Interoperability framework for freshwater biodiversity data

Hi all
NIWA has been awarded a TFBIS scoping project to initiate a process for
defining a "New Zealand Interoperability Framework for Freshwater Bio Data".
This project is lead by Brent Wood, NIWA Wellington.
Over the next months we will work with a key stakeholder group on defining a
roadmap for making interoperability in freshwater reality.

Please find attached a discussion document for comments and to create
discussion.

Regards, Jochen

fbio_interop_primer.docx 18.64kb

Some holiday reading on some useful existing projects/tools/standards in this
domain ...

THREDDS (Thematic Realtime Environmental Distributed Data Services)
http://www.unidata.ucar.edu/projects/THREDDS/

Econinformatics
http://knb.ecoinformatics.org/index.jsp

GBIF Integrated Publishing Toolkit
http://code.google.com/p/gbif-providertoolkit/

and probably worth examining existing biodata sharing networks ...

The New Zealand Virtual Herbarium mobilising around 1 million occurrence
records from a distributed network of data providers
http://www.virtualherbarium.org.nz/home

The infrastructure provided by the Atlas of Living Australia
http://www.ala.org.au/

And the 2.2 million NZ biodata records mobilised by GBIF
http://data.gbif.org/countries/NZ

including many freshwater records, e.g. Galaxias (may not work for you) ...
http://data.gbif.org/occurrences/searchWithTable.htm?c[0]

Hi all
I did some more thinking and modifications to the
"Primer on a NZ freshwater bio information interoperability framework"
Find attached for comments and discussion.

The main question I have is:
Does the abstract model described in the paper fit with your operational
(CADDIS, Ecobase, ???) or conceptual models of biodata information?
Is there anything missing?

Thanks, Jochen

fbio_interop_primer.docx 170.70kb

Jochen,
You have the primary axes of ... 1) Feature of interest, 2) survey/dataset, 3)
collection event, 4) sampling data.

So if a typical use-case is 'show me the national distribution of organism x'
then I assume 'organism x' is retrieved by a call to the subset of sampling
data with data on organisms?

That's OK - providing of course there is something like an NZOR-mediated
disambiguation layer (organism x is also known as organisms y & z, all with
spelling variants ...).
However, it does seem to bury what to me is a primary use-case rather low down
in the conceptual model - but I'm biased being a taxon-focussed person!

Are there a set of use-cases for the framework? Do we have any sense of
priorities?

Jerry

Rest of post

good note!
I will add some use cases.
Jochen

Rest of post

________________________________________
From: interoperability@dataversity.org.nz [interoperability@dataversity.org.nz]
on behalf of Jerry Cooper [<email obscured>]
Sent: Wednesday, January 25, 2012 2:43 PM
To: interoperability@dataversity.org.nz
Subject: Re: [interoperability] Interoperability framework for freshwater
biodiversity data

Jochen,
You have the primary axes of ... 1) Feature of interest, 2) survey/dataset, 3)
collection event, 4) sampling data.

So if a typical use-case is 'show me the national distribution of organism x'
then I assume 'organism x' is retrieved by a call to the subset of sampling
data with data on organisms?

That's OK - providing of course there is something like an NZOR-mediated
disambiguation layer (organism x is also known as organisms y & z, all with
spelling variants ...).
However, it does seem to bury what to me is a primary use-case rather low down
in the conceptual model - but I'm biased being a taxon-focussed person!

Are there a set of use-cases for the framework? Do we have any sense of
priorities?

Jerry

-----Original Message-----
From: interoperability@dataversity.org.nz
[mailto:interoperability@dataversity.org.nz] On Behalf Of Jochen Schmidt
Sent: Wednesday, 25 January 2012 9:24 a.m.
To: interoperability@dataversity.org.nz
Subject: Re: [interoperability] Interoperability framework for freshwater
biodiversity data

― Attachment links are at the end of this email ―

Hi all
I did some more thinking and modifications to the "Primer on a NZ freshwater
bio information interoperability framework"
Find attached for comments and discussion.

The main question I have is:
Does the abstract model described in the paper fit with your operational
(CADDIS, Ecobase, ???) or conceptual models of biodata information?
Is there anything missing?

Thanks, Jochen
Interoperability now contains the following file

http://dataversity.org.nz/r/file/25266-2012-01-24T202143Z
Name: fbio_interop_primer.docx
Type:
application/vnd.openxmlformats-officedocument.wordprocessingml.document
Size: 170KB

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Hi Jochen

Just a couple of comments – mainly because you asked.

You talk of target audience but the one you have defined is the data providers.
What about data consumers?

Your abstract model – is there any room for a hierarchy for the feature of
interest – I.e. A reach is part of a river – not too sure if this matters

What about surveys that have a nebulous feature of interest – a bit of wetland
just south of the bend in the Waikato river 5 km out of Raglan. We have plenty
of data in FBIS that is not linked back to river, lake or reach – it has a site
name but that may be something made up by the surveyor – site 1B – but the only
thing that pins it down is the coordinates.

Does your model include observations that are not taxa based – i.e. Habitat
measurements/observations?
Does it include for observations about the taxa?

