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Last update:  January 7, 2013
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Help page of Allergome
The allergenic molecule section (BLU section) of the Allergome Database is currently up-to-date. In this section as well as in the RED section some data from earlier publications ( < 1987) have not been processed yet. References cited in the GREEN section are up-to-date, but start with 2005. Sections added with the January 2006 release will be completed soon.

This page has been updated on September 13, 2011.


Allergome - A Database of Allergenic Molecules

Version 4.0


The Allergome Database has been designed to be as accessible as possible even to people that are not experienced with database search.

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Home Page

Allows you to access the following pages of the web site: About this site, Help, Links, Allergens, ReTiME, RefArray, Tools, History, Statistics. All the accesses need your authentication. Access to historical copies of the Allergome database needs you registration at that time. If you are a new User and want to visit the History sections please ask for a login and PW to the administrator.

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About this site

Supplies general information about the Allergome web site. It is updated any time relevant modifications in the basic structure or scientific criteria incurred the Allergome Database.

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Help

You are now in this page.

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Links

Contains a continuously updated useful list of links to events, scientific association, and journals.

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Tools

Contains useful procedures and downloads related to the Allergome content.
The AllergomeBlaster is currently available.
Inserting your own sequence you may compare it with the Allergome sequence dataset or with the Uniprot protein database, excluding or including the Allergome dataset.

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Statistics

Displays real time statistics of the most relevant data integrated into the Allergome archives. Statistics are available for yearly copies accessible from the History page.

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History

History page allows access to historical copies of the Allergome database, starting from year 2005.

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Allergens

Represent the main entrance to the core of the Allergome database. Unless named "Allergens" the button allows to enter the Allergome database that also contains IgE-binding molecules from Parasite and Non-IgE-binding molecules (Non-allergens).

Registration The access to the Allergome web site is free, but a registration is required for statistical purposes. If you are a "New User" you have to register yourself first. You have to fill in few fields with information about your interest related to the Allergome web site, and you have to choose a Username (max 16 characters) and a Password (max 16 characters). You may add your e-mail address to receive the monthly issue of the Allergome e-Newsletter. If you already receive the Allergome e-Newsletter skip this step. Once registered you may access the Allergome any time you want just by entry your Username and Password. Save them in a file to avoid multiple registrations.

The Allergome search engine will lead you to the Molecule Monographs in three steps.

1 - Search Form

In the Search page you put your query to the Allergome database.
Molecules in the Allergome Database are located in different sections. They are distinguished by colors. Labels, a legend, and a tooltip on a colored spot help in the search page, in the search result page, and in the molecule monograph, respectively.

Any search is performed using Taxonomy and English source archives. You may add another language by selecting among those available in the pop-down menu. In the case you add an in-language archive you may use special alphabetic characters from a non-international keyboard.

You have two types of Search:
  • The "Quick Search"
  • The "Advanced Search"


QUICK Search:

You may enter one or more words ("string of characters"). The Search engine will retrieve monographs, which contain all the words you are searching for (i.e. "pollen birch" will list all the monographs containing both the words). You may use the "Substring" option that allows you to search the sequence of characters within all the Allergome Database (i.e. "ant" will retrieve both "plants" and "ants").
A quick search field is available in each Allergome page.

ADVANCED Search:

Differing from the Quick search, the words you enter in the Advanced Search fields are considered as a single string of character (i.e. "Dermatophagoides farinae" does not retrieve allergens of the "Dermatophagoides pteronyssinus" species).
You may carry out your Advanced search on "All" the archives of the Allergome Database (default choice in the Select-a-field pop-down menu). This search may be slower, but searches for the text you enter in any part of the Allergome Database.
You may select a specific archive if you know that the term you are searching for is in that archive (e.g. term "Pollen" in the "Tissues" archive).
Data in the "Accession Numbers" section of the Allergen Monograph are not searchable (you can not search for an allergen using an already known accession number). Data in the "References" section of the molecule monograph are not searchable (you can not search for an author's name).

If you want to exclude the Allergen Monographs containing your text simply click on the "NOT" checkbox (e.g. text "Mites" + NOT will retrieve all the Allergen Monographs excluding those containing Allergens from Mites).

If you want to combine terms to refine your search you may enter text in the three fields. The two logical operators "AND" and "OR" will associate or sum your terms. (e.g. "Bet v" AND "Profilin" will retrieve all the Allergenic Molecules containing both terms, whereas "Bet v" or "Profilin" will retrieve all the Allergenic Molecules containing either "Bet v" or "Profilin").

You then enter the text.
The search is not case sensitive.
You may enter letters, signs, number and combination of them.

