Third session of the IODE Steering Group for OBIS, 4-6 December 2013

Meeting Report

Download IOC/IODE-SG-OBIS-III/3

Executive Summary

The third session of the IODE Steering Group for OBIS (SG-OBIS-III) took place on 4-6 December 2013 at the Project Office in Oostende (Belgium). The meeting was well attended with 27 participants. The meeting started with a pre-session day to allow the OBIS task teams to present their ideas and recommendations to prepare the steering group for the more formal session. This format turned out successful and the meeting ended with the adoption of a long list of decisions and recommendations. An important decision was to establish a multidisciplinary scientific advisory task team to steer OBIS into future directions. This new group will meet annually prior to the SG-OBIS meeting. The OBIS steering group also decided on a number of quality control checks for geographical position, dates and taxonomic names, to be implemented by the OBIS nodes before they send data to OBIS. In addition, the Integrated Publishing Toolkit (IPT), developed by the Global Biodiversity Information Facility, will become the standard protocol for exchange of data and metadata between OBIS nodes and the central iOBIS node. Regarding metadata, the Integrated Marine Information System (IMIS) developed by the Flanders Marine Institute, will be used as a central metadata repository. An online project management and issue tracking system will be developed to guide proposals for portal enhancements and new OBIS data content types. The OBIS governance team is tasked to draft an OBIS data policy, and develop a plan to evaluate OBIS nodes and prepare a succession plan in case OBIS nodes become inactive. Two OBIS technical training courses will be organized in 2014 to train data providers and OBIS node managers to access and provide best-quality data to OBIS. In addition, several documents will be published in 2014, such as the OBIS strategic business plan, some outreach material and an OBIS manual for nodes and data providers.

With the recruitment of the OBIS data manager in May 2013, the OBIS international secretariat is now fully operational again. The data from the OBIS nodes are harvested on a regular basis (every 3 months) and the secretariat can fulfill its central role, such as providing training and technical assistance, guiding new data standards and technical developments, and encouraging international cooperation to foster the group benefits of the global network. The OBIS secretariat will also be involved in projects to develop information products and services to support global assessments such as the World Ocean Assessment of the UN Regular Process and the recently established Intergovernmental Science-Platform on Biodiversity and Ecosystem Services.

Recommendations and Decisions

OBIS SCIENCE ADVISORY TASK TEAM

• The SG-OBIS agreed to establish an OBIS Science Advisory Task Team. See here for Terms of Reference and membership.

OBIS TRAINING AND DOCUMENTATION TASK TEAM

• The SG-OBIS agreed that the OBIS training task team will publish a dynamic manual for OBIS node managers and recommended to expand the manual for data providers.

OBIS TECHNICAL TASK TEAM

• The SG-OBIS agreed that OBIS tier 2 nodes shall be using the Matching Strategy for taxonomic Quality (defined by the Taxonomic TT) and the LifeWatch tool for geographic and date quality control (as described by the Training TT)
• The SG-OBIS agreed that OBIS tier 3 nodes shall be recommended to use the Matching Strategy for taxonomic quality control (defined by the Taxonomic TT) and the LifeWatch tool for geographic and date quality control
• The SG-OBIS agreed that data that have not passed the above quality checks will receive corresponding quality flags on the iOBIS data portal, which will allow user to filter data.
• The SG-OBIS recommended to check other Quality Control tools when considering new developments
• The SG-OBIS recommended to check if the Quality Control tools used in OBIS can be implemented as part of the IPT.

