|| Ocean Biogeographic Information System(OBIS)
The Ocean Biogeographic Information System, or OBIS, is an international information system focused on marine biodiversity. OBIS provides spatial query tools for visualizing relationships among species and their environment. This information is readily and freely accessible by the Internet and requires no special software to use.
¡¡¡¡OBIS will integrate biological, physical, and chemical oceanographic data from numerous sources, provide a tools to test hypotheses about marine biodiversity, and assist research on marine ecosystems. Users of OBIS, including researchers, students, and environmental managers, will gain a dynamic view of the distribution of marine species over space and time.
¡¡¡¡Please visit the OBIS Portal website (http://www.iobis.org) for detailed information and data search.
||The OBIS Schema FAQ - General Questions
|| OBIS FAQ
Contributing Data to OBIS
|What is OBIS?
OBIS was established by the Census of Marine Life program (www.coml.org). It is an evolving federation of organizations and people sharing a vision to make marine biogeographic data, from all over the world, freely available over the World Wide Web. It is not a project or program, and is not limited to data from CoML-related projects. OBIS is not incorporated, it does not employ staff, own equipment, or apply for funding. Organizations involved in OBIS take on these responsibilities.|
OBIS provides, on an ¡®open access¡¯ basis through the World Wide Web:
? taxonomically and geographically resolved data on marine life and the ocean environment;
? interactivity with similar databases;
? access to interactive physical oceanographic data at regional and global scales;
? software tools for biogeographic analysis.¡£
Who can join OBIS? Any organization, consortium, project or individual may contribute to OBIS. Contributions typically take the form of data or software tools. The data may be located in part or whole on the OBIS server at Rutgers University, or provided through an on-line connection to another database. To join OBIS contact the Chair of the OBIS International Committee in the first instance. Technical aspects of connecting to the OBIS website will then be planned with the OBIS Webmaster.
What is the OBIS International Committee?OBIS is managed by an International Committee (IC) of invited experts. The IC decides OBIS policy and strategy. It actively fosters OBIS development through data sharing and exchange, making software available, and supervising the OBIS portal development. It may establish working groups, for example to deal with technical data management issues. The IC is responsible for ensuring that contributors have expertise in their field, and have taken reasonable steps to ensure the quality of their data and/or software.
Members of the IC are selected as individuals to represent the constituencies of OBIS, including data providers, software developers, and regions of the world. They bring their expertise, knowledge, and connections to OBIS, and it is anticipated that they would be in regular contact with people and organizations who are potential users of, and contributors to, OBIS. Members do not represent their institutions. The IC elects the OBIS Chair from its members.
Who is on the OBIS International Committee?
Dr. Edward Vanden Berghe
Manager, Flanders Marine Data and Information Centre
Vlaams Instituut voor de Zee (VLIZ, Flanders Marine Institute)
Mr. Robert M. Branton (Chair of the OBIS Management Committee, Manager of the Canada Regional OBIS Node)
Centre of Marine Biodiversity
Bedford Institute of Oceanography
Dartmouth, Nova Scotia, Canada
Dr. Mark J. Costello (Chair of the OBIS International Committee, Chief Executive Officer of OBIS)
Senior Lecturer, Department of Marine Sciences
Leigh Marine Laboratory
University of Auckland
Warkworth, New Zealand
Dr. Daphne G. Fautin
Professor, Department of Ecology and Evolutionary Biology
Curator, Natural History Museum and Biodiversity Research Center
University of Kansas
Lawrence, Kansas, USA
Dr. Rainer Froese (FishBase Coordinator)
Leibniz-Institut f¨¹r Meereswissenschaften an der Universit?t Kiel (Leibniz Institute of Marine Sciences at the University of Kiel)
Dr. J. Frederick Grassle (Director of the OBIS Secretariat, Chair of the CoML Scientific Steering Committee)
Director, Institute for Marine and Coastal Sciences
Rutgers, The State University of New Jersey
New Brunswick, New Jersey, USA
Dr. Patrick N. Halpin (Chair of the OBIS Technology Committee)
Director, Geospatial Analysis Program
Nicholas School of the Environment and Earth Sciences
Durham, North Carolina, USA
Dr. Tony Rees
Manager, Divisional Data Centre
Commonwealth Scientific and Industrial Research Organisation (CSIRO) Marine Research
Hobart, Tasmania, Australia
Dr. Karen Stocks (Vice Chair of the OBIS International Committee)
Assistant Research Scientist, San Diego Supercomputer Center
University of California San Diego
La Jolla, California, USA
Dr. Catherine N. Duckett(OBIS Project Manager)
Rutgers, The State University of New Jersey
New Brunswick, New Jersey, USA
Dr. Yunqing (Phoebe) Zhang (OBIS Portal Manager)
Rutgers, The State University of New Jersey
New Brunswick, New Jersey, USA
What is an OBIS ¡®Contributor¡¯?
