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Report of Workshop on Open Standards Access to Biological Data at the Bedford Institute of Oceanography

Report of Workshop on Open Standards Access to Biological Data at the Bedford Institute of Oceanography

Sponsored by: Centre for Marine Biodiversity

Held in George Needler Boardroom at the Bedford Institute of Oceanography on November 27, 2003.

Reported by:  Robert M. Branton,  Marine Fish Division, Bedford Institute of Oceanography, January 12, 2004.


The Bedford Institute of Oceanography (BIO), as a world leader in development of standards and methods for collection, analysis and exchange of scientific data and the Centre for Marine Biodiversity (CMB), as an internationally recognized organization for scientific activity associated with conservation of marine biodiversity are both seeking to establish a shared vision with regards to open standards based exchange of biological data. CMB recognizes the importance of publishing marine biodiversity data via international standards and expects to strongly influence and in doing so to effectively lead development of a Canadian Ocean Biogeographic Information System (OBIS) portal. BIO, as part of the Canadian Geospatial Data Infrastructure (CGDI), is presently installing data provider and web mapping services, such that marine biological and fisheries data from DFO as well as CMB member sources can be published via the OBIS International and Global Biodiversity Information Facility (GBIF) systems. This workshop brings together several groups involved in this initiative: OBIS & GBIF committee chairs plus a leading taxonomic authority for this region to give first hand accounts of their activities; DFO science and informatics program leaders to describe their efforts to support global ocean observing initiatives; and client groups to give comment on DFO's past performance as well as offer suggestions regarding these latest efforts. General scientific and technical staff, conducting the scientific programs that will eventually appear through these systems were also present. This report includes summaries of each participant's presentation with hyper-links to each of their slide presentations (14) given at the workshop and respective homepages (16). The presentations, when taken together indicate that the data systems now being developed at BIO are rapidly evolving to a point that they can be soon expected to provide direct input to international standards based systems such as OBIS and GBIF. The client groups foresee that open standards will increase their confidence in the data and enable cross-jurisdictional mapping and analysis work not possible with current ad-hoc methods. They also expect that standards based access will allow them to make better and more efficient use of their own resources and of BIO scientific staff's time. Post workshop impressions of the individual participants, included at the end of this report, indicate without exception that there is consensus with regards to overall objectives and course of action being taken with regards to open standards based access to biological data at the Bedford Institute of Oceanography.

Program Outline

Opening Remarks

Michael Sinclair - Bedford Institute of Oceanography (BIO), director  

Commercial fishing, marine transportation as well as oil and gas development (to name a few) are all vital elements of the Canadian economy. Decision-making associated with these activities is very dependant on the broad scale and timely integration of data from a range of ocean science disciplines. The Bedford Institute of Oceanography (BIO) has long been recognized as a world leader in the development of standards and methods for the collection, analysis and exchange of data for many of these disciplines. Marine and fisheries biology data systems now being developed at BIO are rapidly evolving to a point that they can expected to provide direct input to international standards based systems. I am very happy to have representatives of the Global Biodiversity Information Facility (GBIF) and Ocean Biogeographic Information System (OBIS) here today at BIO to provide us all with an opportunity to learn first hand what these developments will bring.

Ellen Kenchington - Centre of Marine Biodiversity (CMB), director

Three Oceans of Biodiversity

The Centre for Marine Biodiversity (CMB) is an internationally recognized organization for scientific activity associated with the conservation of marine biodiversity.  Since inception in 2001, the CMB has used electronic publishing via the website name as a key element of its public outreach activities. CMB recognizes the importance of publishing marine biodiversity data via international standards and expects to strongly influence and in doing so to effectively lead development of a Canadian Ocean Biogeographic Information System portal. CMB strongly encourages the Dept. of Fisheries and Oceans (DFO) in its efforts to establish an open standards data provider service for marine biological and fisheries data at the Bedford Institute of Oceanography (BIO). With that, several non-DFO CMB members are currently developing standards based metadata so that their collections and data may be posted on the BIO system. Depending on the success of this endeavor, the BIO and CMB together could become Canada’s Ocean Biogeographic Information System portal. All data on this Canadian Ocean Biogeographic Information System portal would appear on the International Ocean Biogeographic Information Canadian Biodiversity Inventory portals and hence become part of the Global Biodiversity Information Facility.

GBIF/OBIS and Related Initiatives

Suggested Topics: Overall program objectives and sponsors. Description of relevant standards. Operational description and status.  Recent major accomplishments. Next major milestone(s). Related initiatives. Why we should be interested in this initiative? Demonstration.

