OptimusKG
A modern multimodal knowledge graph with type-specific metadata across biomedical domains.
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최종 버전 다운로드 (.zip)- SKILL.md
- SKILL.md
- SKILL.md
- SKILL.md
- SKILL.md
- SKILL.md
- cognitive-load.md
- heuristics-scoring.md
- personas.md
- SKILL.md
- SKILL.md
- SKILL.md
- SKILL.md
- color-and-contrast.md
- craft.md
- extract.md
- interaction-design.md
- motion-design.md
- responsive-design.md
- spatial-design.md
- typography.md
- ux-writing.md
- cleanup-deprecated.mjs
- SKILL.md
- SKILL.md
- SKILL.md
- SKILL.md
- SKILL.md
- SKILL.md
- SKILL.md
- color_palettes.py
- nature.mplstyle
- presentation.mplstyle
- publication.mplstyle
- color_palettes.md
- journal_requirements.md
- matplotlib_examples.md
- publication_guidelines.md
- figure_export.py
- style_presets.py
- SKILL.md
- SKILL.md
- output-patterns.md
- workflows.md
- init_skill.py
- package_skill.py
- quick_validate.py
- LICENSE.txt
- SKILL.md
- SKILL.md
- adapt
- animate
- audit
- bolder
- clarify
- colorize
- critique
- delight
- distill
- grill-me
- impeccable
- layout
- optimize
- overdrive
- polish
- quieter
- shape
- typeset
- settings.json
- ci.yml
- publish-pypi.yml
- release.yml
- dependabot.yml
- charts-bar-chart.tsx
- text-animations-typewriter.tsx
- text-animations-word-highlight.tsx
- 3d.md
- animations.md
- assets.md
- audio-visualization.md
- audio.md
- calculate-metadata.md
- can-decode.md
- charts.md
- compositions.md
- display-captions.md
- extract-frames.md
- ffmpeg.md
- fonts.md
- get-audio-duration.md
- get-video-dimensions.md
- get-video-duration.md
- gifs.md
- images.md
- import-srt-captions.md
- light-leaks.md
- lottie.md
- maps.md
- measuring-dom-nodes.md
- measuring-text.md
- parameters.md
- sequencing.md
- sfx.md
- silence-detection.md
- subtitles.md
- tailwind.md
- text-animations.md
- timing.md
- transcribe-captions.md
- transitions.md
- transparent-videos.md
- trimming.md
- videos.md
- voiceover.md
- SKILL.md
- remotion-best-practices
- remotion-best-practices
- anatomy.svg
- molecular-function.svg
- phenotype.svg
- schema.webp
- chime.mp3
- pop.mp3
- swish.mp3
- swoosh.mp3
- tick.mp3
- type-key.mp3
- song.mp3
- fade-ramp.ts
- halo-dots.ts
- highlight-sweep.ts
- hold-and-exit.ts
- index.ts
- internal.ts
- iris-wipe.ts
- letter-spacing-collapse.ts
- line-draw.ts
- number-ticker.ts
- particle-swarm.ts
- spring-in.ts
- typewriter.ts
- use-staggered.ts
- window-slide-in.ts
- bullet-reveal.tsx
- hero-line.tsx
- logo.tsx
- scene.tsx
- stat-ticker.tsx
- word-by-word-text.tsx
- graph.tsx
- hook-text.tsx
- index.tsx
- index.tsx
- url.tsx
- index.tsx
- logo-mark.tsx
- snippet.tsx
- heading.tsx
- index.tsx
- index.tsx
- introducing.tsx
- wordmark.tsx
- figure.tsx
- heading.tsx
- index.tsx
- cloud.tsx
- heading.tsx
- index.tsx
- index.tsx
- stats.tsx
- circle.tsx
- heading.tsx
- index.tsx
- paper-qa.tsx
- heading.tsx
- index.tsx
- window.tsx
- heading.tsx
- index.tsx
- index.ts
- index.ts
- sfx.tsx
- composition.tsx
- index.css
- index.ts
- root.tsx
- tokens.ts
- .gitignore
- .prettierrc