People, organizations and projects that provide data, software, expertise, or other resources to OBIS can be recognized as ¡°Contributors to OBIS¡±.
What are the benefits of OBIS?
OBIS provides data and analytical software at no charge to anybody with access to the World Wide Web.
What is the OBIS Portal?
The OBIS portal is the central location that supports the main OBIS website at www.iobis.org. The Institute of Marine and Coastal Sciences at Rutgers hosts the Portal.
Who will use OBIS?
The following communities are expected to use the OBIS portal:
Fishery scientists and resource managers
Who are the OBIS contributors?
? OBIS Data Sources
? OBIS Tools
? OBIS Data Providers
? Regional OBIS Nodes
? OBIS Partners
? OBIS Sponsors
Many scientists have contributed to the development of OBIS, including those on its International Committee, Management Committee, Technical Committee, Editorial Board, and working in its Secretariat. Many others have contributed by providing data, software tools and know-how to OBIS.
OBIS Data Sources
OBIS Data Sources are databases made available through OBIS. One or more may be provided by an organization or person who would be the owners or custodians of the data served. The data is served through an OBIS Data Provider who may or may not be the same organization or person.
OBIS Tools are software that operates through the OBIS portal (e.g. mapping tools), is used in OBIS data management, or that can be downloaded by users.
CMR C-squares Mapper
Distributed Generic Information Retrieval (DiGIR)
Kansas Geological Survey (KGS) Mapper
OBIS Data Providers
OBIS Data Providers are organizations and persons that serve data through the OBIS portal. These data maybe held by themselves or served on behalf of others.
Regional OBIS Nodes
Regional OBIS Nodes are organizations that have committed to a continued support of OBIS within a geographic and/or national region using resources they have obtained. This will include serving data online and developing a data provider and end-user community. Some RON will provide tools, different language versions of the OBIS website, or provide mirror sites for the OBIS portal.
OBIS Partners have a long-term commitment to cooperation with OBIS, through providing data, software, or other infrastructural support.
Commonwealth Scientific and Indutrial Research Organisation(CSIRO)
Food And Agriculture Organization (FAO)
Global Biodiversity Information Facility (GBIF)
International Oceanographic Data and Information Exchange (IODE)
National Center for Biotechnology Information (NCBI)
Pacific Biodiversity Information Network (PBIN)
Rutgers, The State University of New Jersey
OBIS sponsors have provided significant funding that contributed to OBIS development.
Alfred P. Sloan Foundation
Gordon and Betty Moore Foundation
National Science Foundation (NSF)
National Oceanographic Partnership Program (NOPP)
National Oceanic and Atmospheric Administration (NOAA)
What do all the acronyms mean?
Please see Acronyms
Where does OBIS get its data?
OBIS is simply a group of people or organizations that have data relevant to marine biogeography who have agreed to share their data through a central data portal. We are always seeking new data contributors who may want to join the federation.
What kinds of data is OBIS interested in?
OBIS is a marine biogeographic information system, meaning that we concentrate on datasets that record particular species (or higher taxonomic group) from particular marine locations. At present, we can only take information where the locations are recorded as latitude and longitude, not as place names. Our focus is on high taxonomic quality, so datasets where organisms have been identified by professional or trained biologists are our priority. We also have limited staffing, so while we are interested in all data, we may have less time to spend helping those with small datasets (a few observations) than we do those with larger or more comprehensive datasets.
In the near future, we will be expanding to take in environmental datasets (i.e. coverages of physical, chemical, and geological parameters) that are relevant to understanding the distribution of species. So we are interested in hearing from potential contributors of these datasets, and welcome your contact, but are still in the process building this facility.
Will OBIS pay me for my dataset?
No, OBIS does not buy data. It is simply a group of data contributors who have agreed to share their data through a central portal to make it more accessible. However, we may be able to make suggestions for places where you could submit a proposal to fund developing datasets or for digitizing existing datasets.
Who has intellectual property rights to the data?
OBIS claims no ownership nor does it claim any rights to the data sets it provides. All rights remain with you, the data contributor. You may at any time decide to remove your data from OBIS, or restrict its use. This is true whether you serve the data yourself as an OBIS node, or whether you place your dataset in the central OBIS portal for serving.
How will my data be cited/credited in OBIS?
All data served through the OBIS portal are labeled with the organization and database from which the data came. Users are required to cite the data providers when using data from OBIS. Please see the OBIS user agreement for details.
