It's a simple ontology matcher for building a set of cleaned ontologies. These ontologies will be used for building a knowledge graph.
When we want to build a knowledge graph, we always have a problem that the ids of entities are not consistent. The same entity may have different ids in different databases. For example, the entity "Fatigue Syndrom, Chronic" has the following ids in different databases: MESH:D015673 and DOID:8544. But they are the same entity, if we want to integrate the knowledges from different databases which may use different ids to describe the same entity, we need to match the ids of the same entity. This is the purpose of this project.
It is the fundamental step for building a knowledge graph. The knowledge graph is the basis of many applications, such as question answering, knowledge base completion, etc.
NOTICE: It's not production ready, we will continue to improve it.
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Knowledge Graph Studio: A web application for visualizing, editing and discovering knowledge graphs.
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Knowledge Graph Backend: A backend for storing and querying knowledge graph which is built for the Rapex project.
git clone https://github.com/yjcyxky/ontology-matcher.git
cd ontology-matcher
python setup.py installOutput the help information:
onto-match --help
# Usage: onto-match [OPTIONS] COMMAND [ARGS]...
# Options:
# --help Show this message and exit.
# Commands:
# ontology Convert & format ontology ids.
# knowledge Convert & format knowledges which represent as the relations between entities.
# idtypes Which ID types are supported.
# template Generate input file templateOutput the supported id types:
onto-match idtypes --help
# Usage: onto-match idtypes [OPTIONS]
# Which ID types are supported.
# Options:
# -O, --ontology-type [disease|gene]
# Ontology type [required]
# --help Show this message and exit.
onto-match idtypes -O disease
# Outpus as follows:
# OMIM
# DOIDOutput the input file template:
onto-match template --help
# Usage: onto-match template [OPTIONS]
# Generate input file template
# Options:
# -O, --ontology-type [disease|gene]
# Ontology type [required]
# -o, --output-file TEXT Path to output file [required]
# --help Show this message and exit.
onto-match template -O disease -o input.tsv
# Output as follows:
# id name label resource
# DOID:4001 ovarian carcinoma Disease DOID
# MESH:D015673 Fatigue Syndrom, Chronic Disease DOID| Entity Type | Database | Number of Entities | Plan |
|---|---|---|---|
| Disease | DOID;MESH;OMIM | 13,270 | √ |
| Gene | ENTREZ | 589,823 | √ |
| Compound/Chemical/Drug | DRUGBANK;MESH | 175,910 | √ |
| Pathway | KEGG;WIKIPATHWAYS;REACT | 2567 | √ |
| CellularComponent | GO | 1132 | √ |
| MolecularFunction | GO | 2068 | √ |
| BiologicalProcess | GO | 9072 | √ |
| Anatomy | UBERON;MESH | 1844 | √ |
| PharmacologicClass | HETIONET;NDF-RT | 45,605 | √ |
| Protein | Copy from CKG | ||
| SideEffect | To be continued | ||
| Metabolite | To be continued | ||
| Symptom | To be continued |
| Relation Type | Database | Number of Relations | Plan |
|---|