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awesome-biomedical-knowledge-graphs
A curated list of biomedical knowledge graphs and of resources for their construction.
https://github.com/robert-haas/awesome-biomedical-knowledge-graphs
Last synced: 1 day ago
JSON representation
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Curated list
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File formats
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Biomedical knowledge graphs
- Publication (2022)
- API
- Demo
- Publication (2019)
- Data
- Publication (2022)
- Data
- Publication (2022)
- Website
- Code
- Data
- Publication (2023)
- Website
- Data
- Publication (2023)
- Website
- Data
- Publication (2024)
- Data
- Publication (2023)
- Code
- Data
- Publication (2022)
- Website
- Data
- Publication (2023)
- Website
- Data
- Publication (2023)
- Website
- Publication (2024)
- API
- Website
- Data
- Website
- Code
- Code
- Code
- Code
- Code
- Code
- Code
- Code
- Code
- Code
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Tools
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Databases
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Ontologies and controlled vocabularies
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Python package
- kgw - haas.github.io/kgw-docs) enable simple retrieving and conversion of several biomedical knowledge graphs. It is a clean reimplementation of functionality that was explored here previously in Jupyter notebooks. For example, instead of using a CSV file as intermediate format, a file-based SQLite database was chosen for faster and more flexible querying of the knowledge graph contents. This simplifies all downstream conversions and analyses. In future, a greater variety of knowledge graphs may be covered by simply adding an extraction function to get it from its web data repository and a transformation function to convert it into the shared SQLite representation. From there on, all existing conversion functions can be reused immediately. Contributions to the package are welcome and encouraged!
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Introduction
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Notebooks
Programming Languages
Categories
Sub Categories
Keywords
neo4j
4
ncats-translator
4
knowledge-graph
3
bioinformatics
3
rdf
2
monarchinitiative
2
knowledge-graphs
2
linkml
2
solr
1
sqlite
1
database
1
graph-database
1
dataset
1
graph-machine-learning
1
network-medicine
1
nlp-machine-learning
1
precision-medicine
1
semantic-web
1
python
1
linkml-schema
1
kgx
1
mkdocs
1
documentation
1
unicorns
1
resources
1
lists
1
awesome-list
1
yaml
1
standard
1
specification
1
owl
1
obofoundry
1
ncats
1
json-api
1
gene-ontology
1
datamodel
1
biolink
1
biolink-model
1
sql
1
retrieval-augmented-generation
1
rdfs
1
postgresql
1
ontology
1
framework
1
biomedical
1
biochatter
1
ai-ready
1
machine-learning
1
drug-discovery
1
data-science
1