- eslint.config.mjs
- package-lock.json
- package.json
- pnpm-lock.yaml
- README.md
- remotion.config.ts
- tsconfig.json
- optimuskg-logo.svg
- optimuskg.mp4
- __init__.py
- centrality.py
- paperqa.py
- paperqa_figures.py
- power.py
- sample_edges.py
- utils.py
- __init__.py
- adjacency_heatmap.py
- ccdf_degree_distribution.py
- closeness_centrality.py
- degree_distribution.py
- metaedge_bubble_plot.py
- metapath_counts.py
- property_type_distribution.py
- registry.py
- style.py
- __init__.py
- edges.py
- nodes.py
- utils.py
- __init__.py
- schema.py
- types.py
- __init__.py
- __main__.py
- biocypher_config.yaml
- schema_config.yaml
- gene_expressions_in_anatomy.yml
- ctd_exposure_events.yml
- disgenet_diseases.yml
- disgenet_phenotypes.yml
- drug_drug.yml
- drug_gene.yml
- vocabulary.yml
- disease.yml
- drug.yml
- drug_disease.yml
- drug_phenotype.yml
- phenotype.yml
- gene_names.yml
- high_confidence.yml
- go_relations.yml
- go_terms.yml
- hp_relations.yml
- hp_terms.yml
- hp_xrefs.yml
- mondo_relations.yml
- mondo_terms.yml
- mondo_xrefs.yml
- uberon_relations.yml
- uberon_terms.yml
- chembl_drugbank_mapping.yml
- disease.yml
- disease_mappings.yml
- disease_phenotype.yml
- drug_indication.yml
- drug_mechanism_of_action.yml
- drug_molecule.yml
- ensembl_ncbi_mapping.yml
- target.yml
- target_disease_associations.yml
- gene_gene.yml
- reactome_relations.yml
- reactome_terms.yml
- kg.yml
- homo_sapiens_expressions_advanced.yml
- ctd_exposure_events.yml
- disgenet.yml
- full_database.yml
- gene_map.yml
- polypeptide_ids.yml
- vocabulary.yml
- psql_dump.yaml
- gene_names.yml
- high_confidence.yml
- vocab_meddra_adverse_effect.yml
- vocab_rxnorm_ingredient.yml
- biolink.yml
- disease.yml
- go.yml
- hp.yml
- mondo.yml
- orphanet.yml
- uberon.yml
- disease.yml
- disease_phenotype.yml
- drug_indication.yml
- drug_mechanism_of_action.yml
- drug_molecule.yml
- target.yml
- target_disease_associations.yml
- protein_protein.yml
- reactome_pathways.yml
- reactome_pathways_relation.yml
- anatomy_anatomy.yml
- anatomy_gene.yml
- biological_process_biological_process.yml
- biological_process_gene.yml
- cellular_component_cellular_component.yml
- cellular_component_gene.yml
- disease_disease.yml
- disease_gene.yml
- disease_phenotype.yml
- drug_biological_process.yml
- drug_disease.yml
- drug_drug.yml
- drug_gene.yml
- drug_phenotype.yml
- exposure_biological_process.yml
- exposure_cellular_component.yml
- exposure_disease.yml
- exposure_exposure.yml
- exposure_gene.yml
- exposure_molecular_function.yml
- gene_gene.yml
- molecular_function_gene.yml
- molecular_function_molecular_function.yml
- pathway_gene.yml
- pathway_pathway.yml
- phenotype_gene.yml
- phenotype_phenotype.yml
- anatomy.yml
- biological_process.yml
- cellular_component.yml
- disease.yml
- drug.yml
- exposure.yml
- gene.yml
- molecular_function.yml
- pathway.yml
- phenotype.yml
- evals.yml
- parameters.yml
- .gitkeep
- logging.yml
- .gitkeep
- edges.mdx
- meta.json
- nodes.mdx
- index.mdx
- meta.json
- reference.mdx
- citation.mdx
- funding.mdx
- index.mdx
- license.mdx
