Synthetic Pathway dataset

Dataset overview This dataset contains synthetic protein - pathway associations designed to reproduce the structure of a simplified Reactome-like biological knowledge dataset. Each record represents a relationship between a protein and a biological pathway using the relationship type participates_in. The dataset was created for software development, testing, teaching, demonstrations, and workflow validation. It is intended for situations where realistic biological data structures are needed without relying on production databases or experimentally validated records. Dataset contents The dataset contains 28 protein–pathway association records covering: 15 unique proteins or gene symbols 10 unique biological pathways Three organisms: Homo sapiens, NCBI Taxonomy ID 9606 Mus musculus, NCBI Taxonomy ID 10090 Rattus norvegicus, NCBI Taxonomy ID 10116 The data are provided as a tab-separated values file: synthetic_reactome_protein_pathway.tsv Each row describes a protein, its corresponding gene symbol and organism, a pathway identifier and description, and the relationship between the protein and the pathway. Data fields Column Data type Description Example Constraints / Notes uniprot_id String UniProt-style identifier assigned to the protein. P31749 Intended to uniquely identify a protein within the dataset. gene_symbol String Standard gene symbol associated with the protein. AKT1 Multiple rows may contain the same gene because one protein can participate in several pathways. ncbi_tax_id Integer NCBI Taxonomy identifier for the organism associated with the protein. 9606 Examples include 9606 for human, 10090 for mouse, and 10116 for rat. entity_type_source String Type of biological entity represented by the source record. protein Constant value in the current dataset. pathway_id String Synthetic Reactome-style identifier assigned to a biological pathway. R-HSA-1234567 A pathway may be associated with several proteins. pathway_name String Human-readable name of the biological pathway. PI3K/AKT Signaling Describes the pathway identified by pathway_id. pathway_description String Brief description of the biological process represented by the pathway. Regulation of cell survival and growth through PI3K and AKT proteins. Free-text field intended to provide biological context. relationship_type String Type of relationship between the protein and the pathway. participates_in Constant value in the current dataset. evidence_code String Code indicating the type or origin of evidence supporting the relationship. SYNTHETIC Indicates that the relationship was artificially generated rather than obtained from an experimental source. source_database String Name of the database or database-like source represented by the record. Reactome The dataset imitates Reactome-style protein–pathway relationships. is_synthetic Boolean Indicates whether the record was synthetically generated. true All rows in the current dataset are synthetic. Intended uses This dataset may be useful for: testing biological data-processing pipelines validating tabular data import and export workflows prototyping protein - pathway knowledge graphs developing database schemas and APIs testing visualization and network-analysis tools creating software tutorials and educational examples validating data-quality, transformation, and integration procedures developing unit, integration, and regression tests Data quality The dataset contains no missing values and no completely duplicated rows. Protein-to-pathway relationships follow a many-to-many structure: a protein may participate in multiple pathways, and a pathway may contain multiple proteins. Synthetic-data statement All records in this dataset are synthetic. The identifiers, pathway associations, descriptions, and evidence annotations were created for testing and demonstration purposes. They must not be interpreted as experimentally validated biological findings. Although the dataset uses familiar biological naming conventions and Reactome-style pathway identifiers, it is not an official Reactome export and is not intended to reproduce the complete biological accuracy, coverage, or curation standards of Reactome, UniProt, or the NCBI Taxonomy database. Limitations This dataset should not be used for: clinical interpretation biomedical decision-making biological discovery experimental validation pathway enrichment conclusions claims about real protein–pathway relationships Users requiring authoritative biological information should consult the official source databases and their corresponding release documentation. File format The dataset is distributed as a UTF-8 encoded TSV file. The first row contains the column headers, and each subsequent row represents one protein–pathway relationship.