Biodiversity Data Integration IG

IG

Group details

Chair(s): 
Nicola Nicolson, Vince Smith, Paul Kirk, Dimitris Koureas
Case Statement: 
 

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.

Recent Activity

13 Sep 2016

RDA P8 BDI IG Session - update

Dear BDI IG members,
The Biodiversity Data Integration IG acts as a mechanism to enable our wider community to interact with other communities of practice from the Research Data Alliance and also benefit from its outputs.
It is necessary that the group adjusts its agenda based on the current and future needs within our domain and remains responsive to changes and opportunities.

06 Sep 2016

Demo you Software at RDA: Better Description/ Retrieval of Online Scientific Data

Dear Colleagues,
there is an *opportunity to showcase your software* (prototype pr
mature) to:
- enhance the authoring of comprehensive metadata using
community-endorsed standards
- to ensure the annotation of data with terms from standard ontologies
and terminologies, and
- to aid the identification and retrieval of relevant datasets for
exploration and re-analysis.
*BOF: Software for Better Description and Retrieval of Online
Scientific Data*

23 Aug 2016

Heads up on Domain Vocabulary BoF at P8

Will someone from RDA Biodiversity Data Integration IG  be willing to attend and summarize your effort and interest at the Domain Vocabulary Development, Standardization, Registration, Harmonization and Support Breakout  - Saturday17 Sept 11:00 - 12:30?

Since this meeting occurs at the end of P8 it is likly that there will be enough context to have a good exchange of interests and plans.

The idea is that each domain group will provide a brief summary of their work and as available:

05 May 2016

Fwd: Call for papers/abstracts SciDataCon2016

Hello All,
In case anyone is interested. We have a workshop session approved for
SciDataCon2016 at Denver in September 2016 . This session will focus on
environmental data to explore how to make this data published by the
scientific community useful for planners and decision makers and to support
new methods of interpretation and incorporation into working practices.
There is now a call for abstract for presentations for that session. The
session is "The Data requirements and availability for decision makers".

23 Feb 2016

Fwd: Constraint modelling and the SDM course

Hello
I'll be in Japan for the RDA plenary next week if anyone sees anything that
might be of mutual interest in the below.
We've just completed the GBIF data integration for the next release. If
anyone is interested I could get some information together around that
experience and learning etc.
Malcolm
---------- Forwarded message ----------
From: BCCVL <***@***.***>
Date: Thu, Feb 18, 2016 at 11:19 AM
Subject: Constraint modelling and the SDM course
To: ***@***.***

04 Feb 2016

Invitation: RDA P7 BoF - Metadata Standards for attribution of physical and digital collections stewardship

Dear BDI IG members,
Further to my previous email announcing our joint session between our IG and Practical Policy and Certification of repositories Groups, I am happy to announce that RDA programme committee has also approved a BoF breakout session in support of the creation of a new WG on Metadata Standards for attribution of physical and digital collections stewardship.

29 Jan 2016

Biodiversity data repositories: Certification and practical policies | RDA P7 Joint session

Invitation to RDA joint session
RDA P7, Tokyo
The Biodiversity Data Integration, Practical Policies and Certification RGA Groups are co-organising a joint session at the next RDA P7 in Tokyo.
The overarching goal of this joint session is to discuss and plan ahead on top of the outputs of the two technical groups (PP and Certification) and in relation to the needs of institutional and domain repositories for biodiversity data.
Session Title: Biodiversity data repositories: Certification and practical policies
Objectives:

20 Aug 2015

Agenda for the BDI IG breakout session and joint meeting at RDA P6

Dear BDI IG members,
Following a call for abstracts, we received a lot more submissions than originally anticipated. This demonstrates the increasing interest of the community to address the challenges related to the mobilisation of biological/natural history collection data and promote their use. The presentations were selected so that together they form a coherent narrative that takes us from the challenges of data extraction to their use in climate change research.
You may find the agenda for the session at

10 Aug 2015

Call for Presentations - Deadline tomorrow

Final reminder
Dear all,
During the forthcoming RDA plenary in Paris (23-25 Sep) the Biodiversity Data Integration Interest Group will organise a session on data from biological collections.
The title of the session is
"Unlocking the potential of biological collections data for climate change research"
We would like to share experiences, insights and ideas on how we can increase the impact of datasets generated by the ongoing and planned biological collections digitisation programmes across the globe.