Interoperability framework for freshwater biodiversity data.
TFBIS Project 282
Primer / discussion document for comment from project team and wider community
Background
Various organisations across New Zealand hold and / or curate archives and databases of freshwater
biodiversity survey (FBIO) data. To date there is no easy and nationally agreed way to query or
transfer freshwater biodiversity survey information across organisations and systems. New Zealand
needs a biodiversity interoperability framework to achieve that. In this project we conduct a number
of workshops with a key stakeholder group of freshwater biodiversity data managers and architects
to scope key users, components, architecture, and develop a roadmap for a national freshwater
biodiversity interoperability framework. (from NIWA TFBIS proposal)
Key Stakeholder Group
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Jim McLoed, WRC
Jim Fretwell, BOP
Jerry Cooper, LCR
James Lambie, Horizons
Jochen Schmidt, NIWA
Brent Wood, NIWA
Paul Barter, Cawthorn
Norm Thornley, DOC
Lucy Baker, MfE (Observer)
Potentially observer from MSI/MAF
Target audience
Our understanding is that there are different communities with regards to management of FBIO
data:
1.
2.
3.
4.
5.
6.
7.
A range of CADDIS users among regional councils and Cawthorn.
A range of EcoBase (IQUEST) users among regional councils.
Freshwater Fish community feeding data into FFDB and that into FBIS.
NIWA aquatic plants group uses AQPDB which feeds into FBIS.
NIWA freshwater invertebrate groups feed into FBIS.
NIWA freshwater algae groups plan to feed into FBIS.
A large range of NIWA and RC staff use their own excel spreadsheets etc. (= ’wild west’)
It seems to be sensible to focus for now on the question how to integrate the CADDIS/EcoBase/FBIS
communities into an interoperability framework.
What are the fundamental and common concepts of a FBIO Management system?
The key paradigm of the FBIO interoperability framework can be defined as:
Regardless how and where FBIO data is managed, we want stakeholders to be able to discover it in a
taxa, spatial, and temporal context, provide consistent metadata, and be able to access the
information in a consistent way.
To enable interoperability we need to define the same concepts which are common in the
underlying FBIO systems (as an abstract concept).
We suggest they are:
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Feature of interest. The surveyed environmental feature. Typically for freshwater: river
reach, lake, lagoon, wetland, estuary, … In a DB typically represented as a descriptive field or
a link to reference GIS. Typically and simplified described by a geospatial feature (although
we realize that that is a simplification!). Could be exposed as WFS/WMS?
Survey (or dataset). A set of FBIO data collected for one purpose (e.g. project), through one
survey. Typically the scope of what “survey” entails can be variable and is defined by the
curator. Is a survey always related to only one feature of interest? We suggest using ANZLIC?
/ Darwin core? / GBIF? as the common data concept to describe those.
Sampling efforts (or sampling events). A survey always consists of a number of sampling
events. A sampling event is defined by FBIO data collected in one location (coordinate), one
date/time, one method (and more?). What is the common conceptual information model for
sampling efforts?
Sampling Data. The actual data can be quite variable and multi-fold. Therefore currently in
FBIS we have modelled that as a set of (hierarchical) key-value pairs. What is the common
conceptual information model for sampling data?
(Note: We are just focussed on survey data for the purposes of this project, but we do recognise that
other data, e.g. community captured, & opportunistic, exists).
Method
n
1
1
n
n
1
1
Sampling data
Sampling effort
Survey / Dataset
Feature of interest
Taxa / NZOR
1
n
1
Represented through
GIS Polygon
Metadata
Metadata,
point, time
Sampling
data, taxa
Simplified abstract model for an interoperability framework for Freshwater
Biodiversity (FBIO) data.
Key elements of a NZ FBIO interoperability framework
We suggest the following elements need to be dealt with:
1. Interoperable taxa management. To be interoperable all taxa data need to be compatible.
This should be achieved through references to NZOR.
2. Interoperable Feature of Interest Management. To be interoperable references to feature of
interest need to be compatible across the databases.
3. Interoperable spatial references. To be interoperable all spatial references need to be
compatible. Same coordinate system used or well-defined and transformation (on the fly).
4. Interoperable temporal references. To be interoperable all temporal references need to be
compatible. Should not be a big deal??
5. Interoperable methods references. To be interoperable all methods references need to be
compatible. Typically different systems use their own terminology. It will be very hard to
achieve consistency here. Probably best dealt with reference to a locally managed methods
register.
6. Open Standard (web service) to expose survey information. We suggest this should be done
through OGC catalogue services for the web CSW (or others?). Note that this web service
need to include links to (web services exposing) the sampling efforts related to the survey.
7. Open Standard (web service) to expose sampling effort information. We suggest this should
be done through a clearly specified OGC web feature service WFS (Or SOS? Or Others?). Note
that this web service need to include links to (web services exposing) the sampling data
related to the effort.
8. Open Standard (web service) to expose sampling data. Need to develop a standard for that?
Is there an existing one? GBIF/SOS?
Overall architecture of a NZ FBIO framework.
We suggest that the overarching principles and architecture should be defined as follows:
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Every major collector of FBIO data need to feed their data into a “managed FBIO system”.
A “managed FBIO system” uses the fundamental concepts as defined above.
A “managed FBIO system” is consistent with (1), (2), (3), (4), (5) above. (We might be able to
relax 2, 5?).
A “managed FBIO system” stores survey information exposes its information through (6), (7),
(8)