Ref. | KG Specific Functionality | Knowledge Extraction Techniques | Type of KB | KG Resource(s) | KG Stats | Evaluation Measure(s) | Shortcoming(s) | |
---|---|---|---|---|---|---|---|---|
Entity-level | Relation-Level | |||||||
[15] | Cardiovascular domain | LSTM-CR | pattern-based and supervised learning methods | Hybrid | UMLS, EMRs, medical standards, and expert knowledge. | #n: 8,293,284 #e: 32,256,360 | The evaluation is conducted in the embedded modules | • The overall framework requires a detailed case study to evaluate the effectiveness of integrating the proposed modules. |
[45] | Subarachnoid hemorrhage | Semantic analysis (Ontologies: LBO, IAO, etc.,) | Automatic (Rule-based) | Shema-based | clinical notes and brain angiograms | N/A | P, R, F1, and AC | • Limited discussion on the KG statistics • The overall framework requires a detailed case study to evaluate the effectiveness of integrating the proposed modules. |
[76] | Hepatocellular carcinoma | SemRepFootnote 20, rule-based method,and BioIE(with Att-BiLSTM-CRF) | Schema-based | PubMed, SemMedDB, UpToDate, and Clinical TrialsFootnote 21 | #n: 5,028 #e: 13,296 | Accuracy | • The KG was not properly evaluated on real-life case study that addresses hepatocellular carcinoma. • There has been no detailed discussion on the mechanism followed to address the presented disagreements. | |
[80] | Stroke | DNormFootnote 22, tmChemFootnote 23, GNormPlusFootnote 24, PWTEESFootnote 25 | NLTK, PKDE4J, and Bio-BERT | Shema-free | CIDFootnote 26, TCMIDFootnote 27, EU-ADRFootnote 28, ETCMFootnote 29 | #n: 46 k #e: 157 k | P, R, F1 | • The constructed KG is limited to Chinese context and hard to replicate and build a more comprehensive map of medical knowledge. |
[77] | Diagnosis and treatment of viral hepatitis B | N/A | N/A | Schema-based | EMR (8544 patients in China) | #n: 8,563 #e: 96,896 | N/A | • No proper evaluation was conducted. • No discussion on mechanism followed to construct the KG |
[83] | Coronavirus pneumonia-related diseases, | CRF | Bio-BERT | Shema-free | COVID-19 scientific literatures | #n: 10,993 #e: 1,204,234 | Specificity, P, R, F1, and AC | • The entity and relation extraction datasets are provided with lack of discussion on the mechanism followed to conduct the experiments on these datasets. |
[78] | Identifying disease-gene associations | N/A | N/A | Shema-free | CTD, BioGridFootnote 30, MalaCardsFootnote 31 | #n: 103,625 #e: 3,273,215 | N/A | • No discussion on the mechanism followed to extract entities and relationships. • The construction of the KG itself is not evaluated |
[79] | Myopia Prevention | Automatic using python script | Schema-based | Baidu Encyclopedia, Chinese Wikipedia, and professional websites | #n: N/A #e: N/A | NA | • KG is not described in terms of mechanisms used to extract entities and relationships. • No proper evaluation is undertaken. | |
[93] | Depression disorder | XMedlan, Semantic Queries with regular expressions, | Hybrid | PubMed, Clinical Trials5 DrugBankFootnote 32, DrugBook, Wikipedia, SIDERFootnote 33, and UMLS | #e: 8,892,722 | Use cases | • Lack of proper evaluation, • insufficient use of other important medical repositories, • lack of discussion on both the methodology used for knowledge integration and KG statistics. | |
[91] | Autism spectrum disorder | MinHash lookup/UMLS | Skip-gram and kmeans++ | Schema-free | PubMedFootnote 34 (autism spectrum disorder-related article abstracts) | #n: 6827 #e: 16,192 | Hit@k | • Extracted relations are coarse-grained. • Difficult to distinguish semantically related relations, • Insufficient overall evaluation to the model |
[94] | Depression | SemRepFootnote 35,OpenIE and rule-based method | Schema-based | SemMedDB, PubMed | #n: 3,055 #e: 30 | Jaccard | • Poor data quality • The utility of KG was not well-proven | |
[95] | Metabolism-depression associations | Manual curation and extraction by domain expert (traditional logical rules) | Schema-based | KEGG and scientific literature | #n: 3,724,526 #e: 5,725,821 | Case study | • Ineffective inferences due to the incorporated traditional logical rules. • Automatic extraction methods are required to enrich the functional diversity of the depression KG. |