How do I to contribute data to OBIS?
There are two models for sharing data through the OBIS system:
1. You become a distributed data contributor. This means that you keep your dataset locally, and set up a server that can respond to OBIS queries. This requires "mapping" your dataset to the OBIS schema (which is not as hard as it sounds!) and installing a free software package called DiGIR to communicate with the portal. There are more details on this under the "Becoming an OBIS Distributed Data Provider" section of the Technical Resources page.
2. You provide your data set in electronic form to the central data portal, and it is served from there.
Which choice is right for you depends on whether you are interested in maintaining your own server, and also whether you expect to be making regular updates to the data set. OBIS prefers groups to be distributed data contributors, because we think it is best for the data contributor, who knows the dataset best, to maintain it. That way you can add data, make corrections, etc. easily. But for groups not able or willing to set up a server, we are happy to host data at the portal. In either case the data will be credited to you.
What if I have sensitive data which should not be openly accessible?
The short answer is that OBIS is committed to free, open, public access to date, so if you have sensitive data you probably don't want to share it through OBIS. However, there are some particular concerns we may be able to help with. For example, if you are concerned about giving the precise location of a rare or commercial species, then we may be able to represent your data at a lower spatial resolution, or to give a bounding box instead of a point location the information. Also, if you have data that you would like to share but want to wait until it is published, we can help you set up your dataset appropriately now, but agree not to serve it for a certain amount of time.
If I want to contribute data to the OBIS system, what should I do next?
Please contact us, so that we can assist you. Catherine Duckett, the OBIS project manager, will direct you to the right person. Please email: obissupport (at) marine.rutgers.edu
|The Basics of Databasing and Data Serving
How do I start designing a database?
First, figure out what information you have or plan to have. If you already have datasets, either in electronic or paper formats, look at the data that are included. Make a list of these fields (i.e. the column headings in your data table). Then go through the OBIS schema. If there is one or more fields in the OBIS schema that cover information that you want to hold, then use that field name and the suggested format. If there are one or more fields in the OBIS schema that do not apply to your data, just leave them out. If there is additional information that you want to keep in your database that is not covered by the OBIS schema, then you can add additional fields.
Do I need to use a relational database?
A relational database is a class of software that allows you to hold data in linked tables. You do not need to use a relational database, as you can hold your information in a "flat file" such as an Excel worksheet. However, a relational database offers some advantages. First, it lets you enter information more efficiently. For example, you can enter a scientific name once into a table of names. Then for every record or observation you have for that species, you won't need to type that name in again, you can just pick it from a drop-down list. So it is faster and you don't have to worry about making typing or spelling mistakes. In addition, relational databases can be queried in more complex ways than a spreadsheet. For example, you can ask for "all the records for species X that were caught north of 30¡ã North, shallower than 300m, and between 1980 and 1985."
A note on text files. Delimited text files are good for archiving data (saving it in such a way that someone years from now will probably still be able to get to it), but not very good if you actually want to do things with the dataset, like extract certain data of interest, update it, or serve it.
Which relational database should I use, if I use a relational database?
Several products are available, and many are quite similar and have similar functionality, so this isn't a critical decision. Microsoft Access and Filemaker Pro are common desk-top commercial software packages. Oracle and Sybase are common "industrial-strength" databases. This means that they are designed to be efficient with large volumes of data. Generally, if you expect a dataset with hundreds of thousands of records, then you should consider one of the industrial databases. If you have tens of thousands of records or fewer, then Access or Filemaker Pro should be fine. The trade-off is that the industrial packages tend to cost more and also be a little less user-friendly.
MySQL is a free, open-source relational database package that is quite good. You can find more information on MySQL at http://www.mysql.com (note that companies may sell packages that include extra documentation, etc., but the core software is free).
Whichever one you choose, just make sure it is "ODBC compliant" ¨C this means that it can communicate with other sources (for exporting, for serving data, etc.). Most of the relational database packages are ODBC complaint, but some "home-grown" systems are not.
What hardware/software do I need to do to serve data through the web, either through OBIS or to have my own website?
If you want to serve data to OBIS, you will need a computer with an operating system that has your database, server software, and DiGIR installed. If you would like to set up your own web page, you will also have to program to create your web pages and the search functions users will access. HTML is the language that web pages are built in; several languages such as Perl/CGI can be used to create search forms for users to enter data into, and these will need to include the SQL or other commands that actually search your database. Software such as Dreamweaver helps to make programming web pages easier.
For those on a budget, there are some good freeware options. Linux is a free operating system, Apache is a server, and MySQL is a free relational database.
|The OBIS Schema FAQ - General Questions
What is the OBIS Schema?
