1  Introduction

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 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 training@obis.org or added as issues at https://github.com/iobis/manual/issues.

1.1 Guidelines on the sharing and use of data in OBIS

It is important that our data providers as well as all the data users are aware and agree on the OBIS guidelines on the sharing and use of data in OBIS, which was adoped at the 4th OBIS Steering Group.

1.2 Acknowledgements

This manual received contributions from: Leen Vandepitte, Mary Kennedy, Philip Goldstein, Pieter Provoost, Samuel Bosch, Ward Appeltans, Abby Benson, Yi-Ming Gan, Carolina Peralta Brichtova, Saara Suominen, Serita van der Wal, and Elizabeth Lawrence.

1.3 Data Policy

1.3.1 Guidelines on the sharing and use of data in OBIS

Adopted at SG-OBIS-IV (Feb 2015) and IODE-XXIII (March 2015).

The OBIS data policy is based on the principles of timely, free and unrestricted access to biodiversity data for the benefit of science and society, as defined in the:

Unless data are collected through activities funded by IOC/IODE, neither UNESCO, IOC, IODE, the OBIS Secretariat, nor its employees or contractors, own the data in OBIS and they take no responsibility for the quality of data or products based on OBIS, or the use or misuse that people may make of them nor can it control or limit the use of any data or products accessible through its website, other than through the use of a published Data Sharing and Use Terms and Conditions.

1.3.1.1 Data sharing agreement

The data providers retain all rights and responsibilities associated with the data they make available to OBIS via the OBIS nodes. The OBIS nodes warrant that they have made the necessary agreements with the original data providers that it can make the data available to OBIS data under the Creative Commons licenses.

The data providers are responsible for the completeness of the data and metadata profiles. When data is made available to OBIS, OBIS is granted permission to:

  • Distribute the data via its data and information portal
  • Build an integrated database, use the data for data quality control purposes, complement the data with other data such as climate variables and build value-added information products and services for science and decision-making
  • Serve the data to other similar open-access networks such as GBIF in compliance with the terms and conditions for use set by the data providers.

In pursuance of copyright compliance, OBIS endeavours to secure permission from rights holders to ingest their datasets. In the event that the inclusion of a dataset in OBIS is challenged on the basis of copyright infringement, OBIS will follow a take-down policy until there is resolution.

1.3.1.2 Data use agreement

The data in OBIS are freely available to everyone, following the principles of equitable access and benefit sharing and supporting capacity development and participation of all IOC Member States in global programmes. However, data users are expected to give attribution to the data providers (see Citations) and the use of data from OBIS should happen in the light of fair use, i.e.:

  • Recognize that the OBIS portal holds the master copy of the integrated database and hence users should refrain from online redistribution of the OBIS database. Because the OBIS database is updated regularly (every so months) with new datasets and revisions of existing datasets, copies of the OBIS database will become out of date quickly. If you wish to build access web services on top of OBIS, please contact the OBIS secretariat.
  • Respect the data providers, and provide helpful feedback on data quality.
  • In the case you are a custodian of biogeographic data yourself you should take action to also publish these data through OBIS.
  • Consider sponsoring or partnering with OBIS and its OBIS nodes in grant proposal writing. Creating a global database like OBIS cannot happen without the, often voluntary, contribution of many scientists and data managers all over the world. Several activities, such as the coordination, data aggregation, quality control, database and website maintenance require resources including manpower at national and international level. A list of sponsors can be found here

1.3.1.3 Disclaimer

Appropriate caution is necessary in the interpretation of results derived from OBIS. Users must recognize that the analysis and interpretation of data require background knowledge and expertise about marine biodiversity (including ecosystems and taxonomy). Users should be aware of possible errors, including in the use of species names, geo-referencing, data handling, and mapping. They should crosscheck their results for possible errors, and qualify their interpretation of any results accordingly.

Unless data are collected through activities funded by IOC/IODE, neither UNESCO, IOC, IODE, the OBIS Secretariat, nor its employees or contractors, own the data in OBIS and they take no responsibility for the quality of data or products based on OBIS, or the use or misuse.

1.4 Getting Help in OBIS

If you require additional assistance with OBIS we recommend you first get in touch with the most relevant OBIS node. We also have a support channel on Slack where you can communicate with the OBIS community for help. Please feel comfortable posting to this channel before reaching out to the OBIS Secretariat (). The OBIS community is quite active on Slack and GithHub (see below) so you are more likely to receive a quick answer to your question by posting in either place, as the Secretariat receives many requests.

You can submit issues and questions on relevant Github repositories:

We strongly recommend creating a GitHub account to engage with the OBIS community, document issues, ask questions, find datasets that need endorsing, etc. GitHub gives threads a more permanent home and allows for open communication and transparency. If you are unfamiliar with GitHub, the Carpentries have these training resources which you can reference.