Table of Contents

1.0         General Information. 2

1.1 System Overview.. 2

1.2 User access levels. 2

1.2.1 Public (EUginius.eu) 2

1.2.2 AuthoriSed Users. 2

1.3 Points of Contact. 2

1.4 OrganiSation of the Manual 2

1.5 Nomenclature. 2

1.6 Abbreviations. 2

2.0         Getting Started. 2

2.1 Access and Login. 2

2.1.1 Access. 2

2.2 System Menu. 2

2.2.1 Homepage. 2

2.2.2 GMO.. 2

2.2.3 Detection. 2

2.2.4 Analysis. 2

2.2.5 Authorisation. 2

2.2.6 Search. 2

2.3 Homepage Search Module. 2

2.3.1 GMO Search. 2

2.3.2 Literature Search. 2

2.4 Help Module. 2

3.0         Using the System.. 2

3.1 GMO.. 2

3.1.1 List with GMOs and their Identifiers. 2

3.1.2 List with GMOs and Traits. 2

3.1.3 List with GMOs and Genetic Element 2

3.1.4 GMO details. 2

3.2 Detection. 2

3.2.1 Detection Methods. 2

3.2.2 Method Verification. 2

3.2.3 Reference Material 2

3.2.4 Detection Search. 2

3.3 Analysis. 2

3.3.1 Entering Screening Data. 2

3.3.2 Analysis Results. 2

3.4 Authorisation. 2

3.4.1 Authorisation Symbols. 2

3.4.2 Generic Approval 2

3.4.3 Traffic Light Search. 2

3.4.4 Authorisation Search. 2

3.5 Search Module. 2

3.5.1 GMO Search. 2

3.5.2 Literature Search. 2

3.5.3 Element Search. 2

3.5.4 Navigating Search Results. 2

3.6 Exporting data. 2

4.0         Workflow.. 2

4.1 Analysis Tool 2

4.2 Designing a Screening. 2

5.0         Input and Feedback. 2

5.1 Input and Feedback. 2

5.1.1 Suggest New GMO.. 2

5.1.2 Give Feedback. 2

6.0         Appendix. 2

6.1 Appendix Glossary. 2

6.2 GMO-related websites. 2

6.3 Thesauri 2

6.3.1 Elements. 2

6.3.2 STraits. 2

6.4 Terms and Conditions of Use. 2

6.4.1 Terms of use. 2

6.4.2 Conditions of use for registered users. 2

 

1.0                          General Information


 

1.1 System Overview

EUginius, The European GMO Reference Database

EUginius (European GMO Initiative for a Unified database System) is an initiative of BVL - the Federal Office of Consumer Protection and Food Safety (Berlin, DE) and RIKILT Wageningen University and Research (Wageningen, NL) to support competent authorities and private users who seek accurate information on GMOs.

EUginius provides accurate information of major and relevant issues regarding the presence, detection and identification of GMOs with a focus on the situation in the European Union as well as world-wide coverage.

 

1.2 User access levels

  

1.2.1 Public (EUginius.eu)

Access to the EUginius.eu database is open for use by anyone and is intended to support competent authorities as well as private users.

1.2.2 AuthoriSed Users

For unrestricted access to EUginius you must have an account with proper authorisations. For the terms and conditions regarding authorised use consult 6.4 Terms and Conditions of use.
Access can be granted by BVL staff and can be requested via databasemanager@euginius.eu.

EUginius has 3 authorised access levels.

1.2.2.1 read-only

Read Only grants additional access to confidential information as well as modules that are under construction. This includes:

·          BLAST Module

·          Safety Literature Module

1.2.2.2 Expert

Expert users have access to all levels which Read Only cover, plus access to the Data Entry module.

Expert accounts are either BvlExpert or RikiltExpert. Authorized BVL staff should have a BvlExpert status, RikiltExpert status is set aside for Rikilt staff. This is part of EUginius’ 6-eyes data entry system.

1.2.2.3 Administrator

The administrator has access to all modules, and can edit these. For any help, information or feedback contact an administrator via databasemanager@euginius.eu.

 

1.3 Points of Contact

General

For general questions about EUginius you can contact the office of Dr. Esther J. Kok via email esther.kok@wur.nl or at +31(0)317480256 or the office of Emilie Dagand via email 405@bvl.bund.de or at +49(0)30184456504.

Input or Feedback

For any input find the hyperlinks on the homepage or consult 5.0 Input and Feedback

Database

In case of questions about the database, contact database@euginius.eu

Website

In case of questions about the website, contact webmaster@euginius.eu

Relevant Institutions
EUginius is a collaborative effort between BVL - the Federal Office of Consumer Protection and Food Safety (Berlin, DE) and RIKILT Wageningen UR (Wageningen, NL). 

 

RIKILT Logo

BVL Logo

RIKILT - Institute of Food Safety
Afdeling Wettelijke Onderzoeks Taken

Bundesamt für Verbraucherschutz und Lebensmittelsicherheit
Abteilung Gentechnik

T +31 (0)317 480256
F +31 (0)317 417717
info.rikilt@wur.nl
www.rikilt.wur.nl

T +49-(0)3018-445-6000
F +49-(0)3018-445-6099
gentechnik@bvl.bund.de
www.bvl.bund.de

Visiting address:
Akkermaalsbos 2
Building no. 123
6708 WB WAGENINGEN
The Netherlands

Visiting address:
Mauerstraße 39 - 42
10117 Berlin
Germany

 

Mail address:
PO Box 230
6700 AE WAGENINGEN
The Netherlands

Mail address:
PO Box 11 02 60
10832 Berlin
Germany

 


 


1.4 OrganiSation of the Manual

This manual offers internal hyperlinks that allow you to travel through it more efficiently. These are written as 1.4 Organisation of the Manual in dark blue font. They will take you to the place in the manual which the text references.

The manual is divided into 7 major sections:

1.0

General Information

Basic information about EUginius, such as functions performed and a description of the program.

2.0

Getting Started

General walk-through of the system including getting into EUginius.

3.0

Using the System

Detailed description of the system functions from start to finish.

4.0

Workflow

An example for using the analysis tool, finding detailed information and designing your own screening.

5.0

Reporting Errors

The standard procedure for system malfunction or improvement opportunities.

6.0

 

Appendix

Additional data to assist you when working in EUginius.

 

1.5 Nomenclature

 

GMO

Genetically Modified Organism.

Event

Used when describing one particular GMO derived from a transformation process.

UID

Unique Identifier which is given to events for standardisation between databases.

Stack

A traditional crossing of two GMO plants to create a plant that exhibits both features.

Element

A DNA sequence that can be inserted into an organism where it will perform a specific function.

Coding Sequence

An element that consists of DNA encoding for a protein.

Promoter

An element that initiates transcription of a particular coding sequence.

Terminator

An element that marks the end of a particular coding sequence, ending transcription.

Construct

Two or more genetic elements aligned next to each other.

BLAST

Basic Local Alignment Search Tool.

Authorisation

Official permission for the use of specific GMOs.

Food

Product for human consumption.

Feed

Product for animal consumption.

Cultivation

Growing the GMO crop.

Transformation

Genetic alteration of a cell resulting from the direct uptake and incorporation of exogenous genetic material.

Insert

DNA sequence that has integrated into the genome of a species during transformation.

Vector

DNA fragment that was used in the process of transformation.

Free-text search

A search which allows for manual entry of any word/phrase you choose.

Query-building search

A search which allows for multiple keywords which can be selected from a dropdown.

 

1.6 Abbreviations

General

GMO

Genetically Modified Organism

UID

Unique Identifier

BLAST

Basic Local Alignment Search Tool

PCR

Polymerase Chain Reaction

Genetic Elements

CS

Coding Sequence

E

Enhancer

GS

Gene Silencing

G

Genomic Sequence

I

Intron

L

Leader

P

Promoter

R

Regulatory Element

T

Terminator

TP

Transit Peptide

U

Unknown Origin

V

Vector Fragment

Detection Methods

QL-

Qualitative (PCR method)

QT-

Quantitative (PCR method)

-CON-

Construct specific method

-ELE-

Element specific method

-EVE-

Event specific method

-TAX-

Taxon specific method

Institutions

EUginius

EUropean GMO INItiative for a Unified database System

BCH

Biosafety Clearing-House

NCBI

National Center for Biotechnology Information

ISO

International Organization for Standardization

CEN

European Committee for Standardization (Comité Européen de Normalisation)

EU-RL

European Union Reference Laboratories

 

2.0                          Getting Started

 

2.1 Access and Login

  

2.1.1 Access

Public (euginius.eu)

Access to EUginius.eu is public and does not require an account. Terms of use can be found in EUginius’ footer under Terms of use. This public version has the following modules:

·         Home

·         GMO

·         Detection

·         Analysis

·         Search

·         Help

 

2.2 System Menu

  

2.2.1 Homepage

Upon launching the system, you are presented with the homepage (pictured above). By clicking the labelled tabs, you can move to the following sections:

·         GMO

·         Detection

·         Analysis

·         Authorisation

·         Search

·         Help

 

2.2.2 GMO

The GMO tab provides you with four different functions (pictured above). All functions in this tab allow you to search for GMOs using different criteria.

List with GMOs and their Identifiers lets you view, sort and filter GMOs by their identifiers. It shows the name, UID, species, traits, companies, developers, tradenames and EU authorisation of GMOs.

List with GMOs and Traits provides you with GMOs and their associated traits. It shows the name and traits of a GMO and offers additional filtering for these traits. The traits are organized in an hierarchical tree (Trait thesaurus).

List with GMOs and Genetic Elements provides you with GMOs and their genetic elements. It shows the name and all genetic elements of GMOs while offering additional filtering for these genetic elements. The genetic elements are organized in an hierarchical tree (DNA thesaurus).

The Search for GMO section is a text-free search which scans the List with GMOs and their Identifiers section for any matching terms. All other sections use a query-building search.
For more information on this module, consult 3.1 GMO.

2.2.3 Detection

The detection tab provides you with four different functions (pictured above). All functions in this tab provide you with information regarding GMO detection.

Select Detection Methods lets you search PCR methods designed for GMO screening, identification and quantification.

Select Method Verification lets you find information on the specificity of PCR methods and their abilities to detect GMOs. A set of methods can be selected and filtered by specific criteria. You are then given a table displaying the verification data.

Select Reference Material lets you search for GMO reference materials and provides concentrations, percentages and catalogue numbers with sources.

The Search bar section is a text-free search which scans the Select Detection Methods section for any matching terms. All other sections use a query-building search.
For more information on this module, consult 3.2 Detection.

2.2.4 Analysis

The analysis module consists of twelve input fields containing information on GMO detection results. It supports you in sample analysis and provides explanations for detected elements.
Import result file lets you import an Excel file with screening outcomes, saving you from entering data manually.
For more information on this module, consult 3.3 Analysis. NB the Import result file feature will be introduced in EUginius release 1.8.

2.2.5 Authorisation

The authorisation tab provides you with three different functions (pictured above). All functions in this tab provide you with information regarding GMO approval status.

Search for Generic Approval lets you find information on the approval status of a specific GMO for use in food, feed, cultivation or other uses.

Traffic Light Search lets you include or exclude a set of search terms about a GMO and combine this with legal status requirements for the GMO(s). This allows for a very refined search.

The Search bar section is a text-free search which works independently of the other three sections. It shows GMO, recipient, file reference, intended use, status, legislation, decision date, UID, traits, genetic elements, companies, developers, tradenames, country and national authorisation status from EUginius matching the search terms. All other sections use a query-building search.
For more information on this module, consult 3.5 Authorisation.

2.2.6 Search

The search module lets you do a free-text keyword search on GMOs and literature. An advanced search option is also available for GMOs and literature. Additional search options are available for authorisation, methods, reference material and genetic elements with an extra free-text search being possible for genetic elements.

For more information on searching in EUginius, consult 3.6 Search Module.

