Development of an Integrated Regional, National and International Data System for Oceanography

Lead PI: Dr. Peter Cornillon, University of Rhode Island

This consortium will plan and implement a network based system that will provide for the discovery of and seamless access to oceanographic data. The system will build on the rapidly growing Distributed Oceanographic Data System (DODS) framework. As part of the effort, the system will be seeded with a broad suite of oceanographic data and tools will be developed to facilitate unsolicited contributions to the system in the future. In that many of the components required to build such a system already exist, the planning process will focus on determining the modifications that might be required for these components as well as on defining components that are missing. The implementation will focus on assembling these components into an integrated system. This effort will:

  • Result in the design and implementation of an infrastructure for the Virtual Ocean Data Hub (VODHub) system, an integrated – interoperable- oceanographic data environment;
  • Link in excess of two terabytes of oceanographic data held in over 250 data sets at approximately 40 sites via this system;
  • Establish a diverse group from the ocean data user community committed to the success of the system; and
  • Build the basic infrastructure required to couple data providers and users in the science community with data providers and users in the geographic information system (GIS) community

Number of Years: 3

Start Year: 2000

End Year: 2003

Partners:

  • University of Rhode Island – project lead, systems
  • Oregon State University – regional coordinator
  • University of Wisconsin – regional coordinator
  • University Corporation for Atmospheric Research – project manager, user support (UNIDATA)
  • Massachusetts Institute of Technology – systems
  • Texas A&M University – regional coordinator
  • University of Maryland – data provider
  • U.S. Geological Survey (Coastal and Marine Programs) – data provider
  • National Aeronautics and Space Administration
  • Jet Propulsion Laboratory – data provider
  • Goddard Space Flight Center – systems and directory/search
  • Naval Research Laboratory – data provider
  • National Oceanic and Atmospheric Administration
  • Coastal Services Center – regional coordinator, workshops
  • National Geophysical Data Center – GIS
  • Pacific Marine Environmental Laboratory – WebCrawler, web interface
  • State of Maine Department of Marine Resources – regional coordinator
  • Meteo-France – data provider
  • Bureau of Meteorology Research Centre – data provider
  • Minerals Management Service – data provider
  • Science Application International Corporation – data provider
  • Environmental Systems Research Institute, Inc. – GIS

FY 2003 PI Report


Development of a Dynamic Biogeographic Information: A Pilot Application for the Gulf of Maine

Lead PI: Dr. Dale Kiefer, Wrigley Institute of Environmental Studies, University of Southern California

The Gulf of Maine, and contiguous waters, has been recently designated as a pilot site for the Sloan Foundation’s program “Census of Marine Life.” This partnership will contribute to this pilot project by developing a Biogeographical Information System for the region. The Gulf of Maine Biogeographic Information System (GMBIS) will contain the tools and characteristics necessary for integration, analysis, visualization, and communication of the diverse types of information necessary for assessing the habitats and sizes of marine populations. The databases that will be integrated into the system include those of the Bedford Institution of Oceanography in Halifax, the Northeast Fishery Science Center in Woods Hole, and the Atlantic Reference Center in St. Andrews. These databases contain abundant and historic information on the ecological conditions with the Gulf, distributions and abundance of species, fishery exploitation, taxonomic collections and life history information, and allelic characterization of key commercial stocks. Although these databases have been developed independently, when fully integrated into GMBIS they will provide a more complete picture of biogeographic conditions within the region. GMBIS will also contain EASy (Environmental Analysis System) an advanced oceanographic system developed by Systems Science Applications, Los Angeles. EASy is unique among geographic information systems because it provides a dynamic (time dependent) three-dimensional environment for data processing and visualization. The development of GMBIS will not only provide a model for the global Ocean Biogeographical Information System, but it also will provide a powerful tool to meet the new international and Canadian national demands for integrated and ecologically responsible management of marine resources.

Number of Years: 2

Start Year: 2000

End Year: 2002

Partners:

  • University of Southern California – Coordinator, database developer
  • BIO, Department of Fisheries and Oceans (Canada) – Coordinator, data manager, fisheries biology, oceanography, genetics
  • Atlantic Reference Center, Huntsman Marine Science Center (Canada) – taxonomy
  • System Science Applications – Systems engineers: interfacing of GIS with databases

For more information on this project, click here.

