Ontologies at MMI

What's This?

This page contains information about the ontologies hosted by MMI on this site.

The ontologies on this site were stored as static files on the site. Please note that MMI intends to support all its ontologies using the MMI semantic repository software at http://mmisw.org/orr, and has begun this transition. Until we have fully integrated the two sites, unfortunately you will have to look at both sites to learn about all the ontologies we have. (As soon as possible, we will upload all these files to that repository.)

If you click directly on the link to the OWL file from within your browser, you will see the ontology in its native OWL format, which uses the XML representation language. (Using Safari on a Mac, you will see a blank window. You can view the XML OWL file by selecting "View Source" from the VIew menu.) This is briefly interesting, but not the best way to view these files.

How Do I Use The Ontology Files?

Ontologies that are stored in the OWL format may be viewed and edited with many different tools. Some references are provided below and elsewhere on the MMI site.

For a quick look at the ontology file via your browser, you may use a tool such as Dumpont. To do this, copy the URL of the ontology you are interested in, then go to the Dumpont page and paste the ontology URL into the field on that form. You should see the ontology represented in your browser.

To actually work with the ontology, the application most used by MMI is Protege. We have produced some tutorials on working with this tool, including a basic introduction. To search terms and do mappings you can use VINE, the  tool created at MMI.

There are many other applications which support viewing and editing OWL ontologies. You may wish to look at the references in the Tools section of this site for more options.

List of Ontologies at MMI

aerd_ctd
NS: http://marinemetadata.org/2005/08/aerd_ctd
HTML view of the ontology
aerd_underway
NS: http://marinemetadata.org/2005/08/aerd_underway
HTML view of the ontology
AGU Index Terms
NS: http://marinemetadata.org/agu
description: AGU index Terms
HTML view of the ontology
AOSN - Autonomous Ocean Sampling Network Parameters
NS: http://marinemetadata.org/2005/08/aosn-param
description: parameters with description and units
contributor: Mike Godin
source: parameters from an ASCII file created by an SQL query, version June 8, 2005
subject: parameters
URLMoreInformation: http://mammoth.shore.mbari.org:8080/las/servlets/dataset
HTML view of the ontology
ARGO - Instruments
NS: http://marinemetadata.org/2005/08/argo-inst
description: Instrument types
source: Manual v. 2.0.1 15/12/2003 from table 8
subject: Instruments
URLMoreInformation: http://www.ifremer.fr/coriolis/cdc/argo/argo-dm-user-manual.pdf
HTML view of the ontology
ARGO - Parameteres
NS: http://marinemetadata.org/2005/08/argo-param
description: Parameters and valids.
source: Manual v. 2.0.1 Version 15/12/2003
subject: Parameters
URLMoreInformation: http://www.ifremer.fr/coriolis/cdc/argo/argo-dm-user-manual.pdf
HTML view of the ontology
Aquatic Science and Fisheries Abstracts Thesaurus (ASFA) Thesaurus
NS: http://marinemetadata.org/2005/08/asfa
contributor: FAO (UN Food and Agriculture Organization)
subject: glossary terms
URLMoreInformation: http://www.fao.org/fi/asfa/asfa.asp
        Acknowledgments: MMI thanks the FAO ASFA Secretariat and the ASFA Partners for their permission to use the ASFA Thesaurus.

