cimr-d: client and database for continuously integrated metaresource

cimr-d is not yet ready for public use! check back for updates and public releases

YoSon Park <cimrroot at gmail dot com>

Using data in cimr-d

If you are looking for processed files, you do not need to clone the cimr-d GitHub repository. All information you need is provided in the catalog.txt, which you can download by clicking the link and viewing raw file or by typing the following in a terminal:

wget https://raw.githubusercontent.com/greenelab/cimr-d/master/catalog.txt

Cloning the full repository will not download all data stored in the cimr-d Google Cloud Storage bucket. So you may safely clone the repository to keep a local copy of the catalog:

git clone git@github.com:greenelab/cimr-d.git

Frequent pulling is recommended as cimr-d may be updated with new or improved information:

cd cimr-d
git pull

While data processing can be streamlined, any data used in research studies should be carefully reviewed in the context of its original publication. To make this as convenient as possible, we provide doi of each citable publication in the catalog.txt, .bib file to be used in the bibtex directory, and the full reference.

Regarding Licence and Usage of cimr-d

All citations and references for data stored in cimr-d are added to cimr-d references. Recommended acknowledgement and citation information from the original data providers are available as a guideline.

All data deposited here have been either

• contributed by researchers who own the copyright or license to the data, or
• reprocessed and deposited from a public source.

We take every caution to make sure data stored and used via cimr-d suite are approved for public sharing and reuse for research purposes. If any data currently available here require more strict licenses, different citation/acknowledgement rules, or any special usage guidelines, contact us and we will take appropriate actions.

For cimr usage independent of cimr-d, see the cimr manual. For any PR including new data, we strongly recommend including appropriate citations, metadata and other relevant information regarding the data to be added to cimr citations.

Contributing data

cimr-d is built to be a community resource and benefits greatly by contributors of all levels, from research data to development. For details regarding how to contribute data to cimr-d, please see the cimr-d contributions doc.

Briefly,:

1. make a GitHub account
2. fork this repository
3. clone the forked repository
4. copy your yaml file(s) into the "submitted" directory
5. use git commands to add, commit and push your changes to the forked repository

cimr-d references

• If you find cimr and cimr-d useful, please cite:
  • Park Y., Hu D. & Greene C., (2019). "Deciphering complex trait genetics using a continuously integrated meta-resource, cimr-d", Manuscript in Preparation
  • Park Y. (2019), cimr, https://github.com/greenelab/cimr