FY 2002 PI Report


The Fishnet Distributed Biodiversity Information System

Lead PI: Dr. Edward Wiley, Natural History Museum, University of Kansas

This partnership will develop an innovative community network architecture for accessing marine biodiversity data across the Internet by employing Z39.50 technology to link 21 fish specimen databases, providing access to over 39×106 specimens documenting species’ distributions on a global scale. This architecture is timely because information technology has matured to the point that global information networks linking and integrating heterogeneous and scattered information sources are feasible. The FISHNET prototype demonstrates the feasibility of the project. The ichthyological community has a long tradition of capturing museum records electronically and sharing these data openly, and thus is positioned to act as a leader in pioneering efforts to link biodiversity data sources worldwide. This partnership will also provide workshop training for representatives from each partner institution in order to disseminate this technology, allowing for the natural expansion of the network to other groups of marine organisms. As an Ocean Biogeographical Information System (OBIS) node, FISHNET can provide an immediate product that meets the goals of OBIS to institute the Global Biological Information Facility’s biodiversity information mandate by federating marine biodiversity data sources in a system freely and openly available via the Internet.

Number of Years: 2

Start Year: 2000

End Year: 2002

Partners:

  • University of Kansas – Coordination of FISHNET with partner institutions, develop Z39.50 interface and other aspects of the project
  • Cornell University Ichthyology Collection – Provide and maintain database, attend workshop, coordinate placing of server
  • University of Southern Mississippi, Gulf Coast Marine Laboratory – Provide and maintain database, attend workshop, coordinate placing of server
  • Harvard University Museum of Comparative Zoology – Provide and maintain database, attend workshop, coordinate placing of server
  • Scripps Institution of Oceanography – Provide and maintain database, attend workshop, coordinate placing of server
  • University of Texas, Texas Memorial Museum – Provide and maintain database, attend workshop, coordinate placing of server
  • Tulane University Natural History Museum – Provide and maintain database, attend workshop, coordinate placing of server
  • University of Alabama – Provide and maintain database, attend workshop, coordinate placing of server
  • University of Michigan Museum of Zoology – Provide and maintain database, attend workshop, coordinate placing of server
  • Australian Museum – Provide and maintain database, attend workshop, coordinate placing of server
  • Museum National d’Histoire Naturelle – Provide and maintain database, attend workshop, coordinate placing of server
  • Swedish MNH – Provide and maintain database, attend workshop, coordinate placing of server
  • Smithsonian Institution – Provide and maintain database, attend workshop, coordinate placing of server
  • American Museum of Natural History – Provide and maintain database, attend workshop, coordinate placing of server
  • Bernice P. Bishop Museum – Provide and maintain database, attend workshop, coordinate placing of server
  • Canadian Museum of Nature – Provide and maintain database, attend workshop, coordinate placing of server
  • Field Museum of Natural History, Chicago – Provide and maintain database, attend workshop, coordinate placing of server
  • Natural History Museum of Los Angeles County – Provide and maintain database, attend workshop, coordinate placing of server
  • Florida Museum of Natural History – Provide and maintain database, attend workshop, coordinate placing of server
  • Philadelphia Academy of Sciences – Provide and maintain database, attend workshop, coordinate placing of server
  • Royal Ontario Museum – Provide and maintain database, attend workshop, coordinate placing of server

FY 2002 PI Report


Biogeoinformatics of Hexacorallia (Corals, Sea Anemones, and their Allies): Interfacing Geospatial, Taxonomic, and Environmental Data for a Group of Marine Invertebrates

Lead PI: Dr. Daphne Fautin, University of Kansas

As part of the Census of Marine Life, this partnership will create a taxonomic database of the Hexacorallia (phyllum Cnidaria) that adds to the inventory of sea anemones compiled by Fautin all species of orders Ceriantharia (tube anemones; by Molodtsova), Scleractinia (“stony” or “true” corals; by Cairns and Veron), and Zoantharia (zoanthids; by Ryland). Specimen-based, it will contain three-dimensional distribution data (including geospatial precision of each record) and bibliographic reference to description of each species. In addition to current features, an application by Ardelean will permit retrieval of data by all synonyms of species, flagging taxonomic and nomenclatural problems. Interacting with this database will be physicochemical and ecological databases important to marine biogeography. The core databases will be those assembled and linked (by Buddemeier) as part of the United Nations Environment Programme/Global Environment Facility-funded program within the Typology effort of the Land-Ocean Interactions in the Coastal Zone (LOICZ) Project of the International Geosphere-Biosphere Programme (IGBP). This partnership will develop and adapt tools to allow interactive analyses of the biological and environmental data, including visualization on map displays. This project will: link across spatial scales; greatly augment the minimal biogeographic data available for most benthic marine invertebrates; permit formulation and testing of biogeography and biodiversity models; and support forecasting and hindcasting of distribution changes due to environmental change.

