Download XML in the Oceanographic Community An Open Discussion

XML in the Oceanographic
Community
An Open Discussion
Woods Hole Information Technology Group
Smith Conference Room
November 9, 2004
Robert C. Groman
What’s XML
• eXtensible Markup Language - A
subset of SGML making up a particular
text markup language for interchange of
structured data. XML allows one to
create customized tags that describe
data structure, but not the style.
• Originally created to deal with
electronic publishing.
• SGML – Standard Generalized Markup
Language
What or Who is W3C®?
•
•
“The World Wide Web Consortium
(W3C®) develops interoperable
technologies (specifications, guidelines,
software, and tools) to lead the Web to
its full potential.”
One usually adds to XML, the Document
Type Definition (DTD) file or schema file
(XSD), and style sheets (XSLT,
eXtensible Stylesheet Language
Transformations and CSS, Cascading
Stylesheets.)
Ontology
• Ontology combines both a vocabulary
and a taxonomy, together with a
hierarchy of concepts, relationships,
and axioms (that is, relevance).
[Edgington, 2004]
• But I digress ….
What’s XML Look Like?
<?xml version="1.0" standalone="no"?>
<basin_people>
<person invitee_location="NorthAmerican">
<name>
<first>Chris</first>
<middle>A.</middle>
<last>Jones</last>
</name>
<address>
<line>WHOI</line>
<line>"Redfield 226, MS #23"</line>
<line>"Woods Hole, MA 02543"</line>
</address>
XML Tools
• XML toolbox for Matlab
• http://www.w3.org/Tools/HTML-XML-utils/
• Growing support within existing word
processing applications
• Ties to NetCDF; Perl and other languages
• Altova’s XMLSPY
– http://www.softwarecasa.com/publ/altova.htm
Why Am I Playing with XML?
• http://globec.whoi.edu/
• http://globec.whoi.edu/jg/dir/globec/gb/
• http://globec.whoi.edu/jg/serv/globec/gb/BMP2_ess.brev0
• http://globec.whoi.edu/jg/info/globec/gb/BMP2_ess
• WebCOAST is the portal for data and information products
developed by COOA researchers at the University of New
Hampshire.
– http://webcoast.sr.unh.edu/home.jsp
• “Info file”  DIF record  XML
What’s Happening in Oceanography Circles
• There is much evidence of implementing
XML technologies at other oceanographic
sites and WHOI is not part it.
• What is “it”? Using XML technologies to
foster data and information exchange.
• WHOI isn’t fully in the game (yet).
Review of Some of the Projects
•Texas A & M
•ICES-IOC Study
Group on the
Development of
Marine Data
Exchange
•Ocean Biological
Information System
•Monterey Bay
Aquarium Research
Institute
•WHOI
• I was initially confused by
the multiplicity of efforts.
There seemed to be many
groups doing the same
thing.
• Why? It is still in the
“research phase.”
Texas A&M University
• SURA SCOOP Project
• Gerry Creager ([email protected])
• “The problem’s going to be getting the
researchers to A) agree to get involved
with data standards, metadata standards,
data transport and archive, retrieval and
catalogs, etc.; and B) perform the work
they agreed to in (A) above.”
Texas A&M University (cont.)
• “I've been working with Ken Keiser and
Sara Graves from UA/Huntsville on some
of the data issues. I think we can have a
serious positive impact on the Oceans
Community if we can get some
demonstrations of LDM and THREDDS
running to provide the model community
with some easier methods of getting the
data .…”
Texas A&M University (cont.)
• “The SURA SCOOP project has funded a
study to extend the OCEAN.US work on
metadata standards and see about codifying
some of these recommendations into a
concrete document. I'm not directly working
on that ….”
An Aside: Ocean Observing Systems and
Ocean Observatories and
• Gulf of Maine Ocean Observing System
(GoMOOS, Philip Bogden).
• Texas Mesonet is a network of
meteorological monitoring instruments,
broadly dispersed across the State.
• Funding just really starting for the OOS.
Texas A&M University (cont.)
• “The SURA SCOOP project has funded a study to
extend the OCEAN.US work on metadata
standards.”
• “IODE and MBARI have some things.”
• “UCAR/NCAR CF has potential.”
• “MBARI should, by now, have some NSF funding
from last year's money to do about a $500K piece
on […] data standards work for tethered
observatories.”
