3.1 GMO

Figure 6 - GMO module sections

When entering the GMO module, you are presented with four different sections (Figure 6). All sections in this tab allow you to filter and search for GMOs using differing criteria. The Search for GMO function is identical to the homepage GMO search function. For more information on this search function consult 3.5.1 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 (Figure 7).

Figure 7 - Result of list with GMOs and their identifiers

1.	GMO	Most commonly used name for the GMO Clicking the GMO name will lead you to the GMO detailed information page. For more information on this page consult 3.1.4 GMO detailed information.
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 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(s) or company(ies)that 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 3.5.1.1 Advanced GMO Search.

Sorting and Navigating Pages can be done using the arrows, for an explanation on navigating search results consult 3.5.4 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 detailed page. For more information on this page consult 3.1.4 GMO detailed information.
2.	Traits	A list of traits expressed by the GMO that are not found in the wild species.

3.1.2.1 Navigating the traits page

Figure 8 - Defining filter criteria to find GMOs with specific traits.

Filtering Data can be done through the select a trait field (Figure 8). When clicking the field, you are presented with a drop-down list. A trait from this drop-down list 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 drop-down list 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 (Figure 9). 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 (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

Figure 9 - Part of traits tree

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. By default, stacks are excluded. Including stacked events can be done by unchecking the box next to Exclude stacked events.

Sorting and Navigating Pages can be done using the arrows, for an explanation on navigating search results consult 3.5.4 Navigating Search Results.

3.1.2.2 Search Results

Figure 10 - Search results GMOs and traits

After filtering you get a list of GMOs and traits (Figure 10). Clicking the GMO name will bring you to the GMO details tab, for more information on this consult 3.1.4 GMO detailed information. In the traits-column each row of text in a cell represents one trait exhibited by the GMO.

Example:

EF2-114 expresses two traits as result of genetic modification: reduced ethylene synthesis, which falls in the category altered ripening or flowering within the category alteration in growth, development or product quality, and Altered carotenoid biosynthesis which is in the Colour modification category within the main category Composition alteration.

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 detailed information page. For more information on this page consult 3.1.4 GMO detailed information.
2.	Genetic Elements	A list of all elements involved in genetic modification of the GMO.

3.1.3.1 Navigating the Genetic Elements page

Figure 11 - Define filter criteria to find GMOs containing specific genetic elements

Filtering Data can be done through the select a genetic element field (Figure 11). When clicking the field, you are presented with a drop-down list. An element from this drop-down list can be selected by clicking it. Limiting the list of shown elements in this drop-down list 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 (Figure 12). 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 level (1) has been expanded by clicking it. A corresponding Level 2 below (2) was also opened, displaying the genetic elements (level 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

Figure 12 - Part of genetic elements tree

By clicking show tree details next to hide tree EUginius will display more information about the elements in the tree (Figure 13). 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 element’s function in the GMO and Definition gives the unabbreviated name of the element. BCH gives record IDs of the corresponding elements in the Biosafety Clearing-House (http://bch.cbd.int).

Figure 13 - Details of a genetic element

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. By default, stacks are excluded. Including stacked events can be done by unchecking the box next to Exclude stacked events.

Please note: The tree has a hierarchical structure where lowest levels are related to a unique higher level.

The highest level (level_1) describes the general functional types of the genetic element. The next level (level_2) is composed of an abbreviation of the element type plus a generally comprehensive long name referring to the detailed biological function. Below level_2, genetic elements of common/homologous origin and/or with comparable/analogous features are grouped. Those level_3 terms serve as a label for the actual genetic elements.

When you select a higher level, all the elements belonging to lower linked levels will be considered in the search.

3.1.3.2 Search Results

Figure 14a - Search results GMOs and genetic elements

After filtering you get a list of GMOs and genetic elements (Figure 14a). Clicking the GMO name will take you to the GMO details tab, for more information on this consult 3.1.4 GMO detailed information. 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 (Figure 13b).

Example:

Above, filtering happened for CS-accD-PSECL (which is related to Coding Sequence > CS-1-amino-cyclopropane-1-carboxylic acid deaminase). By default, the genetic element column only shows the filtered element. By hitting show all associated elements for the GMO can be shown (below).

Figure 14b – Part of Search results GMOs and genetic elements with the activated show function

Sorting and Navigating Pages can be done using the arrows, for an explanation on navigating search results consult 3.5.4 Navigating Search Results.

3.1.4 GMO Detailed information

When clicking the name of a GMO in any of the EUginius sections, you will be redirected to GMO detailed information tab (Figure 15). This tab presents you with all information which is linked to the selected GMO. Displayed tables can be exported into MS-Excel.

