web components for genetic resources site, observation methodology and evaluation data
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www.jki.bund.de
Web components for genetic resources site, observation methodology and
evaluation data
Ch. U. Germeier & L.Frese
WBN 2012, Capelle en Pevele
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
WBN 2012, Capelle en Pevele
WBN 2012, Capelle en Pevele
- 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)
WBN 2012, Capelle en Pevele
Ex Situ
Accession
In Situ
An Integrated Model for In Situ and Ex Situ Data
Occurrence is collected n1
is within a1
n
CharacterisationEvaluation
Site
(Protected) Area
Location(administrative unit)
is within a1
n
Political Environment
is within a1
n
Ecogeography:ClimateSoilHabitatVegetation
Individual
Patch 1
n
n1
Monitoring1 n
Nat
ural
Env
ironm
ent
WBN 2012, Capelle en Pevele
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
WBN 2012, Capelle en Pevele
Protected area (Natura 2000) inside outsideGenebank representation no yes no yesBeta 4 109 34 896
Beta corolliflora 4 137Beta intermedia 266Beta lomatogona 3 181Beta macrocarpa 18 27 90 87
Beta macrorhiza 4 65Beta nana 8 68 3 9
Beta patula 2 10
Beta trigyna 5 2 111 38Beta 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 66Patellifolia procumbens 1 13 9 31Patellifolia webbiana 6 1 12
Analysis of occurrences for Beta
WBN 2012, Capelle en Pevele
Searching through a geographic hierarchy
WBN 2012, Capelle en Pevele
Map occurrences in protected or non-protected areas
WBN 2012, Capelle en Pevele
Interactive correction of occurrence data
WBN 2012, Capelle en Pevele
Would it work with BioGeomancer ?
WBN 2012, Capelle en Pevele
Interactive correction of occurrence data
WBN 2012, Capelle en Pevele
Interactive correction of occurrence data
WBN 2012, Capelle en Pevele
Searching through a taxonomic hierarchy
WBN 2012, Capelle en Pevele
Mapping a Large Taxon (B. vulgaris ssp. maritima)
WBN 2012, Capelle en Pevele
- 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
WBN 2012, Capelle en Pevele
Online repository for observation methodologies
WBN 2012, Capelle en Pevele
Methodology roadmap for evaluation experiments
WBN 2012, Capelle en Pevele
Online – Fieldplan Generation
WBN 2012, Capelle en Pevele
Online – Fieldplan Generation
WBN 2012, Capelle en Pevele
Generate Lists and Excel Templates for Field Observations
WBN 2012, Capelle en Pevele
Generate Lists and Excel Templates for Field Observations
WBN 2012, Capelle en Pevele
Edit Experiment Details
WBN 2012, Capelle en Pevele
Edit Treatment Details
WBN 2012, Capelle en Pevele
Edit Pathogen Strains
WBN 2012, Capelle en Pevele
Calculators: - Percentages- Area extrapolation- Sample moisture harmonization
Map and Upload Excel Files
WBN 2012, Capelle en Pevele
Documentation of Plot Pictures
WBN 2012, Capelle en Pevele
OutlookVision:- 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.
WBN 2012, Capelle en Pevele
Thanks for your attention
Acknowledgements:Carsten Höhne, Stefan Unger, Alexander Henning (Software Development)All project partners
European Commission, DG AGRI council regulation 870/2004Peter Koelln KGaA, Elmshorn, GermanyEmco Ltd., Praha, Czech RepublicGemeinschaft zur Förderung der privaten deutschen Pflanzenzüchtung e.V. (GFP), Bonn, Germany
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