2.3 Homepage Search Module

The homepage free-text search module has two different modes of use, GMO search and Literature search. Both work with the same search bar but advanced searches are available at the links below the search buttons. More search types are available on the Search Module tab, for information on this tab or on search results consult 3.6 Search Module.

 

Tip:

In the Search Module Tab you can click on Element search to find GMOs, DNA inserts, donors and traits which are attributed to certain elements. For more information on this consult 3.6.3 Element Search

 

 

  

2.3.1 GMO Search

The standard free-text GMO search can find GMO, UID, species, traits, company and trade names.

Advanced GMO search presents you with six fields, these correlate to the above mentioned six features and also genetic elements.
The main advantage of the advanced search is filtering out unwanted results, as it allows exclusion of stacked events and closer specification of search terms. The advanced search is a query-building search as opposed to a free-text search.
Some examples of free-text searches and search terms are listed below:

 

Search Term(s)

Finds GMOs with

Bt*

names "Bt11", "Bt10 maize", "BT10 potato", "FR-Bt1", etc.

305423

with UID "DP-3Ø5423-1"

MON 00810 6

UID "MON-ØØ81Ø-6"

RRS

alias "RRS" (=GTS 40-3-2)

zea

species "Zea mays"

soybean

species "Glycine max"

syngenta

UID "Syngenta Seeds, Inc"

yieldgard

tradename "YieldGard VT PRO", "Yieldgard™", "Maxguard/Yieldgard", etc.

bt11

name "Bt11" and stacks containing Bt11

insect

trait "Insect resistance"

 

For more information on search functions or tips for search strategies, consult 3.6 Search Module.

2.3.2 Literature Search

The standard free-text literature search can find GMO name, abstract, citation and keywords.

The advanced literature search presents you with three search options, GMO, Genetic Element and DNA search. Each of these include a search field for name, publishing authority and publication date. Keywords entered in other sections will not be taken into account when you click the search button (see example). The main advantage of the advanced search is filtering out unwanted results, as it allows closer specification of search terms. The advanced search is a query-building-search as opposed to a free-text search.

 

Example:

If you hit search on the DNA search section, only data in this section will be taken into account. Any data entered in GMO or Genetic Element search will be ignored.

 

 

For more information on search functions or tips for search strategies, consult 3.6 Search Module



2.4 Help Module

The help module provides you with this user manual. It can be accessed from most modules by clicking the blue help button in the top right corner (see above).

Clicking the blue help button while in a module will take you to the matching section of this manual.

 

3.0                          Using the System

 


3.1 GMO

When entering the GMO section, you are presented with four different functions (pictured above). All functions in this tab allow you to filter and search for GMOs using differing criteria. The Search for GMO section is identical to the homepage GMO search function. For more information on this search function consult 3.6.1 GMO Search.

 

3.1.1 List with GMOs and their Identifiers

List with GMOs and their Identifiers lets you view, sort and filter GMOs by their identifiers. It shows the name, UID, species, traits, companies, developers, tradenames and EU authorisation of GMOs.

1.

GMO

Most commonly used name for the GMO
   Clicking the GMO name will lead you to the GMO details section. For
   more information on this section consult
3.1.4 GMO Details

2.

UID

The (UID) Unique Identifier which is given to the GMO.
   This is useful in gathering information from other databases

3.

Species

Species which the organism belongs to.

4.

Traits

A list of traits expressed by the GMO which are not found in the wild species.

5.

Companies

All companies producing or selling the GMO.
   Clicking the company name will lead you to the list of all GMOs related to
   (or produced or sold by) this company

6.

Developers

The institute which developed the GMO, if available.

7.

Tradenames

The name which the GMO is commonly sold under by companies.

8.

EU Authorisation

Approval status of the GMO for food, feed, cultivation and other uses.
   Clicking the icon in the table will lead you to a list with the EU applications
   of this GMO (if available)

   Additional information on EU authorisation can be found in the
   Authorisation tab. For more information on this, consult
3.5 Authorisation

Applying a filter can be done by clicking the apply filter hyperlink at the top of the page. This will take you to the Advanced GMO Search. For more information on this consult 3.6.1.1 Advanced GMO Search.

Sorting and Navigating Pages can be done using the arrows, for an explanation of navigating searches consult 3.6.4 Navigating Search Results.

3.1.2 List with GMOs and Traits

List with GMOs and Traits provides you with GMOs and their associated traits. It shows the name and traits of a GMO and offers additional filtering for these traits.

1.

GMO

Most commonly used name for the GMO
   Clicking the GMO name will lead you to the GMO details section. For more
   information on this section consult
3.1.4 GMO Details

2.

Traits

A list of traits expressed by the GMO which are not found in the wild species.

 

3.1.2.1 Navigating the traits page

Filtering Data can be done through the select a trait field. When clicking the field you are presented with a dropdown. A trait from this dropdown can be selected by clicking it, adding it to the query. By typing text into the field, the shown traits will be limited to traits matching the search term. One or more traits from the dropdown can be selected.

A selection of traits can also be made through the traits tree.

The Traits Tree is opened by clicking the show tree hyperlink at the top of the page. This presents you with a list of categories with   next to them. Clicking the  will add the category to the searched traits, clicking the category will expand it, showing subcategories or specific traits. See example below:

Example:

Here the main category (1) has been expanded by clicking it. The subcategory under this (2) was also opened, displaying the traits.

Any of these parts can be filtered for by clicking the plus symbols next to them. This will add them to the filter field

A list of all traits in EUginius (as of July 2018) is included in 6.3 Thesauri

Filter options can be adjusted by selecting either AND or OR. AND will filter for GMOs that possess all specified traits while OR will filter for GMOs that possess any of the traits. Excluding stacked events can be done by checking the box next to Exclude stacked events. This will further limit the shown results by removing any crossed or stacked GMOs.

Sorting and Navigating Pages can be done using the arrows, for an explanation of navigating searches consult 3.6.4 Navigating Search Results.

3.1.2.2 Search Results

After filtering you get a list of GMOs and traits (see example above). Clicking the GMO name will bring you to the GMO details tab, for more information on this consult 3.1.4 GMO Details. In the traits column each row of text in a cell represents one trait exhibited by the GMO.

 

Example:

Aedes aegypti OX513A expresses two traits as result of genetic modification; reproductive alteration, which falls in the category Composition Alteration, and DsRed2 Activity which is in the Selection Marker and Reporter Genes category.

 

 

3.1.3 List with GMOs and Genetic Element

List with GMOs and Genetic Elements provides you with GMOs and their genetic elements. It shows the name and all genetic elements of GMOs while offering additional filtering for these genetic elements.

1.

GMO

Most commonly used name for the GMO
   Clicking the GMO name will lead you to the GMO details section. For
   more information on this section consult
3.1.4 GMO Details

2.

Genetic Elements

A list of all elements involved in genetic modification of the GMO.

  

3.1.3.1 Navigating the Genetic Elements page

Filtering Data can be done through the select a genetic element field. When clicking the field you are presented with a dropdown. An element from this dropdown can be selected by clicking. Limiting the list of shown elements in this dropdown can be done by entering text into the field.

A selection of elements can also be made through the genetic elements tree.

The Genetic Element Tree is opened by clicking the show tree hyperlink at the top of the page. This presents you with a list of categories with   next to them. Clicking the  will add the category to the searched traits, clicking the category will expand it, showing subcategories. See example below:

Example:

Here the main category (1) has been expanded by clicking it. The subcategory under this (2) was also opened, displaying the genetic elements in said group (3)..

Any of these parts can be filtered for by clicking the plus symbols next to them. This will add them to the filter field

A list of all elements in EUginius (as of July 2018) is included in 6.3 Thesauri

By clicking show tree details next to hide tree EUginius will display more information about the elements in the tree (see example below). Synonyms displays other names for the element, donor shows the organism from which the element is taken, trait shows the trait that the element confers to the GMO, function gives the elements function in the GMO and definition gives the unabbreviated name of the element. BCH record ID gives element IDs of the corresponding elements in the Biosafety Clearing-House (http://bch.cbd.int).

Filter options can be adjusted by selecting either AND or OR. AND will filter for GMOs that possess all specified elements while OR will filter for GMOs that possess any of the elements. Excluding stacked events can be done by checking the box next to Exclude stacked events. This will further limit the shown results by removing any crossed or stacked GMOs.

 

3.1.3.2 Search Results

After filtering you get a list of GMOs and genetic elements (see example above). Clicking the GMO name will take you to the GMO details tab, for more information on this consult 3.1.4 GMO Details. By default only the filtered genetic elements are shown, but by pressing show in the heading of the table you can bring up all genetic elements associated with the GMOs in alphabetical order.

Sorting and Navigating Pages can be done using the arrows, for an explanation of navigating searches consult 3.6.4 Navigating Search Results.

 

Example:

Above, filtering happened for Coding Sequence > CS-acetohydroxy acid synthase. By default the genetic element column only shows the filtered element. By hitting show all associated elements for the GMO can be shown. (below)

 

 

3.1.4 GMO details

When clicking the name of a GMO in any of the EUginius modules, you will be redirected to GMO Molecular Characterization Details. This tab presents you with all information which is linked to the GMO you clicked on.

3.1.4.1 Navigating GMO Details

The basic information on the GMO is always shown at the top, regardless of the tab you are in. This information includes GMO name, alias, UID, Tradename, Company, Developer, Species and Traits. Company also provides a link which brings you to the GMO Identifier List. This list will exclusively show GMOs which the company has produced.

By clicking the symbols at the top of the module, you can call upon different information. These symbols relate to the following information:

GMO Detail tabs

Molecular Characterization

Modification of the GMO on the molecular level

Detection Methods

Methods to detect the GMO

Reference Material

Material with known concentrations of the GMO

Literature

Literature describing the GMO

 

3.1.4.2 GMO Molecular Characterization

GMO Molecular Characterization provides information on the nature of the genetic modification and provides links to sources of information regarding the GMO. For an explanation of the module consult the image and table below.

1.

Description:

General overview of the GMO.

2.

Number of insertion sites

Number of places in the plant genome where the insert was integrated.
  

3.

Transformation Technique

The way in which a vector is introduced into an organism may differ. EUginius currently includes 8 techniques.
   For more information on these techniques consult: Rivera, A.L.
   et al. (2012) Physical methods for genetic plant transformation. Physics
   of Life Reviews, 9, 308–45

4.

Insert/vector Name

DNA starting with insert_ has been confirmed in the GMO.
DNA starting with vector_ describes the vector which was used for the transformation.
   Clicking the insert/vector name will take you to DNA composite
   details, for more information on this consult
3.1.4.2.1 Insert/Vector
   Detail.

5.

Insert/vector Comment

Any additional notes which EUginius staff have about the DNA.
   This is generally hidden from public users.

6.

Insert/vector Map

If a DNA map is available this will be inserted here in a picture format.
   This is currently left empty.

7.

 

Reference Sequence

The reference sequence section lists accession, reference and elements.
 - Accession is a unique code for genetic sequences (e.g. in GenBank).
 - Reference is the source used for entering the molecular
   characterisation into EUginius.
 - Elements lists all elements in the insert/vector with general data.
   Clicking the element name will take you to Genetic Element
   Information, for more information on this consult
3.1.4.2.2 Element
   details.

  

3.1.4.2.1 DNA details

Clicking the insert/vector name will take you to DNA composite details, which provides information on the composite DNA.

1.

Name

DNA called insert_ has been confirmed in the GMO.
DNA starting with vector_ or ending with (putative) describes the vector which was used for the transformation.

2.

DNA Function

The function which the insert serves in the GMO
   This field is generally left empty.

3.

Derived From

The material from which the DNA sequence was obtained:
 - Insert Only, just the sequence of the insert.
 - Covers Integration Site, insert and flanking GMO genome.
 - Vector, the DNA as present in the vector.

4.

Accession Number

This is a unique code for genetic sequences, it can be used to search for genetic sequences online
   e.g. GenBank or EUginius

5.

