The OBIS manual
This manual provides an overview on how to contribute data to OBIS and how to acess data from OBIS. It provides guidelines for OBIS nodes and data providers on the OBIS standards and data management best practices to ensure that data published via OBIS are of high quality and follows internationally recognised standards. It also provides guidelines for data users on how to access, process and visualize data from OBIS.
The OBIS node manual is a dynamic document and is revised on a regular basis. Suggestions for additions and changes to this document are welcome and can be sent to the OBIS Capacity Development Task Team by email to firstname.lastname@example.org.
- How to contribute data to OBIS?
- How to access data in OBIS?
- How to process and visualize data from OBIS?
This manual is written to a large extend by Leen Vandepitte, Mary Kennedy, Philip Goldstein, Pieter Provoost and Ward Appeltans with input from and in consultation with the IODE Steering Group for OBIS.
Guidelines on the sharing and use of data in OBIS
How to contribute data to OBIS?
Become a data provider or an OBIS node
OBIS accepts data from any organization, consortium, project or individual who wants to contribute data. OBIS Data Sources are the authors, editors, and/or organisations that have published one or more datasets through OBIS. They are the owners or custodians of the data, not OBIS! However, OBIS only harvests data from recognized OBIS nodes. If you own data or have the right to share data with OBIS, you can contact the OBIS secretariat or one of the OBIS nodes. Your organization or programme can also become an OBIS node:
Biodiversity data standards
From the very beginning, OBIS has championed the use international standards for biogeographic data. Without agreement on the application of standards and protocols, OBIS would not have been able to build a large central database. OBIS uses the following standards:
- Darwin Core (species occurrence data)
- Ecological Metadata Language (dataset metadata)
- Darwin Core Archive including OBIS-ENV-DATA (sampling events and facts, species occurrences and measurements)
Data publication and sharing
OBIS nodes can accept any data files from its data sources or data providers, and they publish these data on their OBIS nodes IPT, which are harvested by central OBIS. The Integrated Publishing Toolkit (IPT) is developed and maintained by the Global Biodiversity Information Facility (GBIF). GBIF maintains an IPT manual. See here for specific OBIS instructions:
OBIS data quality control procedures
OBIS ignores records that do not meet a number of standards. For example, all species names need to be matched against an authoritative taxonomic register, such as the World Register of Marine Species. In addition, quality is checked against the OBIS required fields as well as against any impossible values. OBIS checks, rejects and reports the data quality back to the OBIS nodes, but never change records. The OBIS tier 2 nodes are responsible for the data quality and communicate errors back to the data providers. A number of QC tools are developed to help data providers and OBIS nodes:
How to access data in OBIS?
OBIS provides a portal or gateway to many datasets containing information on where and when marine species have been recorded. The datasets are integrated so you can search them all seamlessly by species name, higher taxonomic level, geographic area, depth, and time; and then map and find environmental data related to the locations. The OBIS portal has a large spectrum of users: researchers, fishery scientists and managers, policy maker, educators, amateur naturalists, environmental NGOs, consultants, nature conservation organisations, and students.
There are several ways to access OBIS data:
How to process and visualize data from OBIS?
There is an OBIS R-package that can be used for statistical analysis and besides the OBIS mapper, you can also use other GIS tools to visualize and analyse OBIS data:
Introduction to R
R is a great tool for accessing and processing OBIS data, as well as for preparing your datasets for OBIS.