taxonomicClassification> information from multiple documents and is 
> not generally recommended for data set documentation."
>
> I have also cc'd Matt Jones at NCEAS and Margaret who is an LTER 
> information manager to see if they have any comments or insight into 
> your "best practice" question.
>
> Callie
>
>
> Gail Steinhart wrote:
>> Hi Callie,
>>
>> We're wondering if there is a "best practice" when it comes to 
>> specifying taxonomic coverage in EML. We have some data sets where 
>> there are a couple of dozen species (fish), and others where there 
>> might be hundreds (phytoplankton). In most cases we have or can make 
>> (without too much effort) a complete table of species and upload that 
>> as a data table, but is that overkill? Would it be better to simply 
>> specify a higher taxa - (phytoplankton rather than all of the 
>> species)? Can you offer any advice on that?
>>
>> Thanks,
>> Gail
>>
>>
>>
>> Gail Steinhart
>> Research Data & Environmental Sciences Librarian
>> Albert R. Mann Library
>> Cornell University
>> Ithaca, NY 14853
>>
>> Phone: 607-255-7251
>> Fax: 607-255-0318
>> E-mail: GSS1 at cornell.edu
>>