Reference

The source for the genetic sequence
   e.g. NCBI – GenBank, BCH or RIKILT

6.

Sequence

This either says No if no sequence is available, or Yes if a sequence is available. If it says Yes this is also a hyperlink to said sequence.
   If you click Yes it will take you to the sequence string page. For more
   information on this consult
3.1.4.2.3 Sequence String.

7.

Size

The size of the sequence in base pairs (bp).

8.

Annotation

The name which the sequence is annotated under in the reference database/source.

  

3.1.4.2.2 Genetic Element details

Clicking the element name will take you to Genetic Element Information, this gives information on the element.

1.

Name

Element names have a hierarchy which is defined in the thesaurus.
   Specificity increases with level number.
  
 

2.

Synonyms

Contains synonyms for class III
   if available.

3.

Accession Number

This is a unique code for genetic sequences, it can be used to search for genetic sequences online

4.

Donor

The organism from which the genetic element is originally derived

5.

Function

The function that the genetic element performs in a GMO

6.

Definition

A description of the element
   if abbreviations are used in the name.

7.

Modified Trait

Trait which is attributed to the genetic element’s presence in a GMO

8.

Element

Level III of the element name.

9.

Derived from

The material from which the DNA sequence was obtained:
 - Insert Only, just the sequence of the insert.
 - Vector, the DNA as present in the vector.

10.

Reference

The source used for obtaining information about the insert which the element belongs to.
   e.g. scientific journal or organisation
   For more information consult
3.1.4.2 GMO Molecular
   Characterization, section 7. Reference Sequence .

11.

Sequence

This either says No if no sequence is available, or Yes if a sequence is available. If it says Yes this is also a hyperlink to said sequence.
   If you click Yes it will take you to the sequence string page. For more
   information on this consult
3.1.4.2.3 Sequence String.

12.

Size

The size of the element in base pairs (bp).

  

3.1.4.2.3 Sequence String

Clicking Yes in the sequence column of Insert/Vector details brings you to the sequence page, this gives information on the sequence and provides the sequence string.

1.

DNA Name

DNA called insert_ has been confirmed in the GMO.
DNA starting with vector_ or ending with (putative) describes the vector which was used for the transformation.

2.

Comment

This field is often used for description of the source of the information/detailed information on nucleotide changes in the insert.

3.

Derived From

The material from which the DNA sequence was obtained:
 - Insert Only, just the sequence of the insert.
 - Vector, the DNA as present in the vector.

4.

Accession Number

This is a unique code for genetic sequences, it can be used to search for genetic sequences online
   e.g. GenBank

5.

Reference

The source used for entering the composite DNA into EUginius.
   e.g. NCBI – GenBank, BCH or RIKILT

6.

Annotation

The name which the sequence is annotated under in the reference database/source.

7.

Size

The size of the sequence in base pairs (bp).

8.

Sequence String

The full sequence as given in the reference.

  

 

BLAST the sequence

The BLAST site link will only take you to the BLAST site, this will not automatically BLAST the sequence string.

You are asked to copy the sequence and paste this into the BLAST module manually.

 

 

3.1.4.3 GMO Detection Methods

The detection method page displays the GMO Details header with general information on the GMO.
Below this is an extended Select Detection Methods search, with your GMO as filter.
The additional column is added on the right and displays method verification for your GMO. Values in this table can range from 1 to 3 with the following meaning:

1:       Detection of the target is based on other information in EUginius (database, plasmid map etc.)

2:       Detection of the target is verified by sequence alignment

3:       Detection of the target is experimentally verified using reference material

 For more information on the detection methods table, consult 3.2.1 Detection Methods.

3.1.4.4 Reference Material of one Gmo

The reference material page displays the GMO Details header with general information on the GMO.
Below this is a smaller version of the Reference Material search with your GMO as filter. For more information on the Reference Material search section, consult 3.2.3 Reference Material.

Clicking the catalogue number will bring you to the material details page, which provides you with extra information on the reference material.

1.

Catalogue number

A unique identifier given to the reference material by the material provider. This identifier is used for ordering the material.

2.

Description

A description of the reference material stating material amount and type.

3.

Material Type

The type of material.
   Reference material can vary from dried powder to DNA or even
   bacterial strains.

4.

Concentration

Concentration of the reference material.
   cp/µl is the measure for DNA concentration, it refers to genome copies
   (or haploid genome equivalents) per microliter

5.

Certified

Certified material comes with a certificate proving the material’s quality and composition.

6.

Available

Indicates availability of the reference material at the source provider.

7.

Source Provider

The institution which provides the reference material.
   This can be AOCS, EURL, Genescan, IRMM/ERM, SIGMA-ALDRICH or
   the Pasteur Institute.

8.

Comment

Any additional notes which EUginius staff have about the DNA are added here. This field is often used for hyperlinks/references.
   Generally used for hyperlinks to the reference material on the source
   providers website.

 

3.1.4.5 gmo Literature references list

The literature page displays the GMO Details header with general information on the GMO.
Below this is the Advanced Literature search with your GMO as filter.

Clicking the article citation will take you to the literature details page. For more information on this, consult 3.6.2.3 Literature Details.

For more information on the Literature search section, consult 3.6.2 Literature Search.


 

3.2 Detection

When entering the Detection section, you are presented with four different functions (pictured above). All functions in this tab provide you with information regarding GMO detection.

­­­­­­­

3.2.1 Detection Methods

Select Detection Methods lets you search PCR methods designed for GMO screening, identification and quantification. Based on the selected search and dependent on filter criteria chosen you can find methods of GMO detection for your specific query and your desired applications.

For filtering, EUginius makes use of Boolean operators, specifically AND and OR.
   AND requires all provided keywords to match the search results, narrowing down the number of results.
    OR   means you are shown all results that match either of the keywords, broadening the number of results.

In the detection methods search, keywords in Validation, Standardisation, Method set and Method type would all have to match for a detection method to show up in your search. If keywords are entered in either Target event, construct, species or element these do not have to match each other, one of your entered keywords will have to match the keywords in the previously mentioned AND searches. Any method entered in the method field will automatically show up in the search results.

The search fields in this section are query-building searches. Selecting two values in one field means EUginius puts an OR between the keywords. This means either of the keywords have to match the others, they do not both have to match.

Below you can find the meaning of all keywords that can come up in your detection methods searches.

Method set

All

A set of methods which is not restricted and contains every method in EUginius.

Screening

A set of methods which is restricted to methods designed to detect GMOs.

ABC

Set of screening methods which is constantly checked and adjusted by the German National Reference Laboratory (NRL) in collaboration with the national network of GMO laboratories.

  

Validation

In-house validation

The method has been validated in one laboratory using reference materials as sample.

Ring validation

The method's performance (sensitivity, specificity, repeatability, reproducibility) has been evaluated using identical samples in several laboratories under control of a supervising laboratory.

Unknown

Validation of the method is unknown or the method is not validated.

  

Standardisation

CEN standard

Standardised by the European Committee for Standardisation (CEN).

EU reference method

Standardised by the Joint Research Centre of the European Commission or the EU-RL GMFF.

ISO standard

Standardised by the International Organization for Standardization.

National standard

Performed according to national standards (country not specified).

  

Method

When clicking this field you are presented with a dropdown. A method from this dropdown can be selected by clicking. Limiting the list of shown methods in said dropdown can be done by entering text into the field.

The dropdown list contains all methods contained in EUginius.

Method Type

Construct specific

Specific for detecting the presence of two elements that are in close proximity.

Element specific

Specific to a single element.

Event specific

Specific to a single GMO.

Taxon specific

Specific to an entire taxon.

  

Target Event

When clicking this field you are presented with a dropdown. One or more events from this dropdown can be selected by clicking. Limiting the list of shown events in said dropdown can be done by entering text into the field.

The dropdown list contains all events that EUginius has detection methods for.

Target Construct

When clicking this field you are presented with a dropdown. One or more constructs from this dropdown can be selected by clicking. Limiting the list of shown constructs in said dropdown can be done by entering text into the field.

The dropdown list contains all constructs that EUginius has detection methods for.

Target Species

When clicking this field you are presented with a dropdown. One or more species from this dropdown can be selected by clicking. Limiting the list of shown methods in said dropdown can be done by entering text into the field.

The dropdown list contains all species that EUginius has detection methods for.

Target Element

When clicking this field you are presented with a dropdown. One or more elements from this dropdown can be selected by clicking. Limiting the list of shown elements in said dropdown can be done by entering text into the field. The dropdown list contains all elements contained in EUginius.   

DETECTION METHODS SEARCH RESULT

Below an example of the result of a specific query. For more explanation about the different columns see above. The content of the table can be exported as an Excel file (see 3.8).

 

3.2.2 Method Verification

Select Method Verification lets you find information on the specificity of a PCR method and its ability to detect GMOs. A set of methods can be selected and filtered by specific criteria. You then obtain a matrix displaying the verification data.

By hitting search without entering criteria EUginius will show the full matrix of verification methods and GMOs.

3.2.2.1 Navigating The Matrix

Except for GMO, Authorisation, Species and RM available, all column headers are detection methods in EUginius. This list of detection methods can be limited by using keywords in the Filter Criteria for Detection Methods section of the search page. For more information on this section consult 3.2.2.2 Filter Criteria for Detection Methods.

All row headers are GMOs in EUginius, this list of GMOs can be limited by using keywords in the Filter Criteria for Detection GMOs section of the search page. For more information on this section consult 3.2.2.3 Filter Criteria for GMOs.

The matrix crosses filtered GMOs with filtered detection methods, assigning a value to each GMO-method combination. The values indicate the reliability with which a method will detect a certain GMO. These values mean the following:

3

Detection of the target is experimentally verified using reference material

2

Detection of the target is verified by sequence alignment

1

Detection of the target is based on other information in EUGINIUS (database, plasmid map etc.)

-1

No expected target detection, based on other information in EUginius (plasmid maps etc.)

-2

No expected target detection, based on sequence alignment

-3

No target detection is experimentally confirmed using reference material

In the GMO column, clicking a GMO’s name will take you to the respective GMO Details tab. For more information on this tab consult 3.1.4 GMO Details. If no GMO filter criteria are applied, only GMOs with values of 3, 2 or 1 will be shown. Clicking show in the GMO column header will also display GMOs with negative verification values.

Authorisation uses coloured symbols to display approval status of the GMO for food, feed, cultivation and other uses. For more information on this, consult 3.5.1 Authorisation Symbols.

RM available tells you about reference material availability. No means no reference material is available for the GMO. If it says Yes, this means reference material is available, at this point the text is a hyperlink. Clicking the hyperlink will take you to the Reference Material tab of GMO Details. For more information on this tab, consult 3.1.4.4 Reference Material.

3.2.2.2 Filter Criteria for Detection Methods

The Filter Criteria for Detection Methods section lets you limit the detection methods which are shown in the verification matrix.

A detailed explanation of keywords and combining them with AND or OR in the detection methods filter/search was given in 3.2.1 Detection Methods.

3.2.2.3 Filter Criteria for GMOs

The Filter Criteria for Detection Methods section lets you limit the detection methods which are shown in the verification matrix.

For filtering EUginius makes use of Boolean operators, specifically AND and OR.
   AND requires all provided keywords to match the results, narrowing down the number of results.
    OR   means you are shown all results that match either of the keywords, broadening the number of results.

In the filter for GMOs, either Species or GMO will have to match the EU authorisation standards. Only matching results will show in the GMO list of the verification matrix.

The fields in this section are query-building. Selecting two values in one field means EUginius puts an OR between the keywords. This means that only one of the keywords in a field has to match.

 

3.2.3 Reference Material

Select Reference Material can perform searches on the availability and on the source of GMO reference materials, providing you with the information you need to validate or perform your experiments.

3.2.3.1 Searching

OR

For its searches EUginius makes use of Boolean operators, specifically AND and OR.
   AND requires all provided keywords to match the search results, narrowing down the number of results.
    OR   means you are shown all results that match either of the keywords, broadening the number of results.

