Via the Target Identification panel users can collect identification information about targets of interest (genes), store this information and use it for their own research purposes.
Target identification panel can be opened via the VIEWS menu and includes sub-tabs:
- Targets (opened by default) - sub-panel where user can manage targets
- Identifications - sub-panel where user can view and manage target identification reports
Targets management sub-tab contains the following objects:
- Table of previously created (added) targets. For each target in that table, there are columns:
- Name - target name. Name is displayed as a hyperlink. By click it, the target details form will be opened
- Genes - genes/transcripts that are included in this target
- Species - species that are included in this target
- Diseases - diseases that are associated with the target
- Products - products that are associated with the target
- Owner - name of the user who created the target
- Column that contains buttons to launch identification process for the selected target
- Button to add a new target
Note: if there are more than 2 items in any column of the targets table, additional items will be hidden and only their summary number is shown. Click that number to view details, e.g.:
To sort the Targets table by the Name column - click the corresponding header. To invert the sorting order, click the header again, e.g.:
Targets table supports filtering. To filter displayed targets - use one or more parameters to filter items in the table.
To enable filters - use the menu 
in the right upper corner of the panel. The approach is fully the same as described for the Variants panel:
To clear all filters - use the menu 
in the right upper corner of the panel.
To create a new target, there are following ways:
- Via GUI:
- Add a new target manually from the Targets sub-tab
- Create a target from any found orthogroup (using the Homologs panel)
- Via CLI
To create a new target:
- Click the "Create target" button at the Targets sub-panel:
- The following form will appear:
This form contains:- button to return to the targets table form
- field to specify the name of the creating target
- button to add a gene/transcript to the target
- button to add an associated disease to the target
- button to add an associated product to the target
- button to save the creating target
- Specify the new target name.
- Click the button "Add gene" to add a gene/transcript to the target.
A new row with empty fields will appear - for the specifying info for a gene - Gene ID, Gene Name, Tax ID (taxonomy ID of species), Species Name and Priority (priority of the adding gene in the current target's genes list):
- Specify all fields for a gene/transcript (Priority field is non-required, others - mandatory).
There are abilities for specifying genes:- fully manual way when you shall specify the value in each field as a plain text
- "autofilling" with automatically suggested values of genes using appearing ones during the input Gene ID/Gene Name - these values are being suggested from the existing genes database, e.g.:
When the gene/gene ID is selected from the suggested list - all other fields (except Priority) will be autofilled in:
- mix of the manual and "autofilling" ways
- Priority can be left empty or manually selected from the list:
- By the described way (steps 4-6), add desired number of genes/transcripts. Near each gene/transcript, there is a button to remove gene from the list, e.g.:
- Add disease(s) associated with the target (optionally).
To add a disease, click the corresponding field and specify the disease manually. After the input, press Enter key, e.g.:
You may add any count of associated diseases by the described way. To remove a disease from the list - use the cross button near the disease name. - Add product(s) associated with the target (optionally).
To add a product, click the corresponding field and specify the product manually. After the input, press Enter key, e.g.:
You may add any count of associated products by the described way. To remove a product from the list - use the cross button near the product name. - Once all desired values are added - click the Create button.
Target will be saved, the Remove button will appear, the Save button will become disabled:
Click the button
to return to the Targets table. Just created target will appear in the list:
To create a new target from the "Homologs" panel:
- Open the Homologs panel and any sub-tab with the found list of homologous orthogroups ("Homologene" or "Orthologs & Paralogs")
- Right-click any orthogroup from the search results list to view the context menu, e.g.:
Select the item "Create target" from the context menu. - The pre-filled form of the target creation will appear:
Here, list of all genes from the selected orthogroup will be autofilled in. - Specify the name for the creating target.
- Specify another missing info, if necessary.
- Otherwise, the procedure is the same as in the section above.
To edit previously created target:
- Click the target row/name in the Targets table, e.g.:
- The form similar to the target's creation form will be opened:
Here, you can edit the target (edit target name, add/edit/remove genes from the list, add/remove diseases and products) and then save changes or remove the target - by the corresponding buttons.
To launch a new identifying process:
- Find the target in the Targets table and click the button to launch identification process, e.g.:
- The pop-up will appear according to the selected target - to define parameters (species of interest and translational species):
- Here, the following items shall be specified:
- Genes of interest - list of species of interest. Corresponds to species for which gene (target) the identification will be performed. Species can be selected only from ones that were added to the current target. Multiselect is supported
- Translational genes - list of species to which the gene comparison shall be performed during the identification. Species can be selected only from ones that were added to the current target. Multiselect is supported
- Once all fields are specified, click the Identify button to launch the identification, e.g.:
Identifications sub-tab contains identification results. Here, users can:
- view summary results of the current/selected identification process
- view the current/selected identification details
- go up a level to view a list of previously identifications with the ability to open any of them
Once the new identifying process is finished, the Identifications sub-tab will be automatically opened with the identification results (report):
Identification report form contains:
- Button to go up a level to view identification reports' list form
- Label with the target name
- List of species of interest and list of translational species used for the identification
- Button to store the report. Note: if this button is not clicked for a report - it will be removed once closed
- Description section with short overview of the main target gene with link(s) to the source(s) from which the description is
- Set of expandable sections - these sections contain detailed info of the target identification
Below, there are details by each expandable block.
