Using Knowledge Graph
Download the Formatted Data¶
The formatted data is available at Google Drive
Now you can download the formatted data and put all data you expected in the graph_data folder. Other codes will read the data from this folder.
ID Format¶
Entity ID¶
We use entity_id to represent an entity. It is a string of the following format:
such as Gene::ENTREZ:1234, Disease::OMIM:1234, Drug::DRUGBANK:DB1234.
Relation ID¶
We use relation_id to represent a relation. It is a string of the following format:
such as STRING::INTERACTS_WITH::Gene:Gene, STRING::INTERACTS_WITH::Gene:Disease.
Data Format¶
Entity File¶
The entity file is a tab-separated file with the following format:
id name label resource description synonyms pmids taxid xrefs
SYMP:0000149 obsolete sudden onset of severe chills Symptom SymptomOntology
SYMP:0000259 dry hacking cough Symptom SymptomOntology A dry cough that is characterized by a rough and loud sound.
Relation File¶
The relation file is a tab-separated file with the following format:
raw_source_id raw_target_id raw_source_type raw_target_type relation_type resource pmids key_sentence source_id source_type target_id target_type
ENTREZ:2261 CHEMBL:CHEMBL100473 Gene Compound DGIDB::OTHER::Gene:Compound DGIDB ENTREZ:2261 Gene MESH:C113580Compound
ENTREZ:2776 CHEMBL:CHEMBL100473 Gene Compound DGIDB::OTHER::Gene:Compound DGIDB ENTREZ:2776 Gene MESH:C113580Compound
Raw User Defined Knowledge Graph File¶
Raw user defined knowledge graph dataset uses the Raw IDs. The knowledge graph can be stored in a single file (only providing the trainset) or in three files (trainset, validset and testset). Each file stores the triplets of the knowledge graph. The order of head, relation and tail can be arbitry, e.g. [h, r, t]. A delimiter should be used to seperate them. The recommended delimiter is \t.
Gene::ENTREZ:8350 Hetionet::GiG::Gene:Gene Gene::ENTREZ:54583
Gene::ENTREZ:1022 bioarx::HumGenHumGen::Gene:Gene Gene::ENTREZ:890
Gene::ENTREZ:2534 STRING::REACTION::Gene:Gene Gene::ENTREZ:5063
Knowledge Graph File¶
The knowledge graph file is a tab-separated file with the following format:
relation_type resource pmids key_sentence source_id source_type target_id target_type source_name target_name
DGIDB::INHIBITOR::Gene:Compound DGIDB ENTREZ:4311 Gene MESH:D015244 Compound membrane metalloendopeptidase Thiorphan
DGIDB::INHIBITOR::Gene:Compound DGIDB ENTREZ:4311 Gene MESH:C097292 Compound membrane metalloendopeptidase aladotrilat
Annotated Knowledge Graph File¶
The annotated knowledge graph file is a tab-separated file with the following format:
relation_type resource pmids key_sentence source_id source_type target_id target_type source_name source_description target_name target_description
DGIDB::INHIBITOR::Gene:Compound DGIDB ENTREZ:4311 Gene MESH:D015244 Compound membrane metalloendopeptidase The protein encoded by this gene is a type II transmembrane glycoprotein and a common acute lymphocytic leukemia antigen that is an important cell surface marker in the diagnosis of human acute lymphocytic leukemia (ALL). The encoded protein is present on leukemic cells of pre-B phenotype, which represent 85% of cases of ALL. This protein is not restricted to leukemic cells, however, and is found on a variety of normal tissues. The protein is a neutral endopeptidase that cleaves peptides at the amino side of hydrophobic residues and inactivates several peptide hormones including glucagon, enkephalins, substance P, neurotensin, oxytocin, and bradykinin. [provided by RefSeq, Aug 2017]. Thiorphan A potent inhibitor of membrane metalloendopeptidase (ENKEPHALINASE). Thiorphan potentiates morphine-induced ANALGESIA and attenuates naloxone-precipitated withdrawal symptoms.
DGIDB::INHIBITOR::Gene:Compound DGIDB ENTREZ:4311 Gene MESH:C097292 Compound membrane metalloendopeptidase The protein encoded by this gene is a type II transmembrane glycoprotein and a common acute lymphocytic leukemia antigen that is an important cell surface marker in the diagnosis of human acute lymphocytic leukemia (ALL). The encoded protein is present on leukemic cells of pre-B phenotype, which represent 85% of cases of ALL. This protein is not restricted to leukemic cells, however, and is found on a variety of normal tissues. The protein is a neutral endopeptidase that cleaves peptides at the amino side of hydrophobic residues and inactivates several peptide hormones including glucagon, enkephalins, substance P, neurotensin, oxytocin, and bradykinin. [provided by RefSeq, Aug 2017]. aladotrilat