In the reference material search all fields need to match reference material for it to be shown in the search results. The search fields in this section are query-building searches. Selecting two values in one field means EUginius puts an OR between the keywords. This means that only one of the keywords have to match.

Below is a list with descriptions of the search parameters.

1.

GMO

The name(s) of GMOs for which you want to find reference material.

2.

Species

The species for which you want to find reference material.

3.

Source

The institution which provides the reference material.
   This can be AOCS, EURL, Genescan, IRMM/ERM, SIGMA-ALDRICH or the
   Pasteur Institute.

4.

Material Type

The type of material you would like to have as reference material.
   Reference material can vary from dried powder to DNA or even
   bacterial strains.

5.

Description

A description of the GMO material.
   This field is very specific and entering a value here will generally give
   only one result.

6.

Certified

Checking this box will mean only certified materials are shown.
 

3.2.3.2 reference material search result

Below, an example of the result of a specific query. For more explanation about the different columns see the search criteria above. The column Value is not a search criterion but indicates the concentration of the GMO in the sample. The content of the table can be exported as an Excel file (see 3.8).


3.2.4 Detection Search

The standard free-text detection method enables searching for detection methods based on Method Name, Target Type, Forward Primer Name, Forward Primer Sequence, Reverse Primer Name, Reverse Primer Sequence, Probe Name, Probe Sequence and Amplicon Sequence. The search results will also provide you with the Amplicon Size but this is not a searchable metric.

In EUginius’ free-text searches at least one word will need to match the search term. Parts of a word matching will not be picked up. e.g. searching for “VW0” will not show MON810 primers VW01 or VW03. Searching for ”event” will however show all event-specific methods, as EUginius views phrases with hyphens as two separate words.

Wildcards give you results when you only know part of a keyword. The wildcard symbol in EUginius is *.
For example, searching for “VW*” will show all data containing “VW” even without a full word match (i.a VW01, VW03). Wildcards can be added to both left and right sides of the word. A wildcard on the left will only apply to additional characters to the left, a wildcard on the right will only apply to the right.

Clicking advanced search on the search results page will take you to the Detection Methods Search page. For more information on this page, consult 3.2.1 Detection Methods.


 

3.3 Analysis

The analysis module consists of 12 input fields containing information on GMO detection results. It supports you in sample analysis and can provide explanations for detected events.

3.3.1 Entering Screening Data

The fields can be filled with the following information:

1.

Species

Species detected with a taxon/species specific method.

2.

GMO

GMOs detected with an event specific method.

3.

Promoter

Promoters detected with an element specific method.

4.

Terminator

Terminators detected with an element specific method.

5.

Coding Sequence

Coding sequences detected with an element specific method.

6.

Other Elements

Other elements detected with an element specific method.

7.

Construct

Constructs detected with a construct specific method.

8.

Step 2, not detected

Here you should enter any event-, element- or construct-specific methods which you used but that did not yield positive results.

 

3.3.2 Analysis Results

After clicking the Analyse button, EUginius will begin to calculate which parts of your screening data add up and which GMOs may be present that have not been accounted for in your screening.
First it shows GMOs whose presence you demonstrated:

1.

Analysis Report

Lists parameters which EUginius used in the analysis.
   This should match what you entered in the module

2.

Refine Search

Brings you back to the GMO analysis module
   All entered values should be preserved

4-11

GMO information

See separate table on the next page

GMO Prediction views shows you GMOs which may explain unexplained elements which you observed in your sample.

1.

Detected Species Only

Ticking this box means only GMOs will be shown from species that you detected.
   This is especially useful if you are sure what kind of material you  
   have.

2.

Verified Methods Only

Ticking this box means EUginius will analyse based purely on 3+ verified methods for GMOs.
   Theoretical matches between method and GMO will not be
   considered.

3.

Exclude Undetected

This will exclude any GMOs that match targets which you tested for but did not detect.
   This also counts for species.

4-11

GMO information

See separate table on the next page.

 

GMO Information is provided in a matrix with colour coding and symbols in it. These colours and symbols have the
   following meanings:

Unexplained Detected Target

Confirmed Negative Detected Target

Explained Detected Target

 

GMO Table (4-11)
  
The table has seven columns for the Analysis Report and eight columns for Prediction view, these give you
   information about the following:

4.

Species

Species of the GMO

5.

GMO

GMOs name
   Clicking the GMO name will lead you to the Detection Method
   Details section. For more information on this section consult
  
3.1.4.3 Detection Methods

6.

Importance Sorting

Shows the amount of unexplained targets over the amount of explained targets. (in prediction view only)
   Checking the box will put the most likely GMOs on top.

7.

Promoter

All Promoters which are present in the GMO

8.

Terminator

All Terminators which are present in the GMO

9.

Coding Sequence

All Coding Sequences which are present in the GMO

10.

Construct

All Constructs which can be detected in the GMO

11.

EU Authorisation

Approval status of the GMO for food, feed, cultivation and other uses.
   Additional information on EU authorisation can be found in
   Authorisation tab. For more information on this, consult
3.5
   Authorisation.

 


 

3.4 Authorisation

When entering the Authorisation section, you are presented with three different functions (pictured above). All functions in this tab provide you with information regarding GMO approval.


 

3.4.1 Authorisation Symbols

Many of EUginius’ modules have columns for EU Authorisation. These use coloured symbols to display approval status of the GMO for food, feed, cultivation and other uses. These symbols indicate the following:

Not Approved

food - not approved

Food

Not approved for human consumption in the EU

feed - not approved

Feed

Not approved for animal consumption in the EU

cultivation - not approved

Cultivation

Not approved for cultivation in the EU

other uses - not approved

Other uses

Not approved for any other uses in the EU

Approved with Restrictions or Phasing Out

FOOD approved with restrictions or phasing out image

Food

Approved for human consumption in the EU with restrictions or phasing out

FEED approved with restrictions or phasing out image

Feed

Approved for animal consumption in the EU with restrictions or phasing out

CULTIVATION approved with restrictions or phasing out image

Cultivation

Approved for cultivation in the EU with restrictions or phasing out

OTHER_USES approved with restrictions or phasing out image

Other uses

Approved for any other uses in the EU with restrictions or phasing out

Approved

FOOD approved image

Food

Approved for human consumption in the EU

FEED approved image

Feed

Approved for animal consumption in the EU

CULTIVATION approved image

Cultivation

Approved for cultivation in the EU

OTHER_USES approved image

Other uses

Approved for any other uses in the EU

 

As of 2018:

MON810 is the only GMO with limited approval for European cultivation. All other GMOs are not approved for cultivation.

 

 

­­­­­­­

3.4.2 Generic Approval

Search for Generic Approval lets you find information on the approval status of a specific GMO for use in food, feed, cultivation or other uses.

3.4.2.1 Searching

AND

For its searches EUginius makes use of Boolean operators, specifically AND and OR. All searches in this module use AND meaning that all provided keywords have to match the search results, narrowing down the number of results.

Below you can find the meaning of all keywords that can come up in your detection methods searches.

1.

GMO

The name(s) of GMOs of which you want to know the authorisation status.

2.

Species

The species for which you want to know the authorisation status.

3.

Country

The country/region for which the authorisation applies.
   for regulatory reasons, EU is considered a “country” in EUginius.

4.

Country-Zone

A larger region which the authorisation applies for.
   e.g. Europe

5.

Authorisation

Section that lets you specific your search based on authorisation status of GMOs.

  

3.4.2.2 Search Results

Changing your search can be done by clicking Refine Search at the top of the page. When clicking the link you are taken back to the generic approval search page. All previously entered keywords will be maintained in their fields. You can hit the reset button to clear these.

Sorting and Navigating Pages can be done using the arrows, for an explanation of navigating searches consult 3.6.4 Navigating Search Results.

1.

GMO

The name of the GMOs which the approval is for.
   Clicking the GMO name will take you to GMO details, for more
   information on this consult
3.1.4 GMO details.

2.

Species

The species for which you want to know the authorisation status.

3.

Continent

Continent in which the shown authorisation status applies.

4.

Country

Country in which the shown authorisation status applies.
   This can also be EU for EFSA decisions

5.

National Authorisation

Authorisation of the GMO for food, feed, cultivation and other uses.
   EUginius uses symbols to indicate authorisation status, for more
   information on this consult
3.5.1 Authorisation Symbols.

 

 

 

3.4.3 Traffic Light Search

Here you can include or exclude a common set of search parameters describing the identity of a GMO. In addition to these two options to "select positive" or "negative values" you can apply search criteria specifying the legal status of the GMO(s).

This is EUgenius’ most extensive search module.

3.4.3.1 Searching

AND

For its searches EUginius makes use of Boolean operators, specifically AND and OR. All searches in this module use AND meaning that all provided keywords have to match the search results, narrowing down the number of results.

Below you can find the meaning of all keywords that can be used in the application searches.

1.

GMO

Name(s) of GMOs for which you want to find information

2.

Species

Species for which you want to find information

3.

UID

Unique Identifier code for GMOs

4.

Traits

Traits which can be exhibited by GMOs

5.

Genetic Elements

Elements which can be inserted in GMOs

6.

Company

Company which produces/sells the GMO

7.

Developer

Institution which developed the GMO

8.

Tradename

The name which the GMO is commonly sold under

9.

Country-Zone

The country/zone where the application applies

All values entered here will go towards showing results. Below this section you can also Select Negative Values, which will exclude search results from your query.

 

3.4.3.2 Search Results

Changing your search can be done by clicking Refine Search at the top of the page. When clicking the link you are taken back to the traffic light search page. All previously entered keywords will be maintained in their fields. You can hit the reset button to clear these.

Sorting and Navigating Pages can be done using the arrows, for an explanation of navigating searches consult 3.6.4 Navigating Search Results.

1.

GMO

The name(s) of GMOs which the application belongs to.

2.

Species

The species of the GMO.

3.

Continent

Continent in which the authorisation applies.

4.

Country

Country in which the authorisation applies.

5.

National Authorisation

Approval status of the GMO for food, feed, cultivation and other uses.
   EUginius uses symbols to signify approval status, for more information
   on this consult
3.5.1 Authorisation Symbols.

6.

UID

Unique Identifier code for the GMO.

7.

Traits

List of traits expressed by the GMO which are not found in the wild species.

8.

Elements

List of genetic elements in the GMO which are a result of the transformation.

9.

Companies

All companies producing or selling the GMO.

10.

Developers

The institute/company which developed the GMO is listed here.

11.

Tradenames

The name which the GMO is commonly sold under.

 

3.4.4 Authorisation Search

The authorisation search lets you find GMO authorisation status based on GMO Name, Recipient Species, File Reference, Intended Use, Status, Legislation, Decision Date, UID, Traits, Genetic Elements, Companies, Developers, Tradenames, Country. This search will also provide you with the National Authorisation Status though this is not a searchable metric.

In EUginius’ free text searches at least one word will need to match the search term. Parts of a word matching will not be picked up. e.g. searching for “1829” will not show Regulation 1829/2013 as it is only a part of the word. Searching for ”EFSA” will however show all EFSA applications, as EUginius views phrases with hyphens as two separate words.

Wildcards give you results when you only know part of a keyword. The wildcard symbol in EUginius is *.
For example, searching for “EFS*” will show all data containing “EFS” even without a full word match. Wildcards can be added to both left and right sides of the word.

The search result is a combination of the search for EU application details (3.5.3.2) and the traffic light search (3.5.4.2).

 Additional filtering can be done on the top of the result page by checking the boxes for Use Category and Status Category filters. If a box is checked only information matching that use/status is shown.


3.5 Search Module

In the search module you can do a free-text keyword search on GMOs and literature.

An advanced search option is also available for GMOs and literature, clicking the hyperlink for advanced GMO search will bring you to a new page, for more information on this consult 3.6.1.1 Advanced GMO Search.

Clicking the hyperlink for advanced Literature search will also take you to a new page, for more information on this consult 3.6.2.1 Advanced Literature Search.

