System Capabilities

System Features

Database Design Details

Sources of Data

Compliance with Data Standards

System Capabilites- See Output section for examples

For a given species (or higher taxon) of interest, OBIS can:

• Produce a table of locations where the taxa have been found (suitable for export and further analysis)
• Produce a map of these locations, either globally or for a user-defined region.
• Overlay maps of environmental factors (such as sea surface temperature, or primary productivity) onto the range map, to investigate possible correlations between environmental factors and distribution patterns.
• Detail who first described the species, give references for relevant published work, web sites, or graphics, and indicate where specimens of each taxon are held and who to contact regarding the specimens.

• list all species found in that region
• produce a map of the region with locations of different species marked
• overlay environmental data onto the regional map
• produce tables of counts of species richness, for export into statistical analysis software

• link the above capabilities to a web interface which is freely accessible to the public
• produce range maps from point location data using the GARP model (developed by David Stockwell). This model, which is currently used by the Australian ERIN system and the Mexican Bird Project, uses available physical data to produce estimates of ranges, including confidence estimates.

System Features

Expert Review

All data sets for OBIS will be provided by systematists specializing in the given taxa. The role of the systematist is to be aware of current state of the taxonomy and to reexamine and confirm identification of specimens. For many groups the taxonomy has changed greatly over time, and determinations attached to specimens in museums represent a variety of schemes. Having a single expert directly examine specimens and resolve taxonomic conflicts is a prerequisite for a uniform dataset. It will also ensure that as later revisions are made, the data set can be updated and conflicts resolved.

 

Specimen based

For every record of a species found at a certain location, there should exist a preserved specimen. This ensures that the original specimen can be reexamined should later taxonomic revisions occur, or questions about that record arise. Since the taxonomy of many marine groups is understudied and likely to change, this is the only way to ensure that the database remains current and conflicts can be resolved.

 

We do acknowledge that, for some groups, the taxonomy is relatively stable and identification is straightforward, and restricting the data base to specimen-based records may limit the geographic coverage available. We have therefore designed OBIS so that it can also hold information on samples that are not specimen based, and will make determinations on a case-by-case basis about requirements for specimens.

 

Distributed capability

Initially, OBIS is collecting data sets into a central data bank at the Institute of Marine and Coastal Sciences at Rutgers University. The OBIS designers have worked with David Vieglais of the Z39.50 Biological Implementers Group, who is currently developing a client-server application to allow distributed networks of biological collections information. OBIS will be compatible with the application, allowing it to take part in the distributed system.

 

Advantages of a distributed system are:

• as the data set grows, it can be stored in multiple locations, avoiding the hardware requirements of having a single, very large, data set. Computer requirements for the application are modest: just a Windows NT server. All software is free and self-maintaining (has automated maintenance features).
• systematists providing data sets can retain control of the data by setting up their own data server. They can continually update their own data sets, instead of OBIS having to coordinate periodic data transfers and updates, and work with multiple versions of the data set. The systematists can also screen portions of the data set, to protect sensitive information. Systematists who do not wish to set up a server can still transfer their data set to the central archive for storage.
• there is no perceptible change to the user of the OBIS system. Users may create queries and maps as if they were working off a single system. The distributed system is "hidden" behind the application.
• the OBIS user can also access museum collection data for those institutions on the system

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Sources of Data Sets

All data sets within OBIS have been freely contributed by the researchers who created them. These researchers are interested in seeing their data used by a larger audience, and saved in a managed archive. As OBIS grows, it will rely on the desire of experts to share their information. If you have or know of data sets that are appropriate for the OBIS database please contact Jen Gregg at jgregg@imcs.rutgers.edu.

Data currently in the system, and future data sources, are listed on the input data page.
 

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Standards Compliance

National Standards

1. Content Standards

OBIS should be fully compliant with the Content Standard for Digital Geospatial Metadata, developed by the Federal Geographic Data Committee, which is the current national standard for spatial data.

2. Transfer Standards

The Spatial Data Transfer Standard is the national standard. It describes protocols for the exchange of information, not the structure of information while it is stored. OBIS has been designed to hold the information necessary to meet this transfer standard.

Other Standards

Darwin Core Profile for Biological Collections and Taxonomic Data/ANSI Z39.50 Information Retrieval Protocol

ANSI Z39.50 is the reigning standard for information retrieval. Currently, the Z39.50 Biological Implementers Group (ZBIG) are developing a profile to apply Z39.50 to collections and taxonomic data, and are creating client-server applications which will allow data sets using the profile to be linked.

ASC Biological Collections Reference Model

The Association of Systematics Collections, Computerized Networking Committee developed a model in 1992 describing the information categories and relationships that should appear in a database for biological collections. It has since been updated by Stan Blum at the University of Kansas. Because it was developed for specimen collections, it requires some information not relevant to spatial diversity and range information, and excludes other information necessary for our purposes. Therefore, our database model diverges somewhat from their reference model. However, meetings with Stan Blum at the University of Kansas have assured us that our general design is in-line with the design of the reference model, and that there is enough compatibility to allow cross-transfer of information between data sets in OBIS and data sets based on the ASC reference model. We have also relied heavily on the ASC model for parts of our database design, notably the Agent/Person/Organization section.

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