Fig. 1 Trait-regulated-genes ontology model framework

Fig. 2 Hierarchical knowledge structure of trait-regulated-genes knowledge graph A: Multi-dimensional scientific data association retrieval of gene LOC_Os01g40094. B: Data attributes of protein P49597. Different colored circles and arrow lines represent different entity types and relationship types in figure A, respectively. The numbers in parentheses indicate the number of nodes and relationships of different types. Taking node types as an example, red circles represent “trait” nodes, and the number is 3. The light blue circle represents the “protein” node, the number is 4. The orange circle represents the “gene” node, and the number is 2. For example, taking relationship types as an example, the light green arrow line represents the “has protein domain” relation type, and the number is 1. The dark green arrow line represents the “ belongs to “ relation type with a number of 2

Fig. 3 Prediction of gene-regulated- trait The circles and arrow lines in different colors in the figure represent different entity types and relationship types respectively, and the numbers in brackets represent the number of nodes and relationships of different types. Taking node types as an example, the red circle represents a “trait” node and the number is 1. The light blue circle represents the “protein” node, the number of which is 7. The orange circle represents the “gene” node, with a number of 7. Take relationship types as an example, the light green arrow line represents the “has protein domain” relationship type, the number is 6. The dark green arrow line represents the “ belongs to” relation type with a number of 7. This figure shows that there are 8 association paths between the gene “TraesCS4B02G060000” node and the trait “plant height” node

Fig. 4 Mining of the elite pleiotropy gene TraesCS3D02G078500 The circles and arrow lines in different colors in the figure represent different entity types and relationship types respectively, and the numbers in brackets represent the number of nodes and relationships of different types. Taking node types as an example, the red circle represents the trait node and the number is 5. The light blue circle represents the “protein” node, the number of which is 5. The orange circle represents the “gene” node, and the number is 5. Take relationship types as an example, the orange arrow line represents the “located in” relationship type, and the number is 5. The yellow red arrow line represents the “ corresponding to “ relationship type, and the number is 5. This figure predicts that the gene “TraesCS3D02G078500” may regulate the traits of drought resistance, salt resistance, grain weight and plant height

Fig. 5 Prediction of gene function across species The circles and arrow lines in different colors in the figure represent different entity types and relationship types respectively, and the numbers in brackets represent the number of nodes and relationships of different types. Taking node types as an example, the red circle represents a “trait” node and the number is 1. The light blue circle represents the “protein” node, with a number of 10. The orange circle represents the “gene” node, with a number of 4. Take relationship types as an example, the orange arrow line represents the “located in” relationship type, and the number is 13. The yellow red arrow line represents the “ corresponding to “ relationship type, and the number is 10. This figure establishes the association path between wheat gene “TraesCS2D02G261300” and Arabidopsis gene “AT1G48520”, rice gene “LOC_Os11g34210” and maize gene “Zm00001d052622”