Element Search can only be accessed through this module and it allows you to search for genetic elements based on GMO, Donor, Species, Elements and Traits. For more information consult 3.6.3 Element Search.

All other links and functions from this page can be accessed from outside this module as well. Information on these other functions and pages was previously discussed in this manual. The Table of Contents can help you navigate to their specific chapters.

 

3.5.1 GMO Search

The standard free-text GMO search can find GMO, UID, tradename, species, company, traits and genetic elements.

Some examples of free-text searches and search terms are listed below:

 

Search Term(s)

Finds GMOs with

Bt*

names "Bt11", "Bt10 maize", "BT10 potato", "FR-Bt1", etc.

305423

with UID "DP-3Ø5423-1"

MON 00810 6

UID "MON-ØØ81Ø-6"

RRS

alias "RRS" (=GTS 40-3-2)

zea

species "Zea mays"

soybean

species "Glycine max"

syngenta

UID "Syngenta Seeds, Inc"

yieldgard

tradename "YieldGard VT PRO", "Yieldgard™", "Maxguard/Yieldgard", etc.

bt11

name "Bt11" and stacks containing Bt11

insect

trait "Insect resistance"

 

 

3.5.1.1 Advanced GMO Search

Advanced GMO search presents you with seven fields, these correlate to the seven features mentioned above.
The main advantage of the advanced search is filtering out unwanted results, as it allows exclusion of stacked events and closer specification of search terms. The advanced search is a query-building search as opposed to a free-text search. Advanced GMO Search has two search sections: Select GMOs and Stacks, Search GMOs.

Select GMOs and Stacks lets you filter for specific GMOs by picking event-specific GMO names or UIDs.

 

Example:

Entering MON810 will show MON810 and all stacks containing MON810. These results will be the same as a search for MON810’s UID (MON-ØØ81Ø-6)

 

 

Checking “Exclude stacked events” means only one GMO shows up per entered keyword, this would be the GMO which you entered. No stacks of this GMO will be shown in the result list.

Search GMOs lets you search for GMOs using attributes instead of names or identifiers.

1.

Tradename

The name which the GMO is commonly sold under.

2.

Species

Species for which you want to find reference material.

3.

Company

Company which produces/sells the GMO.

4.

Exclude stacked Events

Checking this stops any stacks from being shown.
   Stacks are crosses between two different GMOs

5.

Traits

Traits which can be exhibited by GMOs.

6.

AND/OR

AND and OR are Boolean operators which determine how search terms are treated.
   -AND means the entered keywords has to match the other keywords
   -OR means all GMOs matching the keyword will be shown regardless
   of other keywords

7.

Genetic Elements

Elements which may be integrated/present in GMOs.

 

Search Results from the advanced GMO search serve the same function as a filter for the GMO list of identifiers. For any questions regarding the search results we recommend you consult 3.1.1 List with GMOs and their Identifiers.


 

3.5.2 Literature Search

The standard free-text literature search is capable of searching for GMO name, abstract, citation and keywords.

The advanced literature search presents you with three search options, GMO search, Genetic Element search and DNA search. Each of these include a name search, publishing authority specifier and a publication date. Keywords entered in other sections will not be taken into account when clicking the search button (see example). The main advantage of the advanced search is filtering out unwanted results, as it allows closer specification of search terms. The advanced search is a query-building search as opposed to a free-text search.

3.5.2.1 Advanced Literature Search

Advanced GMO Search has three search sections: GMO search, Genetic Element search and DNA Name search.

Searching by GMO allows for specification of GMO, publishing authority and publication date.

Useful for when you want to know more about a specific GMO

Searching by Genetic Element allows for specification of genetic element, publishing authority and publication date.

 

Searching by DNA name allows for specification of genetic element, publishing authority and publication date.

 

Publishing authority usually refers to one specific institution, though “Research Group” can also be picked here. Picking Research Group will show any scientific publication matching your criteria.

Publication date may differ from the application or decision date. Keep this in mind when searching for literature.


 

3.5.2.2 Literature Search Results

Changing Search Criteria can be done by clicking Refine Search at the top of the page. When clicking the link you are taken back to the literature search page. All previously entered keywords will be maintained in their fields. You can hit the reset button to clear these.

Sorting and Navigating Pages can be done using the arrows, for an explanation of navigating searches consult 3.6.4 Navigating Search Results.

1.

Citation

Literature citation as generally used in references
   Research groups publications are cited in APA 6th edition

   Clicking the citation will lead you to the Literature details section.
   For more information on this section consult
3.6.2.3 Literature
   Details

2.

Publication Year

Year in which the literature was published

3.

Publishing Authority

Authority which published the literature

4.

Publication type

This shows the type of publication and can show you what the purpose of the publication is.
   e.g. application document, patent, decision or peer-reviewed article

5.

Content Types

This is a tagging system for EUginius literature with multiple content types being assigned to literature for different reasons.
   e.g. application, decision, detection, environment, risk
   assessment and safety.

 

3.5.2.3 Literature Details

Literature Details gives information about the literature citation and provides links to the literature. For an explanation of the module consult the image and table below.

1.

Citation

Literature citation as generally used in references.
   Research groups publications are cited in APA 6th edition
   Most other documents also stick to a similar standard

2.

Publication type

This shows the type of publication and can show you what the purpose of the publication is.
   e.g. application document, patent, decision or peer-reviewed article

3.

Comment

Notes of the EUginius staff about the literature are added here.
   This is generally left empty

4.

Content Types

This is a tagging system for EUginius literature with multiple content types being assigned to literature for different reasons.
   e.g. Application, decision, detection, environment, risk
   assessment and safety.

5.

Keyword

Any words which EUginius staff deemed relevant are added here, in order to aid you in finding the right document.

6.

Publication Year

Year in which the literature was published.

7.

Publishing Authority

Authority which published the literature.

8.

View PDF

If available, a .pdf file of the literature is added here.

9.

View URL

A hyperlink to the citation where you can find the text.
   Clicking the hyperlink will open it in a new tab

 

3.5.3 Element Search

The element search module presents you with nine fields that contribute to one query. This allows specification of GMO, Element Donor, Species and Element or Trait. In this module exclusion of certain known GMOs is possible. This helps in the analysis of detected GMOs when several events are tested for.

3.5.3.1 Element Search

1.

GMO

GMO name
   Using this in a search will show all elements inside your GMO

2.

Donor

Species which the genetic element was taken from.
   The element may also be synthetic, this option is also listed

3.

Species

Species in which the genetic element has been inserted.

4.

Genetic Elements

A query-building search of all elements in EUginius element thesaurus.
   Using this in a search will show all GMOs and inserts that carry the
   selected element

5.

AND/OR

AND and OR are Boolean operators which determine how search terms are treated.
   -AND means the entered keywords has to match the other keywords
   -OR means all GMOs matching the keyword will be shown regardless of
     other keywords

6.

Traits

Traits that are attributed to elements in the thesaurus.

  

 

Searching for information on one specific element:

If you have an element’s name and you would like more information on it you can type the name in the Genetic Elements query-building field.

 

 

 

3.5.3.2 Element Search Results

Changing your search can be done by clicking Refine Search at the top of the page. When clicking the link you are taken back to the element search page. All previously entered keywords will be maintained in their fields. You can hit the reset button to clear these.

Sorting and Navigating Pages can be done using the arrows, for an explanation of navigating searches consult 3.6.4 Navigating Search Results.

1.

GMO

GMO which the element is found in
   Clicking the GMO name will take you to GMO details, for more
   information on this consult
3.1.4 GMO details.

2.

Species

Species of the GMO

3.

DNA

Insert or vector which was used to insert the element into the GMO
   Clicking the DNA name will take you to DNA details, for more
   information on this consult
3.1.4.2.2 Element Details.

4.

Element

The element which matched your search criteria

5.

Donor

Species which the genetic element was taken from
   elements can also be synthetic

6.

Trait

Trait which the element introduces to the GMO
   this is only available for coding sequences

 

3.5.4 Navigating Search Results

Sorting allows you to arrange your filtered results in alphabetical order

Sort

The sort symbol indicates that the feature is not being sorted for

Ascending

The ascending symbol indicates that the feature is currently being sorted for

Descending

The descending symbol indicates that the feature is currently being sorted for

Navigating Pages lets you go through your results, or limit the amount of results you see.

Next Page

Navigate to the next page

Last Page

Navigate to the last page (e.g. page 25 out of 25)

Previous Page

Navigate to the previous page

First page

Navigate to the first page (page 1)

 

3.6 Exporting data

Several modules in EUginius allow you to export data using the                       button.

After clicking this button EUginius will generate an Excel (.xls) file for you with all information that is presented in the matrix. All pages are included in the export.
This may take a while. Your browser will then prompt you with the option to download the exported file. This may differ per browser and computer but below is a common example:

In Internet Explorer on Windows 7:

You are presented with a bar at the bottom of your screen.

Clicking OPEN will directly open the .xls file without saving.
Clicking SAVE will directly save the .xls file to your /Downloads folder
Clicking the arrow next to SAVE will allow you to specify the save location.

Exported files adhere to a set format in EUginius:
   Exportpage_YearMonthDay_HourMinuteSecond_Millisecond.xls

 

4.0                          Workflow


 


4.1 Analysis Tool

In this example we are given a sample of Zea mays which is presumed to be genetically modified.

We would like to know:

·         Are there other species in the sample?

·         What GMO is present in the sample?

·         Which GMO can explain the unexplained elements?

o    How do we detect these GMOs?

·         What can we conclude?

·         Is this sample approved for animal feed in the EU?

 

4.1.1.1 Screening Results

In this hypothetical screening we test for five species, six elements, one construct and six GMOs. These test gave the following hypothetical outcomes:

Test

EUginius code

Outcome

Species: Canola fatA

QL-TAX-FatA Primer1/Primer2

N.D.

Species: Maize HMG

QT-TAX-ZM-002

Detected

Species: Rice SPS

QT-TAX-SPS primer f/r

N.D.

Species: Soya Lec

QT-TAX-GM-002

N.D.

Species: Sugar beet GS

QT-TAX-BV-013

N.D.

Element: P-35S CaMV

QT-ELE-P35S 1-5'/P35S 1-3'

Detected

Element: P-act1-ORYSA

QL-ELE-P-Rice actin-F/R

Detected

Element: T-rbcS_E9-PEA

QL-ELE-00-024

N.D.

Element: T-nos-RHIRD

QT-ELE-NOS ter 2-5' /NOS ter 2-3'

Detected

Element: CS-cry1Ab/Ac-BACTU

QL-ELE-00-016

Detected

Element: CS-pat-STRVR

QL-ELE-00-025

N.D.

Construct: ctp2/cp4-epsps

QL-CON-00-008

N.D.

GMO: 3272 maize

QT-EVE-ZM-019

N.D.

GMO: 5307 maize

QT-EVE-ZM-023

N.D.

GMO: 98140 maize

QT-EVE-ZM-021

N.D.

GMO: Bt11 maize

QT-EVE-ZM-006

N.D.

GMO: DAS40278 maize

QT-EVE-ZM-004

N.D.

GMO: MON810 maize

QT-EVE-ZM-020

Detected

Here we manually inserted the results into EUginius’ analysis module:

Clicking Analyse makes EUginius analyse your entered screening results. This may take a while.

 

4.1.1.2 Confirmed Output

Confirmed output tells us which elements can be explained by the GMOs that we have detected.

In this case four of the elements belonging to our selected methods can be explained with the GMOs in the sample. In the matrix below we can also see that MON810 matches the detected elements well.

Two other elements could not be explained by the detection of MON810. This means there must be another GMO in the mixture that was not tested for. Prediction view can help us figure out what GMO this might be.

4.1.1.3 GMO Prediction View

In this case, Prediction View presents us with 120 different GMOs that might be in our sample.

Many of the listed GMOs come from different species though, and in this case we are certain that it is Zea mays. Checking the Restrict GMOs to detected species box will remove all GMOs that we did not detect. In this case we are only left with Zea mays GMOs after applying this filter.


