Login Page
For
accessing the complete set of Drug2Gene features the user should be logged in. The
login option can be accessed from the upper right corner of each Drug2Gene
page.
NB: New user accounts are created only by the
Drug2Gene administrators.
Search Page
The
Search Page consists of three main
sections:
Main Search
Alternative Search
Statistics
Main
Search
The
Main Search provides an easy way for searching in Drug2Gene database suitable
for all users irrespective of their experience level.
The
main options are:
Select
database field - select a search index (for more information please see
below)
Operators
drop down list – select an operator connecting the database field and the query
(depends on the selected index). Available values: “=”, “=(fulltext)”, “=(strict)”, “!=”, “!=(fulltext)”, “!=(strict)”, “>”, “>=”, “<” and
“<=”
Enter
search term – type the query to be searched
BOOLEAN
operator drop down – The available values are: AND, OR and AND NOT. The meaning of the operators is as follows:
<Query1>
AND <Query2> - returns all
the records that match both queries
<Query1>
OR <Query2> - returns all
the records that match either of the two queries
<Query1>AND NOT <Query2> - returns all records that match query1 and do not
match query2
Remove
button – removes the selected search fields
Add Field
button – provides additional search fields for more complex searches
Search
button – starts the search process
Reset
button – resets the Main Search fields
Include
Flagged Entries check box – by default all entries that contain
relations which are flagged as FALSE are excluded form
all searches. If the user wants to add them to his/her search results the Include Flagged Entries box must be checked.
Indexes
The Indexes represent the Drug2Gene
searchable categories in which the user can search for a particular keyword. For
example if you want to search in all possible categories you have to choose the
All Text index. If you prefer to search into a particular category you may
choose it from the index drop down menu.
There are two types of indexes:
Fulltext – the fulltext indexes are designed to examine all the words of a
query in any given category of a drug2gene entry
Strict – the strict
indexes provide an exact match search and the results are returned only in case
of exact match between the query string and the respective index category
content
NB: The All Text index
combines all other indexes in it and it is not stringently fulltext
or stringently strict as it possesses the properties of its ingredient indexes.
The indexes’ data could be three types:
String – Phrases to search can be text phrases,
names, etc. Wildcards can be used. The available operators are: “=” and “!=”
Integer – Phrases to search can only be database
IDs or other type of identificators. Wildcards cannot
be used. The available operators are: “=”, “!=”, “>”, “>=”, “<” and
“<=”
Float – Phrases to search can be digits
with/without decimal points. Wildcards cannot be used. The available operators
are: “=”, “!=”, “>”, “>=”, “<” and “<=”
NB: Wildcards are supported ONLY at the end of the word or phrase. The wildcard symbol is ‘*’. Use the wildcard to replace one or more letters of a keyword
with only one * symbol.
For some of the Indexes an auto-complete option
is available: Activity Unit, Activity Source, Activity Status, Activity Type,
Relation Source, Official Gene Symbol, Gene Name, Gene Synonym, Gene Symbols
And Synonyms, Organism Name and Compound Name.
Alternative
Search
The
Alternative Search is designed for more advanced users. It provides a possibility
for writing directly search queries. The correct syntax is:
[<IndexName>]<QueryToBeSearched>
<IndexName> is
the name of the index to search the query in (the names are the same as in the
Main Search)
<QueryToBeSearched>
is the query string that will be used for performing the search. If it consists
of more than one word it must be enclosed in quotation marks
NB: The alternative search supports wildcards
(“*”) and BOOLEAN operators, too. For determination of the BOOLEAN priority the
bracket symbols must be used.
Example:
[Official Gene
Symbol]= (strict)"UGT*"
AND ([Compound Name] =(fulltext)"Farne*" OR
[Compound Name] =(fulltext)"Furose*")
Statistics
The
statistics section provides brief statistical information about the count of
genes (grouped by common organism name), the count of compounds and the count
of genes and compounds joined in relations. Two values are displayed: the
number of all genes/compounds and the number of genes/compounds joined in
relation.
NB: When new records are inserted into
Drug2Gene database the statistics information is updated automatically.
View Database
Statistics
The
database statistics page consists of two sections. The first one contains the
list of all Drug2Gene sources. Brief description, release number (if available),
particular release date, number of genes in relations, number of compounds in
relations and unique relations are also provided.
NB: Depending on the source type some of the
columns may not contain information. The gene sources contain only the Genes in
Relations count, the compound sources contain only the Compounds in Relations
count.
The
second section provides statistics for the activity types available in
Drug2Gene. Two types of counts are possible - one for the Number of Activities,
and one for the Number of Relations. For more simplicity only the activity
types with more than 10 000 relations are displayed. The other activity
types could be shown by using the “Show all activity types” link at the bottom
of the table.
Middle Result Page
The
Middle Result Page appears when you have already performed a search (upon
completion of the search process). You can see the database hits summarized in
a table view, divided into multiple columns.
Current
Query String
The
Current Query String section contains the exact text and syntax of the current
query. It is possible for the user to copy the query and to paste it into the
Alternative Search to execute again the same search.
Sub-query
Section
This
section allows you to refine your search by performing a sub-query. The new
keyword(s) will be searched only into the current results set returned by the
previous query.
All
controls and fields are the same as in the Main Search.
NB: The Include
Flagged Entries option can not be changed and
will be applied as in the main search query.
Statistics
Section
The
Statistics section contains the amount of hits found. Four count values are
available:
Relations – the count of all returned relations
Genes without interactions – the count of all returned
single (not joining in relation) genes
Compounds without interactions - the count of
all returned single (not joining in relation) compounds
Total – the count of all entries
NB: If the search query returns more than
10 000 entries, only the first 10 000 will be displayed because of performance
issues. To see the total hit count of all entries use the Calculate Total Count link.