This block contains summary description of the target gene(s) with the link(s) to the source(s) from which the description is constructed.
Description is being obtained for all species of interest and merged.
Example of view:
This block contains info about drugs with investigational or approved indications targeting the current target gene(s) according to their curated mechanism of action.
When the block is collapsed - its header contains short info about the count of associated drugs to the target gene(s):
When the block is expanded - it contains a table with known drugs that treat diseases associated with the current target:
Information for this block is obtained from different sources (different databases).
Therefore information from each database can vary - switching between sources is being performed by the corresponding dropdown list in the right upper corner of the block:
For Open Targets source (see the image above), table includes columns:
- Target - gene/transcript name. Allows to filter the table by the specific gene from the target
- Drug - drug name. Each drug is presented as a hyperlink to the corresponding page in Open Targets platform
- drug details columns:
- Type - drug type (antibody, cell, enzyme, molecule, protein, etc.)
- Mechanism of action - drug action to the target (includes action type and target name)
- Action type - drug action type
- Disease - disease name treated by the drug. Each disease is a hyperlink to the corresponding page in Open Targets platform
- clinical trials info columns:
- Phase - current stage of a clinical trial studying a drug
- Status - state of the current clinical trial phase
- Source - hyperlink to the corresponding page of the clinical trial
For DGIdb source, table includes columns:
- Target - gene/transcript name. Allows to filter the table by the specific gene from the target
- Drug - drug name. Each drug is presented as a hyperlink to the corresponding page in DGIdb platform
- Interaction claim source - source (knowledge base) from which the info about drug is received
- Interaction types - type(s) of the drug interaction
For PharmGKB source, table includes columns:
- Target - gene/transcript name. Allows to filter the table by the specific gene from the target
- Drug - drug name. Each drug is presented as a hyperlink to the corresponding page in PharmGKB platform
- Source - source (knowledge base) from which the info about drug is received
By default (no matter which source is selected), table is sorted by the Drug column.
Table supports sorting by any column. Click the column header to sort by this column. To invert the sorting order, click the header again.
Table supports filtering. To filter displayed drugs - specify the desired value(s) to the filter field(s) under headers row.
This block contains info about diseases associated with the current target gene(s).
When the block is collapsed - its header contains short info about the count of associated diseases to the target gene(s):
When the block is expanded - it contains info about diseases associated with the target gene:
Information for this block is obtained from different sources (different databases).
Therefore information from each database can vary - switching between sources is being performed by the corresponding dropdown list in the right upper corner of the block:
For different source databases, there could be several views of data representation - each view can be selected by the special control (tab selector) inside the block, on the upper side.
Available views for Open Targets source:
Table view (default)
In this view, diseases associated with the target are presented as a table.
The table includes columns:
- Target - gene/transcript name. Allows to filter the table by the specific gene from the target
- Disease - disease name associated with the target. Each disease is the hyperlink to the corresponding page in Open Targets platform. Allows to filter the table by the specific disease associated with the target
- Overall score - summary score of all target-disease association scores
- other columns - specific target-disease association scores. For more details see Associations info page.
Table itself is colorized as a heatmap - according to the score value in each cell.
By default, table is sorted descending by the Overall score column.
Table supports sorting by any column. Click the column header to sort by this column. To invert the sorting order, click the header again.
Bubbles view
This view provides a hierarchical representation of the associated diseases using encapsulated bubbles:
- Each associated disease is presented as a bubble colored by its overall association score.
- Big circles represent all the therapeutic areas (from the Open Targets platform). Such circles contain associated diseases bubbles inside.
- As the same disease can belong to more than one therapeutic area, diseases bubbles can be duplicated.
- There is the ability to select a gene from target genes for which the representation of the associated diseases will be displayed.
There is the ability to adjust the view of bubbles using a minimum score filter in the upper side of the view (slider control).
By setting this score, only bubbles with overall score above it will be displayed at the diagram, e.g.:
Hovering over any disease bubble, a tooltip appears with details:
-
associated disease name and ID
-
overall association score of this disease
-
hyperlink to the corresponding disease page in Open Targets platform
Graph view
This view shows the subset of the directed acyclic graph containing the therapeutic areas (from the Open Targets platform) on the left side and associated diseases for the current target on the right.
Disease nodes are colored by their overall association scores.
There is the ability to select a gene from target genes for which the representation of the associated diseases will be displayed.
There is the ability to adjust the view of nodes using a minimum score filter in the upper side of the view (slider control).
By setting this score, only nodes with overall score above it will be displayed at the diagram, e.g.:
Hovering over any disease node, a tooltip appears with details:
-
associated disease name and ID
-
overall association score of this disease
-
hyperlink to the corresponding disease page in Open Targets platform
For PharmGKB source, only Table view is available.
In this view, diseases associated with the target are presented as a table.
