Rseng Data Management

Research data management for software projects

Most research software exists to turn input data into output data, yet data is routinely the least managed part of the project: undocu- mented CSVs, 2GB files in git, results nobody can regenerate. Treat data as a first-class research output with the same care as code - versioned, documented, licensed and citable. FAIR applies to data even more directly than to software (rseng-fair-software covers the software side; the principles at go-fair.org are the shared root).

Project layout and the data/code boundary

• Separate raw, intermediate and final data explicitly - e.g.

data/raw/, data/processed/, results/ - and treat raw data as READ-ONLY: nothing ever edits a raw file in place; all cleaning is scripted so the pipeline can regenerate everything downstream (rseng-workflows).

• Keep the mapping from data to code explicit: which script produces

which file, recorded in the workflow or a Makefile, not in memory.

• Configuration, not hard-coded paths: data locations belong in a

config file or environment variable so the project runs outside its author's laptop (rseng-reproducible-environments).

Keeping data out of git - but versioned

Git is for text; repositories bloat permanently with every committed binary revision. Before a large or binary data file lands in git, intervene:

• Small, stable reference data (kilobytes, test fixtures) may live in

the repository - that is fine and convenient.

• For everything else use a data versioning layer: DVC or git-annex

track content by hash in git while the bytes live in ordinary storage; DataLad builds full dataset management on git-annex and is widespread in neuroscience and beyond. All three keep code and data revisions linked, which is the actual requirement: "which data did commit X use?" must have an answer.

• Published, frozen inputs are often best NOT copied at all: record

the DOI or URL plus a checksum, and fetch in a scripted step.

• Git LFS exists but suits media assets better than evolving research

data; hosting quotas bite and history stays coupled to one forge.

Documenting a dataset

A dataset without documentation is a puzzle, not a resource. Minimum per dataset:

• A README (or datasheet) stating: what the data is, how it was

collected or generated, its units, coordinate systems and conventions, known limitations, license, and how to cite it.

• A data dictionary for tabular data: every column's name, type,

units, allowed values and meaning. Generate it from the data where possible so it cannot drift silently.

• Formats: prefer open, well-specified formats (CSV with a stated

dialect, Parquet, HDF5, NetCDF, domain standards) over proprietary ones; for domain metadata standards and format registries, point users to FAIRsharing and the ELIXIR RDMkit rather than inventing a schema ad hoc.

Depositing, DOIs and citation

Data that supports a publication belongs in a data repository, not in supplementary ZIPs or the code repo:

• Zenodo is the general-purpose default (free, DOI per version,

versioned records); domain repositories are better when one exists - RDMkit and FAIRsharing list them per field.

• Give the dataset its own DOI and its own citation entry; link data

DOI and software DOI both ways so each cites the other (rseng-citation-metadata, rseng-publishing-releasing).

• License the data explicitly - and note that code licenses do not

fit data well: CC0 or CC-BY are the common choices for open data, while ODbL and domain-specific terms exist for databases (rseng-licensing). "No license" means "all rights reserved", for data exactly as for code.

Sensitive and personal data

When data involves people, patients, protected locations or commercial restrictions:

• Never commit sensitive data, even briefly - git history is forever

and forges cache aggressively. Add ignore rules and pre-commit guards BEFORE the first sensitive file exists in the project.

• Keep sensitive data in the access-controlled storage the

institution provides; the repository carries only synthetic or anonymized samples plus the code that ran on the real thing.

• Anonymization is a research task, not a rename: removing names is

not de-identification. Route the user to their data steward or ethics board rather than improvising GDPR compliance.

• A data management plan (DMP) may already govern the project - ask;

when one exists it decides storage, retention and sharing, and the software should implement it rather than contradict it. Writing and maintaining DMPs is rseng-data-management-plans.

Records and transparency

When AI assistance produced or transformed datasets, record it in the project's AI declaration - dataset entries are a supported content type in aidecl.yaml (rseng-ai-declaration). Data provenance and AI provenance are the same habit applied to different artifacts.

Working with this skill

This skill is source-independent: its authority is the FAIR data principles and the community resources linked below.

Learn more (verified):

• https://www.gofair.foundation/fair-principles - the FAIR principles
• https://rdmkit.elixir-europe.org - ELIXIR RDMkit, per-domain and

per-task RDM guidance

• https://fairsharing.org - registry of metadata standards and

data repositories

• https://zenodo.org - general-purpose data repository with DOIs
• https://dvc.org - Data Version Control
• https://www.datalad.org - DataLad dataset management

Related skills

Check whether any of these applies before moving on:

• rseng-archiving - long-term data deposit
• rseng-citation-metadata - data DOIs and two-way citation
• rseng-data-management-plans - funder plan over the practice
• rseng-regulatory-compliance - sensitive and personal data obligations
• rseng-scientific-file-formats - choosing and engineering the format
• rseng-workflows - scripted regeneration of derived data

Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

• Author: fdiblen
• Source: fdiblen/rseng-agent-skills
• License: MIT

Install and usage instructions live in the source repository linked above.