HTML view of the ontology
 
 
BIOMAR classification of Marine Biotypes
NS: http://marinemetadata.org/2005/08/biomar
description: BioMar classification of marine biotopes by Joint Nature Conservation Committee in Britain
contributor: Mark Costello
source: version 2005-05-02
subject: Habitat classification
URLMoreInformation:
HTML view of the ontology
BODC Parameter- Group Dictionary
NS: http://marinemetadata.org/2005/08/bodc-group
description: Parameter Group codes
contributor: BODC - British Oceonographic Data Centre - Roy Lowry
source: version 2005-05-02
subject: Parameters group
URLMoreInformation: http://wwwtest.bodc.ac.uk/data/codes_and_formats/parameter_codes/
HTML view of the ontology
BODC Instruments
NS: http://marinemetadata.org/2005/08/bodc-inst
HTML view of the ontology
BODC Parameter Markup Dictionary
NS: http://marinemetadata.org/2005/08/bodc-param
description: Parameter codes for using of markuping up data
contributor: BODC - British Oceonographic Data Centre - Roy Lowry
source: version 2005-05-02
subject: Parameters
URLMoreInformation: http://wwwtest.bodc.ac.uk/data/codes_and_formats/parameter_codes/
HTML view of the ontology
BODC UNITS
NS: http://marinemetadata.org/2005/08/bodc-units
description: Units codes: id, short name and long names
contributor: BODC - British Oceonographic Data Centre - Roy Lowry
source: version 2005-05-02
subject: Units
URLMoreInformation: http://wwwtest.bodc.ac.uk/data/codes_and_formats/parameter_codes/
HTML view of the ontology
Biological Ocean Group(BOG) CTD Bottle Fields
NS: http://marinemetadata.org/2005/08/bog-bctd
description: CTD bottle data (up cast), productivity, physical, and chemical data. One record for each CTD rosette bottle
contributor: MBARI - BOG Francisco Chavez (P.I.), Tim Pennington (Project Manager), Reiko Michisaki�
source: Version Jan 2002
subject: fields
URLMoreInformation: http://www.mbari.org/bog/mmug/MMUG_table.htm
HTML view of the ontology
Biological Ocean Group(BOG) Profiling CTD Fields
NS: http://marinemetadata.org/2005/08/bog-pctd
description: Profiling CTD (down cast), productivity and physical parameters (sensor data). One record for each meter in depth.
contributor: MBARI - BOG Francisco Chavez (P.I.), Tim Pennington (Project Manager), Reiko Michisaki�
source: Version Jan 2002
URLMoreInformation: http://www.mbari.org/bog/mmug/MMUG_table.htm
HTML view of the ontology
Calco Cast
NS: http://marinemetadata.org/2005/08/calcocast
HTML view of the ontology
calcofi_eggcounts
NS: http://marinemetadata.org/2005/08/calcofi_eggcounts
HTML view of the ontology
calcofi_p_bot
NS: http://marinemetadata.org/2005/08/calcofi_p_bot
HTML view of the ontology
calcofi_p_cast
NS: http://marinemetadata.org/2005/08/calcofi_p_cast
HTML view of the ontology
calcofi_p_proto
NS: http://marinemetadata.org/2005/08/calcofi_p_proto
HTML view of the ontology
calcofi_p_station
NS: http://marinemetadata.org/2005/08/calcofi_p_station
HTML view of the ontology
calcofi_species_codes
NS: http://marinemetadata.org/2005/08/calcofi_species
HTML view of the ontology
calcofi_station
NS: http://marinemetadata.org/2005/08/calcofi_station
HTML view of the ontology
calcofi_tows
NS: http://marinemetadata.org/2005/08/calcofi_tows
HTML view of the ontology
Coastal Data Information Program (CDIP)
NS: http://marinemetadata.org/2005/08/cdip
description: Julie Thomas
contributor: Julie Thomas
source: Shoreline protection manual ARMI CORPS of Eng.
subject: Waves measurement and models
URLMoreInformation: http://cdip.ucsd.edu
HTML view of the ontology
CMECS HABITAT CLASSIFICATION FRAMEWORK
NS: http://marinemetadata.org/2005/08/cmecs
description: Habitat classification taken from COASTAL MARINE ECOLOGICAL CLASSIFICATION STANDARD (CMECS): HABITAT CLASSIFICATION FRAMEWORK - Madden and Grossman 2004
HTML view of the ontology
NetCDF CF - Standard Name table
NS: http://marinemetadata.org/2005/08/cf

