Biodiversity Data Integration IG

IG

Group details

Case Statement: 
IG Established
 

Biodiversity is infinitely complex and must be generalised, approximated and abstracted in order to be represented and understood. However, this should not contradict the epistemological richness of biodiversity science as a discipline or deprive biodiversity scientists the flexibility to express their knowledge regardless if their precise terminology has been standardised.

This interest group would like to increase the effectiveness of biodiversity e-Infrastructures by promoting the adoption of common tools and services establishing data interoperability within the biodiversity domain, enabling the convergence on shared terminology and routines for assembling and integrating biodiversity data.

In this context taxon names provide the key element for connecting biodiversity data. The absence of an appropriate global name-reference system hinders an efficient and dynamic cross-referencing of taxon names, the functional re-use of biodiversity information and a single access to 'all names in use'. It also hinders the further development of a communal (virtual) research environment, supporting science as a community effort.

As an example, the Global Names Architecture (GNA) would like to create more stability, compatibility and community in names resolution, by including an objective (nomenclatural) layer, stabilising the cross-referencing of taxon names and by including advanced indexing services for name discovery, recognition and re-use, which will also optimise the use and uptake of all associated biodiversity information.

GNA will optimise the discovery and integration of biodiversity data by developing and improving authority files and names backbones (like CoL and PESI), checklist mapping routines and repositories (like the GBIF Checklist Bank), harmonise web portal APIs, build workflows to secure the proper resolution and data cleaning for e-Science application, and support the on-going virtualisation of the research domain. Gradually the names architecture will advance towards a global names references system, including necessary components like the Global Names Usage Bank (GNUB) and Global Names Index (GNI).

Other recognised essential foundations for data interoperability includes systems for developing, managing and sharing controlled vocabularies and ontologies such as Biodiversity Information Standards TDWG terms wiki (http://terms.tdwg.org) and the National Center for Biomedical Ontology (NCBO) BioPortal and infrastructure models allowing an integrated access to vernacular names, also serving the non-scientific community.

The promotion and adoption of common standards tools and best practices amongst biodiversity researchers as well supports the further internationalisation of existing infrastructures. Therefore an initial focus of this IG includes the drafting of an agenda contributing to the rationalisation of species (data) management, reducing redundancy and fragmentation on species information tools and resources.

Members of this Interest Group are supposed to collaborate with relevant other RDA Working and Interest Groups on data citation, meta-data, persistent identifiers, big data analysis, data publishing, and so on.

Announced short term subgroups and potential Working Groups includes:

  • Global Names Architecture
  • Defragmentation of species data-management
  • Vernacular names infrastructure

The general objective is to make this Interest Group a sustainable component of major biodiversity informatics initiatives, like LifeWatch, EU BON, GBIF, Encyclopedia of Life and Atlas of Living Australia. Preparatory activities are supported by EC FP7 projects, like PESI, ViBRANT, OpenUp!, BioVel and pro-iBiosphere and global organisations like TDWG.

Contacts and chairs

Yde de Jong <mail@yjong.net>

Nicola Nicolson <n.nicolson@rbgkew.org.uk>

Vince Smith <vince@vsmith.info>

Dimitris Koureas <d.koureas@nhm.ac.uk>

References:

Alex Hardisty, Dave Roberts and The Biodiversity Informatics Community, 2013. A decadal view of biodiversity informatics: challenges and priorities. BMC Ecology 2013, 13(16):1-23. doi:10.1186/1472-6785-13-16.

Alex Hardisty et al., 2013. Horizon 2020: A call to forge EU biodiversity links. Nature 502, 170–171 (2013). doi:10.1038/502171d.

Yde de Jong et al., 2015. PESI - a taxonomic backbone for Europe. Biodiversity Data Journal 3: e5848. doi: 10.3897/BDJ.3.e5848.


File Attachment: 
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File BDI_IG_v3.docx46.03 KB

Recent Activity

24 Jun 2019

Plenary 14 Session Submission Deadline Is Thursday!

With Plenary 14 (P14) scheduled to occur from October 23-25, the deadline for session submission is this Thursday, 27 June at 16:00 UTC.

Submissions for meeting sessions are open to working groups, interest groups, joint groups and birds of feather (BoF) meetings.

Please note, however, submissions are accepted from group chairs only. If you submit a session request for a group, please notify the other chairs of that group.

17 May 2019

Open position: Computational Scientist (m/f/d) - Monheim (Germany)

(apologies for cross-posting)
Dear colleague,
We are looking for a 'computational scientist' with the following profile:
* Scientific master degree in bioinformatics or similar
* Experience in building and maintaining (bio-)ontologies as well as in
automatizing ontology maintenance tasks (e.g. using scripts)
* Experience/exposure with master data management (data stewardship and
governance) and with biological data integration as well as algorithms
design and implementation

16 May 2019

Plenary 14: Call for Sessions, Collocated Events, Posters and Registration Now Open!

Taking place from 23-25 October 2019, the 14th RDA Plenary will take place in Dipoli, the nature-immersed building of Aalto University, Helsinki, in Finland, “one of the happiest countries in the world”, states Per Öster, CSC-IT Center For Science Director and Co-Chair of the P14 Programme Committee.

 

23 May 2018

Time to renew leadership and objectives of the group - Call for applications

Dear Biodiversity Data Integration IG members, 

Disciplinary groups play a pivotal role in the RDA ecosystem. Not only they provide a mechanism for engaging with the outputs of the RDA community, they are instrumnetal in providing input to the cross-cutting technical and socio-cultural groups.The number disciplinary groups has significantly increased over the last few years, from a handful (the biodiversity community was there from the start) to around 20 Interest Groups.

20 Apr 2018

presentation at RDA P11

Dear Biodiversity Data Integration IG members,
The Biodiversity Data Integration IG presentation given at the RDA P11
Joint meeting:
IG ELIXIR Bridging Force, IG Biodiversity Data Integration, WG BioSharing
Registry
is now available at:
https://www.rd-alliance.org/biodiversity-data-integration-ig-presentatio...
Kind regards,
Wouter Addink
Coordinator research-data and e-infrastructure
ICT Systems Officer Species 2000

13 Sep 2017

Using R to manage metadata and promote interoperability (FDI-WG)

Dear IG's / WG's,

We would like to invite you to an RDA related event that we believe to be relevant to your activities; "Use R to manage metadata of especially time-series (in our case related to Tuna Fisheries) and comply with OGC standards while using controlled vocabularies." 

Most of the presented software is Open Source, and we will demonstrate how it can help (you) to manage time-series and geospatial data. We welcome feed-back, and if this of your interest, please consider to join the FDI-WG

You can read details here: 

14 Jun 2017

Next steps for BDI IG and online meeting

Dear members of the Biodiversity Data Integration IG,

 

Disciplinary groups play a pivotal role in the RDA ecosystem. Not only they provide a mechanism for engaging with the outputs of the RDA community, they are instrumnetal in providing input to the cross-cutting technical and socio-cultural groups.

The number disciplinary groups has significantly increased over the last few years, from a handful (the biodiversity community was there from the start) to around 20 Interest Groups.