OBIS DATA CONTENT ENHANCEMENT TASK TEAM

• The SG-OBIS agreed when evaluating enhancements of the OBIS System (database and portal), we should consider the business case / justification for doing so, and consider potential clients and funding opportunities.
• The SG-OBIS agreed to set up an issue tracking system for data enhancements: as OBIS adopts Ratified Darwin Core, we desire consensus in our use of terms and we anticipate some usage will require discussion and resolution of questions and issues. For on going handling of terminology questions, implement a method and tools that support collaboration among globally distributed participants, such as an issue tracking system.
• The SG-OBIS agreed to use ISO-8601 for date (only one field)
• The SG-OBIS agreed to add a scientific name qualifier (resulting in adding a new field in OBIS scheme).
• The SG-OBIS agreed to implement Ratified Darwin Core recognizing that individual network components may need a transition period before this can be fully adopted throughout the network.
• The SG-OBIS recommended to consider the impact of the transition to Ratified Darwin Core on OBIS program office technology - particularly the database. Initiate a task to assess and evaluate requirements, technical options, and cost /benefit/risk factors, followed by a task to select, plan and implement technology changes.
• The SG-OBIS recommended to consider the impact of the transition to Ratified Darwin Core on OBIS nodes. Plan to develop Ratified Darwin Core education and assistance for nodes, while encouraging nodes self-reliance.
• The SG-OBIS recommended to collaborate with GBIF, IODE/GE-BICH and SeaDataNet to help develop vocabularies for additional data types.
• The SG-OBIS recommended to apply the following policy with respect to opportunities to enhance OBIS content by making wider use of existing Darwin Core terms and extensions or by developing new terms and extensions:
  • Encourage application-based and requirements-driven use of terms,
  • Encourage leadership by OBIS nodes, teams, or individuals, to develop enhancements,
  • Do not restrict enhancement by blanket prohibition, however,
  • Do warn content enhancers to manage scope, complexity, and risk exposure in the enhancements they pursue,
  • Refer to and follow Darwin Core practices as a guide for all enhancements (a guide is available at http://rs.tdwg.org/dwc/index.htm),
  • OBIS wants to encourage node independence to develop enhancements to meet their needs, but OBIS wants to establish consensus on enhancements that are adopted into OBIS program-wide practices.
• The SG-OBIS recommended that iOBIS includes the original data if it offers a full-scale public IPT of all OBIS datasets
• The SG-OBIS recommended the OBIS data content enhancement Task Team to investigate the addition of a “georeference protocol” to the OBIS schema (verbatim location, GPS, closest degree)
• The SG-OBIS recommended to add georeferencing precison (decimal places, trailing zeros) as part of the geographic Quality Control procedure.
• The SG-OBIS recommended to determine coordinate uncertainty (m) as part of the geographic Quality Control procedure.
• The SG-OBIS recommended to develop more Darwin Core expertise within OBIS by:
  • Establishing more interaction with Darwin Core experts via GBIF, TDWG, and other Darwin Core communities.
  • Setting-up data enhancement meetings with users/data providers (i.e. those that can explain to us what their needs and requirements are, e.g. ICES, PICES.). Be user driven, incl. sponsorship.
• The SG-OBIS recommended to investigate the possibility to use extended data types to link the OBIS system with other systems, e.g. SeaDataNet.
• The SG-OBIS agreed that iOBIS will gather the metadata in any format (no single metadata format for OBIS nodes). iOBIS will capture at least a minimal set of metadata information for every dataset (abstract, citation, title, contact).
• The SG-OBIS agreed that IMIS will be central metadata repository for iOBIS.
• The SG-OBIS agreed that OBIS nodes are not required to have web accessible metadata; OBIS/IMIS can capture richer metadata contents than the minimum set for these nodes.
• The SG-OBIS agreed that iOBIS will use IMIS to export to multiple formats, ISO (Ocean Data Portal), FGDC, DIF (GCMD)
• The SG-OBIS agreed that IMIS and Darwin Core Archives will point to web accessible metadata for nodes who have web accessible metadata available.
• The SG-OBIS agreed that EML may become a widely used input format due to IPT, but other format possibilities are still open to populate DwC-A.
• The SG-OBIS recommended looking into working with the GCMD organization for their ability to assist with metadata formatting.
• The SG-OBIS recommended to take into consideration that data enhancements will impact the metadata requirements, minimal fields will be increasing
• The SG-OBIS recommended OBIS will investigate requirements and priorities for offering and emphasizing the use ISO 19115 metadata and OBIS will prepare accordingly to implement ISO metadata solutions.

