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Knowledge Graph Relations

Wiki Page: Dependencies
Jupyter Notebook: Data_Preparation.ipynb
Required Inputs: resources/relations_data/RELATIONS_LABELS.txt; resources/relations_data/INVERSE_RELATIONS.txt

Purpose

PheKnowLator can be built using a single set of provided relations (i.e. the owl:ObjectProperty or edge which is used to connect the nodes in the graph) with or without the inclusion of each relation's inverse.


🛑 CONSTRAINTS 🛑
If you would like the knowledge graph to include relations and their inverse relations, you must add the following to the ./resources/relations_data repository (an example of what should be included in each of these is included below):

  • A .txt file of all relations and their labels
  • A .txt file of the relations and their inverse relations

Relations and Inverse Relations Data

Filename: INVERSE_RELATIONS.txt


The owl:inverseOf property is used to identify each relation's inverse. To make it easier to look up the inverse relations when building the knowledge graph, each relation/inverse relation pair is listed twice, for example:

The data in this file should look like:

  RO_0003000  RO_0003001
  RO_0003001  RO_0003000
  RO_0002233  RO_0002352
  RO_0002352  RO_0002233

Relations and Labels

Filename: RELATIONS_LABELS.txt


Not all relations have an inverse (e.g. interactions). Even when an inverse relation is not present, we still want to ensure that all interactions relations are symmetrically represented in the graph. To aid in this process, we need to be able to quickly look-up an edge and determine if it is an interaction. To help make this process more efficient, the algorithm expects a list of all relations and their labels in a .txt file.

The data in this file should look like:

  RO_0002285  developmentally replaces
  RO_0002287  part of developmental precursor of
  RO_0002490  existence overlaps
  RO_0002214  has prototype