Fwd: electronic tagging data base

Wed Feb 4 21:50:44 PST 2004

Hi Bill, John, and others,

Personally, I think they should definitely interact with us at NCEAS due 
to our role in developing Morpho and EML, and they very well might get a 
lot out of contacting PISCO because of the similarity in usage of Morpho 
within PISCO.  I think the LTER has a lot to add regarding EML usage, 
and may also have good insight into Morpho as time passes.  Probably the 
best way to contact the right knowledgeable people is to write to 
'morpho-dev at ecoinformatics.org' for Morpho questions and 
'eml-dev at ecoinformatics.org' for EML questions.  Both lists contain a 
mix of people from NCEAS, PISCO, LTER, and other sites who will be 
responsive to PFRP's quesitons and needs.

I've put some comments below in John's email to try and answer some of 
his initial questions.   Let me know if you'd like further clarifications.

Matt

*********************************************************************
* Matt Jones
* National Center for Ecological Analysis and Synthesis
* UC Santa Barbara
* 907-789-0496             jones at nceas.ucsb.edu
*********************************************************************

wmichene at lternet.edu wrote:

> Matt and James,
> 
> The PFRP is very much interested in eml&Morpho for pelagic fisheries data.  As 
> you can see from the message below, they are interested in points of contact 
> for examining extensibility of morpho for specific needs. 
> 
> Would it be best for them to interact with NCEAS, PISCO, LTER, or all of the 
> above?  
> 
> Note that I have cc'd the director of the program in this message, so you may 
> respond directly to all.
> 
> thanks for your input!
> 
> Bill
> 
> 
> ----- Forwarded message from John Sibert <sibert at hawaii.edu> -----
> Date: Thu, 29 Jan 2004 09:04:35 -0500
> From: John Sibert <sibert at hawaii.edu>
> Reply-To: John Sibert <sibert at hawaii.edu>
> Subject: electronic tagging data base
> To: Bill Michener <wmichene at lternet.edu>
> 
> Dear Bill,
> 
> Thank you very much for you presentation to the PFRP PI meeting in
> December. I may have mentioned to you that some colleagues and I are
> contemplating creating a shared data base for electronic tagging data. Your
> talk opened my eyes to the fact that other people have addressed this
> problem and pointed me to some tools. I downloaded Morpho, created a
> prototype data base for one of our tags, and uploaded it to the KNB web
> site. (It contains only 2 days of raw data, but the full set of processed
> data.) To see it. point your browser to
> http://knb.ecoinformatics.org/index.jsp Then type "fish track" (without
> quotes) in the search box. It should turn up a "package" entitled "Raw data
> and estimated track for mooring tag 97-224" click on it to see a prototype
> shareable data base.
> 
> I'm not quite ready to recommend this to my colleagues, but it has some
> advantages. It makes use of XML and uses the EML "standard" for ecological
> data. 

And the new version that we are working on supports the full EML 2.0.0 
specification.
Hosting is taken care of. Access can be controlled (but I haven't
> figured it out yet). 

Access control is based on unique distinguished names for users in the 
shared community LDAP database.  The interface in Morpho 1.4 is 
difficult to use by anyone other than an EML expert -- the upcoming 1.5 
release of Morpho will have a substantially improved access control 
interface.  If you need help with the existing interface, let us 
know...its not hard but you have to know the right syntax for 
distinguished names of users.

It has a user interface. On the other hand Morpho is
> slightly annoying to use. 

Yep. We've been working on this.  Its an incremental process, and I 
think you'll find the upcoming 1.5 release to be a completely different 
(and better) user experience.  Bear with us...developing good user 
interfaces is not easy, especially with small development teams like 
ours.  And on that note, we appreciate any feedback on things that were 
particularly annoying or that you think would improve the interface 
substantially.  We also would welcome code contribtions that improve the 
interface as long as you work with us to make sure your ideas are 
compatible with the direction we're taking Morpho.  We'd be happy if 
there were broad community participation in the design and development 
of Morpho.

The EML standard lacks some features that we
> might want to have. In particular, additional metadata fields would be
> required for electronic tags and data compression would be required for raw
> data. 

Data compression is completely possible with the current eml-2.0.0 
standard -- you just need to indicate the compression algorithm in the 
eml-physical section of the metadata.  The new EML 2.0.0 standard is 
extensible (it allows arbitrary additionalMetadata sections that can be 
validated or not at the user's choice).  So electronic tags should be 
supported there at a minimum, even if there isn't a specific field in 
EML for that information.  If you think this information is general 
enough to be added to the EML specification, you can propose such an 
enhancement on eml-dev at ecoinformatics.org and it will be discussed and 
considered for a future release of EML.

And it is not strictly under control of the PFRP, an issue that will
> concern some of my colleagues.

Because EML is extensible (you can add your own fields), I hope it would 
meet your needs.  That said, EML development is an open, 
community-oriented process, so you can very easily influence or even 
drive the development of the specification by getting actively involved 
in the EML project.  More information on contributing to EML is 
available at http://knb.ecoinformatics.org/software/eml

> It would seem that since EML is based on XML, it is extensible. Therefore
> we could extend both XML and Morpho to be more suitable for use in
> electronic tagging. Can you suggest someone I should contact in the EML
> community that could give me some feedback?

Anyone on eml-dev at ecoinformatics.org can help with technical issues.  If 
you want you can email me directly and I can try to direct your request 
appropriately.  In any case, you probably want to use the structures 
found under "/eml/additionalMetadata" for customization as an initial 
starting point -- I'd be happy to explain how the reference pointers 
work in that section if it isn't clear to you from the EML specification.

I'm glad to see you're working with the specification, and thanks for 
your comments.  Cheers,

Matt

> Best wishes for the New Year,
> John
> 
> 
> 
> 
> 
> ____________________________________
> 
> John Sibert, Manager
> Pelagic Fisheries Research Program
> University of Hawaii at Manoa
> 1000 Pope Road, MSB 313
> Honolulu, HI 96822
> United States
> 
> Phone: (808) 956-4109
> Fax: (808) 956-4104
> ____________________________________
> 
> Washington DC
> Phone: (202) 861 2363
> Fax: (202) 861 4767
> ____________________________________
> 
> PFRP Web Site:   http://www.soest.hawaii.edu/PFRP/
> email:  sibert at hawaii.edu
> _________________________________
> 
> 
> 
> 
> 
> 
> 
> 
> 
> ----- End forwarded message -----