• “SURA (Southeast Universities' Research
Association) has provided about $150K additional
funds to […] SCOOP ….”
Texas A&M University (cont.)
• “ … Earth Sciences Markup Language from the
University of Alabama/Huntsville…” [information
exchange]
• “… a project from UAH called SensorML (and the
associated Sensor Web) which have also seen
interest from the OpenGeospatial Consortium.”
[data exchange]
• “Graphics are another issue.” “ … using the Wide
Area Information Server (WAIS) which is a natural
language index/database system.”
• Sees benefits in working with WHOI to benefit
TAMU and SCOOP.
International Oceanographic Data and
Information Exchange (IODE)
• http://www.iode.org/
• IOC and the International Council for the
Exploration of the Sea (ICES) are
cooperating in the development of a marine
XML and have formed the ICES-IOC Study
Group on the Development of Marine Data
Exchange Systems using XML (SGXML).
• http://www.marinexml.net/
Ocean Biogeographic Information System
(OBIS)
• http://www.iobis.org/
• OBIS is the information component of the
Census of Marine Life (CoML), a growing
network of researchers in more than 45
nations engaged in a 10-year initiative to
assess and explain the diversity, distribution,
and abundance of life in the oceans - past,
present, and future.
• OBIS is a web-based provider of global georeferenced information on marine species.
Monterey Bay Aquarium Research Institute
(MBARI)
• Mike McCann ([email protected])
• Shore Side Data System (SSDS)
• “[W]e are still working on our SSDS system
and use XML quite a bit for describing our
metadata. We have a schema and a database
and all of the supporting Java code to make it
all work. It's still very much a work in
progress.”
Monterey Bay Aquarium Research Institute
(cont.)
• John Graybeal
• SensorML work under the auspices of the
OpenGIS Consortium
(http://vast.uah.edu/SensorML) [Likes this effort;
some XML schema specified
• Ontologies for marine terminology
– SWEET, GCMD, and BODC
– http://wiki.mbari.org/marinemetadatawiki/StandardNam
eExercise
•
•
•
•
Monterey Bay Aquarium Research Institute
(cont.)
Leading the Marine Metadata project
http://marinemetadata.org
“Al Plueddemann and Bob Weller are strong
participants in the Marine Metadata project.”
“We are particularly interested in exemplars
(as you are clearly working on one) and
references.” [Referring to our effort to create
XML-based tags for US GLOBEC metadata.]
Marine Biological Laboratory (MBL) and
WHOI
• Dave Remsen, with WHOI’s Ralph Stephen,
Andy Maffei, etc.
• XML-based ontology and classification
systems.
• Has experience with Web Services using
SOAP
• owl - Ontology Web Language [????]
Conclusion
• There is much activity in the oceanographic
community, embracing the XML
technologies in order to share, exchange and
(re)serve data
• WHOI is a new player here but can offer a
lot, including experience with lots of data.
References
• http://www.cencoos.org/ - Central and Northern California Ocean
Observing System
• http://www.ices.dk/ocean/iode.htm - International
Oceanographic Data and Information Exchange (IOC)
• Edgington, Theresa, Beomjin Choi, Katherine Henson, T.S. Raghu, and
Ajay Winze, Adopting Ontology to Facilitate Knowledge Sharing,
Communications of the ACM, November 2004, Vol 47, No. 11.
• http://www.mbari.org/iag/workshops/dmv/index.html – Monterey Bay
Area Workshop on Data Management and Visualization, 2003
• http://www.w3c.org/ World Wide Web Consortium
• http://dodsdev.gso.uri.edu/ - DODS Developer's Web site (evolving DDS
plus DAS into XML version (DDX)
References (cont.)
• http://www.w3.org/2001/sw/Europe/reports/final_r
eport/ - W3C Semantic Web Advanced
Development for Europe (EU MarineXML
project, SEEGrid, IOC-UNESCO);
http://www.marinexml.net/
• Dublin Core, FGDC and Global Change
Master Directory DIF records
–
–
–
–
http://helium.gsfc.nasa.gov/User/difguide/
http://helium.gsfc.nasa.gov/Aboutus/standards/
http://dublincore.org/
http://www.fgdc.gov/standards/standards.html
[Federal Geographic Data Committee]
References (cont.)
• http://www.geongrid.org/about.html GEOsciences Network (GEON)