 

After restricting to detected species we are left with 20 GMOs.

We could test for the presence of these 20 GMOs, but since we are confident that we correctly performed our screening we can eliminate a few more GMOs from this list.
Checking the Exclude GMOs that contain targets that have not been detected box, will remove all GMOs with elements that we tested for but did not detect. These are GMOs with elements that are underlined in yellow.

After filtering out not-detected species and not-detected elements we are left with 10 GMOs.

By checking Importance Sorting we move GMOs to the top that best explain the unexplained events.

In this particular case events GA21 and MON87460 best explain the unexplained elements as they contain both of the unexplained elements. If possible, we would test for all 10 of these GMOs with event specific methods but since MON87460 and GA21 are most likely a test for only these two should suffice.

You can find methods to test for these GMOs by clicking their names in the GMO column.

 

4.1.1.4 Detection of Predicted GMO

Clicking the GMO name will take you to Detection Method GMO Details, which provides you with a list of all detection methods that will give a positive result for your GMO. In the case of GA21 we are presented with 21 methods that will show positive for GA21, but not all 21 are useful to us.
Since we want a method that is specific to GA21 it should be an event-specific method. In this case there are two options since both QT-EVE-ZM-007 and QT-EVE-ZM-014 are ring trial validated EU reference methods that are specific to GA21.
If no event-specific methods are available for your GMO of interest we recommend you use multiple construct or element-specific methods to be as certain as possible that you are making the correct call.

4.1.1.5 Conclusion

In doing this analysis we found out that:

·         There are no other species in the sample.

·         Event MON810 is definitely present in the sample.

·         Most likely, either GA21 or MON87460 are in the sample.

·         GA21 can be detected with QT-EVE-ZM-007 and QT-EVE-ZM-014.
MON87460 can be detected with QT-EVE-ZM-005.

·         MON810 is approved for animal feed in the EU, as are GA21 and MON87460. The sample is most likely
approved for animal feed in the EU, but a few more tests need to be done.

 

4.2 Designing a Screening

In this example we are given samples of multiple species which are presumed to be genetically modified.

We would like to know:

·         Which tests we can run to help identify GMOs

4.2.1.1 Aims of this screening

In this screening we would like to detect at least the following GMOs:

·         Bt11

·         DAS59122

·         DAS40278

·         GA21

·         MIR162

·         MIR604

·         MON87427

·         NK603

4.2.1.2 Finding methods

For this purpose we go to the Detection Method Verification module under the Detection tab. Here we enter the GMOs we would like to detect and set the Method Set to SCREENING:

4.2.1.3 Selecting Methods

Method Verification Search Results gives us a matrix of GMOs and detection methods showing which methods can detect which GMOs. For an explanation of this matrix consult 3.2.2 Method Verification.

When designing a screening we want to pick methods in such a way that all GMOs are detected at least once with as few as possible methods in the screening. Here method-GMO verifications of category 3 are preferred as they are most reliable.

 Zoomed in we see that several methods detect six of our nine GMOs but and could be utilized. T-nos-RHIRD (QL-ELE-00-011) offers the highest reliability here as its effectiveness for these GMOs has been confirmed.

Now we need to find a method that fills in most of the gaps, the more additional GMOs are detected here the better. Having two matches will make identification easier. Several GMOs have a total of five matches and fill two of the three gaps. Here E-35S-CaMV, P-35S CaMV (QT-ELE-00-004) has the highest reliability.

After this there is only one GMO that our screening cannot detect yet (DAS40278). There is only one method listed which can detect DAS40278 (P-ubi1-MAIZE (QL-ELE-P-Ubi-F/P-Ubi-R ) which we will also add to the screening.


4.2.1.4 Conclusion

Using EUginius’ Detection Method Verification Search we determined the optimal screening test for Bt11, DAS59122, DAS40278, GA21, MIR162, MIR604, MON87427 and NK603. This is composed of:

·         T-nos-RHIRD (QL-ELE-00-011)

·         E-35S-CaMV, P-35S CaMV (QT-ELE-00-004)

·         DAS40278 (P-ubi1-MAIZE (QL-ELE-P-Ubi-F/P-Ubi-R))

 

5.0                          Input and Feedback


 


5.1 Input and Feedback

On its homepage EUginius offers two links that allow you to give feedback or to provide input on interesting GMOs.

 

5.1.1 Suggest New GMO

Clicking Suggest new GMO opens your local e-mailing software (e.g. Microsoft Office Outlook) with numerous filled in fields. This is the standard layout for suggesting GMOs (see right).

As of EUginius version 1.7.5 the To... field should say database@euginius.eu with Suggested new GMO for EUGINIUS as subject.

Below this we would like you to provide the name of the GMO you would like to see added to EUginius, your name, e-mail address, your affiliation and a source of information.

It greatly benefits EUginius staff if you provide as much information as you have available.

 

 

5.1.2 Give Feedback

Clicking Give feedback opens your local e-mailing software (e.g. Microsoft Office Outlook) with numerous filled in fields. This is the standard layout for giving feedback on EUginius (see right).

As of EUginius version 1.7.5 the To... field should say databasemanager@euginius.eu with Feedback on EUGINIUS as subject.

Below this we would like you to provide your name, e-mail address, your affiliation and your comment/feedback for the EUginius staff.

It greatly benefits EUginius staff if you provide as much information as you have available.

 

 

6.0                          Appendix


 

6.1 Appendix Glossary

The appendix contains the following documents

6.2 GMO-Related Websites

An up-to-date list is available from the EUginius homepage under GMO-related websites

6.3 Thesauri

Currently the Trait and Element lists are only available through this manual.

6.4 Terms and Conditions of Use

The latest version can be found in EUginius’ footer under Terms of Use

 

6.2 GMO-related websites

Certified Reference Material

AOCS

AOCS’ library of Certified GMO Reference Materials.

JRC IRMM 

JRC Institute for Reference Materials and Measurements.

Legal Status of GMOs

APHIS USDA 

USDA’s standard website for GMO applications, petitions and legal status.

APHIS USDA biotechnology permit and notification 

USDA’s interactive website for GMO applications, petitions and legal status.

EFSA Register of Questions 

EFSA’s large register of questions, applications and other inquiries. Not only useful for GMOs.

OECD BioTrack product database 

OECD’s BioTrack Database tracks GMO approval in multiple nations for use by officials and stakeholders.

GMO Databases / GMO Registries

Biosafety Clearing-House (BCH) 

BCH is a mechanism set up by the Cartagena Protocol on Biosafety that aims to have a complete registry of all GMO plants.

CERA GM Crop Database *

Currently offline

EU Register of authorised GMOs 

GMO Register of the European Commission.

EU-RL GMFF

GMO Register of the European Union Research Laboratory for GM Food and Feed.

GMO Compass GMO database *

Currently offline

ISAAA GM Approval Database 

ISAAA’s GMO approval database for various biotechnology stakeholders.

GMO Related news

EMM MedISys GMO 

News and general information on GMOs retrieved from 4000 dedicated websites.

Europe Media Monitor - Newsbrief 

European news tracking software to show you the highlights and hot topics in your field.

Safety

FAO GM Foods Platform 

Platform for general information on food safety, also tracks GMO information.

Risk Assessment Searching Mechanism (RASM) 

Online collection of risk assessment documents for genetically modified organisms

Detection Methods

CropLife International Detection Methods Database 

CropLife’s collection of detection methods for GMOs

GMO Detection method Database (GMDD) 

General database for the GMO detection methods

JRC - GMO Methods database 

European Joint Research Centre’s collection of GMO detection methods

Other

RASFF portal 

Food-safety communication network for urgent matters

GMOseek project 

Software to aid in GMO screening analysis

6.3 Thesauri

As of the release of this of this user manual (see cover) EUginius has the traits and elements as listed in the paragraphs below. More details about the thesauri can be found earlier in the manual (e.g.  1.6 for the prefixes and 3.1.3 for the structure). More details about the element thesaurus will be presented in a paper (in progress). The most recent versions of the thesauri are available in the thesaurus trees on www.euginius.eu.