Number of Years: 2

Start Year: 2000

End Year: 2002

Partners:

  • University of Kansas – Project lead, coordinator for taxonomy, taxonomy of sea anemones
  • Kansas Geological Survey – co-project lead, coordinator for environmental databases, GIS
  • Nova University, NCRI – Development of databases for website on coral and reef biodiversity/vulnerability
  • University of Wales – Taxonomy of zoanthids: assembly and entering of taxon list, literature, synonymies
  • Shirshov Institute of Oceanology – Taxonomy of cerianthids: assembly and entering of taxon list, literature, synonymies
  • Australian Institute of Marine Science – Taxonomy of hermatypic corals: assembly of taxon list, literature, synonymies
  • National Oceanic and Atmospheric Administration, Biogeography Program – Coordination and sharing of databases and applications being developed; dissemination and liaison
  • Natural History Museum, Smithsonian Institution – Taxonomy of ahermatypic corals: assembly of taxon list, literature, synonymies
  • Bits and Parity – Software and database development and maintenance
  • LOICZ (IGBP) – Development of global shallow-water databases plus synthesis and analysis tools; liaison with other IGBP (GLOBEC, JGOFS) and international programs (SCOR, IOC/UNESCO, UNEP)
  • International Center for Living Aquatic Resources Management – Integration with existing community-level databases; distribution of products

FY 2002 PI Report


Diel, Seasonal, and Interannual Patterns in Zooplankton and Micronekton Species Composition in the Subtropical Atlantic

Lead PI: Dr. Deborah Steinberg, Virginia Institute of Marine Sciences (The grant was awarded when Dr. Steinberg was with the Bermuda Biological Station for Research.)

Planktonic communities comprise an incredibly wide diversity of organisms that form the basis of marine food webs. We propose a multi-species inventory of zooplankton and micronekton at the Bermuda Atlantic Time-series Study (BATS) station, an 11-year, ongoing oceanographic time series situated in the western North Atlantic subtropical gyre or Sargasso Sea. The program will provide high-resolution species data that covers diel, seasonal, interannual, and decadal time scales. Detailed accompanying environmental data already available from BATS cruises (e.g., water column temperature, oxygen, nutrients, and plant pigment concentration) add additional value to the data set. Both species and environmental “metadata” will be formatted using techniques already well developed and in use at BATS for compilation and provision of data of interest into OBIS. This project will involve participation from both academia and government and will provide a high quality time series of zooplankton and micronekton species composition which will enable the investigators to determine the difference between natural variability and real ‘change’ in the diversity of the plankton community. This will be critical for testing and validation of ecosystem models, and for understanding the effects of long term climate change on ecosystems.

Number of Years: 2

Start Year: 2000

End Year: 2002

Partners:

  • Virginia Institute of Marine Sciences – Project coordination; species identification; compilation and integration of species data into existing BATS database
  • Woods Hole Oceanographic Institution – Species identification; compilation of species database
  • Russian Academy of Sciences, Zoological Institute – Species identification; compilation of species database
  • Bermuda Biological Station for Research – original sample collection and linking of zooplankton species composition data with BATS hydographic data
  • Museum of Natural History, Smithsonian Institution – Consult on species identifications; provision of laboratory facilities and resources

FY 2002 PI Report


ZooGene, a DNA Sequence Database for Calanoid Copepods and Ephausiids: An OBIS Tool for Uniform Standards of Species Identification