The OBIS schema is a list of data fields with names, descriptions, and format notes. It is an extension to the Darwin Core Version 2 standard. When the OBIS portal sends queries out to its distributed data contributors, the portal will request data using these fields and needs to have data returned using these fields. The DiGIR software provides the programming to turn an OBIS query into a search on your particular database, but in order to install DiGIR you need to "map" the OBIS schema fields to the fields in your database.
What is DiGIR?
DiGIR is the software through which OBIS communicates with its distributed data contributors. When a user of the OBIS portal inputs in a query (such as 'show me all the locations where the fish, Beryx splendens, has been found'), DiGIR allows the portal to send that query to the data contributors, for the data contributors to translate that query into a search on their local database, and to send the data back to OBIS. More information on DiGIR can be found on digir.sourceforge.net. Please contact OBIS before installing the DiGIR software to ensure that you are using a compatible version and have the OBIS configuration details.
Is the OBIS Schema compatible with the Darwin Core standard?
Yes. The OBIS schema was built as an extension to the Darwin Core version 2 standard (http://tsadev.speciesanalyst.net/documentation/ow.asp?DarwinCoreV2). [The Darwin Core is a standard that is used by the Global Biodiversity Information Facility and several networks of museum collections] So it contains all of the Darwin Core fields with the same names. The OBIS Schema also contains some additional fields for holding information that the Darwin Core does not handle. So, if you implement the OBIS Schema in your database, you will be compliant with both the Darwin Core standard and the OBIS standard.
The OBIS schema has many fields - isn't it hard to implement them all?
Think of the OBIS schema as a menu of options. There are only four fields that are required in order to be compatible (latitude, longitude, taxonomic name, and date/time of last modification). For all of the other fields you only need to include them if you want to have that information in your database. If you don't plan to hold a particular type of information, you can leave it out of your database. However, if you do include a type of information covered by a field in the OBIS schema, you should represent it as described in the OBIS schema.
Do I have to use the same field names in my database as the OBIS Schema?
No, you can use any field names you like. When you implement DiGIR, it will ask you to tell it which fields relate to which OBIS Schema field. You should keep track of this and make sure that there is a one-to-one mapping of fields in the OBIS schema to your database and that you use the required format for the field. For example, because the OBIS Schema has separate fields for day, month, and year of the record, it is best to hold these in three separate fields and not in a single date field (or at least have a plan for how to separate the pieces for serving to OBIS).
Note that most database software will allow you to do automatic operations on fields. You may prefer to enter your location information as degrees and minutes for latitude and longitude instead of decimal degrees. That's fine, because it will be easy for you to create a database view with a latitude field in decimal degrees calculated from (latitude degrees + (latitude minutes/60)).
Using an OBIS view
It may be easiest for you to implement DiGIR by creating a table "view" in your database that has all the OBIS schema fields in one table. You may have separate tables for "species names", "observations" etc., but may create one virtual view that does all the joins necessary for the OBIS query. You can also have it do any reformatting (such as the latitude degrees and minutes calculation mentioned in the above question) required. Then it will be easy during DiGIR installation to map onto the OBIS schema.
Why do you have so many fields for place names that don't apply in the ocean (County, State Province, etc.)?
Because these are Darwin Core fields. To be compliant with the Darwin Core, OBIS must allow all Darwin Core fields to be entered. But remember, these are all optional fields. Don't even put them in your database if you don't need them - most OBIS datasets won't. OBIS operates off latitude and longitude locations, which are why these two are the only required locality information.
What do you mean by the terms "Collected" and "Observed"?
The OBIS databases hold information on the locations where different species have been found. The act of finding a species at a place is called a "collection" or an "observation" throughout the schema documentation. This term is meant to apply very broadly, and includes cases where species were literally seen during a visual search, were collected in a sample of any kind (research survey, fisheries catch date, etc.), where a specimen in a museum indicates the location where it is from, etc.
OBIS Schema data types
The schema indicates the data type for each field. These are general categories, and your particular database software may use different terms. Where there are additional restrictions placed on the data format, this will be indicated in the Description.
Can the OBIS Schema accomodate tagging data, or multiple sightings of a single individual?
Yes, the OBIS Schema can accommodate data from multiple observations of a single individual organism, such as data produced by tagging studies. To implement this, the user should 1) create a record in their database for the individual and use the Catalog Number as a unique identifier for that individual; and 2) each observation for that individual should be entered as a separate record in the database and tied to the individual by setting the Related Catalog Item field equal to the Institution Code, Collection Code, and Catalog Number of the individual record, and the Relationship Type field to 'point observation for tagged animal of.' (see the Technical Resources page for more on the OBIS Schema fields).