pmc-publication-metadata
A Snakemake workflow to produce accessible datasets for PMC publication metadata
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Repository
A Snakemake workflow to produce accessible datasets for PMC publication metadata
Basic Info
- Host: GitHub
- Owner: sdruskat
- Language: Python
- Default Branch: main
- Size: 65.4 KB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 1
Metadata Files
README.md
Snakemake workflow: Extract LUTs from PMC OA non-commercial, commercial and other bulk metadata
A Snakemake workflow for extracting accessible lookup tables for PMC publication dates.
The workflow attempts to extract the earliest publication date for each publication from
the metadata and maps them to publication identifiers. The lookup tables are in JSON,
where identifiers have the format PMC<numerical identifier and dates have the format
YYYY[-MM[-DD]].
json
{
"PMC1234567": "2020-02-20",
"PMC1234568": "2020-02",
"PMC1234569": "2020"
}
Documentation
The technical documentation and description of outputs is in workflow/documentation.md.
Running the workflow
You need to have conda installed to create and activate a new environment.
bash
conda env create -n pmc-metadata --file conda-environment.yaml
conda activate pmc-metadata
Run with -–keep-storage-local-copies to avoid downloading resources over and over again.
Also run with --software-deployment-method conda to use global conda packages.
shell
snakemake --keep-storage-local-copies --software-deployment-method conda -c <number-of-cores-to-use>
You can use run.sh to run the workflow this way, and with 12 cores.
Running on a cluster with Slurm
Create a Snakemake profile, then run as follows.
```yaml
~/.config/snakemake//config.v8+.yaml
executor: slurm jobs: 100 local-storage-prefix: /scratch/$USER/snakemake-scratch latency-wait: 300 default-resources: slurmpartition: cpu nodes: 1 tasks: 1 cpusper_task: 1 ```
shell
nohup snakemake --keep-storage-local-copies --software-deployment-method conda --profile <profilename> --directory <working directory> --configfile config/config.yml &
Citation
If you use this workflow in your work, please cite it using the metadata provided in CITATION.cff.
License
This work is licensed as specific in the REUSE 3.0 Specification. Please consult the single file licenses.
Owner
- Name: Stephan Druskat
- Login: sdruskat
- Kind: user
- Location: Berlin
- Company: German Aerospace Center (DLR)
- Website: http://sdruskat.net
- Twitter: stdruskat
- Repositories: 12
- Profile: https://github.com/sdruskat
Software Engineering PhD candidate @DLR-SC, Research Software Engineer (https://hexatomic.github.io)
Citation (CITATION.cff)
# SPDX-FileCopyrightText: 2024 German Aerospace Center (DLR)
# SPDX-FileContributor: Stephan Druskat <stephan.druskat@dlr.de>
#
# SPDX-License-Identifier: CC0-1.0
# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!
cff-version: 1.2.0
title: PMC metadata extraction workflow
message: >-
If you use this software, please cite it using the
metadata from this file.
type: software
authors:
- given-names: Stephan
family-names: Druskat
email: stephan.druskat@dlr.de
affiliation: German Aerospace Center (DLR)
orcid: 'https://orcid.org/0000-0003-4925-7248'
abstract: >-
A Snakemake workflow for extracting metadata for PMC
publications.
license: MIT
version: 0.1.0
date-released: '2024-05-27'
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Top Committers
| Name | Commits | |
|---|---|---|
| Stephan Druskat | s****t@d****e | 87 |
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