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Use cases and Query Paths

Query paths are used for advanced query to give you fine-grained control over the data you want to find. Even for the same origin and destination, different paths can give you different results. Choosing the right path depends on your scientific question.

To understand query paths, we first need to look at the Module schema.

Module schema​

The connections between the nodes change the meaning of what the node is representing. For example, if you want the species of the TCR, you would follow the path TCR --> Species. If you want the species of the PMhc, you would follow the path PMhc --> Species.

Semantic meaning of paths​

To give an example of how the path changes the meaning of the data, let's consider the following examples.

Example 1: TCR and PMhcs​

Path: TCR --> Study --> PMhc​

This means finding the peptide-MHC complexes that bind to your TCRs.

To explain further, this path finds pMHC complexes that have been experimentally identified to bind with specific TCRs in the context of a study. Here, the Study node implies that only pMHC-TCR bindings that were actually observed in experimental conditions are returned.

Use Case: Useful for researchers interested in known binding interactions between TCRs and pMHCs, as confirmed by a specific study.

Path: TCR --> Individual --> PMhc​

This path identifies all pMHC complexes produced by the individual from whom the TCR is sourced, regardless of whether the TCR binds to these complexes.

Use Case: Useful for understanding the complete immune context of an individual, showing all possible MHC complexes available for presentation, whether or not they interact with the TCR of interest.

Example 2: PMhc and Species​

Path: PMhc --> Study --> Individual --> Species​

This path identifies the species of individuals who participated in studies involving specific pMHC complexes. It shows which species' individuals were included in the study context for those pMHCs.

Use Case: Useful for researchers looking to understand the species distribution of individuals whose pMHC complexes were studied, providing insights into cross-species immune response research.

Path: PMhc --> Individual --> Species​

This path identifies the species of individuals who produce specific pMHC complexes. It traces the origin of the pMHC back to the individual and then to the species of that individual.

Use Case: Useful for researchers interested in understanding which species produce certain pMHC complexes, providing insights into species-specific immune responses.

Example 3: Individual and TCR​

Path: Individual --> TCR​

This path identifies all TCRs sourced from a specific individual. It directly links the individual to their TCR repertoire without considering any intermediate nodes like studies or pMHCs.

Use Case: Useful for researchers who want to explore the complete set of TCRs present in an individual, providing a comprehensive view of the individual's TCR diversity.

Path: Individual --> Study --> TCR​

This path finds TCRs from individuals who participated in a particular study. Here, the TCRs are specifically those sampled within the study context, which may not represent all TCRs an individual possesses.

Use Case: Useful for researchers analyzing TCR profiles studied in specific contexts or datasets.

Path: Individual --> PMhc --> Study --> TCR​

This path identifies TCRs that have been studied in the context of pMHCs produced by a specific individual. The relationship goes through the pMHC and study nodes, indicating that the TCRs were observed in studies involving the individual's pMHCs.

Use Case: Useful for researchers interested in TCRs that have been experimentally studied in relation to the pMHCs from a specific individual, providing insights into observed immune interactions within study contexts.

Example 4: Species​

Path: Species --> TCR​

This path identifies the species from which specific TCRs are sourced. It directly links the TCRs to their originating species without considering intermediate nodes like studies or individuals.

Use Case: Useful for researchers interested in the species-specific origin of TCRs, providing insights into the diversity of TCRs across different species.

Path: Species --> PMhc​

This path identifies the species that produce specific pMHC complexes. It directly links the pMHCs to their originating species, providing a clear view of species-specific pMHC production.

Use Case: Useful for understanding which species produce certain pMHC complexes, aiding in comparative studies of immune responses across species.

Path: Species --> Individual​

This path identifies all individuals belonging to a specific species. It directly links the species to its individuals, providing a comprehensive list of individuals within that species.

Use Case: Useful for researchers who need to identify all individuals of a particular species, facilitating studies on species-specific immune responses or genetic diversity.