You may access the "New Molecules" added to the BLUE section of the Allergome database by selecting number of weeks of your interest and clicking the BLUE arrow on the right end of the first line.
You may access the "Modified Molecules" in the BLUE section of the Allergome database by selecting number of weeks of your interest and clicking the BLUE arrow on the right end of the second line.
You may list all the Molecules of the Allergome database by clicking the BLUE arrow on the right end of the third line.
You may access the "All the New Sources", the modified ones, and all of them.
You may access the "New Allergenic Sources having identified allergenic molecules" added to the GREEN section of the Allergome database by clicking the GREEN arrow on the right end of the fifth line.
You may list all the modified Allergenic Sources in the RED and GREEN sections of the Allergome database by clicking the RED/GREEN arrow on the right end of the sixth line.
You may list all the Allergenic Sources in the RED and GREEN sections of the Allergome database by clicking the RED/GREEN arrow on the right end of the seventh line.

A refined advanced search can be performed by using Allergenicity Scoring parameters as follows:
  • Species of Interest: You may select one or more of the options. If you don't make any selection, all kinds are true. Species of interest is updated real time.
  • Data Generation: You may select one of the three options. If you don't make any selection, all kinds are true. Data generation is updated real time.
  • Sequence: All the available sequences are considered. You may select one of the two options. If you don't make any selection, all molecules will be displayed. If you select "available", you are asked to select one or more sequence type. Sequence availability in the Allergenicity Scoring is updated once a day. Click once to select, double click to deselect.
  • Tests: You may check one or two options. If you don't check any option, the test will not be used for searching. Tests are updated real time.
  • Epidemiology from Literature: You may enter range values for searching on tested subject, positive subjects, percentages. Epidemiology values are extracted from the corresponding Allergome table and updated real time.
  • ReTiME: You may enter range values for searching on tested subject, positive subjects, percentages. ReTiME values are extracted from the corresponding Allergome page and updated once a day.
TIPS

Do not enter in a single text field of the ADVANCED Search form a combination of words like "birch pollen" or "mite proteases". Combined Search must be performed using the QUICK search or the three text fields and the logical operators.

Use simple words and refine the Search after scrolling the list of the search results. The shorter is the string of character you use the longer will be the retrieved list.

If you don't remember the exact term use the QUICK search with the substring option.

The searching engine is not case sensitive.

2 - Molecule Found

If no Molecules are retrieved using your terms the following message appears:
"No Items Available in the Allergome Database using [ your term ] "

If you used one of the filter checkboxes the Allergome database could return the following message:
"You can Obtain Information without the Current Selections"
If you go back to the Search Form and remove the checkbox selection you will retrieve information from the previously excluded Allergome sections.

If you add the search in one of the available language archive the Allergome Database could return the following message:
"If you are doing a search using a term in your own language that is not present in the Allergome database, send us an e-mail indicating the language, the term, and the corresponding English or Taxonomic term."

If you retrieved one or more Molecule Monograph a list will appear by column as follows:
1) A progressive number. The background color identifies the molecule section;
2) A Red dot, a Yellow dot or a blank space marking the items as "NEW", "MODIFIED", or "UNMODIFIED", respectively;
3) The Molecule Name;
4) The inclusion in the WHO-IUIS Official Nomenclature List (www.allergen.org). The WHO-IUIS Allergen Nomenclature Sub-committee logo marks the molecule;
5) The way the data are generated. In silico generated monographs are marked;
6) The Sources of the Molecule. Taxonomy and English terms are always displayed. In-language terms are listed if the search has been performed using a language archive;
7) The date of last molecule updating;
8) The Allergome unique Code.

Clicking on the Allergenic Molecule Name you want to look for, you enter the Allergenic Molecule Monograph.

Some Allergenic Molecules may have the same abbreviation as in the IUIS official nomenclature, followed by a Common molecule name (e.g. Aln g Profilin) or an acronym (e.g. Ara h LTP). They refer to Allergenic Molecules characterized in terms of biological and IgE reactivity.

3 - Allergenic Monograph

BLUE, GREEN, RED monographs are identified by a spot with a tooltip.

The Allergenic Molecule Monograph may have up to eight pages:

"General Information" page contains data for the identification of the molecule and its relationship with other Allergens within the Allergome. Data on "Epidemiology", information on available "Reagents", and a complete list of "References" are provided.
"Sequences" page contains data Allergen sequences. It is not present if no sequence is available.
There are two kinds of Links in these pages: "Native Form" page contains data on allergenicity of the Allergen in its natural conformation.
"Recombinant Form" page/s contains data on allergenicity of the molecule obtained by means of molecular biology techniques. "Recombinant Form" pages are named by the expression vector used to express the molecule.
"Epidemiology from Literature" page.
"ReTiME" page contains real time data on IgE sensitization from the ReTiME module.
"Reference" page.