3.1.4.1 Navigating GMO Detailed Information

Figure 15 - GMO detailed information

The basic information on the GMO is always shown at the top. This information includes GMO name, Alias, UID, Tradename, Company, Developer, Species, Traits and EU authorisation. Company also provides a link which brings you to the GMO Identifier List. This list will exclusively show GMOs which the company has produced. Clicking the traffic light authorisation symbols takes you to the GMO-specific authorisation details, which provides the same information as EU Application Details Search, with your GMO as filter. For more information on the application details, consult 3.5.3 Search for EU Application details.

By clicking the arrows, text or blue bar the sections described below will expand, revealing additional information.

GMO detailed information tab

General Information	General information on GMO
Inserts / Modification	Modification of the GMO on the molecular level / Sequence information when available
Transformation vectors	Vectors used to transform the GMO
Detection Methods	Methods to detect the GMO
Reference Materials	Material with known concentrations of the GMO
Authorisation	Approval status of the GMO in the European Union
Literature reference	Literature describing the GMO

3.1.4.2 General Information

General Information provides basic information on the nature of the genetic modification and provides links to sources of information regarding the GMO (Figure 16). For an explanation of the module consult the image and table below.

Figure 16 - Explanation of general information about a GMO

1.	Description	General overview of the GMO.
2.	Links regarding to this GMO	Hyperlinks to sources, relevant documents and databases regarding the GMO.
3.	Transformation /Modification technique	The transformation or modification technique used to develop an organism may differ. EUginius currently includes 15 techniques. For more information on these techniques consult for example: Ramkumar T.R., Lenka S.K., Arya S.S., Bansal K.C. (2020) A Short History and Perspectives on Plant Genetic Transformation. In: Rustgi S., Luo H. (eds) Biolistic DNA Delivery in Plants. Methods in Molecular Biology, vol 2124. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0356-7_3

3.1.4.3 Inserts / Modification

Inserts / Modification provides more detailed information on the nature of the genetic modification (Figure 17). Here you can find elements in the composite DNA and all of EUginius’ sequences associated with the GMO. For an explanation of the module, consult the image and table below.

Figure 17 - Explanation of the inserts/modification section

1.	Name	DNA called insert_ has been confirmed in the GMO. DNA starting with vector_ describes the vector that was used for the transformation. DNA ending with (putative) describes information about the insert, based on the transformation vector.
2.	Comment	Contains more detailed information on the insert/insertion site. e.g. deletion, rearrangements, insertion etc.
3.	Map	If a DNA map is available this will be inserted here in a picture format. Please note that this function is not used until now due to copyright issues.
4.	Genetic Elements	Information following this header regards the elements contained in the insert/vector
4.1	Reference	The source used for obtaining information about the insert which the element belongs to. e.g. scientific journal or organisation
4.2.	Elements	All elements in the insert/vector with general data.
	4.2.1 – 4.2.8	A summary of the element, as also described on the Genetic Element Information page. If available the order of elements in the insert/vector is also provided 4.2.1). Clicking the element name (4.2.2) will take you to Genetic Element Information, for more information on this consult 3.1.5.1 Genetic Element details.
5.	DNA Sequences	All sequences associated with the GMO and general data.
	5.1 – 5.5	A summary of the available sequences, as also described on the Sequence String Information page. The Sequence column (5.1) can link you to additional information. 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 3.1.5.2 Sequence String.

3.1.4.4 Transformation vectors

Transformation Vectors provides more detailed information on the vector used for the development of the GMO. For an explanation of the module consult the paragraph above: 3.1.4.3 Inserts / Modification.

3.1.4.5 Detection Methods

Detection Methods provides a detection search, with your GMO as filter. The additional column Verification 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. For more information about the verification values, consult 3.2.2 GMO/method matrix.

3.1.4.6 Reference Materials

Reference Materials provides 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 GMO reference material page, which provides you with extra information on the reference material. For more information on the GMO reference material page, consult 3.1.5.3 Reference Material Details.

3.1.4.7 Authorisation

Authorisation provides detailed information on applications that were submitted for the GMO with information on intended use, legal status and legislation.

Clicking the Application reference number will take you to the GMO application page. For more information on this, consult 3.1.5.4 Application Details.

3.1.4.8 Literature reference

Literature reference provides the same information as advanced Literature search, with your GMO as filter.

Clicking the article citation will take you to the GMO literature details page. For more information on this, consult 3.5.2.3 Literature Details. For more information on the Literature search section, consult 3.5.2 Literature Search.

3.1.5 Detail Pages

3.1.5.1 Genetic Element details

Clicking the element name will take you to the tree with genetic elements, with the selected element in focus. More information about the tree can be found on the 3.1.3.1 Navigation the genetic elements page.

3.1.5.2 Sequence String

Clicking Yes in the Sequence column in the Related DNA Sequences table of Inserts / Modification or Vector brings you to the Sequence string page (Figure 18), this gives information on the sequence and provides the Sequence String.