          An updated version can be found here: http://marinemetadata.org/cf

description: Controlled vocabualry use in the NetCDF Climate and Forecast (CF) Metadata Convention
contributor: Brian Eaton et. al.
source: version 2005-08-01
subject: Parameters
URLMoreInformation: http://www.cgd.ucar.edu/cms/eaton/cf-metadata/standard_name.xml
HTML view of the ontology
CORIS - Coral Reef Information System of NOAA
NS: http://marinemetadata.org/2005/08/coris
description: The glossary contains terms concerned with ecology, biogeography, evolution, taxonomy, morphology, physiology, cell and molecular biology, genetics, mapping, development, fisheries, oceanography, geosciences, conservation programs, remote-sensing, physics, chemistry, and data and information management.
contributor: Mark Costello
source: Online glossary dowloaded 2005-08-01
URLMoreInformation: http://coris.noaa.gov/glossary/welcome.html
HTML view of the ontology
NAVOCEANO's Master Oceanographic Observation Data Set (MOODS) CTD related Parameters
NS: http://marinemetadata.org/2005/08/ctd_moods_param
source: Version 04/21/2004
subject: glossary terms
URLMoreInformation: http://co-ops.nos.noaa.gov/publications/glossary2.pdf
HTML view of the ontology
EPIC - Pacific Marine Environmental Laboratory - Units
NS: http://marinemetadata.org/2005/08/epic-units
source: May 04, 2005
URLMoreInformation: ftp://www.epic.noaa.gov/epic/epic.key
HTML view of the ontology
EPIC software package attributes convetion based on netDCF
NS: http://marinemetadata.org/2005/08/epic
description: PMEL-EPIC/CTD convention for writing netCDF data files with the EPS library,for use with the EPIC software package for oceanographic data. This document is an addendum to the PMEL-EPICdocument in the Unidata /pub/netCDF/PMEL-EPIC directory,describing those characteristics which are specific to CTD-type data.This includes CTD, XBT and bottle data.
contributor: NOAA Pacific Marine Environmental Laboratory Seattle, WA
source: 22 October, 1993
subject: Attributes CTD
URLMoreInformation: ftp://ftp.unidata.ucar.edu/pub/netcdf/Conventions/PMEL-EPIC/
HTML view of the ontology
The European Nature Information System (EUNIS)
NS: http://marinemetadata.org/2005/08/eunis
description: "The European Nature Information System (EUNIS) classification is a pan-European system, which was developed between 1996 and2001 by the European Environment Agency in collaboration with experts from throughout Europe. It covers all types of natural andartificial habitats, both aquatic and terrestrial. The National Marine Habitat Classification for Britain and Ireland was fully incorporated into the EUNIS classification system. The marine section of the EUNIS classification is currently undergoing revision through the Osloand Paris Convention (OSPAR). "
contributor: FAO (UN Food and Agriculture Organization)
subject: glossary terms
URLMoreInformation: http://eunis.eea.eu.int/habitats-code-browser.jsp?habCode=A#factsheet
HTML view of the ontology
FNMOC - Fleet Numerical Meteorology and Oceanography Center- Interpolated Sea Level Pressure
NS: http://marinemetadata.org/2005/08/fnmoc
contributor: Jerome King - contact: Lynn Dewitt (ERD - Pacific Grove) NOAA/NMFS
source: Received by email July 28 2005
URLMoreInformation: http://www.pfeg.noaa.gov/products/las/docs/wind_from_pressure.nc.html
HTML view of the ontology
GCMD Instrument Keywords
NS: http://marinemetadata.org/2005/08/gcmd-inst
description: Instruments keywords with short name and long name
contributor: Olsen, L.M., G. Major, S. Leicester, K. Shein, J. Scialdone, H. Weir, S. Ritz, C. Solomon, M. Holland, R. Bilodeau, T. Northcutt, R. Vogel. 2004. NASA/Global Change Master Directory (GCMD) Earth Science Keywords. Version 5.1.1
source: version 2005-06-28 15:08:21
subject: instruments
URLMoreInformation: http://gcmd.nasa.gov/Resources/valids/keyword_list.html
HTML view of the ontology
GCMD Science Keywords
NS: http://marinemetadata.org/2005/08/gcmd-keyw
        An updated version can be found here: http://marinemetadata.org/gcmd
 