- mcp-bundle.mdx
- meta.json
- showcase.mdx
- calculator.png
- calendar.png
- editor.svg
- finder.png
- mail.png
- music.png
- notes.png
- photos.png
- safari.png
- terminal.png
- anatomy-dark.svg
- anatomy-light.svg
- biological-process-dark.svg
- biological-process-light.svg
- cellular-component-dark.svg
- cellular-component-light.svg
- code-library.svg
- data-pipeline.webp
- disease-dark.svg
- disease-light.svg
- drug-dark.svg
- drug-light.svg
- exposure-dark.svg
- exposure-light.svg
- figure.webp
- gene-dark.svg
- gene-light.svg
- molecular-function-dark.svg
- molecular-function-light.svg
- pathway-dark.svg
- pathway-light.svg
- phenotype-dark.svg
- phenotype-light.svg
- hillside-village.png
- lakeside-village.png
- mountain-overlook.png
- valley-stream.png
- logo.svg
- generate-docs.mjs
- schema-tab-content.tsx
- index.tsx
- themed-svg-tab-content.tsx
- index.tsx
- index.tsx
- shiki-block.tsx
- shiki-themes.ts
- index.tsx
- snippet.tsx
- index.tsx
- index.tsx
- editor-window.tsx
- mac-os-dock.tsx
- index.tsx
- tabbed-editor.tsx
- window-tabbed-editor.tsx
- index.tsx
- menu-toggle-icon.tsx
- index.tsx
- code-block.tsx
- cta-section.tsx
- download-button.tsx
- footer.tsx
- hero-section.tsx
- stats-scroller.tsx
- tree.tsx
- landing.css
- layout.tsx
- opengraph-image.tsx
- page.tsx
- route.ts
- page.tsx
- docs.css
- layout.tsx
- route.ts
- route.ts
- route.ts
- route.tsx
- global.css
- icon.svg
- layout.tsx
- citation-block.tsx
- docs-schema-tree.tsx
- index.tsx
- tree.tsx
- index.tsx
- logo.tsx
- markdown.tsx
- cn.ts
- layout-shared.tsx
- shared.ts
- source.ts
- .gitignore
- .mise.toml
- biome.jsonc
- next.config.mjs
- package.json
- pnpm-lock.yaml
- pnpm-workspace.yaml
- postcss.config.mjs
- proxy.ts
- README.md
- source.config.ts
- tsconfig.json
- vercel.json
- __init__.py
- data.py
- db.py
- index.py
- profiling.py
- schema.py
- server.py
- tools.py
- run_stdio.py
- conftest.py
- test_benchmark.py
- test_tools.py
- .gitignore
- .mcpbignore
- build.py
- icon.png
- manifest.json
- pyproject.toml
- README.md
- uv.lock
- quickstart.ipynb
- __init__.py
- json_dataset.py
- parquet_dataset.py
- __init__.py
- docker-compose.yaml
- sqldump_query_dataset.py
- __init__.py
- lxml_dataset.py
- owl_dataset.py
- zip_dataset.py
- __init__.py
- base.py
- bioontology.py
- drugbank.py
- http.py
- opentargets.py
- __init__.py
- origin_hooks.py
- __init__.py
- checksum_hooks.py
- quality_checks_hooks.py
- __init__.py
- drug_drug.py
- drug_gene.py
- vocabulary.py
- __init__.py
- go.py
- hp.py
- mondo.py
- uberon.py
- __init__.py
- chembl_drugbank_mapping.py
- disease.py
- disease_mappings.py
- disease_phenotype.py
- drug_indication.py
- drug_mechanism_of_action.py
- drug_molecule.py
- ensembl_ncbi_mapping.py
- target.py
- target_disease_associations.py
- __init__.py
- reactome_pathways.py
- __init__.py
- bgee.py
- ctd.py
- disgenet.py
- drugcentral.py
- gene_names.py
- onsides.py
- ppi.py
- __init__.py
- pipeline.py
- __init__.py
- neo4j.py
- parquet.py
- __init__.py
- export_kg.py
- __init__.py
- biocypher.py
- __init__.py
- pipeline.py