Figure 18 - Explanation of sequence information

1.	DNA Name	DNA called insert_ has been confirmed in the GMO. DNA starting with vector_ describes the vector which was used for the transformation. DNA ending with (putative) describes information about the insert, based on the transformation vector.
2.	Comment	This field is often used for description of the source of the information/detailed information on nucleotide changes in the insert.
3.	Accession Number	This is a unique code for genetic sequences, it can be used to search for genetic sequences online e.g. GenBank
4.	Reference	The source used for entering the composite DNA into EUginius. e.g. NCBI – GenBank, BCH, BVL or WFSR
5.	Annotation	The name under which the sequence is annotated in the reference database/source.
6.	Size	The size of the sequence in base pairs (bp).
7.	Sequence String	The full sequence as given in the reference.

3.1.5.3 GMO Reference Material

The GMO Reference Material page displays the GMO detailed information 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 (Figure 19), which provides you with extra information on the reference material.

Figure 19 – Explanation of GMO 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 (JRC), Eurofins 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.
9.	Extra Comment	The Extra Comment field is to indicate issues with the material in combination with specific method(s) (e.g. unexpected positive signal).

3.1.5.4 Application Details

The GMO application page can be accessed by clicking the Application reference number hyperlink in the Authorisation table. It displays the GMO Details header with general information on the GMO.
Below this, there are three sections: Application details (Figure 20), a Use/Status table and Documents.

Application Details shows general information on the application.

Figure 20 - Explanation of application details

1.	Application reference number	A unique identifier for the application, assigned to it by the institute which received the application. e.g. for applications under Regulation (EU) No 1829/2003: EFSA-GMO-Country-Year-Number
2.	Country	The country/region for which the approval applies.
3.	Applicant	Company/institution which submitted the application.
4.	Legislation	Legislation under which the ruling was made.
5.	Comment	Any notes which EUginius staff have about the application are added here. This field is often used for short summaries on related applications.
6.	Decision date /Expiry date	The period in which the decision applies.
7.	Related applications	Hyperlinks or application references for previous applications of this GMO and use-combination.

The Use and Status table shows intended uses and approval status for said uses.

Attached Documents can be found below in the Documents table, this generally includes the summary of application, EFSA or EU Scientific Panel and EFSA risk assessments and decision documents with any other documents the EUginius staff deemed relevant.

3.2 Detection

Figure 21 - Functions in the Detection module

When entering the Detection section, you are presented with three different functions (Figure 21). All functions in this tab provide you with information regarding GMO detection.

3.2.1 Detection Methods -> PCR methods for GMO detection and identification

3.2.1.1 All methods for one GMO

Figure 22 - Search All methods for one GMO with GMO drop-down list

The methods search for one GMO (Figure 22) enables finding methods, related to a specific GMO, out of the pool of species-, element-, construct- and event-specific methods by selecting this GMO in the drop-down list.

Names of detection methods in EUginius have a specific syntax. Methods designed for quantification have the prefix QT- (quantitative), methods starting with QL- (qualitative) have been designed for qualitative analysis. This prefix is followed by a three-letter code: -CON- stands for construct-specific, -ELE- is an element-specific method, -EVE- indicates an event-specific method, and -TAX- is a taxon-specific method. If relevant, the species code (e.g. ZM – Zea mays, GM – Glycine max, and 00 if species is not relevant) is added to the method’s name. The last part indicates the primers used, or, for methods that are common with GMOMETHOD database (https://gmo-crl.jrc.ec.europa.eu/gmomethods/), only consist of a three-digit number.

3.2.1.2 Free-text search for methods

The standard free-text detection method enables searching for detection methods based on the name of the method, the primers or the probe or based on the sequence of the primers, of the probe or of the amplicon. 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”, however, will 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.e. 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 main Detection Methods page.

3.2.1.3 All methods corresponding to defined criteria

Based on the selected search and dependent on filter criteria chosen you can find PCR methods for your specific query and your desired applications: GMO screening, identification and quantification (Figure 23).

Figure 23 - Preselect a method set

Figure 24 - Define a query for specific methods

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.

The Target fields Events, Constructs, Elements and Species are all OR operators. The fields Target type, Validation and Standardisation are AND operators to restrict the list. If multiple keywords are entered in fields Target type, Validation and Standardisation at least one of those keywords have to be present (Figure 24).

Any method entered in the Method field will automatically show up in the search results additionally to the methods of the set (Screening or ABC). If no method set has been selected (=ALL) only the method(s) selected in the Method field will show up.

Below, you can find the meaning of all keywords that can come up in your detection methods searches (Figures 23 and 24).

ALL

Entire pool of methods.

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.

EventS

One or more events from this drop-down list can be selected by clicking. Limiting the list of shown events in said drop-down list can be done by entering text into the field.

The drop-down list contains all events that EUginius has detection methods for.

ConstructS

One or more constructs from this drop-down list can be selected by clicking. Limiting the list of shown constructs in said drop-down list can be done by entering text into the field.