Guy Baillargeon- GBIF Nodes Committee, chairman

Global Biodiversity Information Facility
The Canadian Biodiversity Information Facility

The Global Biodiversity Information Facility (GBIF) is an international scientific cooperative project aimed at making the world’s biodiversity data freely and universally available via the Internet.  GBIF is establishing a distributed information infrastructure to serve primary biodiversity data (specimens, observations, names, and associated metadata) and act as a global integrator.  Agreed-upon conventions, open processes and of data exchange standards are key enablers to make distributed biodiversity databases interoperable, and to share primary biodiversity data across the different levels of biological organization and with other scientific information domains.  Currently, 39 countries and 22 international organisations are participating in GBIF.  The Canadian effort is coordinated by the Federal Biodiversity Information Partnership (FBIP), supporting the development of the Canadian Biodiversity Information Facility to promote the GBIF information model nationally, and to assist in bringing new Canadian data providers and datasets into GBIF.

Mark Costello - OBIS International Committee, chairman

Mapping Marine Life over the Internet

The Ocean Biogeographic Information System (OBIS) is becoming the leading on-line source for marine species distributions in the world.  The bringing together of this information through a federation of databases with instant access to analytical tools and maps, will deliver new insights of what lives where in the world oceans.  Synthesis of this information will aid understanding of collective patterns in biodiversity, such as species relationships, food web structure, and effects of climate change on ecosystems. OBIS provides an 'open access' basis through the World Wide Web for: taxonomically and geographically resolved data on marine life and ocean environment; data from museums, fisheries, and ecological studies; data from all ocean environments; seabed to plankton, coastal to deep sea; interactivity with many other databases, including other on-line databases; access to physical oceanographic data at regional and global scales; software tools for checking species names, mapping, modelling, and biogeographic analysis. OBIS is for use by students, researchers, fishery scientists and managers, educators, amateur naturalists, industry, consultants, environmental and nature conservation organizations. This information infrastructure is networking marine biologists, taxonomists, ecologists and oceanographers at regional and global scales.  OBIS was created as the information component of the Census of Marine Life.  It is an Associate Member of the Global Biodiversity Information Facility and subscribes to the GBIF policy on data sharing.

Lou VanGuelpen - Canadian Atlantic Marine Species Information System, project leader

Canadian Atlantic Species Information System

The Atlantic Reference Centre is a research museum of Canadian Atlantic organisms, and thus an archive of biodiversity information.  This presentation describes the objectives of the ARC 1) to be an on-line provider of regional biodiversity information, 2)  to develop an on-line Canadian Atlantic Species Information System, and 3) to develop an on-line North Atlantic Register of Marine Species, all using open standards for access to biological data.

DFO Maritimes Programs

Suggested Topics: Overall objectives and sponsors. Related initiatives such as Geoconnections. Other data sources at BIO. Reliability, sustainability  and threat management. Past experience and recent accomplishments. Future plans. Expected costs.  Demonstration.

Richard Eisner - DFO Science and Oceans Committee, chairman     

Marine Program Informatics - A Success Story in Integrated Data/Information Partnering

Effective data and information/knowledge management practices are a fundamental element of all of the Science and Ocean programs at BIO, including: Fisheries Science, Aquaculture, Oceanography, Hydrography, Environmental Science, Habitat Management, Oceans and Coastal Management. The present infrastructure is the result of a number of initiatives and arrangements, such as Y2K, MEDS, strong CHS Informatics. It is supported by Non core Informatics- Application Development, Applications Roll out, Client operations ( server support) and by Core Maritimes Informatics-National and Regional Network, Telephony, LAN Servers and Workstations, Help Desk, Security, Document Management, Library, Linkages to Oceans and NRCAN at BIO plus Regional staff in all Sectors and with external stakeholders. New directions include: invasive species, climate studies in the Labrador Sea and eastern arctic, fish aquaculture and environment interactions, stock assessment for under- assessed, economically valuable species, science in support of integrated management, ecosystem structure- descriptive tools, discovery corridors, genetic effects of Fishing, lobster meta-population structure, and noise in the aquatic environment. The way ahead will include continued data management research and development coupled with enhanced external partnering such as: Geoconnections, the Ocean Biogeographical Information System, collection of data by industry, and research at universities.

Robert Branton - Marine Fish Division, lead data manager

Open Standards Access to Biological Data

Marine Fish Division (MFD) and the Atlantic Reference Centre (ARC) together have been major contributors to a number of international and national data publishing programs including: Census of Marine Life (CoML); Geoconnections - Canadian Marine Geospatial Data Infrastructure (CMGDI), and Environmental Studies Research Fund (ESRF). Currently, under sponsorship of the Geoconnections, we are preparing to provide annually updated population & distribution products for 400+ species encountered by Canadian and USA research trawl surveys. We intend this to be the first product emerging from the internet portal currently under development at BIO. The BIO Portal facility will employ a number of standards, including OBIS and the Open GIS Web Mapping Services. We plan to also use this service as a local test bed for extending the OBIS standard to include concepts like: length, age, maturity, thus permitting separation of populations into juvenile and adult stock components and to estimate mortality. We intend to assist other fisheries research groups to establish similar facilities, thereby creating electronic atlas facilities for all Atlantic Canada data and taxonomic collections.and in the longer term provide services covering all 3 of Canada’s oceans.

