Posts in Interoperability: Dataversity

Hi all
First of all thanks for your participation and contribution to the workshop
“Working towards a ‘New Zealand bio information infrastructure’”,
we held last Friday at TePapa. (Apologies for people I missed in this
distribution list.)

I feel it was another important step working towards our joint goal as
expressed in the workshop title.
To me it also highlighted the importance of having these events (“biodata
enthusiast gatherings”) to keep us all informed, engaged, and aligned. I will
endeavour to have these events regularly.

I like in particular thank Peter for his time and energy to contribute from an
ALA perspective.

Next Steps:

Susan Waugh, James Lambie and I are at the moment preparing formal minutes.

We have identified some key actions at the workshop, here I note in particular
the urgent ones:

- Develop a project concept. Outlining the “why”. What are the key questions
to be answered by a new “system”, what are the key outcomes (environmentally,
economically). What are the core steps of a work programme (i.e. gap analyses,
data catalogues).
Elaine Wright and Aaron Wilton to champion a draft 2-pager by July 31st.
- Jerry Cooper to use this material as “ammunition” for project case within
NSC.
- Does ALA provide Functionalities in terms of data access/ visualisation /
data analyses for NZ use cases? All to check ALA and comment on functionality.
- Governance questions:
Sue to draft TOR for a governance group.
NZ reps on ALA governance group possible – Peter to check.
- Need to approach: MfE, MPI, Stats NZ, Biosec groups, Regional Councils
(through James Lambie) once we have written material as per above.

Thanks again for your enthusiasm!
And always remember: The Path Is The Goal.
Regards, Jochen

Jochen Schmidt
Chief Scientist, Environmental Information National Institute of Water &
Atmospheric Research (NIWA) PO Box 8602, Christchurch, New Zealand, MOB 027 298
5886

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.

Working towards a Data Infrastructure for Biodiversity
At the recent workshop held at Te Papa (5th December) participants agreed that:

* Small working groups should be formed to work on two aspects of a
federated framework for managing and sharing biodiversity data, with a focus on
the guiding role provided by Landcare Research, NIWA, Te Papa and DOC as
relevant national agencies. At that workshop there was a consensus that a
pragmatic way forward is to develop a collaborative project with key
deliverables which encapsulated and demonstrated the value of a national
federated data-sharing network. At the same time, we also agreed there was need
to progress the technical framework supporting the interoperability of bio- and
geospatial data for to the tiers of metadata, biodiversity observation data and
taxonomic data.

* Those working groups will keep the December workshop participants
informed of plans and progress. Subsequently this has been set up on the
Dataversity site by Dan Ranbow.
The next step is to hold a meeting of the working groups to progress the
federated framework for managing and sharing biodiversity data.
Agenda
Collaborative project: Species Occupancy as the primary use case + two
others.
Exploring how a project to develop a national species occupancy toolset will
deliver national benefit? Consider data sources, covariates, design, analysis,
uncertainty, reporting, and use.
What other use-cases could be developed to prove value of a federated biodata
infrastructure.

Potential Workgroup: Jerry Cooper, Peter Bellingham(LCR); Brent Wood, Barb
Hayden (NIWA), Barry Polley, Elaine Wright(DOC);

Technical Framework: Implementation of a federated bio information system
What does a fundamental biodata model look like?
What are the core components? (Metadata, Obs, Taxa?)
What agreements / standards are required?
Working towards a biodata
services framework.
What agreements / standards are required?
Vocabularies required?

Potential Workgroup: Jerry Cooper, Susan Wiser, Alistair Ritchie (LCR);
Brent Wood, Jochen Schmidt (NIWA), Barry Polley, Elaine Wright (DOC); Susan
Waugh (TePapa)

Jochen Scmidt (NIWA) has agreed to progress a meeting in February around these
Work Groups.

Rob Allen
Ph 64 3 321 9601
Cell Ph 027 620 7117
Fax 64 3 321 9998
E-mail <email obscured><mailto:allenr@landcareresearch.co.nz>
P.O. Box 40, Lincoln 7640, New Zealand

[Description: Description: Description: cid:<email obscured>8816E0]

Rest of post

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

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

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

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

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>>

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

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."

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

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

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 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

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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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

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

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]

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/

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