The drop-down list contains all constructs that EUginius has detection methods for.

ElementS

One or more elements from this drop-down can be selected by clicking. Limiting the list of shown elements in said drop-down list can be done by entering text into the field.

The drop-down list contains all elements contained in EUginius.

Species

One or more species from this drop-down list can be selected by clicking. Limiting the list of shown methods in said drop-down list can be done by entering text into the field.

The drop-down list contains all species that EUginius has detection methods for.

TARGET Type

One or more target types from this drop-down list can be selected by clicking.

Construct-specific	Specific for detecting the presence of two elements that are in proximity.
Element-specific	Specific to a single element.
Event-specific	Specific to a single GMO.
Taxon-specific	Specific to an entire taxon.

Validation

One or more validations from this drop-down list can be selected by clicking.

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

One or more standardisations from this drop-down list can be selected by clicking.

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

One or more methods from this drop-down list can be selected by clicking. Limiting the list of shown methods in said drop-down list can be done by entering text into the field.

The drop-down list contains all methods in EUginius.

Detection Methods Search Result

Figure 25 shows 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 section 3.6 Exporting data).

Figure 25 - Result of detection method search

Detailed examples on how to use the functions in the detection module can be found in 4.1 Detection: search workflow for detection methods.

3.2.2 GMO/method matrix

The GMO/method matrix section lets you find information on the specificity of a PCR method and its ability to detect GMOs (Figure 27). A set of methods can be selected and filtered by specific criteria. You can also select specific GMOs and/or species of interest or filter for GMOs with a specific authorisation status in the EU. If no GMOs are selected and no status filter applied the matrix will contain all GMOs present in EUginius.

3.2.2.1 Select methods foR the GMO/method matrix

The Filter Criteria for Select methods for the GMO/method matrix 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 3.2.1.3 All methods corresponding to defined criteria.

3.2.2.2 select GMOs for the GMO/method matrix

The Filter Criteria for Select GMOs for the GMO/method matrix section lets you limit the GMOs which are shown in the verification matrix. You can select specific GMOs, species of interest or filter for GMOs with a specific authorisation status in the EU.

Figure 26 - Define a query for the GMOs for the GMO/method matrix

For filtering EUginius makes use of Boolean operators, specifically ‘AND’ and/or ‘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.

The list of GMOs to be shown in the matrix (Figure 27) can be restricted by different filters (Figure 26).

Specific GMOs or Species can be selected.

Stacks can be excluded (default) or included.

The list of GMOs can be restricted by authorisation status. The authorisation options are combined with AND. This means that GMOs in the list should comply with all the options.

By hitting search EUginius will open up the option to show three result matrices, which all can be exported as an Excel file (see section 3.6 Exporting data).

· GMOs detected by selected methods

· GMOs not detected by selected methods

· All GMOs

3.2.2.3 Navigating The Matrix

Figure 27 - Verification matrix

Except for GMO, Authorisation, Species and Reference material (RM) available, all column headers are detection methods in EUginius. This list of detection methods can be limited by using filters in the Select methods for the GMO/method matrix section of the search page. For more information on this section consult 3.2.2.2 Select methods for the GMO/method matrix.

All row headers are GMOs in EUginius. This list of GMOs can be limited by using filters in the Select GMOs for the GMO/method matrix section of the search page. For more information on this section consult 3.2.2.3 Select GMOs for the GMO/method matrix.

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 (literature, plasmid map etc.)
-1	No expected target detection, based on other information in EUginius (literature, 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 detailed information.

Authorisation uses coloured symbols to display the 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. 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 3.1.4.5 Reference Materials.

Specific examples on how to use the functions in the GMO/method matrix module can be found in 4.2 GMO/method matrix: Optimisation of a screening strategy and 4.3 GMO/method matrix: Designing a Screening strategy .

3.2.3 Reference Material

The Reference material section allows to perform searches on the availability and on the source of GMO reference materials (Figure 28), providing you with the information you need to validate or perform your experiments.

3.2.3.1 Searching

Figure 28 - Define a query for reference materials

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 has 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 (JRC), Eurofins 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.	Certified	Checking this box will mean only certified materials are shown.

3.2.3.2 reference material search result

Figure 28 shows an example of the result of a specific query. For more explanation about the different columns, see the search criteria above (Figure 29). 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 section 3.6 Exporting data). Clicking catalogue number takes you to the details. For more information on this page, consult 3.1.5.3 GMO reference material.

Figure 29 - Reference material search result

3.3 Analysis

The Analysis module consists of 14 input fields containing information on GMO detection results (Figure 30). It supports you in sample analysis and can provide explanations for detected events. Import result file lets you import an Excel file with screening outcomes from your laboratory, saving you from entering data manually. A detailed example workflow showing how to use the functions can be found in 4.4 Analysis Tool.