David Swetnam, Tobias Spears - Informatics Branch

Informatics Branch - A partnering service provider
Implementing an Enterprise GIS Infrasrtucture – A Beginner’s Guide

The Regional Director of Informatics made a presentation about the Informatics services avaliable in the Maritimes region in support of its clients in the other sectors such as Science.  Science in turn partners with outside agencies for projects of mutual benefit.  The presentation dealt with the varied nature of the services available and the secure aspect of those services.  Highlighted were the application development services and the data storage management systems.  The focus was on the infrastructure behind the presentation layer that clients typically only see. Tobias Spears gave a demonstration integrated web and desktops geographic information system technologies currently under development at BIO.

Client Group Perspectives

Suggested Topics: Overall objectives, interests and sponsors. Experience obtaining biological data from DFO and others. Would open standards have made this easier?  What data will you need  in the future? Suggest ways of cooperating with open standards initiatives.

Jennifer Smith - World Wildlife Fund

WWF - Canada and Marine Conservation Data Needs

WWF-Canada's Marine program has been a major consumer of data from BIO in the past 2-3 years. Our experience has been one of inconsistent standards. Open standards would help us to use our own resources, as well as the staff time resources of BIO scientists, more efficiently; would facilitate our cross-jurisdictional mapping and analysis work; and would increase our confidence level in the data we use. Our future data needs centre around strategically-chosen indicators, high-quality fundamental data sets (i.e. multibeam) and physical proxies for modeling non-existent biological data, and other high-quality pre-processed data products, while maintaining the flexibility of access to raw data: whatever standard is adopted should facilitate sharing of analysis products. The majority of our work takes place in a GIS environment, so adherence to or compatibility with standards in use by the larger geomatics community would be preferred.

Ransom Myers - Dalhousie University, Future of Marine Animal Populations

The Future of Marine Animal Populations - Visions for the Integration of Models and Data

Large marine animals that once were very abundant in the world's oceans have all but disappeared from their environment. Meta-analytical methods to investigate such global ecological problems require the compilation of large datasets from disparate sources. This process would be facilitated through the standardisation of biogeographic data collection, storage and distribution.

Stephen Smith – DFO, Invertebrates Fisheries Division, Molluscan Section Head

Access to Data - Needs and Experiences

Constructing ORACLE databases and rescuing data have been the main focus for data access in Invertebrate Fisheries Division over the last 5 years.  While the processing of a large portion of the numeric data has been initiated, other diverse kinds of data including digital photographs, video and multibeam data need to be included.  As this process nears completion, emphasis will change to linking these data sets, especially on a geographic basis to other related data bases in DFO and elsewhere.  

Kate Bredin - Nature Serve Canada, Atlantic Canada Conservation Data Centre

Atlantic Canada Conservation Data Centre  - part of NatureServe Network

The AC CDC is unique within the NatureServe network of Conservation Data Centres and US Natural Heritage Programs by virtue of its NGO status and regional, Atlantic Canada, mandate.  AC CDC has used marine biodiversity data throughout NatureServe methodology (listing and ranking species, compiling georeferenced species occurrences, and mapping and distributing data) for three projects.  Marine data obtained by the AC CDC included ECNASAP groundfish trawl survey data, ichthyoplankton survey data (for spawning and larval fish concentrations), rare species records from the ARC, and population and distribution trend information for commercial fish species for the WWF Nature Audit.  Open standards access to marine biological data would have facilitated project completion by eliminating the need to: 1) discover the types of datasets available, 2) determine who to contact for particular datasets, and, 3) negotiate data transfer. Otherwise, AC CDC encountered few obstacles in obtaining marine biodiversity data from DFO.  Knowledge of the gaps, nuances, and sampling biases inherent in datasets, that influence to what degree data is an accurate reflection of reality, could, however, only be gained by talking to the scientists who collect and manage marine biodiversity data.  We would not have been able to correctly interpret and apply marine biodiversity data without this expert consultation. There is a requirement to indicate data gaps and sampling information with each available dataset in the movement towards open standards access to biological data.


Suggested Topics: Are we on the right track?  What are the alternatives?  What are risks?

Questions and/or discussion at the end of each presentation and at the end of the session as a whole showed an overall and enthusiastic support for open standards at the Bedford Institute of Oceanography as well as for ongoing collaboration with the Centre for Marine Biodiversity. Following are impressions of the workshop participants.

