README.md

# DEEP Computational Metadata

## Identification

This repository can be cited in publications using the following DOI:

[DOI: 10.17617/1.2W](http://doi.org/10.17617/1.2W "https://github.molgen.mpg.de/DEEP/comp-metadata")

Also consider citing the corresponding publication listed under *References*.

## Process documentation

In DEEP, standardized computational analysis pipelines are documented in form of so-called *Process* specifications.
A *Process* document lists required input and reference files, specifies the output generated by the pipeline and
provides a step-by-step description of the computational analysis.
*Processes* are in XML format and are rendered into a readable form when opened in a standard web browser
(assuming an active internet connection). They are lightweight enough to be send via e-mail to collaboration partners.

[Proceed to Process documents](docs/)

## Creating and validating Process documents

If you want to document a new analysis type, i.e., a standardized pipeline, or if you just want to document
an analysis specific for a DEEP publication, you can download the *Process* template file
and some basic introductory material in this repository:

[Proceed to Process template](template/)

## Analysis documentation

Each run of a standardized pipeline is supposed to produce an *Analysis* metadata document at the end
(named like this: `DEEP-ID.PROCESS.DATE.amd.tsv`). These are simple tab-separated text files listing all input,
output and reference files as well as non-default parameters in form of *key-value* entries.
Whereas a *Process* document has to be manually created and describes an analysis pipeline in generic form,
an *Analysis* metadata file is created automatically. Consequently, these files are not accessible via this repository.

If you are looking for the *Analysis* metadata files, please refer to the official [DEEP data portal](http://deep.dkfz.de) hosted
by the DEEP *Data Collection Center* (DCC - DKFZ Heidelberg).

## References
See the corresponding publication in Oxford Database for details:

["A general concept for consistent documentation of computational analyses", *Database* 2015](https://dx.doi.org/10.1093/database/bav050)

The [supplemental material](publication/) is also available in this repository. Please note that this material is just kept for reference, and is considered outdated. Please **do not use it** to create new *Process* documents.