OBIS TAXONOMY TASK TEAM

• The SG-OBIS agreed to add a ScientificNameID to the OBIS schema. Use LSIDs when available. AphiaID (from WoRMS) is the preferred LSID.
• The SG-OBIS agreed to add the original (non valid, misspelling, misapplied, …) name to the OBIS schema
• The SG-OBIS agreed if the species name is a synonym, to not change the original name; and use the synonym name ScientificNameID.
• The SG-OBIS agreed that uncertain identifications should be matched to the first higher level (ScientificNameID is associated with the parent). Flag the uncertainty in the TaxonRemarks field.
• The SG-OBIS agreed that fossil data can be included, but is not a priority for OBIS.
• The SG-OBIS recommended to include authorship in scientific names (using ScientificAuthorship field)
• The SG-OBIS recommended that iOBIS builds its own DwC extension if required, and liaises closely with the Darwin Core community
• The SG-OBIS recommended hosting the annotated list of non-marine scientific names

OBIS TECHNICAL TASK TEAM

• The SG-OBIS agreed to make dot size on data portal according to precision
• The SG-OBIS agreed that unknown species names should not be removed, but flag accordingly
• The SG-OBIS agreed to show taxonomy from WoRMS on OBIS portal (live connection)
• The SG-OBIS agreed to create a giant iOBIS IPT Server
• The SG-OBIS agreed that the iOBIS database shall not be extended with new data types unless we use the extra data types on the portal
• The SG-OBIS agreed that all new OBIS nodes shall use IPT (no new DiGIR servers be created)
• The SG-OBIS agreed that MS Excel sheets, Word etc are no longer acceptable formats for data exchange with OBIS node tier 1 (iOBIS)
• The SG-OBIS agreed that iOBIS will develop an OBIS advanced search
• The SG-OBIS agreed that iOBIS will only store metadata that is really needed and link to page (EML) with more (need a WAF (web accessible folder)
• The SG-OBIS agreed that web services should point to the iOBIS Stage (or mirror) System to avoid performance problems with live system.
• The SG-OBIS agreed that the OBIS Project Office should be contacted directly for requests for data in historical versions of the iOBIS database.
• The SG-OBIS agreed to use of the OBIS internal website to store internal documentation (link to any existing documentation on the Google drive).
• The SG-OBIS recommended that existing OBIS nodes move to IPT, but can still use DiGIR
• The SG-OBIS recommended that the Project Office offers IPT set up to Nodes. Tier 2 Nodes can facilitate the transfer of data from EXCEL to IPT.
• The SG-OBIS recommended that the Project Office should make an agreement with VLIZ that they enter metadata into IMIS, or provide a means of semi-automating the entry of minimum metadata into IMIS
• The SG-OBIS recommended upgrading the Drupal CMS in the future and the O/S, and database, but not Geoserver (as the portal will break).
• The SG-OBIS recommended updating the Shapefiles and Oceanographic Variables used in the iOBIS Database indexing process with newest versions.
• The SG-OBIS recommended promoting the use of existing OBIS Web services.
• The SG-OBIS recommended that OBIS should monitor data usage, via the portal and webservice and to provide these statistics online.
• The SG-OBIS recommended setting up a system to reference versions of the OBIS database with DOIs, and setting up a repository of database versions.
• The SG-OBIS recommended the following enhancements to the iOBIS web portal:
  • Enable Multiple Species Selection in the Portal Search,
  • Implementing OBIS SEAMAP improvements:
    • Drawing areas on a map and calculating diversity indexes etc. dynamically.
    • Enhanced area selection: such as an area outside a zone or selection.
    • Stateful Search
  • Enhance / Correct display of taxonomy (accepted names vs synonyms) on the iOBIS portal.
  • Tools to aid the construction of an OGC webservice URL.
  • Pre-calculated webservice URLS for common requests.
  • Better summarise OBIS data for outputs such as Biodiversity Maps, species checklists, summaries for pre-defined areas / taxa, species e.g. IUCN Red List, range maps
  • Better display of time series / adding time dimension to maps e.g. spread of invasive species.
  • Implementation of better system monitoring tools e.g. MUNIN

OBIS WEBSITE TRANSLATIONS

• The SG-OBIS agreed that a multilingual website is important and translations should be continued
• The SG-OBIS recommended to show the English version if pages are not translated.

OBIS GOVERNANCE

• The SG-OBIS agreed to publish the OBIS Strategic Business Plan considering the last modifications provided by the meeting participants; see Strategic Plan for the Ocean Biogeographic Information System, including resource requirements
• The SG-OBIS recommended to review the OBIS Data policy
• The SG-OBIS recommended to develop a plan to evaluate OBIS nodes
• The SG-OBIS recommended to develop a succession plan in case OBIS nodes become inactive