description: Science keywords categorized by: category topic term and variable
contributor: Olsen, L.M., G. Major, S. Leicester, K. Shein, J. Scialdone, H. Weir, S. Ritz, C. Solomon, M. Holland, R. Bilodeau, T. Northcutt, R. Vogel. 2004. NASA/Global Change Master Directory (GCMD) Earth Science Keywords. Version 5.1.1
source: version 2005-07-27 13:46:02
subject: parameters
URLMoreInformation: http://gcmd.nasa.gov/Resources/valids/keyword_list.html
HTML view of the ontology
GCMD Platform Keywords
NS: http://marinemetadata.org/2005/08/gcmd-platf
description: Platform keywords with short name and long name
contributor: Olsen, L.M., G. Major, S. Leicester, K. Shein, J. Scialdone, H. Weir, S. Ritz, C. Solomon, M. Holland, R. Bilodeau, T. Northcutt, R. Vogel. 2004. NASA/Global Change Master Directory (GCMD) Earth Science Keywords. Version 5.1.1
source: version 2005-07-26 13:46:14
subject: Platform
URLMoreInformation: http://gcmd.nasa.gov/Resources/valids/keyword_list.html
HTML view of the ontology
Sea Surface Temperature (GTS - Global Telecommunications System)
NS: http://marinemetadata.org/2005/08/gts
description: Sea Surface Temperature (GTS - Global Telecommunications System)
contributor: Jerome King - contact: Lynn Dewitt (ERD - Pacific Grove) NOAA/NMFS
source: Received by email July 28 2005
URLMoreInformation: http://www.pfeg.noaa.gov/products/las/docs/sst.nc.html
HTML view of the ontology
IOC STANDARD GF3 SUBSET FOR CTD DATA
NS: http://marinemetadata.org/2005/08/ioc-gf3
description: Fields for data collected by a CTD or similar profiling instrument,lowered from a single location and sampling temperature, conductivity and perhaps other variables.
contributor: Working Committee OCEANOGRAPHIC on IODE Group of Experts�
source: Version Jun 1983
URLMoreInformation: http://ioc.unesco.org/oceanteacher/resourcekit/M3/Formats/Integrated/GF3/ctd.pdf
HTML view of the ontology
IOOS - Integrated Ocean Observing System
NS: http://marinemetadata.org/2005/08/ioos
description: Core variables draft (not yet recommended) for the initial IOOS
contributor: Stephanie Watson
source: IOOS Implementation, Part II, Building the Initial IOOS, Version 8/1/2005, from Table 3 and 5
subject: parameters
URLMoreInformation:
HTML view of the ontology
Juvenile Rockfish Survey Parameters
NS: http://marinemetadata.org/2005/08/juv-rock
description: Paramters from Juvenile Rockfish Survey
source: from Juvenile Rockfish Survey - Data Manager Keith Sakuma (831) 420-3945, Keith.sakuma@noaa.gov
subject: Parameters
URLMoreInformation:
HTML view of the ontology
Classifying benthic terrains with multibeam bathymetry, bathymetric position and rugosity
NS: http://marinemetadata.org/2005/08/lunblad-05
source: As described in Lundblad, E., Wright, D.J., Miller, J., Larkin, E.M., Rinehart, R., Battista, T., Anderson, S.M., Naar, D.F., and Donahue, B.T., Classifying benthic terrains with multibeam bathymetry, bathymetric position and rugosity: Tutuila, American Samoa, Marine Geodesy, in review, 2005,and based on Lundblad, E., The Development and Application of Benthic Classifications for Coral Reef Ecosystems Below 30 m Depth using Multibeam Bathymetry: Tutuila, American Samoa, M.S. Thesis, Corvallis, OR, Oregon State University, 137 pp.description=
HTML view of the ontology
Manly Hydraulics Laboratory Glossary
NS: http://marinemetadata.org/2005/08/manly
URLMoreInformation:
HTML view of the ontology
MEDS - Marine Environmetal Data Services
NS: http://marinemetadata.org/2005/08/meds-param
description: Parameters codes and accuracies
source: Version 6/16/2004 12:58:27 PM online HTML page
subject: Parameters
URLMoreInformation: http://www.meds-sdmm.dfo-mpo.gc.ca/meds/About_MEDS/Code_Tables/standard_code_e.asp
HTML view of the ontology
MMI Sensors
NS: http://marinemetadata.org/2005/08/mmi-sensors
HTML view of the ontology
NDBC Waves
NS: http://marinemetadata.org/2005/08/ndbc_waves
HTML view of the ontology
NOAA Tide and Current Glossary
NS: http://marinemetadata.org/2005/08/noaa-tide-current
contributor: NOAA
source: Version Jan 2002
subject: glossary terms
URLMoreInformation: http://co-ops.nos.noaa.gov/publications/glossary2.pdf
HTML view of the ontology
NOAA Waves terms compiled by Richard Bouchard
NS: http://marinemetadata.org/2005/08/noaa-waves
description: Waves glossary of NOAA with synonyms of NDBC, MEDS and others
contributor: Richard Bouchard
source: Richard Bouchard's Excel file v. July 28th 2005
HTML view of the ontology
prd_ctd
NS: http://marinemetadata.org/2005/08/prd_ctd
HTML view of the ontology
PRD XBT
NS: http://marinemetadata.org/2005/08/prd_xbt
HTML view of the ontology
RDI ADCP Currents and Waves Glossary
NS: http://marinemetadata.org/2005/08/rdi
HTML view of the ontology
Southeast Association of Coastal Ocean Observing System (SEACOOS) Dictionary
NS: http://marinemetadata.org/2005/08/seacoos
description: includes standard names that are coordinate-related, time_date names, atmospheric data, physical oceanographic, chemicaloceanographic, electromagnetic radiation, ADCP, sensor-related, platform-related,M_aeri data-related, and navigation. For each name, there is a definition, shortname, long name, data type, data class, units, axis, valid range, parameter reference, instrument general, equivalent standard name, and standard.
contributor: Jeremy Cothran
source: Accessed 2005-08-02 11:52:00 am pacific time
URLMoreInformation: http://marinemetadata.org/vocabularies/refs/markup/seacoosdd
HTML view of the ontology
SSDS Parameters
NS: http://marinemetadata.org/2005/08/ssds-param
description: SSDS parameters in an ontology. A CSV was generated from the database and an automatic conversion was created by MMI.
contributor: Kevin Gomez
source: SSDS Shore Side Data System (SSDS)
subject: parameters
URLMoreInformation: http://ssdspub.mbari.org/
HTML view of the ontology

