electronic tagging data base

Sun Feb 29 16:01:51 PST 2004

Chris,

Thanks for your thoughtful reply to my comments and queries. I'm sure we 
will look into Morpho 1.5 in the near future.

Regards,
John

  At 10:27 AM 2/29/2004, Christopher Jones wrote:
>Hi John,
>
>I was just able to catch up on this conversation thread, and thought that 
>I'd chip in since Matt hadn't been able to respond back yet.  He can 
>clarify things as well.  I work for PISCO, and have discussed using this 
>system for a shared tracking database during a workshop at UC Santa Cruz, 
>but at the time, people at the meeting were leaning towards a Microsoft 
>Access type database.  Also, morpho was in an even earlier development 
>stage at that point.  I'll comment where I can inline.
>On Feb 9, 2004, at 8:01 AM, John Sibert wrote:
>
>>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.
>I found it particularly useful when I had multiple roles to fill.  For 
>instance, I use one profile to manage data in my PISCO role, so my profile 
>logs me in as uid=cjones,o=PISCO,dc=ecoinformatics,dc=org. (This is my 
>unique identifier in the distributed LDAP authentication database).  Next, 
>since I collaborate with folks at the Santa Barbara Coastal LTER, I use 
>another profile that logs me on as 
>uid=cjones1,o=LTER,dc=ecoinformatics,dc=org.  What is very powerful about 
>this system is that I can share datasets that I create as my PISCO profile 
>with people outside of that user community.
>
>>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.
>Setting this directory in the Preferences dialog seems like a good 
>idea.  Developers struggled with how accessible this directory should be, 
>because it essential stores the internal Morpho files, and any manual 
>changes to them from outside of Morpho could potentially make them 
>unreadable by morpho.  The reason for this is mostly due to the strong 
>version control in Morpho (and the Metacat database).
>
>>3. The type face used in the field descriptions within Morpho is too 
>>small for old eyes such as mine.
>Noted.
>
>>3. I like the "tree" display of the metadata structure.
>Noted.  This is constantly debated, and new ways of presenting the 
>metadata are also being developed.  If you understand XML, the tree can be 
>easy to navigate.  If you understand EML, it's even easier.  If your 
>metadata management experience largely stems from using tables (ie RDBMS), 
>than it can be a stretch.  It's hard to balance the UI needs of everyone.
>
>>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.
>Ah, that's an interesting issue.  During the development of EML, the 
>GeographicCoverage section largely reflected what was in the USGS's 
>geospatial standard (CSDGM FGDC-STD-001-1998).  The Spatial Domain section 
>(1.5) defined the range of each bounding coordinate to be:
>Domain:  -90.0 <= North Bounding Coordinate <= 90.0
>Domain:  -90.0 <= South Bounding Coordinate <= 90.0
>Domain:  -180.0 <= East Bounding Coordinate <= 180.0
>Domain:  -180.0 <= West Bounding Coordinate < 180.0
>
>And so, that's where the convention came from.  So, it seems that tools 
>like Morpho should 'present' the interface based on a preference, and do 
>the conversion, as you had mentioned in software like GMT.
>
>>5. Need to be able to copy and paste into Morpho fields.
>Noted.  Depending on the version of Morpho that you are using, this may 
>already have been addressed.
>>6. Some of the field documentation is ambiguous, eg. what does 
>>publication place mean? A city or a journal?
>Yes, documentation is a tough one.  The tooltip popups in Morpho are not 
>hard-coded into the application.  Rather, they are parsed from the 
>documentation fields that are embedded into the EML schema documents.
>We've struggled with the 'audience' for the documentation.  Some of the 
>documentation needs to target developers, whereas other field 
>documentation needs to target different user communities.  For instance, 
>people that frequently use GIS are accustomed to the the concepts of 
>'entities' and 'attributes', whereas other folks may only be familiar with 
>'tables' and 'columns'.
>So, the documentation largely relies on EML - but there's nothing to say 
>that you couldn't modify the EML schema prior to compiling Morpho, such 
>that the documentation more closely targeted your user community.
>So you know, the KNB has faculty, graduate students, and postdocs involved 
>in formally testing the KNB software.  There's been a bunch of feedback on 
>documentation, and in particular, there has been an effort to refine the 
>help system within Morpho for the ecology community.
>Okay - well - this is a long subject, but to answer your question - 
>publication place is the city in which the article, book, etc. was published.
>
>>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.)
>Yep. Point well taken.  We need people to take part in this that lean to 
>the domain science side rather than the technology side.
>>
>>A couple of specific questions:
>>1. Can you please tell me how to control access to a specific user or a 
>>group of users?
>If this is Morpho 1.4, access control is linked in at the 'top' level of 
>the dataset, so you need to open the data package, and in the summary box 
>at the top (with the author, title, etc.) click on the 'more' link.  this 
>opens up the general info panel more, and at the bottom there is a link 
>that says "something.x.x provides access control rules for 
>something.x.x".  Click on the first link to view the access control rules. 
>Once you are viewing them, click on the 'edit' button to edit them in the 
>tree editor.
>
>FYI, much of this clunkiness is changing in the Morpho 1.5 release, since 
>it now has support for EML2.0.0.  There has been major improvement to the 
>interface.  The status of this is tracked in the bug database at:
>
>http://bugzilla.ecoinformatics.org/show_bug.cgi?id=88
>
>>2. Must the data be hosted at KNB web site or could host the data at the 
>>PFRP web site?
>You can definitely host the data locally by installing and maintaining 
>your own Metacat database.  At PISCO, we run two metacats, and plan to 
>replicate data between them using the built-in replication feature of 
>Metacat.  When our system is stable, we also plan to replicate to the 
>central KNB servers so that our metadata are viewable to a wider 
>community.  Still, all access control is respected across catalogs, so the 
>KNB metacats will only allow users to view data and metadata that are 
>authorized.
>
>>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?
>Yes.  In the tree editor, you can copy a whole section of a tree (with the 
>children), and paste it into a section of another tree in another window.
>
>
>
>I'm sure Matt and the other developers can go into more detail than I have 
>here.  Also, keep an eye out for the 1.5 release.  You can get an alpha 
>copy if you'd like from the developers, too.  Just say the word.
>
>Take care,
>Chris
>http://www.piscoweb.org
>_________________________________________________________________
>christopher jones     cjones at lifesci.ucsb.edu      (805) 680-5946
>marine science institute  university of california, santa barbara
>_________________________________________________________________

____________________________________

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
_________________________________