- __init__.py
- anatomy_anatomy.py
- anatomy_gene.py
- biological_process_biological_process.py
- biological_process_gene.py
- cellular_component_cellular_component.py
- cellular_component_gene.py
- disease_disease.py
- disease_gene.py
- disease_phenotype.py
- drug_biological_process.py
- drug_disease.py
- drug_drug.py
- drug_gene.py
- drug_phenotype.py
- exposure_biological_process.py
- exposure_cellular_component.py
- exposure_disease.py
- exposure_exposure.py
- exposure_gene.py
- exposure_molecular_function.py
- gene_gene.py
- molecular_function_gene.py
- molecular_function_molecular_function.py
- pathway_gene.py
- pathway_pathway.py
- phenotype_gene.py
- phenotype_phenotype.py
- utils.py
- __init__.py
- anatomy.py
- biological_process.py
- cellular_component.py
- disease.py
- drug.py
- exposure.py
- gene.py
- molecular_function.py
- pathway.py
- phenotype.py
- __init__.py
- constants.py
- __init__.py
- pipeline.py
- __init__.py
- __init__.py
- dry_runner.py
- parallel_runner.py
- __init__.py
- __main__.py
- pipeline_registry.py
- py.typed
- settings.py
- utils.py
- __init__.py
- _config.py
- _dataverse.py
- _graph.py
- _paths.py
- api.py
- conftest.py
- test_api.py
- test_config.py
- test_dataverse.py
- test_graph.py
- test_paths.py
- .gitignore
- LICENSE
- pyproject.toml
- README.md
- uv.lock
- download_landing.sh
- neo4j_entrypoint.sh
- graph-schema.md
- SKILL.md
- .dockerignore
- .gitignore
- .pre-commit-config.yaml
- .python-version
- .telemetry
- AGENTS.md
- CLAUDE.md
- CONTRIBUTING.md
- docker-compose.yaml
- LICENSE
- Makefile
- pyproject.toml
- README.md
- skills-lock.json
- uv.lock
# 설치 가이드
1. 코드 내려받기
git clone https://github.com/mims-harvard/OptimusKG
깃허브에서 프로젝트 코드 전체를 내 컴퓨터로 내려받습니다.
cd OptimusKG
방금 내려받은 프로젝트 폴더 안으로 이동합니다.
2. 공식 설치 스크립트
쉬움 추천사전 준비물
- Python 3 pip 명령어를 쓰려면 Python이 필요합니다.
pip install optimuskg
PyPI에 배포된 패키지를 바로 설치합니다. 소스 클론이 필요 없습니다.
설치 후 새 터미널을 열고, 프로그램의 버전 확인 명령(예: --version)으로 정상 설치됐는지 확인하세요.
이 레포의 README에 적힌 실제 명령어를 그대로 가져왔습니다.
3. Docker
쉬움사전 준비물
- Git GitHub에서 프로젝트 코드를 내려받으려면 필요합니다.
- Docker Desktop 컨테이너를 빌드하고 실행하려면 필요합니다. 설치 후 실행해서 백그라운드에 켜두세요.
docker compose up -d --build
정의된 모든 컨테이너(서버, DB 등)를 한 번에 빌드하고 백그라운드에서 실행합니다.
터미널에 docker compose ps 를 입력해 컨테이너들이 Up 상태인지 확인하세요. README에 포트 번호가 적혀있다면 브라우저에서 http://localhost:포트번호 로 접속해보세요.
4. Node.js
쉬움사전 준비물
⚠️ 이 프로젝트는 규모가 큰 저장소라, 이 방법이 실제 핵심 제품이 아니라 내부 하위 패키지를 가리키는 것일 수 있습니다. README 전체를 함께 확인해보세요.
cd assets/remotion
이 프로젝트의 관련 파일이 하위 폴더 안에 있어서, 먼저 그 폴더로 이동합니다.
npm install
package.json에 명시된 라이브러리들을 내려받아 설치합니다.
npm start
개발/실행 서버를 켭니다.
명령어 실행 후 터미널에 나타나는 주소(보통 http://localhost:3000 형태)를 브라우저에서 열어보세요.
5. Python
쉬움사전 준비물
pip install optimuskg
PyPI에 배포된 패키지를 바로 설치합니다. 소스 클론이 필요 없습니다.
에러 메시지 없이 실행되고 터미널에 안내 문구가 출력되면 정상입니다.
이 레포의 README에 적힌 실제 명령어를 그대로 가져왔습니다.
6. Make
보통사전 준비물
- Git GitHub에서 프로젝트 코드를 내려받으려면 필요합니다.
- Make Linux/macOS는 보통 기본 설치되어 있습니다. Windows는 별도 설치(예: MSYS2, WSL)가 필요합니다.
make
생성된 빌드 설정을 바탕으로 실제 컴파일을 진행해 실행 파일을 만듭니다.
에러 없이 끝나면 성공입니다. 생성된 실행 파일을 직접 실행해보세요.
// repository documentation
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