3.3.1 Entering Screening Data

Figure 30 - Manually entering screening data for Analysis module

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 species-, GMO-, promoter-, terminator, coding sequence, other element-, construct-specific methods that you used but that did not yield positive results.

3.3.2 Importing Screening Data

Import result file lets you import an Excel file with screening outcomes to save time entering data.

Figure 31 - Importing screening data for Analysis module

The Excel file which can be imported (Figure 31) has a layout especially designed for easy entry in either EUginius or a LIMS (laboratory information management system).

Row 1	Row 1 is redundant for data analysis purposes; it purely provides the user of the Excel sheet with a name for the method.
Row 2	EUginius’ method abbreviation. This is required for EUginius’ analysis module. For finding the EUginius method abbreviation that corresponds to your method(s) (see 4.1.2.1 Which method in EUginius corresponds to the P-35S method from my laboratory?).
Row 3	LIMS’ method abbreviation. This is required for LIMS’ data management.
Rows 4+	Each row from 4 onwards is a separate screening. Once the analysis has been run you can switch between screening results by moving pages. This allows you to run multiple analyses at the same time.

Column A	A legend describing the contents of the rows behind them.
Columns B+	A matrix of screening information showing test results per method for the different screening samples.

D	Detected, the test showed a positive result.
ND	Not Detected, the test showed no result.
-	Blank, this test was not performed.

3.3.3 Analysis Results

After clicking the Analyse button, EUginius will begin to calculate which parts of your screening data coincide with the detected GMOs and which other GMOs may be present that have not been accounted for in your screening. When you have used an import file with results, the samples will be shown one by one on separate pages.

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

		Unexplained detected target (detected target not present in any of the identified GMOs)
		Confirmed not-detected target (tested but not detected)
		Explained detected target (detected target present at least in one of the identified GMOs)

3.3.3.1 Confirmed output

The parameters which EUginius used in the analysis are displayed first (Targets detected by used methods/ Targets not detected by used methods).

Then, the analysis report shows the GMOs which were identified with the event specific method(s) as well as the elements which were detected. Additionally, it is indicated if the presence of the detected elements can be explained by the GMOs identified (green underlined) or not (red underlined).

In the table, complementary information on the identified GMOs are displayed (Figure 32).

Figure 32 - Confirmed output

1.	Targets detected by used method/Targets not detected by used method	Parameters which were used in the analysis are listed in this section.
2.	Analysis Report	Lists targets which were detected (GMOs/ constructs/ elements). This should match what you entered in step 1 of the module
3.	Refine Search	Brings you back to the GMO analysis module All entered values should be preserved
4.	Species	Species of the GMO
5.	GMO	GMOs name Clicking the GMO name will lead you to the GMO detailed information section. For more information on this section consult 3.1.4 GMO Detailed information-
6.	Promoter	All Promoters which are present in the GMO
7.	Terminator	All Terminators which are present in the GMO
8.	Coding Sequence	All Coding Sequences which are present in the GMO
9.	Construct	All Constructs which can be detected in the GMO
10.	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 3.4 Authorisation

3.3.3.2 GMO prediction view

The GMO Prediction views shows GMOs which may explain targets detected in the sample but not present in be the GMOs identified (Figure 33). The GMOs are sorted in alphabetical order of the species by default.

Note: It is your choice to restrict the outcome. EUginius can only make calculations based on your input.

Figure 33 - GMO prediction view (note that the importance sorting was used in this example)

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 (practically) verified methods for GMOs. Theoretical matches between method and GMO will not be considered.
3.	Exclude Undetected	This will exclude any GMOs that contains target(s) which you tested for but did not detect. This also counts for species.
4.	Species	Species of the GMO
5.	GMO	GMOs name Clicking the GMO name will lead you to the GMO detailed information section. For more information on this section consult 3.1.4 GMO Detailed information
6.	Importance sorting	Shows the number 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 3.4 Authorisation

3.4 Authorisation

Figure 34 - Authorisation sections

When entering the Authorisation module, you are presented with three different sections: Search for generic approval, Custom search – EU applications, and Free-text search (Figure 34). All sections in this tab provide you with information regarding GMO approval.

3.4.1 Authorisation Symbols

Many of EUginius’ sections 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 for human consumption in the EU
	Feed	Not approved for animal consumption in the EU
	Cultivation	Not approved for cultivation in the EU
	Other uses	Not approved for any other uses in the EU

Approved with Restrictions or Phasing Out

	Food	Approved for human consumption in the EU with restrictions or phasing out
	Feed	Approved for animal consumption in the EU with restrictions or phasing out
	Cultivation	Approved for cultivation in the EU with restrictions or phasing out
	Other uses	Approved for any other uses in the EU with restrictions or phasing out

Approved

	Food	Approved for human consumption in the EU
	Feed	Approved for animal consumption in the EU
	Cultivation	Approved for cultivation in the EU
	Other uses	Approved for any other uses in the EU

Not submitted

	Food	Approved for human consumption in the EU
	Feed	Approved for animal consumption in the EU
	Cultivation	Approved for cultivation in the EU
	Other uses	Approved for any other uses in the EU

As of 2023:

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

3.4.2 Search for Generic Approval

Search for Generic Approval section lets you find information on the approval status of a specific GMO for use in food, feed, cultivation or other uses (Figure 35).

