Fwd: electronic tagging data base

Mon Feb 9 08:01:53 PST 2004

Hi Matt (et al.),

Thanks for your constructive an helpful response.

I will make a few specific comments and queries about this Morpho/EML 
system. I hope you will take the comments as constructive and the queries 
as those of a newbie user.

First, I should clarify our application. The application of electronic tags 
to marine fishes is an new, rapidly developing and highly competitive 
field. As a result there a certain level of mistrust among some members of 
the community. Nevertheless, people are beginning to realize that more data 
are accumulating than can be easily analyzed and that more brains might be 
better. Some of my colleagues have asked the PFRP, as an honest entity, to 
host a data sharing facility. I have felt for some time that fisheries 
people need to move closer to the ecology mainstream. Thefore Bill 
Michener's presentation to the PFRP workshop in December was revelatory 
because it showed me a way to approach the data sharing problem in a way 
that would help fisheries types to become members of the ecology community. 
Thie PISCO connection seem particularly relevant.

So here are my comments and questions (in no particular order).

1. I find the notion of "profile" a bit confusing. It seems more applicable 
to the web site than to the creation of a data base on a local computer.
2. The location of the Morpho files in a W32 system is not where I would 
have placed them and I could find no way to modify the default directory.
3. The type face used in the field descriptions within Morpho is too small 
for old eyes such as mine.
3. I like the "tree" display of the metadata structure.
4. The use of east and west longitude is awkward for those of us who 
operate near the dateline and who track fish that cross it regularly. We 
generally use east longitude for the whole domain, ie. positive longitude 
from 0 to 360 so that west longitude extends from 180 to 360 (instead of 
-180 to 0). Good public domain mapping software, such as GMT, easily 
accommodate this convention.
5. Need to be able to copy and paste into Morpho fields.
6. Some of the field documentation is ambiguous, eg. what does publication 
place mean? A city or a journal?
7. Some of the documentation is a bit jargon heavy. It took me some time to 
figure out that a resource is the data base. (I have had some experience 
building GUIs, and one lesson that I learned is that the developer of the 
software should not write the documentation.)

A couple of specific questions:
1. Can you please tell me how to control access to a specific user or a 
group of users?
2. Must the data be hosted at KNB web site or could host the data at the 
PFRP web site?
3. In our tracking applications, many data fields would be similar and 
would be repeated many times. For example, a track consists of date, 
longitude and latitude. Or the raw data from one model of electronic tag is 
always comprised the same fields. Is there a way to copy meta-data from 
file to file?

Thanks for your help.

Regards,
John sibert
At 12:50 AM 2/5/2004, Matt Jones wrote:
>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 -----
>
>

____________________________________

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
_________________________________