Data
Results Grid
The Data Result
Grid
holds the data of the entries returned by the search query. The data is
organized in five default columns: Relation ID, Official Gene Symbol, Gene
Organism, Compound Name and Activities. The default columns can be changed with
the Select categories option (please
see below for more information).
NB: Relation
ID column can not be removed from the Data
Results Grid
The
Relation ID column contains a drop
down button with three available options:
Relation View – opens a Relation oriented Final
page for a particular entry. It is available only for entries which contain a relation
Gene View - opens a Gene oriented Final page for
a particular entry. It is available for relation- and single gene entries
Compound View - opens a Compound oriented Final
page for a particular entry. It is available for relation- and single compound
entries
The
Data Results Grid contains a
special column with check boxes. Entries can be selected
for export or flagging by using these check boxes.
NB: The main check box (positioned in the
columns header) selects/deselects all entries at the particular page (not all
entries returned by the search query)
Export
The
user can export entries from Drug2Gene database in XML or TSV file format.
All
available for export categories are listed in the export form. Via the check
boxes in front of the categories names you can select the categories for your
export.
You
can choose to export the selected entries on the Middle result page or all
entries returned by the query search.
NB: If your search query returned more than 10 000
entries and the “All entries” radio
button is selected only the first 50 000 entries will be exported. For the
guest users the limit threshold is 10 000 entries. The unlimited exports
require special permission.
If
you try to export more than 500 entries at once you will be redirected to a
special download page. There your export request will be put at the exports queue
if there are other users’ export requests entered before yours. When your
export is ready a link for downloading the exported file will be displayed on
the download page.
Via
the “Create zip archive” option you
can compress your export file using the standard zip algorithm. This will
reduce the size of your export file and will decrease the download time.
Select
Results Columns
The
Select Results Columns form contains all possible categories which can be
displayed on the Middle results page
grid. The Relation ID can not be removed as it provides the opening of the Final result page.
Via
the Make default option the user can
change the categories which should be displayed on the Middle results page.
NB: The Make
Default option is available only for logged users.
Flag
Relations/Evidences
The
Flag Relations/Evidences option provides
a way for the user to set a status of any relation/evidence. There are two
statuses: true and false.
To
set a relation flag first check the
entry check box (the first column from the Data Result Grid) and for evidence check the check box in the
Activities column (there is a check box for each evidence). By checking more
than one entry/evidence check box you can flag multiple relations/evidences
simultaneously.
If
a given relation is flagged as false then it won’t be included in the search
results returned by the user query unless the Include flagged Entries check box is
checked.
If
all evidences for a given relation are flagged as false, the relation will automatically
be flagged as false as well. Conversely, if at least one evidence is set to
true, the entire relation will be automatically flagged as true.
NB: The Flag
Relations/Evidences option is available only for logged users with the proper
permissions. The relation/evidence flag comments are editable from the full
history page. The user can edit only his/her own comments, the administrators
can edit all comments.
Final Result Page
The
Final Result Page contains data grid
with detailed information for a given entry. It consists of two columns. The
first one displays the name of the category field and the second column
displays the actual data for a category.
There
are three different types of final pages:
Relation oriented – displays the information
about one gene, one compound and their relation data
Gene oriented – displays one gene information and
all its related compounds with their relations data or just a single gene
information (for genes not joined in relations)
Compound oriented - displays one compound
information and all its related genes with their relations data or just a
single compound information (for compounds not joined in relations)
The
export and flag relation/evidences options are the same as in the Middle
results Page.
Import
The
Drug2Gene database provides a possibility for proprietary data import thus
enabling users to enrich the database information.
The
import system accepts XML, TSV and SDF/MOL flat files. The exact flat files
format could be seen from the provided templates (right top corner of the
Import page). The flat files should be in the right encoding for successful
import. The allowed characters might be seen at http://www.w3.org/TR/2006/REC-xml-20060816/#charsets.
The
imported data could be deleted. If a particular import is deleted the data will
be erased permanently from the Drug2Gene database.
The
Drug2Gene import system allows only compounds and relations to be imported. The
genes data could only be modified (for example: new gene sources or synonyms could
be added).
NB: The import system accepts only flat files
less than 20 MB, one primary (tsv or xml) file, and maximum
50 files for one import at a time. The import functionality is available only
for logged users with appropriate permissions. The users with non
administrative permissions may view only their own import history.
Users
The
User Management functionality provides a way to administrate the Drug2Gene user
accounts.
Each
user is granted a set of permissions which authorize access to particular
functionality. The possible permissions are:
Meta
Administrator – combines all other permissions and allows the user to create
new user accounts
Everyone – default permission which grants
access to the basic functionality
Drug2Gene Importer/Deleter
– allows the user to import/delete appropriate data into/from the Drug2Gene
database
Drug2Gene Curator – allows the user to flag
relations/evidences
Drug2Gene Unlimited Export – allows the user to
export entries from the Drug2gene database without any limitations
Drug2Gene Admin – combines Importer, Curator and
Unlimited Exports into one permission
NB: The created users could be edited or
deleted by clicking a particular username link from the User Name column. Users
with non administrative permissions could only edit their own accounts.
Link Manager
The
Link Manager provides functionality for adding and editing the database
sources. The “primary database source name” and the “primary database source
full name” fields are mandatory.
As
a particular database source may provide gene, compound and/or relation entries
and there may be different links for them the “url
type” column defines the database source link type. In this way for one
database source multiple links could be set.
The
primary database sources have just edit option and can not be deleted. For all
other sources the delete option is available only if they do not have entries
connected to them.
NB: The Link Manager functionality is
available only for logged users with appropriate permissions.