The table includes columns:
- Target - gene/transcript name. Allows to filter the table by the specific gene from the target
- Disease - disease name associated with the target. Each disease is the hyperlink to the corresponding page in PharmGKB platform. Allows to filter the table by the specific disease associated with the target
This block contains list of sequence(s) corresponding to the target - DNA, RNA, proteins.
When the block is collapsed - its header contains short summary info about the number of found related sequences to the target gene(s):
When the block is expanded - it contains list of sequences related to the specific target gene, e.g.:
Switching between target genes is being performed by the corresponding dropdown list in the right upper corner of the block:
In the top of the block, there is an info about DNA sequence of the gene (if it is found), e.g.:
Such block includes:
- gene DNA accession. If this gene is presented in any dataset of the current NGB deployment - accession is shown as a hyperlink, user may click such link - the gene track will be opened for that gene, e.g.:
- reference to the corresponding NCBI page
List of transcripts related to the specific target gene is presented as a table:
Such table includes columns:
- Target - gene/transcript name
- Transcript - transcript accession. Each transcript is the hyperlink to the corresponding page in NCBI platform
- Length (nt) - transcript length (number of nucleotides in the sequence)
- Protein - protein accession. Each protein is the hyperlink to the corresponding page in NCBI platform
- Length (aa) - protein length (number of amino acid items in the sequence)
- Protein name - name of the protein
This block contains information about homologous genes for the target genes:
- paralogs of the current target gene(s)/transcrition(s) in the species of interest
- orthologs of the current target gene(s) in the translational species
This block contains structures related to the target gene(s)/transcription(s) and allows to view found structure models.
When the block is collapsed - its header contains short summary info about the number of found structures related to the target gene(s):
When the block is expanded - it contains list of structures related to the target:
Information for this block is obtained from different sources (databases), local sources are also supported.
Switching between sources is being performed by the corresponding dropdown list in the right upper corner of the block:
List of structures related to the target is presented as a table:
Such table includes columns (set of columns may vary due to selected source):
- ID - structure ID in a database. It is presented as a hyperlink to the corresponding page of the structure in the selected database (e.g., PDB)
- Name - structure name
- Method - method by which the structure is obtained
- Source - source database of the structure
- Resolution - a measure of the quality of the data (level of details presented in the diffraction pattern)
- Chains - name of macromolecule's polymeric chain of the current gene/protein
- Owner - owner user name of the structure file (only for local sources)
Table supports filtering by ID and Name columns. To filter by any of these columns - specify the filter text to the field under the header of the column, e.g.:
To open the structure model in a viewer - click its row in the table, e.g.:
Structure model is being opened in the 3D viewer.
This viewer is identical to the one using as NGB Molecular Viewer.
This block contains references corresponding to publications, literature, articles that mentioned the target gene(s) in the species of interest.
Main source of these publications - PubMed.
When the block is collapsed - its header contains short info about the summary count of all publications mentioned the target gene(s):
When the block is expanded - it contains list of references to publications mentioned the target gene(s).
Each reference contains:
- publication title - as the hyperlink to the corresponding publication on PubMed
- list of publication authors
- publication source title and date
There is the ability to generate a summary of the found bibliography using AI capabilities.
Note: this summary is generated using pretrained AI language model and its text generation functionality.
For the summary, only abstracts of the several "top" (most relevant) publications are used.
As the summary is generated by AI and this process is poorly controlled, the summary block can vary for each request for the same list of publications.
To generate a summary of the found bibliography - click the corresponding button in the upper side of the block:
It takes some time to generate the summary. Once the summary is prepared - it will appear in the upper side of the block:
You can (re)generate the summary in the described way as many times as you need.
Note: you can change the AI model that will be used for the Bibliography summary generation - select the model from the dropdown list of AI settings - see details in the section below.
Once the model is changed - the summary will be regenerated with that AI model, e.g.:
Additional ability, available for users at the identification results' form - AI chat.
There is a simple build-in chat like ChatGPT where user can try to find answer for medical or bioinformatics questions .
To open chat:
- Click the corresponding hyperlink in the right upper corner of the Identifications tab:
- Chat will be opened in the left bottom corner of the page:
- To start chat - just specify your question in the field and press Enter key, e.g.:
- The answer will appear in a few seconds:
- You may ask any count of questions here by the described way.
You can change the language model that will be used in chat - select the desired model from the dropdown list of AI settings in the right upper corner of the Identifications tab:
Notes:
- not all models are supported for the chat
- changing of the model here affects the process of the summary generation of the Bibliography
Also, you can configure each AI model used here:
- Open the dropdown list of AI models in the right upper corner of the Identifications tab.
- Click the Configure model item in the list:
- The pop-up with model's configuration will appear:
Here, the following options are available:- Model - select the AI model for which settings will be configured.
- Temperature - defines the degree of randomness in model responses. A higher temperature makes the model's answers more varied and creative. A lower temperature makes the answers more focused and consistent.
- Max size - defines the maximum size of tokens that can be used for model responses. Refers to the limit on the number of words, characters, or chunks of text that the language model can handle at once.
- Once options are configured - click the OK button to save them and apply new config.