UCUM Units

           NS: http://marinemetadata.org/ucum

           description:  The Unified Code for Units of Measure in OWL

           contributor: Luis Bermudez

           source: Created from an XML document version 1.6 available at http://aurora.rg.iupui.edu/UCUM/. Using    

                           http://marinemetadata.org/ucumtoowl.xslt

         subject: units

 URLMoreInformation: http://aurora.rg.iupui.edu/UCUM 
 HTML view of the ontology
U.S. GLOBEC Fields Data Thesaurus
NS: http://marinemetadata.org/2005/08/us-globec-fields
description: Field names used by the U.S. GLOBEC Program
contributor: US GLOBEC
source: Revised: July 12, 2005
subject: paramterers
URLMoreInformation: http://globec.whoi.edu/globec-dir/thesaurus.html
HTML view of the ontology
U.S. GLOBEC Instruments
NS: http://marinemetadata.org/2005/08/us-globec-inst
description: Instrument names used by the U.S. GLOBEC Program
contributor: US GLOBEC
source: Globec Thesaurus version: Revised: July 12, 2005
URLMoreInformation: http://globec.whoi.edu/globec-dir/thesaurus.html
HTML view of the ontology
U.S. JGOFS Dictionary of parameters
NS: http://marinemetadata.org/2005/08/us-jgofs
source: version Friday, 10 September 2004 (14:53:29 EDT)
URLMoreInformation: http://usjgofs.whoi.edu/datasys/param_master.html#Org
HTML view of the ontology