RED Links: a new "Search" process starts using the term you are clicking on and the selection you defined in your previous search.
The Allergome searching engine will retrieve a new list of Molecules.


BLUE Links: a new window is opened linking you to another web site containing additional information on the Allergenic Molecule you are looking at.

A third kind of link is used to move to other monograph pages (Prevalence or Reference), or to open pop-up pages.

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General Information page

The General Information page is divided in the following sections:



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- Allergenicity scoring

The Allergenicity Scoring summarizes and visualizes the current characterization status of each molecule. Move on the spots with the mouse pointer to get explanation and values for each of the eleven parameters considered. All the data are updated in real time, excepting Sequence and ReTiME values that are updated once a day. Dots are not clickable.
The icon/s on the left describe the species of interest.
When multiple species of interest are shown, Allergenicity scoring refers to Homo sapiens. When Homo sapiens is not involved, the Allergenicity scoring refers to the most important species for the allergenic molecule.

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- For allergenic sources

The icon/s on the left describe the species of interest.

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- Entry date

Date when the allergen has been entered in Allergome for the first time.

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- Last Update

Date of the last data entry or editing of the monograph.

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- Allergome Code

Univocal progressive code within the Allergome database. Does not distinguish molecules from sources.

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- Name

Allergen Name is assigned by the WHO-IUIS subcommittee for allergen nomenclature. In case the allergen name is followed by a link to the IUIS web site. Allergens lacking an official name have been nominated on the basis of authors' indications, or similarity to homologous proteins. Some structures have been identified by means of bioinformatics procedures. These are labeled as "In Silico Generated". Allergens and allergenic sources are scored in the Appendix A of the CLSI ILA20-A2 Guidelines for IgE detection. Scoring system is between 1 (highest) and 4 (lowest). This reports the strength of documentation of the substance as an allergen, being 1 equal to well documented in literature, 2 moderate documentation, 3 weak documentation, 4 no documentation.

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- Previous Names

Reports names that have been assigned to the same allergen during the time.

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- Common Names

Common names are assigned on the basis of nomenclature of already described molecules. They may be codes used to identify commercial reagents. Some Common Names are selected for grouping purposes of IgE test results in InterAll (the Allergome allergic patient e-records). Selected ones and valid taxonomy nomenclature are in bold.

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- Links to Molecule Sequences

Sequences of molecules are available, along with many other information on dedicated free web sites (UniProt, EMBL, NCBI).

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- Links to Molecule Structure

This section links to molecule structure available at the Protein Data Bank web site. Structure are available from the scientific literature and you may find a specific link in the other pages of this web site.

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- Links to AllFam

This section links to allergenic molecule families as described in the AllFam website.
Last updates of Links to AllFam were uploaded on September 12, 2011. 186 allergen families are considered, grouping 995 allergenic molecules and their isoforms. Allergens with unknown protein family were 96.

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- Biological Function

Function of the molecule is described in the literature. It may be the result of specific studies or may be derived by the sequence homology to molecules whose function is known.

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- Sources

Terms defining the source are reported. Taxonomy and English or most common terms are displayed. If an in-language search has been performed in-language terms are added. The full list of the available in-language terms may be obtained by clicking "...other Source Terms in available Languages ->".
To allow Users to easily identify the sources the Allergome team is adding images in each monograph that are automatically displayed if available. Some Source Names are selected for grouping purposes of IgE test results in InterAll (the Allergome allergic patient e-records). Selected ones are in bold.

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- Links to Source Taxonomy

NEWT, NCBI, and ITIS web sites are linked to supply full information on taxonomy of allergenic sources. Whenever a species is not listed in the two websites additional resources are linked.

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- Links to Source Images

Source images are available by searching on Google images using the correct taxonomy name.

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- Links to Source Calendars

This section links to free web site having data on dispersal of the source material. As these data often do not refer to the allergenic molecule or to a single species, much of the data are reported for families.

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- Tissues

This section describes which part of the source organism releases the molecules. A single molecule may be present in different tissues.

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- Routes of Exposure

Routes of allergen penetration into the human body are reported in this section. Exposure to a single allergenic molecule may happen via several routes.

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- Isoforms or Allergenic Molecules

This section reports the list of isoallergens that have been described and classified for allergenic molecule (BLUE section).
In the case of the GREEN section, it reports the list of allergenic molecules identified within that source.