6.3.1 Elements


Coding Sequence

>CS-1-amino-cyclopropane-1-carboxylic acid deaminase

             >CS-accD-PSECL

>CS-1-amino-cyclopropane-1-carboxylic acid synthase

             >CS-acc-DIACA

             >CS-acc2-SOLLC

>CS-3"(9)-O-aminoglycoside adenyltransferase

             >CS-aadA-ECOLX

>CS-4-hydroxyphenylpyruvate dioxygenase

             >CS-HPPD-AVESA

             >CS-HPPD-PSEFL

>CS-5-enolpyruvylshikimate-3-phosphate synthase

             >CS-CP4epsps-RHIRD

             >CS-epsps-ARTGO

             >CS-epsps-MAIZE

>CS-acetohydroxy acid synthase

             >CS-ahas-ARATH

             >CS-ahas-MAIZE

             >CS-ahas-ORYSA

             >CS-ahas-SOYBN

             >CS-SuRB-TOBAC

             >CS-SuRB_S4-TOBAC

>CS-alpha amylase

             >CS-amy-MAIZE

             >CS-amy797E-SYNTH

>CS-aryloxy alkanoate dioxygenase

             >CS-aad1-SPHHE

             >CS-aad12-DELAC

>CS-B-box32

             >CS-BBX32-ARATH

>CS-barnase

             >CS-barnase-BACAM

>CS-barstar

             >CS-barstar-BACAM

>CS-beta glucuronidase

             >CS-uidA-ECOLX

>CS-bleomycin binding protein

             >CS-ble-ECOLX

>CS-bromoxynil-specific nitrilase

             >CS-bxn-KLEPO

>CS-carotene desaturase

             >CS-crtI-PANAN

>CS-choline dehydrogynase

             >CS-betA-ECOLX

>CS-cold shock protein

             >CS-cspB-BACIU

>CS-crystal delta-endotoxin

             >CS-cry14Ab1-BACTU

             >CS-cry1A.88-BACTU

             >CS-cry1Ab-BACTU

             >CS-cry1Ab_Ac-SYNTH

             >CS-cry1Ab_vip3H-SYNTH

             >CS-cry1Ac-BACTU

             >CS-cry1A_105-SYNTH

             >CS-cry1C-BACTU

             >CS-cry1F-BACTU

             >CS-cry2A.127-BACTU

             >CS-cry2Ab2-BACTU

             >CS-cry2Ae-BACTU

             >CS-cry34Ab1-BACTU

             >CS-cry35Ab1-BACTU

             >CS-cry3A-BACTU

             >CS-cry3Bb1-BACTU

             >CS-cry51Aa2-BACTU

             >CS-cry9C-BACTU

             >CS-ecry3_1Ab-SYNTH

             >CS-mcry3A-SYNTH

>CS-cytochrome

             >CS-cytb5-PETHY

>CS-defensin

             >CS-pdf1.2-ARATH

>CS-delta desaturase

             >CS-delta12D-LACKL

             >CS-delta12D-PHYSP

             >CS-delta4D-DIALT

             >CS-delta4D-REBSA

             >CS-delta4D-THRSP

             >CS-delta5D-REBSA

             >CS-delta5D-THRSP

             >CS-delta6D-MICPC

             >CS-delta6D-OSTTA

             >CS-delta6D-PRIJU

             >CS-fad3-NEUCS

>CS-delta elongase

             >CS-delta5E-OSTTA

             >CS-delta5E-PYRCR

             >CS-delta6E-PYRCR

             >CS-delta6E-THAPS

             >CS-detla6E-PHYPA

>CS-diacylglycerol acyltransferase

             >CS-dgat2A-UMBRA

>CS-dicamba monooxygenase

             >CS-dmo-STEMA

>CS-dihydrodipicolinate synthase

             >CS-dhdps-CORGT

>CS-dihydroflavonol 4-reductase

             >CS-dfr-MAIZE

             >CS-dfr-PETHY

>CS-DNA adenine methylase

             >CS-dam-ECOLX

>CS-DsRed2 fluorescent protein

             >CS-DsRed2-SYNTH

>CS-flavonoid 3', 5' hydroxylase

             >CS-F3_5_H-COMCM

             >CS-F3_5_H-PETHY

             >CS-F3_5_H-SALSN

             >CS-F3_5_H-VIOLA

>CS-glyphosate oxidoreductase

             >CS-gox-OCHAN

>CS-glyphosate-N-acteyltransferase

             >CS-gat-BACLI

>CS-growth hormone

             >CS-GHc2-ONCTS

>CS-homeodomain-leucine zipper

             >CS-HB17-ARATH

             >CS-HD4-HELAN

>CS-hygromycin B phosphotransferase

             >CS-hpt-ECOLX

             >CS-hpt-STRHY

>CS-insulin precursor

             >CS-preINS-SYNTH

>CS-leucine rich repeat

             >CS-rpi1-SOLBU

             >CS-rpi1-SOLVN

             >CS-rpi2-SOLBU

>CS-male fertility gene Ms45

             >CS-ms45-MAIZE

>CS-miraculin

             >CS-mir-SYNDU

>CS-MYB transcription factor

             >CS-pap1-ARATH

>CS-neomycin phosphotransferase II

             >CS-nptII-ECOLX

>CS-nopaline synthase

             >CS-nos-RHIRD

>CS-omega desaturase

             >CS-omega3D-KOMPG

             >CS-omega3D-PHYIT

             >CS-omega3D-PYTIR

>CS-phosphinotricin N-acetyltransferase

             >CS-bar-STRHY

             >CS-pat-STRVR

>CS-phosphomannose isomerase

             >CS-pmi-ECOLX

>CS-phytase

             >CS-phyA-ASPNG

>CS-phytoene synthase

             >CS-psy-CITUN

             >CS-psy-MAIZE

>CS-proteinase inhibitor II

             >CS-pinII-SOLTU

>CS-replicase

             >CS-NIb-PRSV

             >CS-rep-PLRV

>CS-S-adenosylmethionine hydrolase

             >CS-SAMhydrolase-T3

>CS-seed albumin

             >CS-AmA1-AMAPH

>CS-tetracycline-controlled transactivator

             >CS-tTAV-SYNTH

>CS-thioesterase

             >CS-te-UMBCA

>CS-triosephosphate isomerase

             >CS-tpi1-SCHPM

>CS-trypsin inhibitor

             >CS-SCK-SYNTH

>CS-vegetative insecticidal proteins

             >CS-Vip3A-BACTU

             >CS-vip3Aa20-BACTU

>CS-viral coat protein

             >CS-cp-CMV

             >CS-cp-PPV

             >CS-cp-PRSV

             >CS-cp-PVY

             >CS-cp-WMV

             >CS-cp-ZYMV

>CS-WRKY transcription factor

             >CS-WRKY45-ORYSA

 

Promoter

>P-34S FMV

             >P-FMV

>P-35S CaMV

             >P-2ocs_35S-SYNTH

             >P-35S-CaMV

             >P-35S-CaMV_v4

             >P-35S-CaMV_v6

             >P-4AS1-CaMV

             >P-e35S-CaMV

>P-5'e1 stamen specific

             >P-5_e1-ORYSA

>P-5126 anther-specific

             >P-5126-MAIZE

>P-acetohydroxy acid synthase

             >P-ahas-ARATH

             >P-ahas-MAIZE

             >P-ahas-ORYSA

             >P-ahas-TOBAC

>P-actin

             >P-act1-ORYSA

             >P-act2-ARATH

             >P-act5c-DROME

             >P-act8-ARATH

>P-ADP glucose pyrophosphorylase

             >P-Agp-SOLTU

>P-alpha globulin B

             >P-alpha glbB-GOSHI

>P-alpha subunit of beta conglycinin

             >P-7Salpha-SOYBN

>P-alpha-tubulin

             >P-TubA-ORYSA

>P-anthocyanidin synthase

             >P-ans-DIACA

>P-anti freeze protein

             >P-AFP-ZOAAM

>P-arcelin

             >P-arc5a-PHAVU

>P-banana streak virus (Acuminata Vietnam strain)

             >P-BSV(AV)

>P-bromelain inhibitor

             >P-bi-ANACO

>P-CA55 stamen-specific

             >P-CA55-MAIZE

>P-calcium-dependent protein kinase

             >P-cdpk-MAIZE

>P-cassava vein mosaic virus

             >P-CsVMV

>P-cestrum yellow leaf curling virus

             >P-CYLCV

             >P-CYLCV_SMP-SYNTH

>P-chalcone synthase

             >P-chs-ANTMA

>P-citrus yellow mosaic virus

             >P-CiYMV

>P-conlinin

             >P-cnl1-LINUS

             >P-cnl2-LINUS

>P-cruciferin A

             >P-cruA-BRANA

>P-delta mas2

             >P-4ocs_delta_mas-SYNTH

>P-dihydroflavonol 4-reductase

             >P-dfr-PETHY

>P-elongation factor EF-1 alpha

             >P-EF1alpha-ARATH

             >P-EF1alpha-SOYBN

>P-epoxide hydrolase

             >P-ephx-ANACO

>P-ethylene biosynthesis-related

             >P-E8-SOLLC

>P-fatty acid elongase

             >P-fae1-ARATH

             >P-fae1-BRANA

>P-gamma-zein

             >P-gz27-MAIZE

>P-globulin 1

             >P-glb1-MAIZE

>P-glutathione S-transferase

             >P-gst-ORYSA

>P-glutelin

             >P-GluA2-ORYSA

>P-granule-bound starch synthase

             >P-gbss-SOLTU

>P-heat shock protein

             >P-hsp70-DROSP

             >P-hsp80-BRAOL

             >P-hsp81-2-ARATH

>P-histone

             >P-H2B-MAIZE

             >P-H4-ARATH

>P-homeodomain-leucine zipper 4

             >P-HD4-HELAN

>P-Kunitz trypsin inhibitor

             >P-KTi3-SOYBN

>P-legumin

             >P-leg1-MAIZE

>P-linin

             >P-linin_LINUS

>P-lipid transfer protein

             >P-ltp2-HORVU

>P-mac chimeric molecule

             >P-mac1-SYNTH

>P-mannopine synthase

             >P-mas-RHIRD

>P-metallothionein-like

             >P-mtl-MAIZE

>P-napin

             >P-FP1-BRANA

             >P-napA-BRANA

             >P-napin-BRARR

>P-nopaline synthase

             >P-nos-RHIRD

>P-peanut chlorotic streak virus

             >P-PCSV

>P-peroxidase

             >P-pox-WHEAT

>P-peroxiredoxin

             >P-pxr-LINUS

>P-phenylalanine ammonia-lyase

             >P-Pal2-PHAVU

>P-phosphoenolpyruvate carboxylase

             >P-pepc-MAIZE

>P-physical impedance induced protein

             >P-pIIG-MAIZE

>P-Phytophthora resistance

             >P-rpi1-SOLBU

             >P-rpi1-SOLVN

             >P-rpi2-SOLBU

>P-polygalacturonase

             >P-pg47-MAIZE

>P-RuBisCO small subunit

             >P-rbcS-ARATH

             >P-rbcS-ORYSA

>P-S-adenosyl-L-methionine synthetase

             >P-sams-SOYBN

>P-scp1 chimeric molecule

             >P-scp1-SYNTH

>P-SETL

             >B-setl-BRANA

>P-subterranean clover stunt virus

             >P-s7s7-SCSV

>P-sucrose binding protein

             >P-sbp-VICFA

>P-sugarcane bacilliform virus

             >P-SCBV

>P-TA29 tapetal specific

             >P-ta29-TOBAC

>P-tac chimeric molecule

             >P-tac-SYNTH

>P-triosephosphate isomerase

             >P-tpi1-SCHPM

             >P-tpi1-YEASX

>P-ubiquitin

             >P-ubi-ANACO

             >P-ubi-ANDGE

             >P-ubi1-MAIZE

             >P-ubi10-ARATH

             >P-ubi3-ARATH

             >P-ubi4-PETCR

             >P-ubi4-SACOF

             >P-ubi7-ORYSA

>P-USP

             >P-usp-VICFA

 

Terminator

>T-35S CaMV

             >T-35S-CaMV

>T-acetohydroxy acid synthase

             >T-ahas-ARATH

             >T-ahas-ORYSA

             >T-ahas-SOYBN

             >T-SuRB-TOBAC

>T-actin 1

             >T-act1-SORBI

>T-alpha amylase trypsin inhibitor

             >T-Ara5-ORYSA

>T-alpha subunit beta conglycinin

             >T-7Salpha-SOYBN

>T-alpha-tubulin

             >T-TubA-ORYSA

>T-anthocyanidin synthase

             >T-ans-DIACA

>T-anti freeze protein

             >T-AFP-ZOAAM

>T-arcelin

             >T-arc5a-PHAVU

>T-barnase

             >T-barnase-BACAM

>T-barstar

             >T-barstar-BACAM

>T-cathepsin D inhibitor

             >T-CDI-SOLTU

>T-conlinin

             >T-cnl1-LINUS

             >T-cnl2-LINUS

>T-cruciferin A

             >T-cruA-BRANA

>T-dihydroflavonol 4-reductase

             >T-dfr-PETHY

>T-drosomycin

             >T-drs-DROME

>T-E6

             >T-E6-GOSBA

>T-fatty acid elongase

             >T-fae1-ARATH

>T-female sterile (1) K10

             >T-fs(1)K10-DROSP

>T-globulin 1

             >T-glb1-MAIZE

             >T-glb1-PHAVU

>T-heat shock protein

             >T-hsp17_3-WHEAT

>T-herbicide safener inducible In2-1

             >T-In2_1-MAIZE

>T-histone

             >T-H4-ARATH

             >T-H6-GOSBA

>T-Kunitz trypsin inhibitor

             >T-KTi3-SOYBN

>T-lectin

             >T-le1-SOYBN

>T-legumin

             >T-leg1-MAIZE

>T-male fertility gene Ms45

             >T-ms45-MAIZE

>T-mannopine synthase

             >T-mas-RHIRD

>T-metallothionein-like protein

             >T-Mt-ORYSA

>T-NADP-malic enzyme

             >T-NADPme1-FLABI

>T-napin

             >T-napin-BRARR

>T-nopaline synthase

             >T-nos-RHIRD

>T-octopine synthase

             >T-ocs-RHIRD

>T-ORF1

             >T-orf1-RHIRD

>T-ORF23

             >T-orf23-RHIRD

>T-ORF25

             >T-orf25-RHIRD

>T-peroxiredoxin

             >T-pxr-ARATH

>T-phosphate transporter

             >T-Pt1-MEDTR

>T-phospholipids transfer protein

             >T-D8-PETHY

>T-Phytophthora resistance

             >T-rpi1-SOLBU

             >T-rpi1-SOLVN

             >T-rpi2-SOLBU

>T-potato virus Y

             >T-cp-PVY

>T-preferential cationic peroxidase

             >T-per5-MAIZE

>T-proteinase inhibitor II

             >T-pinII-SOLTU

>T-ribosomal protein gene

             >T-rpg-ARATH

>T-RuBisCO small subunit

             >T-rbcS-SOYBN

             >T-rbcS_E9-PEA

>T-SETL

             >t-setl-BRANA

>T-transcript 7

             >T-tr7-RHIRD

>T-triosephosphate isomerase

             >T-tpi1-SCHPM

             >T-tpi1-YEASX

>T-tumor morphology large

             >T-tml-RHIRD

>T-ubiquitin

             >T-ubi-ANACO

             >T-ubi1-MAIZE

             >T-ubi14-ARATH

             >T-ubi3-ARATH

>T-vegetative storage protein

             >T-vsp-SOYBN

>T-zein

             >T-zein-MAIZE

 