Lead PI: Dr. Ann Bucklin, University of New Hampshire

This international partnership will create a zooplankton genomic (ZooGene) database of DNA type sequences for calanoid copepods and euphausiids. The ZooGene database will be designed to include all species of these groups and to allow expansion to additional zooplankton groups. The ZooGene partnership includes four P.I.s and thirteen expert taxonomic consultants from seven countries. Zooplankton samples will be sorted from existing archival collections, obtained in coordination with planned oceanographic research efforts, and collected during National Marine Fisheries Service field surveys. The taxonomic experts will confirm species’ identifications; DNA sequencing will be done at the University of New Hampshire and, in some cases, in other partners’ laboratories. For each species, a DNA type sequence will be determined for a portion of the mitochondrial cytochrome oxidase I (mtCOI) gene; multiple mtCOI sequences will be included as necessary to reflect intraspecific variation. The ZooGene database will be designed, created, managed, maintained, and distributed as part of the proposed work; the data will be integrated into the Ocean Biogeographical Information System (OBIS). Uses for and research applications of the ZooGene database include: 1) uniform standards of species’ identification, 2) evaluation of the taxonomic significance of geographic variation within widespread species, 3) identification of cryptic species, 4) accurate estimation of species’ diversity, 5) determination of evolutionary relationships among species, and 6) design of rapid molecularly-based species’ identification protocols. Education and outreach efforts will include: training of graduate students at UNH and UW; a hands-on Molecular Systematics Workshop at UNH during Summer, 2001; exchanges between the P.I.s, international partners, and their colleagues and students; inclusion of ZooGene molecular and environmental data in the OBIS database, among others; creation and maintenance of a project web site; production of a CD with the ZooGene database and simple search tools; and informal education with the assistance of UNH Sea Grant.

Number of Years: 2

Start Year: 2000

End Year: 2002

Partners

  • University of New Hampshire – Project coordinator; molecular analyses; 2001 Workshop
  • University of Washington – Coordination of copepod collection; taxonomic analyses
  • Woods Hole Oceanographic Institution – Coordination of euphausiid collection; database and web site design
  • Northeast Fisheries Science Center – Coordination with NMFS; U.S. GLOBEC; sampling design for field surveys
  • International ZooGen Partners
  • Laboratoire de Biologie Animale (Plancton), Universite de Provence, Marseille, France – Expert taxonomic consultant for calanoid copepods)
  • Centro de Investigación Cientifica y de Educación Superior de Ensenada, Ensenada, México – Expert taxonomic consultant for euphausiids
  • Institute of Antarctic and Southern Ocean Studies, University of Tasmania, Hobart, Australia – Molecular analysis of euphausiids
  • Ocean Research Institute, University of Tokyo, Tokyo, Japan – Expert taxonomic consultant for calanoid copepods
  • Observatoire Oceanologique, Universite P. et M. Curie, Villefranche-sur-mer, France – Expert taxonomic consultant for calanoid copepods
  • Fisheries Laboratory, Hiroshima University, Hiroshima, Japan – Expert taxonomic consultant for calanoid copepods
  • Observatoire Oceanologique de Banyuls, Universite P. et M. Curie, Banyuls-sur-mer, France – Expert taxonomic consultants for calanoid copepods
  • Institute of Oceanic Research and Development, Tokai University, Shizuoka, Japan – Expert taxonomic consultant for euphausiids)
  • Senckenberg Research Institute, University of Hamburg, Hamburg, Germany – Expert taxonomic consultant for calanoid copepods
  • Center for Marine Environmental Studies, Ehime University, Ehime, Japan – Expert taxonomic consultant for calanoid copepods
  • National Institute of Water & Atmospheric Research, Ltd., Wellington, New Zealand – Expert taxonomic consultant for calanoid copepods
  • Australian Institute of Marine Science, Townsville, Australia – Expert taxonomic consultant for calanoid copepods

For more information on this project, click here.


Expansion of CephBase as a Biological Prototype for OBIS

Lead PI: Dr. Phillip Lee, University of Texas Medical Branch

Cephalopods are an ideal model for development of the Ocean Biogeographical Information System (OBIS) concept because the 700 living species are a manageable slice of marine life. Cephalopods occur worldwide, occupying niches from abyssal to intertidal and from the tropics to the poles, range in size from 100 _g rhynchoteuthions to 1000 kg giant squid, are important prey for top predators, are fished commercially, and have a half-billion year fossil record. Cephalopods are colorful, active and engaging to the public; they are great ambassadors for all marine invertebrates. Mapping cephalopods in 3-D space and time will be a powerful scientific tool and a valuable educational forum.