Guy Baillargeon was impressed by the cohesion of the marine biodiversity science community, but he was also struck by the commonality of needs and constraints of users and producers of biodiversity data in the marine environment as compared to those of users and producers focussing on other types of environments.  This speaks very much in favour of better concerted efforts nationally and also for close alliance with international efforts.

Mark Costello:  Attendance demonstrated the priority and interest in this subject in BIO and the CMB membership. Clearly, the BIO-CMB collaboration is highly successful in bringing government, university and NGO scientists together. Together they represent the collectors and users of marine biological and fishery data, and the public interest. DFO at BIO are already world leaders in providing quality marine biological and fishery data to the public and research communities over the internet.  This meeting showed how through CMB this data will contribute to global megascience projects such as the Ocean Biogeographic Information System, and the Global Biodiversity Information Facility.

Lou VanGuelpen: The meeting had a rational approach to the topic of open standards (the choice of speaker groups and open discussion).  I think the meeting was informative and beneficial for many in the audience, in terms of open standards and in making helpful contacts.

Dave Swetnam: My reaction to the meeting was extremely positive. In general I support the utilization of cooperative interagency projects, with each agency bringing its strengths to the table.  I feel a strength that Informatics can bring to the table is a secure infrastructure and creative application developers.

Jennifer Smith: The majority of participants seemed to be in agreement that the existing architectures and standards can meet our needs: Bob's point that we needn't expend a lot of energy to reinvent these tools is well taken, as is the importance of a link with Geoconnections.  Audiences need to be well-defined and clients should be consulted particularly with regard to the data products to be made available. We applaud this initiative.

Ram Myers: The meeting was a very positive collaboration between governmental agencies, NGOs and academia.  Biogeographic data standards need to facilitate the distribution and sharing of the raw data and should also become a tool to communicate results from modelling analyses.

Stephen Smith: Prior to this meeting I did not know very much about the concept of Open standards for data access or about some of the standards that currently exist.  I felt that this meeting provided a good broad brush introduction to field that I can use to learn more.  As always, I am concerned about providing data to the public that may be used in a manner that it had not been originally designed for.  Hopefully metadata descriptions will include caveats and limitations.

Kate Bredin:  The meeting provided an excellent overview of the many different interlocking and often confusing initiatives to provide open standards to marine data world-wide. It was interesting and exciting to see how far DFO, the ARC and CMB have progressed towards assemblage and provision of marine biodiversity data products and services.


Many thanks to Victoria Clayton, the Centre for Marine Biodiversity administrator for arranging the accommodations and general support and to Lesley Carter for attending to technical details of posting this report on the CMB Website.


  1. Baillargeon, Guy - AAFC
  2. Beanlands, Diane - Marine Fish
  3. Black, Jerry - DFO
  4. Bond, Shelley - Marine Fish
  5. Bourbonnais, Cynthia - MES
  6. Branton, Bob - Marine Fish
  7. Bredin, Kate - ACCDC
  8. Brien, Pierre - DFO
  9. Broughton, Derek - DFO
  10. Burke, Allison - DFO
  11. Clement, Pierre - MES
  12. Comeau, Peter - DFO
  13. Costello, Mark - HMSC
  14. David, Blair - DFO
  15. Eisner, Richard - Science
  16. Fowler, Mark - DFO
  17. Gerriets, Stefen - ACCDC
  18. Gonzalez, Patricial - COD
  19. Gordon, Don - MES
  20. Gouda Rajashree - 
  21. Gregory, Doug - Ocean Science
  22. Harding, Gareth - MES
  23. Harvie, Carolyn - DFO
  24. Head, Erica - Ocean Science
  25. Kenchington, Ellen - CMB
  26. Kennedy, Mary - Ocean Science
  27. King, Marty - WWF
  28. Lamb, Janet - EC
  29. Lautenschlager, R.A. - ACCDC
  30. MacIsaac, Kevin - DFO
  31. Mason, Charles - DFO
  32. McIntyre, Tara - DFO
  33. Myers, Ram - Dalhousie
  34. O’Neill, John - DFO
  35. Pohle, Gerhard - HMSC
  36. Potter, Ted - Oceans
  37. Reid, Jim - Marine Fish
  38. Ricard, Daniel - Dalhousie
  39. Rose-Taylor, Candace - HMSC
  40. Simon, Jim - Marine Fish
  41. Sinclair, Michael - Science
  42. Smith, Jennifer - WWF
  43. Smith, Stephen - IFD
  44. Spears, Tobias - DFO
  45. Spry, Jackie - Spry Tech
  46. Stewart, Patrick - Envirosphere Con
  47. Swetnam, David - DFO
  48. Tremblay, John - IFD
  49. Valdés, Carlos - CEC
  50. Van Guelpen, Lou - HMSC
  51. Varma, Herman - DFO
  52. Wilson, Scott - Marine Fish
  53. Wilson, Trudy - Ocean Science
  54. Worcester, Tana - DFO

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