3.4.2.1 Searching

Figure 35 - Search for generic approval

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 searches for generic approval.

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

Figure 36 - Generic approval search results

Changing your search can be done by clicking Refine Search at the top of the page (Figure 36). 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 on navigating search results consult 3.5.4 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 detailed information
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. For regulatory reasons, the EU is seen as one nation. EUginius uses symbols to indicate authorisation status, for more information on this consult 3.4.1 Authorisation Symbols

3.4.3 Custom Search - EU applications

Here you can use a set of search parameters which are specific to EU applications or which describe the specificity of the GMO(s) subject of EU applications (Figure 37).

The criteria are included when selected under positive criteria and excluded when selected under negative criteria.

You can expand the list of search parameters for both, positive and negative criteria, by adding optional filters. There are seven filters which can be added to or removed from the selection.

Stacks can be included (default) or excluded from the search.

3.4.3.1 Searching – positive criteria

Figure 37 – Explanation custom search

For its searches EUginius makes use of Boolean operators, specifically AND and OR. All fields are combined in the query with AND, meaning that all provided keywords have to match the search results, narrowing down the number of results. Multiple selections in one field are combined with OR, meaning the result should match one of the keywords in this field unless you can choose between AND and OR (fields Traits and Genetic Elements).

Below, you can find the meaning of all keywords that can be used in the EU applications searches. Numbers in parentheses correspond to optional criteria.

1.	Application reference number	A unique identifier for the application, assigned to it by the institute which received the application.
2.	Species	Species for which you want to find information.
3.	GMO	Name(s) of GMOs for which you want to find information.

(4.)	UID	Unique Identifier code for GMOs.
5.	Intended use	Use(s) and EU authorisation status for the GMO(s).
6.	Applicant	The company / institution which submitted the application.
7.	Country	Country in which the authorisation applies.
8.	Commission decision number	Number of the Commission Implementing Decision.
9.	Expiry date	Date on which the authorisation expires.
(10.)	Decision date	Date of the European Commission decision.
(11.)	Legislation	Legislation under which the application was submitted / the authorisation is granted
(12.)	Traits	Traits which can be exhibited by GMOs
(13.)	Genetic Elements	Elements which can be inserted in GMOs
(14.)	Tradenames	The name(s) which the GMO is commonly sold under
(15.)	Companies/Institutions	The company/institution which developed the GMO as well as companies producing or selling the GMO.

All values entered here will be considered in the results.

3.4.3.2 Searching – Negative criteria

Below the section Search for positive criteria you can select negative criteria (Figure 37), which will exclude search results from your query. The fields and queries function as within the positive criteria search (Figure 37).

3.4.3.3 Search Results

EUginius opens up the option to show three result tables, which all can be exported as an Excel file (see section 3.6 Exporting data):

· All applications: all applications that meet the search criteria (Figure 38a),

· Valid applications: applications that meet the search criteria and have at least one authorisation status currently set to approved, approved with restrictions, phasing out or pending,

· Further applications: applications that meet the search criteria and do not have any authorisation status set to approved, approved with restrictions, phasing out or pending.

Figure 38a - Custom 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 custom 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 on navigating search results consult 3.5.4 Navigating Search Results.

1.	Application reference number	Number from the European Food Safety Authority (EFSA) assigned to the application
2.	Species	Species for which you want to find information.
3.	GMO	Name(s) of GMOs for which you want to find information. Clicking the GMO name will lead you to the GMO Detailed information section. For more information on this section consult 3.1.4 GMO Detailed information. e.g. “+2 GMOs” indicates that there are two more GMOs covered by the application. Clicking on the blue arrow symbol ( ) in the first column expands the list with the additional GMOs.
(4.)	UID	Unique Identifier code for GMOs.
5.	Intended use	Use(s) and EU authorisation status for the GMO(s).
6.	Applicant	The company / institution which submitted the application.
7.	Commission decision number	Number of the Commission Implementing Decision.
8.	Expiry date	Date on which the authorisation expires.
9.	Decision date	Date of the European Commission decision.
(10.)	Legislation	Legislation under which the application was submitted / the authorisation is granted
(11.)	Traits	Traits which can be exhibited by GMOs
(12.)	Genetic Elements	Elements which can be inserted in GMOs
(13.)	Tradenames	The name(s) which the GMO is commonly sold under
(14.)	Companies/Institutions	The company/institute which developed the GMO as well as companies producing or selling the GMO.