The CephBase team combines Internet database experience and international influence with a large image library, institutional support, and years of cephalopod research experience. The result will be a searchable, reference dynamic website with images, video, ecology, life history, catch statistics, distribution maps, dissection guides, taxonomy, and identification keys. CephBase will be useful to elementary, undergraduate, and graduate students, research scientists, fishery scientists or anyone interested in marine life. CephBase will be available on-line; its complexity will be transparent to users. A fifth grader will be able to access it, but it will be most useful to persons interested in global biodiversity of the ecologically and economically important class.

Number of Years: 2

Start Year: 2000

End Year: 2003

Partners:

  • National Resource Center for Cephalopods, University of Texas Medical Branch – Project coordinator, design and supervision of hardware and software systems and coordination of data input
  • Dalhousie University – International collaborations and supervision of data input
  • Smithsonian Institution – Taxonomic authority and coordination of specimen and video cataloging

For more information on this project, click here.

FY 2002 PI Report


A Biotic Database of Indo-Pacific Marine Mollusks

Lead PI: Dr. Gary Rosenberg, Adademy of Natural Sciences, Philadelphia

This partnership will use BioLink software to create a biotic database of the estimated 35,000 named species of .mollusks in the Indo-Pacific region. The database will include the fields required by Species 2000 for global species databases, which treat the current classification and synonymy of each species. It will also include summary data on the distribution and ecology of each species, as available in the scientific literature. Point data for more than 200,000 specimen records in the collections at the Academy of Natural Sciences, the Australian Museum and the California Academy of Sciences will be included.

Another objective is to combine Indo-Pacific data with existing species databases for Western Atlantic and Europe marine mollusks and for higher taxa of mollusks to form the basis of a global database of mollusks. Such a database will provide a uniform framework for linking specimen records from worldwide museum collections and data from molluscan fisheries to show spatial and temporal patterns of occurrence and abundance. It will provide on-demand information via the Internet about any species in question, as well as lists of species restricted by geography, taxonomy, bathymetry, or ecology. As such it will be an invaluable tool for scientists and environmental managers, as well as students, amateur biologists and naturalists.

Number of Years: 2

Start Year: 2000

End Year: 2002

Partners:

  • Australian Museum – Coordination of species and bibliography; provision of data for Central Indo-West Pacific mollusks
  • Museum National d’Histoire Naturelle, France – Provision of data on names of supraspecific taxa
  • Academy of Natural Sciences – Project coordinator; database integration; provision of data for outlying Indo-Pacific mollusks
  • California Academy of Sciences – Provision of data for opisthobranch gastropods

Census of Marine Fishes (CMF): Definitive List of Species and Online Biodiversity Database

Lead PI: Dr. William Eschmeyer, California Academy of Sciences

As part of the Ocean Biogeographical Information System (OBIS) initiative, this project will provide: 1) an accurate on-line world checklist of marine and brackish water fishes; 2) an on-line biodiversity database of fish occurrences, based on specimen collections and integrated with key information on fish biology and ecology; and 3) software that will assist collection managers to improve the quality of collection databases. The checklist will be drawn from two existing on-line databases, the Catalog of Fishes, which provides a coherent treatment of over 50,000 original descriptions of fishes, and FishBase, which contains an additional 24,000 combinations and common misspellings of scientific names used for fishes. The biodiversity database will use the checklist to bring together information in computerized fish collection databases and connect it with the biological and ecological data compiled in FishBase. The software to improve the quality of collection databases will build on existing prototypes available in FishBase, and will assist in correcting nomenclatural errors and assign a reliability indicator to every record in a collection database. The goals of this project will be pursued in close partnership with taxonomic specialists and collection managers, and with other initiatives.

Number of Years: 2

Start Year: 2000

End Year: 2002

Partners:

  • Various Institutions to be Named – Assistance with the definitive fish checklist; assistance with identification
  • California Academy of Sciences – Project coordinator; provision of definitive checklist; assistance with nomenclatural problems in collections
  • FishBase, ICLARM – provision of biological information, assignment of reliability marker to collection records, provision of biodiversity database
  • Collection Managers to be Named – Clean up collection databases, provision of core data for mirroring in central database
  • Museums to be Named – Computerization of collections
  • Integrated Taxonomic Information System

FY 2002 PI Report