I hope that helps
Jane

Hi all
I did some more thinking and modifications to the
"Primer on a NZ freshwater bio information interoperability framework"
Find attached for comments and discussion.

I added some crude use cases for how users would like to discover / access
information in a interoperable framework for freshwater biodata.
Would appreciate if you could think about others more cases.

Thanks, Jochen

fbio_interop_primer.docx 171.23kb

Hi all
Thanks to those who joined us for the discussion group on a fbio
interoperability framework yesterday.
Please find attached the Minutes, compiled as condensed notes for easy
digestion.

Best, Jochen

fbio_interop_Minutes_feb12.docx 17.60kb

You might be interested in this project if you haven’t come across it already.
Biofresh – has a data interoperability component.

http://www.freshwaterbiodiversity.eu/

One of many EU FP7 e-infrastructures projects being absorbed into ‘Lifewatch’
I believe …
http://www.lifewatch.eu/

Jerry Cooper

Folks - that might be something to learn / steal from?

http://www.freshwaterbiodiversity.eu/index.php/work-package-1.html

"In order to ensure that the BioFresh portal can be linked to other
biodiversity information initiatives and be integrated in a global information
network on biodiversity, we will only use open-source technology and we will
adhere to the standards and tools proposed by global initiatives such as GBIF,
TDWG and the Open Geospatial Consortium (OGC). These include, amongst others,
the ABCD and DarwinCore2 data schemes, CERIF and DIF format from the Global
Change Master Directory (GCMD) for metadata, DiGIR/TAPIR and BioCase as web
access protocols, and integrating WMS and WFS as basic web services. As GBIF’s
generic data portal scheme will be used as the basis for the BioFresh data
portal, developments proposed by GBIF will be closely followed and implemented.
Experience gained as the Belgian node of GBIF and during the development of the
marine biodiversity network of the Scientific Committee on Antarctic Research
(SCAR-MarBIN) will be instrumental."

This is the technology that I think we should be seriously looking at the NZ
biodiversity. It allows NZ to create and publish our own version of Darwin
Core, plus it's out-of-the-box technology - ready to install. For an example
that I have been shown, check out
http://share.biodiversity.aq/training/ANTABIF%20training.pdf

Cheers,
Kevin MacKay, NIWA

an interesting project that seems to cover a lot of what we are discussing...

http://www.google.co.nz/url?sa=t&;rct=j&;q=&;esrc=s&;source=web&;cd=3&;ved=0CDQQFjAC&;url=http%3A%2F%2Fdata.saeon.ac.za%2Fdocumentation%2Frequirements-and-specifications-repository%2Fuser-requirements-documentation%2FG342.3.2%2520Integrated%2520Observations%2520and%2520Measurements%2520Management.pdf%2Fat_download%2Ffile&;ei=8KlvT9y4MI-0iQfazdmPBg&;usg=AFQjCNEpg4eX5pnjXbVYe0RM5GzE80b4wA

Kevin Richards <<email obscured>>

NIWA and Landcare had a meeting on a NJZ biodiversity interoperability
framework on the 26th of March.
Notes can be found under:

https://teamwork.niwa.co.nz/display/NZEIIF/Biodata+Interoperability+Meeting%2C+NIWA+CHC%2C+26-03-2012

Landcare and NIWA specialists have concluded that

it is worth testing O&M as a container but the profile required development in
the context of existing biodiversity specific vocabularies such as Darwin Core
and EML.

We will work further on that premise and keep you posted.

Jochen

https://teamwork.niwa.co.nz/display/NZEIIF/Biodiversity+Interoperability+through+Open+Geospatial+Standards

Hi all (geeks)
As mentioned in the last blog, NIWA has been working on an OGC O&M profile for
biodiversity data.
This would allow to share biodiversity data through open geospatial standards.
The strawman document can be found under above link and any input / comments
from interested folk much appreciated.

Love, Joy, Freedom to you all! Jochen

Hi Bio Data Interoperability Enthusiasts.

Many things are happening in that space.
I have developed my opinion on what NZ Inc. needs in terms of a "federated
infrastructure", with the basic message of "Adopted and maintained standards"
instead of "Portals" and "Warehouses".
See attached file.
Pretty much the interoperability message anyway ;-)

federated information systems.pptx 5.36mb

To keep you up to speed with some international activities:

I have agreed to "represent NZ in GEO-BON wg 8" through the following two
initiatives:

Paper at EGU 2013, lead author Wim Hugo, title: "Development of Extended
Content Standards for Biodiversity Data"

chapter on "cyper-infrastructure" as part of "GEO HANDBOOK ON BIODIVERSITY
OBSERVATION NETWORKS
CONTENTS "

Want more info: please get in touch with me.

Hi all
I believe I never posted the actual final report for TFBIS project 282.
Find attached.

Apologies. Jochen

chc2012_077.pdf 133.58kb

Hi all
To support communication in our BSS project I have created a simple webpage as
a reference to core information and to advertise upcoming events and news:

https://teamwork.niwa.co.nz/display/NZBSS

If you have any requests / suggestions on content please contact me.

Regards, Jochen

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Interoperability framework for freshwater biodiversity data

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