Associations on the Fly
Learn about the new associations view released in 23.09.
“Associations on the fly” is a revamp the Open Targets Platform association page with new facets and additional built-in functionalities. This view replaced the classic associations page.
In the Associations on the fly page, a target or disease / phenotype is fixed and the prioritised list of alternative entities is displayed. A more detailed explanation on associations is available in the Target - Disease associations section.
Key features
Rapid comparison of evidence for different associations
User control over the weighting of contributing evidence from each data source
Ability to include and filter by specific data sources (Note: this is an OR filter)
Searching and applying filters by various target / disease or phenotype categories
Ability to 'pin' a list of targets to create a customised list
Upload a list of interested entities and export results
Data source score weights
The data source weights are presented as an advanced option in the new user interface. They have been designed to allow users to dynamically modify the relative importance of the different data sources from the defaults set by Open Targets. The view automatically recomputes the association scores based on the new user-defined weights, giving this view its name: Associations On the Fly.
The new feature can be adjusted to modify the preset Open Targets data sources scores and their effect on the global association score “on the fly”. This interaction ultimately enables a more tailored therapeutic hypothesis formulation.
Evidence
Where evidence is available for a data source, clicking on the button will reveal the detail widget for that data source. Evidence displayed in the widget includes indirect evidence, so the user can interrogate evidence annotated with descendants of the disease or phenotype of interest.
Filtering functionality
The Platform comes with a re-designed functionality which allows filtering on the Associations On the Fly and Target Prioritisation pages:
On a disease or phenotype page: Users can search and apply target specific filters which filters the association & prioritisation page by a particular target or a target category (categories details in the table below). The default is All Categories, however you can also select and view filter suggestions for a specific category from the drop down menu.
Names
Name of the target (approvedName)
interleukin 13, tyrosine kinase 2
Symbol
Target symbol (approvedSymbol)
IL13, TYK2
ChEMBL Target Class
Class of drug target from the ChEMBL database
Enzyme, Kinase, Surface antigen
GO:BP
Gene Ontology: Biological Process The larger processes, or ‘biological programs’ accomplished by multiple molecular activities
DNA repair, Intracellular signal transduction
GO:CC
Gene Ontology: Cellular Component A location, relative to cellular compartments and structures, occupied by a macromolecular machine
Cytoskeleton, Clathrin complex
GO:MF
Gene Ontology: Molecular Function Molecular-level activities performed by gene products
Oxidoreductase activity, Transporter activator activity
Reactome
Pathways from the Reactome database
Circadian clock, Interleukin-6 signaling
Subcellular Location
Subcellular location from UniProt and HPA
Cell membrane, Cytoplasm
Target ID (ENSG)
Ensembl gene IDs of the target, beginning with ENSG (id)
ENSG00000169194, ENSG00000105397
Tractability Antibody
UniProt loc high conf, Human Protein Atlas loc
Tractability Other Modalities
Approved Drug
Tractability PROTAC
UniProt Ubiquitination, Half-life Data
Tractability Small Molecule
Structure with Ligand, High-Quality Pocket
All Categories
Search and apply all of the above filters
IL13, ENSG00000105397
On a target page: Users can search and apply disease or phenotype specific filters allowing them to filter the association page by a particular disease/phenotype or a disease/phenotype category [Disease, Therapeutic Area (eg Infectious disease, Endocrine system disease)].
Whenever you select a specific category, a few suggestions from the selected category are shown by default.
When multiple filters from different categories are selected, they are applied using an AND operator. When multiple filters within the same category are selected, they are applied with an OR operator.
Check out this tutorial video to know more about this feature:
Upload functionality
Users can now upload a custom list of targets or diseases or phenotype of interest to obtain a tailored association/target prioritisation view.
The feature is accessible from the "upload" icon on the Associations on the Fly page. This gives users the option of uploading a file containing a custom list of targets or diseases or phenotype. The file should have one entity per row. There are multiple allowed file formats for the uploaded file (.txt)* , (.csv/.tsv/.xlsx)** , (.json). An example format has also been provided for each file format in the feature.
The Platform then suggests potential matches between the entities in uploaded list and the ones in the Platform; the matches are provided through their platform entity ids. The users also have the option to select specific results that they wish to be displayed on the final view. Clicking the 'Pin hits' tab prompts the "Associations on the Fly" page to build up a custom view with the entities from the uploaded list.
Watch our video describing the feature:
* For .txt file format, please create your input list using a text editor.
** For .csv/.tsv/.xlsx file formats, please ensure that the file has a header called id.
Export functionality
We have designed and developed an export functionality for the Associations On the Fly/Target Prioritisation pages, allowing users to download:
Entire dataset view (default status)
Customised dataset view including custom controls changes, subset of data types (aggregations) and/or data from pinned targets only
TSV and JSON formats
Walkthrough of the new Associations on the Fly view
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