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

Principles (Framework)

Na t

i on a

l Le v

el

Data processing

Data packagingData sources

Ce n

t ra l

Lev

e l Data importing Data checkingData access

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

Mechanism

(Responsibilities)

1. Responsible of data sources & merges2. Ensure data quality & accuracy 3. Decide on data availability 4. Commit to provide data in the

EURISCO-MCPD data format Nat

ion

al

1. Responsible of data checking of NI 2. Provide feedback to National Partners 3. Import NI data in EURISCO4. Develop and maintain front endCen

tral

Protocols (Data flow)

First line contains the MCPD columns descriptors. no order restrictions but has to follow the exactname of the descriptors (I.e. INSTCODE)

ASCII Tab delimited format

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 ?

National Inventory data file…

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

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 (Data flows)

FTPODBC

XML

Text file

Now Short-Medium term

Protocols (Database structure)

ACC

COD_INST

COD_TAX

COD_ISO

COD_SAMPSTAT

COD_COLLSRC

COD_XXXXXXX

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.

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….

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

• ...

Essential !!!

Detailed checking

Basic checking

No real checking(for the time being)

Uploading web site

www.ecpgr.org/eurisco-upload/index.php

Import File

View transfer report

View file import report

View data before uploading to

EURISCO

Upload to EURISCO

View EURISCO update

reports

EURISCO web site

DEMO

Demo site: http://ipgri.singer.cgiar.org/

Demo site