Transit Peptide

>TP-5-enolpyruvylshikimate-3-phosphate synthase

             >TP-epsps-ARATH

>TP-acetohydroxy acid synthase

             >TP-ahas-MAIZE

>TP-brittle

             >TP-brittle1-MAIZE

>TP-chloroplast transit peptide

             >TP-ctp-ARATH

             >TP-ctp-SYNTH

             >TP-ctp4-PETHY

>TP-cysteine protease

             >TP-ccp2-MAIZE

>TP-dihydrodipicolinate synthase

             >TP-dhdps-MAIZE

>TP-optimised transit peptide

             >TP-OTP-SYNTH

>TP-RuBisCO small subunit

             >TP-rbcS-ARATH

             >TP-rbcS-MAIZE

             >TP-rbcS-PEA

             >TP-rbcS-SYNTH

 

Unknown origin

>U-sequence of unknown origin

 

Vector Fragment

>V-beta galactosidase

             >V-beta_gal-ECOLX

>V-beta lactamase

             >V-bla-ECOLX

>V-chloramphenicol acetyl transferase

             >V-cat-ECOLX

>V-intervening sequences

             >V-intervening-RHIRD

             >V-intervening-SOLTU

             >V-intervening-SYNTH

             >V-MCS-SYNTH

>V-inverted terminal repeat

             >V-itr-TRINI

>V-loxP recombination site

             >V-loxP-BPP1

>V-neomycin phosphotransferase

             >V-nptII-ECOLX

>V-piggyBac DNA transposable element

             >V-tel-TRINI

>V-pMc5-8

             >V-pMc5_8-SYNTH

>V-pUC

             >V-pUC18-SYNTH

             >V-pUC19-SYNTH

             >V-pUC_oriC-SYNTH

>V-Ti plasmid left border repeat

             >V-LB-RHIRD

             >V-LB-SYNTH

>V-Ti plasmid right border repeat

             >V-RB-RHIRD

             >V-RB-SYNTH

>V-transformation vector backbone

             >V-backbone-SYNTH

 

Enhancer

>E-34S FMV

             >E-FMV

>E-35S CaMV

             >E-35S-CaMV

>E-nopaline synthase

             >E-nos-RHIRD

>E-rb7 matrix attachment region

             >E-as_rb7_mar-TOBAC

             >E-rb7_mar-TOBAC

>E-RuBisCO small subunit

             >E-rbcS-MAIZE

 

Gene Silencing

>GS-1-amino-cyclopropane-1-carboxylic acid  synthase

             >GS-acs2_s-SOLLC

             >GS-acs_as-ANACO

             >GS-acs_s-ANACO

>GS-acid invertase

             >GS-AI_as-SOLTU

             >GS-AI_s-SOLTU

>GS-alpha-glucan water dikinase R1

             >GS-R1_as-SOLTU

             >GS-R1_s-SOLTU

>GS-asparagine synthetase-1

             >GS-Asn1_as-SOLTU

             >GS-Asn1_s-SOLTU

>GS-caffeoyl CoA 3-O-methyltransferase

             >GS-CCOMT_u-MEDSA

>GS-delta desaturase

             >GS-delta12D_as-CARTI

             >GS-delta12D_s-CARTI

             >GS-fad2_1_as-SOYBN

             >GS-fad2_1_s-SOYBN

>GS-delta-cadinene synthase

             >GS-dcs_u-GOSHI

>GS-dihydroflavonol 4-reductase

             >GS-dfr_as-DIACA

             >GS-dfr_s-DIACA

>GS-ethylene-forming enzyme

             >GS-ACO_as-SOLLC

>GS-granule-bound starch synthase

             >GS-gbss_as-SOLTU

             >GS-gbss_s-SOLTU

>GS-lycopene cyclase

             >GS-lycb_as-ANACO

             >GS-lycb_s-ANACO

             >GS-lyce_as-ANACO

             >GS-lyce_s-ANACO

>GS-palmitoyl acyl carrier protein thioesterase

             >GS-fatB1_as-SOYBN

             >GS-fatB1_s-SOYBN

             >GS-fatB_as-CARTI

             >GS-fatB_s-CARTI

>GS-phosphorylase-L

             >GS-phl_as-SOLTU

             >GS-phl_s-SOLTU

>GS-polygalacturonase gene

             >GS-pg_as-SOLLC

             >GS-pg_s-SOLLC

>GS-polyphenol oxidase 5

             >GS-Ppo5_as-SOLVR

             >GS-Ppo5_s-SOLVR

>GS-polyphenol oxidase suppression transgene

             >GS-PGAS-SYNTH

>GS-replicase

             >GS-rep-(ac1)_u-BGMV

>GS-RNA-dependent RNA polymerase

             >GS-RdRp_as-BNYVV

             >GS-RdRp_s-BNYVV

>GS-Snf7 -escrt-III subunit protein

             >GS-Snf7_u-DIAVI

 

Genomic Sequence

>G-endogenous genomic sequence (flanking sequence)

             >G-flank-HOST

             >G-genomic-HOST

 

Intron

>I-actin

             >I-1_act1-ORYSA

             >I-1_act8-ARATH

>I-alcohol dehydrogenase

             >I-1_adh1-MAIZE

             >I-2_adh1-MAIZE

             >I-6_adh1-MAIZE

             >I-adh-DROSP

>I-catalase

             >I-cat1-RIICO

>I-dihydroflavonol 4-reductase

             >I-dfr-PETHY

>I-elongation factor 1 alpha

             >I-1_EF1alpha-ARATH

>I-heat shock protein

             >I-hsp70-MAIZE

>I-histone

             >I-1_H3-ARATH

>I-intron-containing 5'UTR

             >I-AGO4

             >I-At1g01170

             >I-At1g62290

             >I-At1g65090

             >I-At5g63190

>I-phosphoenolpyruvate carboxylase

             >I-9_PEPC-MAIZE

>I-psbr

             >I-2_psbr-SOLTU

>I-pyruvate dehydrogenase kinase

             >I-pdk-FLATR

>I-RuBisCO small subunit

             >I-1_rbcS-MAIZE

>I-ubiquitin

             >I-1_ubi1-MAIZE

             >I-ubi-ANDGE

             >I-ubi4-PETCR

             >I-ubi4-SACOF

 

Leader

>L-5'e1 tapetum specific

             >L-5_e1-ORYSA

>L-5-enolpyruvylshikimate-3-phosphate synthase

             >L-epsps-ARATH

>L-actin

             >L-act8-ARATH

>L-alcohol dehydrogenase

             >L-adh-ORYSA

>L-alpha subunit of beta conglycinin

             >L-7Salpha-SOYBN

>L-beta glucuronidase

             >L-uidA-ECOLX

>L-cestrum yellow leaf curling virus

             >L-CYLCV

>L-chlorophyll a/b-binding protein

             >L-cab-PETHY

             >L-cab-WHEAT

>L-elongation factor 1 alpha

             >L-EF1alpha-ARATH

>L-heat shock protein

             >L-hsp17_9-SOYBN

             >L-hsp70-PETHY

>L-octopine synthase

             >L-ocs-RHIRD

>L-omega tobacco mosaic virus

             >L-omega-TMV

>L-Papaya ringspot virus

             >L-PRSV

>L-peptide

             >L-pep-SYNTH

>L-RNA 4 of alfalfa mosaic virus

             >L-RNA4-AMV

>L-RuBisCO small subunit

             >L-rbcS-MAIZE

>L-tobacco etch virus

             >L-TEV

>L-ubiquitin

             >L-ubi-ANDGE

             >L-ubi-MAIZE

             >L-ubi4-SACOF

 

Regulatory Element

>R-ER retention signal

             >R-SEKDEL-SYNTH

>R-heptamerised tetracycline operator

             >R-tetO-ECOLX

>R-spacer

             >R-gbss_spacer-SOLTU

 

 


6.3.2 STraits


 

Abiotic stress tolerance 

Altered photoperiod sensitivity

Cold or heat tolerance

Drought or water tolerance

 

Alteration in growth, development or product quality 

Altered ripening or flowering

Enhanced growth rate or yield

Fertility restoration

Male sterility

Reduced black spot bruising

Reduced browning

 

Altered ripening or flowering 

Reduced ethylene synthesis

Reduced pectin degradation

 

 

Composition alteration 

Allergen reduction

Amylose/amylopectin ratio

Colour modification

Enhanced bioethanol production

Nutrional composition

Phytate degradation

pro Vitamin A

Reduced acrylamide potential

Reduced lignin

Reduced nicotin

Reproductive alteration

 

Fungus and Oomycetes resistance 

Phytophthora resistance

 

Herbicide tolerance 

2,4-D tolerance

Aryloxyphenoxypropionate tolerance

Bromoxynil tolerance

Carotinoid synthesis inhibitor tolerance

Chlorsulfuron tolerance

Cyanamid tolerance

Dicamba (2-methoxy-3,6-dichlorobenzoic acid) tolerance

Glufosinate tolerance

Glyphosate tolerance

Imidazolinone tolerance

Isoxaflutole tolerance

Mesotrione tolerance

Methotrexate tolerance

Other herbicide tolerance

Paraquat tolerance

Sethoxydim tolerance

Sulfonylurea tolerance

 

 

Nutrional composition 

Altered amino acid composition

Altered fatty acids and oils

 

Pest resistance 

Bacterial resistance

Fungus and Oomycetes resistance

Insect resistance

Virus resistance

 

Production of medical or nutritional compounds

Amino acid, peptide or protein production

Vitamin production

 

Protein secretion 

SEC61 gamma chain protein

 

Selection markers and reporter genes 

Ampicillin resistance

b-glucuronidase (GUS) activity

DsRed2 activity

Firefly luciferase activity

GPF activity

Hexose sugars metabolism

Hygromycin resistance

Kanamycin/neomycin resistance

lacZ (b-galactosidase) activity

Mannose metabolism

Nopaline synthesis

Streptomycin/spectromycin resistance

 

Virus resistance 

Beet necrotic yellow vein virus resistance

Cucumber mosaic virus resistance

Papaya ringspot virus resistance

Potato leaf roll virus resistance

Potato virus Y resistance

Watermelon mosaic virus resistance

Zucchini yellow mosaic virus resistance

 

Insect resistance 

Coleoptera resistance

Lepidoptera resistance

Nematode resistance

 

Colour modification 

Altered caroteinoid biosynthesis

 

 


6.4 Terms and Conditions of Use

6.4.1 Terms of use

The most recent terms of use can be found in EUginius’ footer under Terms of use.

6.4.2 Conditions of use for registered users

EUginius is a web-based database application providing information on genetically modified organisms. It was jointly developed by the German Federal Office of Consumer Protection and Food Safety (BVL) and the Dutch RIKILT- Wageningen UR.

Authorised Users shall receive a username and password with which they can gain access to the secure/protected area of EUginius. This user authorisation is personalised and may not be used by anyone other than the owner.

 

1.       Authorised Users are obliged to keep their password and username secret in order to avoid risk of abuse by third parties. If the Authorised User becomes aware of any abuse of his/her access data, he/she shall be obliged to inform BVL without delay.

 

2.       Authorised Users are obliged to ensure that the contact details they have stored in the EUginius system are kept up to date at all times. Notwithstanding this, all access authorisations will be reviewed on a yearly basis.

 

3.       All data stored in the EUginius system for which this access authorisation is required shall be used for official purposes only. Any entry, recording or preservation of the data and any form of publishing or transfer to third parties is not permitted.

 

4.       The Authorised User shall be liable for any abuse attributable to him/her. In cases of abuse BVL is entitled to block that user’s access immediately.

 

5.       For technical reasons, the user’s name and email address will be transferred to servers of the BVL and to a server of its cooperation partner (RIKILT - Wageningen UR) in the Netherlands for storage once a day during data update. The Authorised User hereby agrees to this.

 

6.       All data stored in the EUginius system by Authorised Users shall be treated confidentially by BVL and by BVL’s cooperation partner in the Netherlands and shall not be transferred to third parties.