renku-bio

This plugin extends Renku to easily annotate biological samples in Renku metadata. Samples can be annotated on either the project or dataset metadata (using --dataset).

Installation

The development version can be installed as a local Python package by running the following command from the root of the repo:

pip install -e .

The stable version is on PyPI and can be installed with pip:

pip install renku-bio

Usage

A CLI is available with entrypoint renku bio the gif belows demonstrates how to use it:

[Click to expand] Full command from example above

➜ renku bio add-sample \
    --description "Culture of liver cells from an adult mouse" \
    --age 2 \
    --taxon "Mus musculus" \
    --collector "SDSC" \
    --gender Male mouse_liver \
    --location "Lausanne" \
    --date 2022-08-10

After adding the biosample above, the project metadata graph would have the following structure:

The new "BioSample" node was created by renku bio add-sample. The information provided for sampling location, collector organization and taxon are enriched using third party APIs. For example, the "Taxon" node now has "scientificName", "taxonRank" and "parentTaxon" in addition to the name provided.

[Click to expand] Compact view of the full biosample metadata

[
        {
          "@id": "https://renkulab.io/projects/renku-bio/mouse_liver",
          "@type": "http://bioschemas.org/BioSample",
          "http://schema.org/dateCreated": "2022-08-10",
          "http://bioschemas.org/collector": {
            "@id": "https://ror.org/02hdt9m26",
            "@type": "http://schema.org/Organization",
            "http://schema.org/name": "Swiss Data Science Center"
          },
          "http://bioschemas.org/isControl": false,
          "http://bioschemas.org/locationCreated": {
            "@id": "https://renkulab.io/projects/renku-bio/mouse_liver/loc",
            "@type": "http://schema.org/Place",
            "http://schema.org/latitude": 46.5218269,
            "http://schema.org/longitude": 6.6327025,
            "http://schema.org/name": "Lausanne, District de Lausanne, Vaud, Schweiz/Suisse/Svizzera/Svizra"
          },
          "http://bioschemas.org/samplingAge": 2,
          "http://bioschemas.org/taxonomicRange": {
            "@id": "https://renkulab.io/projects/renku-bio/mouse_liver/tax",
            "@type": "http://bioschemas.org/Taxon",
            "http://bioschemas.org/parentTaxon": "Mus",
            "http://bioschemas.org/scientificName": "Mus musculus",
            "http://bioschemas.org/taxonRank": "species",
            "http://schema.org/name": "house mouse"
          },
          "http://schema.org/description": "Culture of liver cells from an adult mouse",
          "http://schema.org/gender": "Male",
          "http://schema.org/name": "mouse_liver"
        }
      ]

Current state:

Checklist:

Interactively prompt user to select relevant API result (ROR, EBI, OSM)
Use dataset annotations instead of project
Use Renku API to fetch metadata instead of CLI + subprocess
Change console entrypoint to make into a renku plugin
Add support for experimental assay (potentially with LabProtocol)
- Restructure CLI into renku bio {sample,assay} {add,ls,rm,show}
PoC to query a list of datasets (or projects) based on BioSample annotations.

Metadata

Release files for renku-bio 0.2.0

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for renku-bio 0.2.0
File	Size	Uploaded
renku-bio-0.2.0.tar.gz	12.3 kB	Oct 17, 2022	Details

Built distribution (wheel)

Table of built distributions (wheels) for renku-bio 0.2.0
File	Interpreter	ABI	Platform	Reset
renku_bio-0.2.0-py3-none-any.whl 11.9 kB Oct 17, 2022	Python 3	none	any	Details

Total release size: 24.1 kB

Release files / renku-bio-0.2.0.tar.gz

Download URL	renku-bio-0.2.0.tar.gz
Size	12.3 kB
Tags	Source
SHA-256 checksum How to use checksums	`b1b20a01c54f83993f0510cecbe9321493c2c0530479c37e12a12b6eb9d6cffb`
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Upload date	Oct 17, 2022
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`poetry/1.2.1 CPython/3.9.7 Linux/5.15.0-50-generic`

Release files / renku_bio-0.2.0-py3-none-any.whl

Download URL	renku_bio-0.2.0-py3-none-any.whl
Size	11.9 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`12372b7ea87579e404e9322c8f7d57eb15e922d5e0b7d4d2b63eb82fab65c4fa`
BLAKE2b-256 checksum How to use checksums	`34b5487cd38ff258f2450d4fce915f2717a0e8786178424efc626312af90aa58`
Upload date	Oct 17, 2022
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`poetry/1.2.1 CPython/3.9.7 Linux/5.15.0-50-generic`