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توضیحات

Get metadata and ontological information about all biomedical entities.

ویژگی	مقدار
سیستم عامل	OS Independent
نام فایل	biolookup-0.2.0
نام	biolookup
نسخه کتابخانه	0.2.0
نگهدارنده	['Charles Tapley Hoyt']
ایمیل نگهدارنده	['cthoyt@gmail.com']
نویسنده	Charles Tapley Hoyt
ایمیل نویسنده	cthoyt@gmail.com
آدرس صفحه اصلی	https://github.com/biopragmatics/biolookup
آدرس اینترنتی	https://pypi.org/project/biolookup/
مجوز	MIT

<p align="center"> <img alt="Biolookup Service logo" src="https://github.com/biopragmatics/biolookup/raw/main/src/biolookup/app/static/logo.svg" height="150"> </p> <h1 align="center"> Biolookup </h1> <p align="center"> <a href="https://github.com/biopragmatics/biolookup/actions?query=workflow%3ATests"> <img alt="Tests" src="https://github.com/biopragmatics/biolookup/workflows/Tests/badge.svg" /> </a> <a href="https://github.com/cthoyt/cookiecutter-python-package"> <img alt="Cookiecutter template from @cthoyt" src="https://img.shields.io/badge/Cookiecutter-python--package-yellow" /> </a> <a href="https://pypi.org/project/biolookup"> <img alt="PyPI" src="https://img.shields.io/pypi/v/biolookup" /> </a> <a href="https://pypi.org/project/biolookup"> <img alt="PyPI - Python Version" src="https://img.shields.io/pypi/pyversions/biolookup" /> </a> <a href="https://github.com/biopragmatics/biolookup/blob/main/LICENSE"> <img alt="PyPI - License" src="https://img.shields.io/pypi/l/biolookup" /> </a> <a href='https://biolookup.readthedocs.io/en/latest/?badge=latest'> <img src='https://readthedocs.org/projects/biolookup/badge/?version=latest' alt='Documentation Status' /> </a> <a href="https://zenodo.org/badge/latestdoi/400996921"> <img src="https://zenodo.org/badge/400996921.svg" alt="DOI"> </a> <a href='https://github.com/psf/black'> <img src='https://img.shields.io/badge/code%20style-black-000000.svg' alt='Code style: black' /> </a> <a href="https://github.com/biopragmatics/bioregistry"$> <img alt="Powered by the Bioregistry" src="https://img.shields.io/static/v1?label=Powered%20by&message=Bioregistry&color=BA274A&style=flat&logo=image/png;base64,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" /> </a> </p> Get metadata and ontological information about biomedical entities. ### 🔍 Querying the Biolookup Service The Biolookup Service has an endpoint `/api/lookup/<curie>` for retrieving metadata and ontological information about a biomedical entity via its compact identifier (CURIE). ```python import requests res = requests.get("http://localhost:5000/api/lookup/doid:14330").json() assert res["name"] == "Parkinson's disease" assert res["identifier"] == "14330" assert res["prefix"] == "doid" assert res["definition"] is not None # not shown for brevity ``` The [INDRA Lab](https://indralab.github.io) hosts an instance of the Biolookup Service at http://biolookup.io, so you can alternatively use `http://biolookup.io/api/lookup/doid:14330`. The same can be accomplished using the `biolookup` package: ```python import biolookup res = biolookup.lookup("doid:14330") assert res["name"] == "Parkinson's disease" # ... same as before ``` If you've configured the `BIOLOOKUP_SQLALCHEMY_URI` environment variable (or any other valid way with [`pystow`](https://github.com/cthoyt/pystow) to point directly at the database for an instance of the Biolookup Service, it will make a direct connection to the database instead of using the web-based API. ### 🕸️ Running the Lookup App You can run the lookup app in local mode with: ```shell $ biolookup web --lazy ``` This means that the in-memory data from `pyobo` are used. If you have a large external database, you can run in remote mode with the `--sql` flag: ```shell $ biolookup web --sql --uri postgresql+psycopg2://postgres:biolookup@localhost:5434/biolookup ``` If `--uri` is not given for the `web` subcommand, it uses `pystow.get_config("biolookup", "sqlalchemy_uri)`to look up from `BIOLOOKUP_SQLALCHEMY_URI` or in `~/.config/biolookup.ini`. If none is given, it defaults to a SQLite database in `~/.data/biolookup/biolookup.db`. ### 🗂️ Load the Database ```shell $ biolookup load --uri postgresql+psycopg2://postgres:biolookup@localhost:5434/biolookup ``` If `--uri` is not given for the `load` subcommand, it uses `pystow.get_config("biolookup", "sqlalchemy_uri)`to look up from `BIOLOOKUP_SQLALCHEMY_URI` or in `~/.config/biolookup.ini`. If none is given, it creates a defaults a SQLite database at `~/.data/biolookup/biolookup.db`. ## 🚀 Installation The most recent release can be installed from [PyPI](https://pypi.org/project/biolookup/) with: ```bash $ pip install biolookup ``` The most recent code and data can be installed directly from GitHub with: ```bash $ pip install git+https://github.com/biopragmatics/biolookup.git ``` To install in development mode, use the following: ```bash $ git clone git+https://github.com/biopragmatics/biolookup.git $ cd biolookup $ pip install -e . ``` ## 👐 Contributing Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See [CONTRIBUTING.rst](https://github.com/biopragmatics/biolookup/blob/master/CONTRIBUTING.rst) for more information on getting involved. ## 👀 Attribution ### ⚖️ License The code in this package is licensed under the MIT License.  ### 🎁 Support The Biolookup Service was developed by the [INDRA Lab](https://indralab.github.io), a part of the [Laboratory of Systems Pharmacology](https://hits.harvard.edu/the-program/laboratory-of-systems-pharmacology/about/) and the [Harvard Program in Therapeutic Science (HiTS)](https://hits.harvard.edu) at [Harvard Medical School](https://hms.harvard.edu/). ### 💰 Funding This project has been supported by the following grants: | Funding Body | Program | Grant | |----------------------------------------------------------|-------------------------------------------------------------------------------------------------------------------------------|-----------------| | DARPA | [Automating Scientific Knowledge Extraction (ASKE)](https://www.darpa.mil/program/automating-scientific-knowledge-extraction) | HR00111990009 | ### 🍪 Cookiecutter This package was created with [@audreyfeldroy](https://github.com/audreyfeldroy)'s [cookiecutter](https://github.com/cookiecutter/cookiecutter) package using [@cthoyt](https://github.com/cthoyt)'s [cookiecutter-snekpack](https://github.com/cthoyt/cookiecutter-snekpack) template.

نیازمندی

مقدار	نام
-	tqdm
-	click
-	more-click
>=0.6.3	pyobo
-	flask
-	bootstrap-flask
-	flasgger
-	psutil
-	sqlalchemy
-	psycopg2-binary
-	tabulate
-	sphinx
-	sphinx-rtd-theme
-	sphinx-click
-	sphinx-autodoc-typehints
-	sphinx-automodapi
-	pytest
-	coverage

زبان مورد نیاز

مقدار	نام
>=3.8	Python

نحوه نصب

نصب پکیج whl biolookup-0.2.0:

pip install biolookup-0.2.0.whl

نصب پکیج tar.gz biolookup-0.2.0:

pip install biolookup-0.2.0.tar.gz