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- Hybrids, Polymers & Shuffleds

Hybrids, polymers or shuffleds based on allergenic molecules have their components listed in this section.

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- Epidemiology from Literature

Data reported in the table of "Epidemiology from Literature" are from the literature. Heading of the columns report data classified. It's possible to sort the table by clicking on one of the headings. Columns containing characters are sorted in increasing alphabetical order. Columns containing number are sorted in decreasing value order. Whenever the table exceed twenty rows a "Epidemiology from Literature" page is created. Only the first twenty rows will be displayed in the General Information page. The complete table is available in the "Epidemiology from Literature" page including the first twenty rows by clicking on "... complete "Epidemiology from Literature" listing ->" button or on the "Epidemiology from Literature" label in the menu.

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- Reagents

Links are provided to Companies and Laboratories supplying specific reagents for the allergenic molecule or source described in the monograph.
Several categories are available that classify the reagents:
Source Material;
Molecule;
Antibody;
Diagnostic (in vivo);
Diagnostic (in vitro);
Immunotherapy;
Standardized Allergenic Extracts.

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- References

The very last 20 publications are listed for each category in this page.
Several categories are available to classify references
a) Biochemistry / Structure / Function
b) Molecular Biology
c) Immunochemistry / Allergenicity
d) Immune-mechanisms / Genetics
e-1) Detection - Indoor Environment
e-2) Detection - Outdoor Environment
e-3) Detection - Source Extracts or Food Products
e-4) Detection - Diagnostic and Immunotherapeutic Products
e-5) Detection - Source Tissues
e-6) Detection - Body Biodistribution
f) Epidemiology
g) Diagnosis
h) Immunotherapy
i-1) Experimental Model - Allergic Immune Response
i-2) Experimental Model - Conjunctival Contact-induced Diseases
i-3) Experimental Model - Ingestion-induced Diseases
i-4) Experimental Model - Inhalant-induced Diseases
i-5) Experimental Model - Injection-induced Diseases
i-6) Experimental Model - Skin-induced Diseases
j) Allergic Diseases in Animals
k) Review Citations

A single reference may be assigned to one or more categories depending on its content.
Whenever references in one of the categories exceed twenty a Reference page is created. Only the first twenty References will be displayed in the General Information page. The complete Reference list is available in the Reference page including the first twenty citations by clicking on "...complete Reference listing ->" button or on the Reference label in the menu.

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Sequences

This page display available sequences from sequence databases, from literature, or provided by authors. The following are the sections that can be found in the Sequences page:

- Sequence
Contains sequences as complete, precursor, partial or fragments, N-terminal, C-terminal, and peptides. Each sequence type is defined in the table. You may perform sequence alignments for similarity searches using the AllergomeAligner on either the Allergome or the UniprotKb databases, or both together, using BLAST and FASTA algorithms.

- B-epitope
Defined IgE binding sequences (B-epitope) are displayed. One or more links to the data source are provided. Non IgE-binding sequences might be displayed as well.

- T-epitope
Epitope sequences identified by T cells (T-epitope) are displayed. One or more links to the data source are provided. T cell non reactive sequences might be displayed as well.

- Mimotope
IgE binding sequences identified as conformational epitopes (mimotope) are displayed. One or more links to the data source are provided.

- Sequence Motif
Sequence motifs represent shared amino acid sequences among allergenic molecules. Sequence motifs have been obtained on the basis of a collaborative study with the Institute of Immunology Bern, Inselspital, Bern, Switzerland, by the method described by Stadler MB, Stadler BM (FASEB J 2003;17(9):1141-3). The last allergen motif discovery run has been performed on December 1, 2010, by using 2708 sequences from the Allergome database. This resulted in 115 motifs representing 2154 allergenic molecules. The remaining 554 allergenic molecules did not match a motif.

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The Allergome O-ring

The Allergome O-ring is the current representation of the reciprocal relationships among allergenic molecules. It is dynamically generated at the time you click the button. It works in both Sequence Homology and Cross Reactivity sections. By clicking one of the two buttons, or , the Allergome software runs an analysis of the data available in the selected section. Data are obtained from Native and Recombinant pages of all the related allergens. A graph is generated in a new window. The allergen you are starting from is at the top of the Allergome O-ring. All the related allergens are in clockwise alphabetical order. Arrowheads indicate in which direction the data has been documented. A green line connecting two molecules corresponds to a double-side arrowhead. A red line indicates a single way relationship. If you access the O-ring page via the you may click the name of an allergen opening its monograph in a new page, but you can not modify the image dimension. If you access the O-ring page via the you can not click the name of an allergen to open its monograph, but you can zoom the image. To allow a comparative evaluation, two different windows are opened for the Allergome Sequence Homology O-ring and the Allergome Cross Reactivity O-ring, respectively. Not all the allergens have the same number of studies. If a connecting line is not present it may indicate either absence of relationship or missing data.

