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European Internet Search Catalogue of ex situ PGR accessions

European Internet Search Catalogue of ex situ PGR accessions. EURISCO Uploading mechanism. Principles Framework Data format Responsibilities Mechanism Protocols Import file data format / technology Uploading web site EURISCO demo version. Data sources. Data packaging.

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European Internet Search Catalogue of ex situ PGR accessions

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  1. European Internet Search Catalogue of ex situ PGR accessions

  2. EURISCO Uploading mechanism • Principles • Framework • Data format • Responsibilities • Mechanism • Protocols • Import file data format / technology • Uploading web site • EURISCO demo version

  3. Data sources Data packaging National Level Data processing Principles (Framework) Data access Data importing Data checking Central Level

  4. Principles (Data format) • Data from National Inventory are uploaded to EURISCO in a fixed format • to allow automation • to allow validation • Descriptor list is only for uploading • National Inventory descriptors can be different • Scripts for conversion can be necessary • The EURISCO descriptor list is an extension of the FAO/IPGRI Multi Crop Passport Descriptor List (MCPD) version 2 (December 2001) • the MCPD list v2 is used without changes but with six additions • Download the MCPD: • http://www.ipgri.cgiar.org/publications/pubfile.asp?id_pub=124 • http://www.ipgri.cgiar.org/publications/pdf/124.pdf

  5. Responsible of data sources & merges • Ensure data quality & accuracy • Decide on data availability • Commit to provide data in the EURISCO-MCPD data format National • Responsible of data checking of NI • Provide feedback to National Partners • Import NI data in EURISCO • Develop and maintain front end Central Mechanism (Responsibilities)

  6. First line contains the MCPD columns descriptors. no order restrictions but has to follow the exact name of the descriptors (I.e. INSTCODE) Next lines contains the respective MCPD descriptorsfor each accession submitted. Essential fields required for each line: NICODE= NI identifier = ISO code = From ? INSTCODE= INST identifier = Who ? ACCENUMB= ACC identifier = What ? GENUS= Taxa identifier = Of ? Protocols (Data flow) ASCII Tab delimited format National Inventory data file…

  7. Descr1 -> Descr2 -> Descr3 -> Descr4 …. ->DescrX Data1 -> Data2 -> Data3 -> Data4 …. ->DataX Data1 -> Data2 -> Data3 -> Data4 …. ->DataX Data1 -> Data2 -> Data3 -> Data4 …. ->DataX Data1 -> Data2 -> Data3 -> Data4 …. ->DataX Data1 -> Data2 -> Data3 -> Data4 …. ->DataX Protocols(Import file data format) • TAB delimited text file (for the time being) • TAB=ASCII(9) as field separator • One accession = one line • Line Break=ASCII(10) or ASCII(10)+ASCII(13) as line separator

  8. Text file FTP ODBC XML Now Short-Medium term Protocols (Data flows)

  9. COD_INST COD_SAMPSTAT ACC COD_TAX COD_COLLSRC COD_ISO COD_XXXXXXX Protocols (Database structure)

  10. Protocols (tools and technology) Database software:MySQL (http://www.mysql.com) Scripting language:PHP (http://www.php.net) Web server:Apache (http://www.apache.org) The objective is to develop EURISCO central node with free software.EURISCO should be able to run on most OS (Linux, Windows, Mac…) All developments including codes are freely accessible.

  11. Protocols (Preliminary checks) • Data format (for the time being tab delimited) • Essential descriptors • NICODE • INSTCODE • GENUS • ACCENUMB • Line per Line checking • Uploading report generated • Data provider contacted for approval….

  12. Essential !!! Detailed checking Basic checking No real checking(for the time being) Protocols (Line checks) • Line per Line checking • Required Descriptors • Descriptors coded • Sample status • Collecting source • With INSTCODE (BREDCODE…) • Descriptors semi-coded • Dates • Coordinates • Descriptors un-coded • Taxonomy • ...

  13. Uploading web site www.ecpgr.org/eurisco-upload/index.php

  14. Import File

  15. View transfer report

  16. View file import report

  17. View data before uploading to EURISCO

  18. Upload to EURISCO

  19. View EURISCO update reports

  20. EURISCO web siteDEMO Demo site: http://ipgri.singer.cgiar.org/

  21. Demo site

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