Welcome to the Awesome Biomedical Knowledge Graphs repository! This project aims to curate and share resources related to Biomedical Knowledge Graphs (BKGs), a powerful tool for organizing and analyzing biological data. Whether you are a researcher, developer, or enthusiast in the field of biology or data science, this repository is a valuable resource for you.
2023/9/8 This project is actively under development.
Feel free to STAR and WATCH to stay updated with our progress.
In this repository, we gather recent advancements in BKGs. We provide a taxonomy that effectively categorizes different BKGs, along with explanations of the techniques and applications involved.
Our objective is to assist researchers and practitioners in gaining a deeper understanding of this burgeoning field. Your participation and contributions are highly encouraged to help foster growth and knowledge sharing within the BKG community.
- Biological applications of knowledge graph embedding models (Brief. Bioinformatics, 2021) [paper]
- A Survey on Knowledge Graphs for Healthcare: Resources, Applications, and Promises (Arxiv, 2023) [paper]
- Constructing knowledge graphs and their biomedical applications (CSBJ, 2020) [paper]
| Title | Year | Journal | Specialisation | Application | Resources | Link |
|---|---|---|---|---|---|---|
| Building a knowledge graph to enable precision medicine | 2023 | Scientific Data | Disease | Protein function annotation | - | [1] |
| Building a PubMed knowledge graph | 2020 | Scientific Data | Author | Bio-entity extraction, Name disambiguation | Pubmed | [2] |
| Knowledge Graph-Enabled Cancer Data Analytics | 2020 | JBHI | Patient | Query, Extensibility, Visualization | EHR | [3] |
| Construction of a knowledge graph for diabetes complications | 2020 | CAS | Disease | Risk prediction, Clinical support | EHR | [4] |
| PharmKG: a dedicated knowledge graph benchmark | 2021 | Brief Bioinform. | Gene, Drug | Drug repurposing, Target identification | Multiple | [5] |
| A global network of biomedical relationships derived from text | 2018 | Bioinformatics | Gene, Disease | Information retrieval | PubTator | [6] |
| Systematic integration of biomedical knowledge prioritizes drugs | 2017 | eLife | Gene | Drug repurposing | Multiple | [7] |
| A Literature-Based Knowledge Graph Embedding Method | 2020 | PSB | Gene, Drug | Drug repurposing, Path analysis | Multiple | [8] |
| OpenBioPaper: a benchmarking framework for large-scale biomedical Paper prediction | 2020 | Bioinformatics | Gene | - | OpenBioPaper | [9] |
| Title (Shortened) | KGE Methods | Entity Types | Entity No. | Relation No. | Triple No. |
|---|---|---|---|---|---|
| Building a knowledge graph to enable precision medicine | - | - | - | - | - |
| Building a PubMed knowledge graph | - | - | - | - | - |
| Knowledge Graph-Enabled Cancer Data Analytics | - | - | - | - | 90M |
| Construction of a knowledge graph for diabetes complications | - | 10 | 59K | - | - |
| PharmKG | ConvKB | 3 | 8k | 29 | 500k |
| A global network of biomedical relationships derived from text | - | 3 | - | 36 | 2.2M |
| Systematic integration of biomedical knowledge prioritizes drugs | - | 11 | 47k | 24 | 2M |
| A Literature-Based Knowledge Graph Embedding Method | DisMult | 3 | 63k | 32 | 584k |
| OpenBioPaper |