1. How is data organized in Causaly?
2. How does Search work in Causaly?
3. Do I have to incude all synonyms when searching for a Concept?
4. Do keywords used in the free text box include synonyms?
5. How can I find the best terms for my Search?
1. How is data organized in Causaly?
All entry terms are associated with Concepts that are linked to ontologies of the Unified Medical Language System (UMLS™), maintained by the National Library of Medicine. Each Concept is associated with narrower (child) and broader (parent) Concepts as defined by UMLS™.
You can preview the ontologies for a specific Concept, for example “Non-Small Cell Lung Carcinoma” in the Overview page as seen in Figure 1.
Figure 1. Preview ontologies for “Non-Small Cell Lung Carcinoma”
For more information on the ontologies and dictionaries used, please visit UMLS Metathesaurus Vocabulary Documentation.
2. How does Search work in Causaly?
The easiest way to begin your Search is by typing a Concept in the search box. As you start typing, a full or abbreviated entry term, Causaly suggests the top 7 relevant Concepts, as found in the ontologies. Suggestions include narrower and broader Concepts as indicated in Figure 2.
Figure 2. Narrower and broader Concepts suggested when typing in the Search box
3. Do I have to include all synonyms when searching for a Concept?
No - when searching for a Concept in Causaly, synonyms are included automatically as defined by the UMLS™ vocabularies. For more information visit the UMLS™ Metathesaurus Vocabulary Documentation.
For example, when searching for the gene PD-L1, Causaly recognizes its synonyms, such as CD274, and suggests it below as shown in Figure 3.
Figure 3. Synonyms are recognized and suggested when typing a Concept
Causaly also recognizes drug brand names and suggests their associated pharmacological ingredients. For example, when searching for Humira®, Causaly will also suggest adalimumab (Figure 4).
Figure 4. Pharmacological substances are suggested when typing a drug’s trade name
4. Do keyword used in the free text box include synonyms?
In the free text box keywords can be used to refine a Search (Figure 5). Keywords include synonyms and narrower Concepts as defined by the MeSH dictionary.
To find out more about synonyms included, please visit MeSH - NCBI.
Figure 5. Free text box keywords also include synonyms
In cases where the free text box is used, Causaly first finds all the articles that meet the keyword search criteria and then finds the relevant relationships within these articles. For more details on how to construct free text keyword queries visit the keyword search section.
5. How can I find the best terms for my Search?
When performing a Search, Causaly includes narrower Concepts by default. You can inspect these by clicking on the down arrow next to the concept name and click on the "View related concepts" as shown in Figure 6.
Figure 6. Click on the “View related concepts” button to see all Concepts included in your Search
Select broader or narrower Concepts to identify the most relevant evidence to your research question (see Figure 7).
Figure 7. Explore ontologies, select broader and narrower Concepts
If you require further assistance, please contact support@causaly.com.