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ReTiME

The "Real Time Monitoring of IgE sensitization" (ReTiME) module is a database created to acquire and store real time data.
Data on IgE sensitization can be supplied by any contributor willing to share his/her own data with the international scientific community.
Data from the ReTiME database are displayed in each allergen monograph in a dedicated page.
The ReTiME search engine, allowing to explore available data in deep, is not a free access area. This area can be accessed by data providers, Allergome scientific collaborators, or financial contributors to the Allergome project.
If you want to know more about ReTiME please contact the Allergome administrator.
If like to have a two week trial period to test the ReTiME module please contact the Allergome administrator.

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RefArray

RefArray is a module created to ease the access to references stored in the new Allergome Reference Archive. The Allergome Reference Archive contains all the processed papers available from the literature, beyond PubMed citation.
Data can be retrieved from the Allergome Reference Archive by using a number of optional filters, and by selecting the molecule/source of interest.
Data are displayed in an array. On the top of the RefArray are listed the Reference Classes for molecules (left) and sources (right). On the left of the RefArray are listed the selected items.
The crossing point represent the references matching the two criteria. A figure in the tooltip indicates the available number of references.
Clicking the red dotted square activates a popup listing the references.
Additional information can be obtained by selecting "show abstract".
Further listing can be activated by selecting either one item name on the left side of the RefArray or one of the Reference classes on the top.
The RefArray is a free resource from the Allergome platform.

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Allergome Contacts

We greatly appreciate your feedback if you find any error in the Allergenic Molecule Monograph data.
If you don't find what you expected in a search or you are aware of any identified allergen that is not in the Allergome Database, please contact us.

General purposes and contacts with the Allergome team and collaborators: allergome@allergome.org

To contact the administrator: adriano.mari@allergome.org

For your valuable feedback: your.feedback@allergome.org

To place your link in the Links page: links@allergome.org

To contact the Allergy Data Laboratories: allergy.data.laboratories@allergome.org

Physical Address:

Dr. Adriano Mari
Allergy Data Laboratories s.c.
Via Malipiero 28
04100 Latina, Italy
tel +39 330860005


To follow the examples access to the Allergome website by activating your browser in a new window.

Example 1

Start in the Search page. Enter "Birch" in the text field of the QUICK search;
A page with a list of Allergens appears. Click on "Bet v 1" and have a look to the General Information, Native and Recombinant pages;
Go back to the General Information page and click on the "Blue" links. New windows will be opened linking you with other web sites. Close the new windows;
Click now on "Betula verrucosa". You get the same list as for "Birch". Click now on "Bet v 4";
The Bet v 4 General Information page appears. Have a look and then click on "Calcium-binding Proteins";
A new Search result appears containing all the Calcium-binding Proteins. You may go on clicking on any of the listed molecules and have a look at the results. You can go back to the Search page using the Search button on the heading line.

Example 2

You are in the Search page. Enter "Profil" in the text field of the QUICK search and select the "substring" checkbox;
You get a list of Profilins. Some of them have not the official IUIS name;
Go back to the Search page using the "Back to Allergenic Molecule Search Form" button;
Click on the IUIS checkbox and do a new Search with Profilin;
You get a new list where the non-officially named molecules are excluded;
Click on any of the Profilins and explore the data;
Go back to the Search page using the Search button on the heading line.

Example 3

Enter "Ailanthus" in the text field of the ADVANCED Search;
You get a single line. Instead of the Allergen name the message "No Allergenic Molecules Identified" appears;
If you click on the message you will get information on an Allergenic source still lacking any identified allergenic molecule.
Go back to the Search page using the Search button on the heading line;
Click on the "All the Identified Allergens" checkbox and do the Search again with "Ailanthus";
The allergenic source monograph is no more available;
Go back to the Search page using the Search button on the heading line.


Example 4

Search page. You may use either the Quick or the Advanced Search forms;
Select a language from the menu;
Enter a term in selected language;
Search for the term:
You get a list of allergens and in the source column in-language terms are listed along with taxonomic and English terms;
Select one of the allergens;
Locate the Source section;
Click on "... other Source Terms in available Languages -> "
You get a pop-up window where terms identifying the source are listed in all the available languages.
Close this window.
Go back to the Search page using the Search button on the heading line
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