web components for genetic resources site, observation
TRANSCRIPT
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www.jki.bund.de
Web components for genetic resources site,
observation methodology and
evaluation data
Ch. U. Germeier & L.Frese
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An Integrated European In Situ management work plan:
implementing genetic reserves and on farm concepts (AEGRO)
Avena Genetic Resources for Quality in Human Consumption (AVEQ)
Population level information systems for model crops (e.g. Beta).
An integrated model for in situ and ex situ data.
Data sources and analysis for Beta.
Searching, mapping and editing in PLIS Beta.
Web based components for AEGRO and AVEQ
Online repository and roadmap for observation methodologies in
evaluation.
Field plan generation.
Generate lists and spreadsheet templates for field observations.
Edit experiment and treatment details including strains for artificial
inoculation.
Import spreadsheets and upload plot pictures.
Outlook
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- Development of information models for in situ management of plant
genetic resources field work on the population level.
- Integration of historical occurrence (distribution) data.
- Propose concepts for data exchange and the integration of project results
in existing information systems (e.g. the European Central Crop
Databases).
- Development of a web application for information on already known sites
and additional tools supporting in situ field work (mobile application based
on the CyberTracker development framework).
Population level information systems
for model crops
(Avena, Beta, Brassica, Prunus)
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Ex Situ
Accession
In Situ
An Integrated Model for
In Situ and Ex Situ Data
Occurrence is collected n 1
is within a 1
n
Characterisation
Evaluation
Site
(Protected)
Area Location
(administrative unit)
is within a
1
n
Political Environment
is within a
1
n
Ecogeography:
Climate
Soil
Habitat
Vegetation
Individual
Patch 1
n
n
1
Monitoring
1 n
Na
tura
l E
nvir
on
men
t
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Biological Data Sources
GBIF Excel downloads (2007)
EURISCO Excel downloads (2007)
PCGRIN DBase download (2007)
ECCDB: IDBB (2007)
Number of entries
(accession, cataloguenumber)
20 355 *
7 155*
2 506**
10 435**
* restricted to Europe ** worldwide
EUROSTAT (NUTS / LAU, 2003) * 111 074 locations
described on 4 levels
Natura 2000 Database (J.Iriondo to detect occurrences in protected areas)
Geographic Data Sources
Data Sources Beta
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Protected area (Natura 2000) inside outside
Genebank representation no yes no yes
Beta 4 109 34 896
Beta corolliflora 4 137
Beta intermedia 266
Beta lomatogona 3 181
Beta macrocarpa 18 27 90 87
Beta macrorhiza 4 65
Beta nana 8 68 3 9
Beta patula 2 10
Beta trigyna 5 2 111 38
Beta vulgaris 333 239 2400 1973
Beta vulgaris L. subsp. adanensis 6 23 22
Beta vulgaris L. subsp. maritima 967 131 5600 823
Beta vulgaris L. subsp. vulgaris 63 105 1280 1381
Patellifolia patellaris 6 19 48 66
Patellifolia procumbens 1 13 9 31
Patellifolia webbiana 6 1 12
Analysis of occurrences for Beta
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Searching through a geographic hierarchy
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Map occurrences in protected or non-
protected areas
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Interactive correction of occurrence data
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Would it work with BioGeomancer ?
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Interactive correction of occurrence data
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Interactive correction of occurrence data
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Searching through a taxonomic hierarchy
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Mapping a Large Taxon (B. vulgaris ssp. maritima)
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- Online repository for observation methodologies,
Develop web solutions for managing cooperative multisite genetic
resources evaluation and facilitate the inclusion of project data into
a central database by promoting standardized ways of
documentation and data generation:
- Online description of field experiments and treatments,
- Online fieldplan generation, download of pdf and Excel templates,
- Spreadsheet upload with routine calculations (e.g. emergence, yield,
seed weight)
AVEQ: Avena genetic resources for quality in
human consumption
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Online repository for observation methodologies
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Methodology roadmap for evaluation
experiments
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Online – Fieldplan Generation
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Online – Fieldplan Generation
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Generate Lists and Excel Templates for
Field Observations
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Generate Lists and Excel Templates for
Field Observations
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Edit Experiment Details
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Edit Treatment Details
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Edit Pathogen Strains
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Calculators:
- Percentages
- Area extrapolation
- Sample moisture harmonization
Map and Upload Excel Files
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Documentation of Plot Pictures
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Outlook Vision:
- The user community manages the database themselves by using the
online tools.
- They are able to adapt and further develop these tools for their purposes
themselves with the source code available in an open source repository.
Next steps:
- All source code developed for AEGRO and AVEQ will be made available in
CropForge together with journal publications.
New projects:
- Mobile apps for using the IDBB in exploration and monitoring of
in situ CWR resources?
- Using and improving the online tools developed for AVEQ in a
Beta evaluation and characterization project?
- Still to be done: update of passport data and / or stronger
integration with EURISCO and GRIN passport data – will be
difficult to attract funds for that.
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Thanks for your attention
Acknowledgements:
Carsten Höhne, Stefan Unger, Alexander Henning
(Software Development)
All project partners
European Commission, DG AGRI council regulation 870/2004
Peter Koelln KGaA, Elmshorn, Germany
Emco Ltd., Praha, Czech Republic
Gemeinschaft zur Förderung der privaten deutschen
Pflanzenzüchtung e.V. (GFP), Bonn, Germany