This guide will take approximately 10 minutes to complete.
What is Causaly Target Ontology?
Causaly Targets is a custom ontology curated and maintained by Causaly, enabling our users to perform target-related searches more rapidly and effectively.
The current version of Causaly Target Ontology consists of 40,000+ targets, updated monthly.
It has the following key features and benefits:
- Saves time – All relevant target-related UMLS categories are selected with a single click, whether they are proteins, genes, or molecular functions.
- Increases sensitivity – Insights are synthesized from all aggregated target concepts, making sure that you don’t miss any critical evidence.
- Reduces noise – Targets are grouped into target families and specific targets to give you a more focused view.
- Better precision – Explore a specific functional target class to finetune your results for optimal precision and relevance.
This guide will take approximately 10 minutes to complete.
Search for targets associated with an indication of interest
To explore all targets associated with a disease of interest, use Causaly Discover in the Causaly home page (Figure 1).
Figure 1. Causaly Discover on the Causaly homepage
Begin your search by typing your question into the Causaly Discover search bar in natural language (Figure 2). “What are the targets for glioblastoma?” will be used as an example (link).
Figure 2: Directly ask a question in natural language in the Causaly Discover search bar
Click "Search" or hit Enter on your keyboard to run the search, which will direct you to the Causaly Discover results page.
Causaly Discover offers an AI-generated summary, complete with in-line citations for transparency into the results, based on the top 20 articles. You can scroll down to view all the documents retrieved in response to your search query.
In addition, Causaly Discover will prompt you to visit the Bio Graph to review thetargets in a dendrogram list and be able to deep dive into their unique relationships with the disease of interest. Click on View analysis to open the Causaly Bio Graph knowledge card (Figure 3).
Figure 3: Causaly Bio Graph card linking your search query to Causaly dendrogram results.
TIP! If you are used to working with keywords on Intelligent Search and/or would like to review the results directly in the Causaly Biograph, you can select the option to return to your previous Causaly experience and initiate your search there by clicking the “Intelligent Search” option under “Biograph” on top of your Causaly homepage (Figure 4).
Figure 4: Access the previous Causaly interface, by clicking on Biograph and selecting the “Intelligent Search” option.
Look for a specific target or target family
In the results page, you can open the collapsible filters panel on the left denoted by the 3 lines. In the Causaly Targets filter, you will notice the pre-selected filters: Specific target and Generic target i.e. target families (Figure 5).
Figure 5: Within the Causaly Targets filter, “specific target” and “generic target” have been pre-selected.
With these filters selected, the dendrogram view will categorize the targets based on whether they are specific targets (“specific”) or target families (“generic”).
Scroll through the dendrogram to explore the Causaly Specific targets (Figure 6) or Generic targets (Figure 7) for your indication of interest. You can further refine the results to focus on just one of the categories.
Figure 6: The category “specific targets” within the dendrogram view.
Figure 7: The category “generic targets” within the dendrogram view.
TIP! Results in "specific targets" have been compiled across various categories, such as genes, proteins, alleles, gene products, receptors, and signaling pathways. For example, concepts across these categories may be aggregated under terms like 'MTOR,' which is associated with glioblastoma in the literature, as shown in Figure 8. Similar aggregations can be applied to other targets in different contexts.
Figure 8: Aggregation of relevant target concepts under “MTOR”.
Under specific targets, you can further fine-tune the results using the Target Class categories (Figure 9). As part of Causaly’s custom target ontology, the Target Classes filters have been designed to give greater clarity on the types of targets that can influence a biomedical concept. Exploring your results with a focus on protein/molecular functions may enable more informed decision making.. Visit this link to find out more about the Target Classes filters.
Figure 9: Refine to a protein class using the Target Classes filter under “specific targets”.
Explore or validate targets in Intelligent Search
Learn about the roles and effects of your target of interest by performing a target search. Causaly’s Target Ontology gives you the option to include all relevant target concepts so you can quickly uncover supporting evidence in the literature with better coverage and reduced noise. If you wanted to validate a target-disease association, you can type in the name of the target and disease in the Intelligent Search Bar. The example used below is looking at the relationship between BRCA2 and Colorectal Cancer.
To explore this use case in Causaly, use Intelligent Search to investigate the relationship between BRCA2 and colorectal cancer (link). Causaly detects BRCA2 in its Target Ontology and returns the matching target with all relevant UMLS terms aggregated (Figure 10).
Figure 10: Causaly Targets aggregates the relevant UMLS terms under “BRCA2”.
Any direct relationships between BRCA2 and colorectal cancer found in the literature are presented in the results, including those describing different molecular forms and conditions of BRCA2 (Figure 11). This functionality ensures that you don’t miss any critical insights and validates gene-disease associations with additional, related information.
Figure 11: Colorectal carcinoma is associated with multiple concepts under “BRCA2”.
TIP! To see the UMLS terms covered by ‘BRCA2’ in the search, click on the down arrow next to ‘BRCA2’ and view related concepts (Figure 12). Examine the narrower and related concepts of BRCA2 automatically included to increase sensitivity.
Figure 12: Click on the down arrow within the concept to view related concepts.
You can exclude specific concepts in this view to reduce noise in the search. Simply click on the checkbox to de-select the concept (Figure 13).
Figure 13: Narrower concepts of ‘BRCA2’ from the UMLS ontologies.
If you already have a specific concept in mind, you can search directly with the UMLS concept for highly specific results. Simply select one of the concepts aggregated under a target, or directly enter the UMLS concept into the search field. For example, search for the association between “egfr exon 20 mutation” (Figure 14) and NSCLC (link).
Figure 14: Use a specific UMLS concept for a more restricted and focused search.
Want to learn more about how to find evidence in Causaly?
Find more information and examples on how to search posts by clicking here.