The blue arrow symbol ( ) in the first column indicates that there are more GMOs covered by the application. When you click on the symbol these additional GMOs are displayed as well (Figure 38b).

Figure 38b - Custom search results – expanded GMOs display

3.4.4 Authorisation Free-text Search

The authorisation free-text search lets you find all applications submitted in the European Union for authorisation of GMO(s). It allows the use of application related terms (name of the applicant, the name of the EFSA application file reference, the Commission Decision Number), as well as GMO related terms (GMO name, GMO alias, UID, species name (Latin name or common name), trade name(s), company/institution). The search terms are highlighted in the result table.

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

Search Term(s)	Search result(s)
*	Finds all applications in EUginius
Bt*	names "Bt11", "Bt10 maize", "BT10 potato", "FR-Bt1", etc.
305423	GMO “DP305423” and its’ UID "DP-3Ø5423-1"
Ms8 OR Rf3	GMOs “Ms8” and “Rf3” or stacks with one or both (e.g. “Ms11 x Rf3” or “Rf3 x GT73”)
Moon*	Tradenames “Moonlite” and “Moonberry”; additionally, Carnation lines which contain “Moon*” in their Alias – please note that the latter results are not highlighted in yellow as the GMO alias is not displayed.
Gossypium	species "Gossypium hirsutum”
Cotton	species " Gossypium hirsutum”
syngenta	Applicant or Companies/Institutions e.g. "Syngenta Seeds SAS", “Syngenta Crop Protection”
“Syngenta Seeds SAS”	Specifically finds “Syngenta Seeds SAS”
EFSA*	Finds all Application reference numbers containing “EFSA”
“EFSA-GMO-RX-GA21”	Specifically finds application “EFSA-GMO-RX-GA21”
Directive 90/220/EEC	All applications submitted under legislation “Directive 90/220/EEC”
98/292 OR 2017/1207	Applications with the respective Commission decisions “(EU) 2017/1207” OR “(EC) 98/292”
98/292 AND 2017/1207	No result – no application decided with both Commission decisions “(EU) 2017/1207” AND “(EC) 98/292”

The display of the result table can be amended using the box on the right of the page (Figure 39). It allows you to show/hide some of the columns.

Figure 39 - Results of authorisation free-text search

3.5 Search

Figure 40 - Collected search options

In the Search module (Figure 40) 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 3.5.1.1 Advanced GMO Search.

Clicking the hyperlink for advanced Literature search will also take you to a new page, for more information on this consult 3.5.2.1 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 3.5.3 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 free-text search for detection methods is explained in Chapter 3.2.1.2 Free-text search for methods. The Table of Contents lists all other chapters and can help you navigate to the specific search functions.

3.5.1 Search GMO

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"
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

The advanced GMO search (Figure 41) 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. Exclude stacked events is selected by default.

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

Figure 41 - Advanced GMO search

For its searches EUginius makes use of Boolean operators, specifically AND and OR. Searching for traits or genetic elements allows to choose between the two search operators.

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.	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 Search Literature

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 for a 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 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

Figure 42 - Literature search results

Changing Search Criteria can be done by clicking Refine Search at the top of the page (Figure 42). 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 on navigating search results consult 3.5.4 Navigating Search Results.

1.	Citation	Literature citation as generally used in references Research groups publications are cited in APA 6^th edition Clicking the citation will lead you to the Literature details section. For more information on this section consult 3.5.2.3 GMO 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 GMO Literature Details

GMO literature details gives information about the literature citation and provides links to the literature. For an explanation of the module consult Figure 43 and table below.

Figure 43 - GMO literature details

1.	Citation	Literature citation as generally used in references. Research groups publications are cited in APA 6^th 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 type	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.	Authority	Authority which published the literature.
8.	View PDF	If available, a .pdf file of the literature can be downloaded 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 presents you with six fields that contribute to one query (Figure 44). This allows specification of GMO, Element Donor, Species and Element or Trait.

With similar fields exclusion of certain known GMOs, genetic elements or traits is also possible. This helps in the analysis of detected GMOs when several events are tested for.

3.5.3.1 Element Search

Figure 44 - Explanation of Element search

For its searches EUginius makes use of Boolean operators, specifically AND and OR. AND means the result needs to contain all entered keywords. OR means all GMOs matching the keyword will be shown regardless of other keywords.

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.	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 about it, you can type the name in the Genetic Elements query-building field.

3.5.3.2 Element Search Results

Figure 45 - Element search results

Changing your search can be done by clicking Refine Search at the top of the page (Figure 45). 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 on navigating search results consult 3.5.4 Navigating Search Results.

1.	GMO	GMO wherein 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 detailed information
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 3.1.5.1 Genetic 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 that was introduced into the GMO This is only available for coding sequences.

