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rtx-kg2-gateway

Enabling RTX-KG2 data access through various means.

https://github.com/cu-dbmi/rtx-kg2-gateway

Science Score: 52.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
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    Academic publication links
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    Academic email domains
  • ✓
    Institutional organization owner
    Organization cu-dbmi has institutional domain (medschool.cuanschutz.edu)
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.8%) to scientific vocabulary
Last synced: 9 months ago · JSON representation ·

Repository

Enabling RTX-KG2 data access through various means.

Basic Info
  • Host: GitHub
  • Owner: CU-DBMI
  • License: bsd-3-clause
  • Language: Jupyter Notebook
  • Default Branch: main
  • Size: 653 KB
Statistics
  • Stars: 0
  • Watchers: 2
  • Forks: 1
  • Open Issues: 2
  • Releases: 1
Created over 2 years ago · Last pushed about 2 years ago
Metadata Files
Readme License Citation

README.md

RTX-KG2 Gateway

Enabling RTX-KG2 data access through various means.

Overview

RTX-KG2 provides a knowledge graph composed of many different data sources. The output data from the RTX-KG2 project can benefit from the use of additional specialized graph database tools for analysis purposes. Please find a brief overview of these technologies below for a better understanding of how they're used in context with the RTX-KG2 data.

Graph Database Technologies

Installation

Python

Usage of the contents found within this repository depend on Python being available on the system. One suggested way to use and manage Python is through pyenv (there are many other ways too!). Please reference the pyproject.toml file for more information on Python versions which are compatible with this project.

Poetry environment

Please use Python poetry to run and install a Python environment related to this project. The Poetry environment for this project includes dependencies which help run IDE environments, manage the data, and run workflows. See here for more information about installing Poetry within your environment.

```bash

context: within the root of the repository

after installing poetry, create the environment

poetry install ```

Development

Running and updating Jupyter notebooks

Please follow installation steps above and then use a related Jupyter environment to open and explore the notebooks under the notebooks directory. These notebooks leverage Jupyter Lab extensions (such as jupytext) through the related Poetry environment for this repository. Usage of the notebooks outside of Jupyter Lab as an IDE may have varied experiences.

```bash

context: within the root of the repository

after creating poetry environment, run jupyter

poetry run jupyter lab ```

Executing sequences of Python modules as tasks

We use Poe the Poet to define and run tasks defined within pyproject.toml under the section [tool.poe.tasks*]. This allows for the definition and use of a task workflow when implementing multiple procedures in sequence.

For example, use the following to run the notebook_sample_data_generation task:

```bash

context: within the root of the repository

run data_prep task using poethepoet defined within pyproject.toml

poetry run poe notebooksampledata_generation ```

Existing tasks:

  • notebook_sample_data_generation: generates a sample parquet dataset and adds to a kuzu database.
  • notebook_full_data_generation: generates full dataset and adds to a kuzu database.
  • notebook_full_data_generation_with_metanames: generates full dataset with metanames specificity and adds to a kuzu database in similar fashion.

Citation and Acknowledgements

Data used by this repo includes RTX-KG2 which was published at the NCATS Biomedical Data Translator repository. Special thanks goes to those mentioned in the RTX-KG2 credits. Further data acknowledgments may be found within the data sources documentation.

Owner

  • Name: University of Colorado Department of Biomedical Informatics
  • Login: CU-DBMI
  • Kind: organization
  • Location: University of Colorado, School of Medicine, Anschutz Medical Campus

Citation (CITATION.cff) 

# CITATION.cff file for software work and references.
---
cff-version: 1.2.0
title: rtx-kg2-gateway
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: David
    family-names: Bunten
    orcid: 'https://orcid.org/0000-0001-6041-3665'
  - given-names: Negar
    family-names: Janani
    orcid: 'https://orcid.org/0009-0000-7308-926X'
  - given-names: Faisal
    family-names: Alquaddoomi
    orcid: 'https://orcid.org/0000-0003-4297-8747'
  - given-names: Casey
    family-names: Greene
    orcid: 'https://orcid.org/0000-0001-8713-9213'
repository-code: 'https://github.com/CU-DBMI/rtx-kg2-gateway'
url: 'https://github.com/CU-DBMI/rtx-kg2-gateway'
abstract: >-
  Enabling RTX-KG2 data access through various means.
keywords:
  - python
  - knowledge-graph
  - rtx-kg2
license: BSD-3-Clause
references:
  - title:  >-
      RTX-KG2: a system for building a semantically standardized knowledge graph for translational biomedicine
    type: article
    url: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-022-04932-3
    authors:
      - family-names: Wood
        given-names: E. C.
      - family-names: Glen
        given-names: Amy K.
      - family-names: Kvarfordt
        given-names: Lindsey G.
      - family-names: Womack
        given-names: Finn
      - family-names: Acevedo
        given-names: Liliana
      - family-names: Yoon
        given-names: Timothy S.
      - family-names: Ma
        given-names: Chunyu
      - family-names: Flores
        given-names: Veronica
      - family-names: Sinha
        given-names: Meghamala
      - family-names: Chodpathumwan
        given-names: Yodsawalai
      - family-names: Termehchy
        given-names: Arash
      - family-names: Roach
        given-names: Jared C.
      - family-names: Mendoza
        given-names: Luis
      - family-names: Hoffman
        given-names: Andrew S.
      - family-names: Deutsch
        given-names: Eric W.
      - family-names: Koslicki
        given-names: David
      - family-names: Ramsey
        given-names: Stephen A.
    date-released: 2022-09-29
    identifiers:
      - type: doi
        value: 10.1186/s12859-022-04932-3
    notes: >-
      RTX-KG2 data is referenced from https://github.com/ncats/translator-lfs-artifacts as part of this project.
  - title:  >-
      Kùzu Graph Database Management System
    type: software
    url: https://github.com/kuzudb/kuzu
    authors:
      - family-names: Feng
        given-names: Xiyang
      - family-names: Jin
        given-names: Guodong
      - family-names: Chen
        given-names: Ziyi
      - family-names: Liu
        given-names: Chang
      - family-names: Salihoğlu
        given-names: Semih
  - title:  DuckDB
    type: software
    url: https://github.com/duckdb/duckdb
    authors:
      - family-names: Raasveldt
        given-names: Mark
      - family-names: Muehleisen
        given-names: Hannes

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Dependencies

.github/workflows/pre-commit-checks.yaml actions
  • actions/checkout v4 composite
  • actions/setup-python v5 composite
  • pre-commit/action v3.0.0 composite
poetry.lock pypi
  • 148 dependencies
pyproject.toml pypi
  • black ^24.0.1 develop
  • isort ^5.13.0 develop
  • jupyterlab ^4.0.0 develop
  • jupyterlab-code-formatter ^2.2.1 develop
  • jupytext ^1.16.0 develop
  • awkward ^2.6.0
  • duckdb ^0.10.0
  • genson ^1.2.2
  • ijson ^3.2.3
  • kuzu ^0.3.0
  • pandas ^2.2.0
  • poethepoet ^0.24.4
  • poetry ^1.7.1
  • pyarrow ^15.0.0
  • python >=3.10,<3.13
  • requests ^2.31.0
  • tabulate ^0.9.0