3.5.4 Navigating Search Results

Figure 46 - 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 sections 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 depending on the amount of data you want to export. Your browser will then prompt you with the option to download the exported file.

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


Wageningen Food Safety Research Department Statutory Tasks	Federal Office of Consumer Protection and Food Safety Department Genetic Engineering
T +31 (0)317 480256 euginius.wfsr@wur.nl www.wur.eu/wfsr	T +49-(0)3018-444-40000 gentechnik@bvl.bund.de www.bvl.bund.de
Visiting address: Akkermaalsbos 2 Building no. 123 6708 WB WAGENINGEN The Netherlands	Visiting address: Gerichtstraße 49 13347 BERLIN Germany
Mail address: PO Box 230 6700 AE WAGENINGEN The Netherlands	Mail address: PO Box 11 02 60 10832 BERLIN Germany

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’s 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	Input and Feedback	The standard procedure for system malfunction or improvement opportunities.
6.0	Terms and Condition of Use	Additional data to assist you when working in EUginius.

GMO	Genetically Modified Organism
Event	Used when describing one particular GMO derived from a transformation process as well as genome edited organisms (GE-GMO)
UID	Unique Identifier which is given to events for standardisation between databases
Stack	A traditional crossing of two GMO events 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. In case of GE-GMO, DNA sequence which has been modified.
Coding Sequence	An element that consists of DNA coding 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 as 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 drop-down list

BLAST	Basic Local Alignment Search Tool
GE	Genome Edited
GMO	Genetically Modified Organism
PCR	Polymerase Chain Reaction
UID	Unique IDentifier

CS	Coding Sequence
E	Enhancer
I	Intron
L	Leader
O	Other sequences
P	Promoter
R	Regulatory element
T	Terminator
TP	Transit Peptide
V	Vector fragment

QL-	Qualitative (PCR method)
QT-	Quantitative (PCR method)
-CON-	Construct-specific method
-ELE-	Element-specific method
-EVE-	Event-specific method
-TAX-	Taxon-specific method

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)
EURL	European Union Reference Laboratory

1.2.1 Public (euginius.eu)

1.2.2.1 Read-only

1.2.2.2 Data entry

1.2.2.3 Expert

1.2.2.4 Administrator

1.4 Organisation of the Manual

2.1 Access and Login

2.2.1.1 Homepage toolbar (left)

2.2.1.2 Homepage body (center)

2.3 Homepage Search section

3.1 GMO

3.1.1 List with GMOs and their Identifiers

3.1.2 List with GMOs and Traits

3.1.2.1 Navigating the traits page

3.1.2.2 Search Results

3.1.3 List with GMOs and Genetic Element

3.1.3.1 Navigating the Genetic Elements page

3.1.3.2 Search Results

3.1.4 GMO Detailed information

3.1.4.1 Navigating GMO Detailed Information

3.1.4.2 General Information

3.1.4.3 Inserts / Modification

3.1.4.4 Transformation vectors

3.1.4.5 Detection Methods

3.1.4.6 Reference Materials

3.1.4.7 Authorisation

3.1.4.8 Literature reference

3.1.5 Detail Pages

3.1.5.1 Genetic Element details

3.1.5.2 Sequence String

3.1.5.3 GMO Reference Material

3.1.5.4 Application Details

3.2 Detection

3.2.1 Detection Methods -> PCR methods for GMO detection and identification

3.2.1.1 All methods for one GMO

3.2.1.2 Free-text search for methods

3.2.1.3 All methods corresponding to defined criteria

ALL

SCREENING

ABC

EventS

ConstructS

ElementS

Species

TARGET Type

3.2.2 GMO/method matrix

3.2.2.1 Select methods foR the GMO/method matrix

3.2.2.2 select GMOs for the GMO/method matrix

3.2.2.3 Navigating The Matrix

3.2.3 Reference Material

3.2.3.1 Searching

3.2.3.2 reference material search result

3.3 Analysis

3.3.2 Importing Screening Data

3.3.3 Analysis Results

3.3.3.1 Confirmed output

3.3.3.2 GMO prediction view

3.4 Authorisation

3.4.1 Authorisation Symbols

3.4.2 Search for Generic Approval

3.4.2.1 Searching

3.4.2.2 Search Results

3.4.3 Custom Search - EU applications

3.4.3.1 Searching – positive criteria

3.4.3.2 Searching – Negative criteria

3.4.3.3 Search Results

3.4.4 Authorisation Free-text Search

3.5 Search

3.5.1 Search GMO

3.5.1.1 Advanced GMO Search

3.5.2 Search Literature

3.5.2.1 Advanced Literature Search

3.5.2.2 Literature Search Results

3.5.2.3 GMO Literature Details

3.5.3 Element Search

3.5.3.1 Element Search

3.5.3.2 Element Search Results

3.5.4 Navigating Search Results

3.6 Exporting data