Chemistry Data Repositories and Databases

Last updated on 2026-03-24 | Edit this page

Overview

Questions

  • Where should I deposit chemistry data to make it findable and reusable?
  • What chemistry-specific repositories exist and what do they accept?
  • What should I do when my paper includes several different types of data?

Objectives

  • Identify domain-specific repositories for chemistry data
  • Understand when to use a specialist repository rather than a general-purpose one
  • Decide how to handle data deposits when a paper involves multiple data types
  • Find and evaluate a chemistry repository relevant to your own research area

Why Use a Chemistry-Specific Repository?

You can deposit almost any data in a general-purpose repository like Zenodo or Figshare, satisfy most funder requirements, and obtain a DOI. So why bother with a domain-specific repository?

The answer is discoverability and reusability. A general repository stores your files and mints a DOI, but a chemistry-specific repository understands your data. It can index compounds by chemical structure, enforce community metadata standards, validate file formats, and link your deposition directly to established databases. A crystal structure deposited in the Cambridge Structural Database (CSD) becomes part of a curated collection of over a million structures, searchable by geometry, connectivity, or space group. The same file sitting in Zenodo is just a file.

The hierarchy of preference introduced in Episode 5 applies directly here:

  1. Domain-specific repository: always the first choice if one exists for your data type
  2. Institutional repository: required by many UK universities for reporting purposes
  3. General-purpose repository: (Zenodo, Figshare) – always a valid fallback

Key Chemistry Repositories

The table below covers some of the repositories most relevant to chemistry researchers in the UK.

Repository What it holds Notes
Chemotion Repository Reaction data, NMR, MS, IR, UV-Vis Free, open; integrates with Chemotion ELN; DOI minting
Cambridge Structural Database (CSD) Small-molecule crystal structures Free to search; academic licence for full access; mandatory deposition for many journals
NOMAD Computational materials science data Strong metadata standards for DFT, molecular dynamics
ioChem-BD Computational chemistry (DFT, MD, etc.) Accepts Gaussian, ORCA, CP2K, VASP outputs
RADAR4Chem General chemistry research data Part of NFDI4Chem; accessible internationally
Protein Data Bank (PDB) Protein and macromolecular structures Essential for biochemistry and structural biology
Zenodo Anything Best fallback for data types without a specialist home
Challenge

Check Your Understanding: Which Repository?

A researcher produces the following datasets during a project. For each one, select the most appropriate repository from the options given and explain your reasoning.

1. A set of single-crystal X-ray diffraction data for a new organic small molecule.

  • A. Zenodo
  • B. Cambridge Structural Database (CSD)
  • C. NOMAD
  • D. Protein Data Bank

2. DFT input and output files from geometry optimisations of a series of transition metal complexes.

  • A. Chemotion Repository
  • B. Cambridge Structural Database (CSD)
  • C. ioChem-BD or NOMAD
  • D. Figshare

3. Reaction yield data, ¹H NMR spectra, and mass spectra from a synthetic chemistry project – no crystal structures or computational data.

  • A. NOMAD
  • B. Protein Data Bank
  • C. Chemotion Repository
  • D. Zenodo is the only valid option for spectroscopic data

1. B: Cambridge Structural Database (CSD). Crystal structure data for small organic molecules belongs in the CSD. Deposition is mandatory for most crystallography journals, and the CSD is the world’s curated reference collection for this data type. Zenodo is a valid fallback but provides none of the structural search, curation, or community visibility that the CSD offers.

2. C: ioChem-BD or NOMAD. Both are designed for computational chemistry output files and understand DFT codes. ioChem-BD is particularly well-suited for molecular systems; NOMAD has broader coverage of solid-state and materials codes. Chemotion is oriented towards experimental synthetic chemistry and does not handle DFT input/output files.

3. C: Chemotion Repository. Chemotion is built for exactly this type of data: it understands reactions and spectra, accepts JCAMP-DX and other open formats, links records to chemical structures, and integrates with the Chemotion ELN. Answer D is wrong: Zenodo is a valid alternative, but it is not the only option and is not the best choice when a domain-specific repository exists.

When a Paper Has Multiple Data Types

Most chemistry papers draw on several techniques simultaneously. A single publication might combine crystal structures, NMR and mass spectra, and DFT calculations, each of which has a different natural repository home. This situation is extremely common, and knowing how to handle it is as important as knowing which repositories exist.

Splitting across repositories is usually the right approach. Deposit each data type where it fits best: crystal structures to the CSD, computational output files to ioChem-BD or NOMAD, reaction and spectroscopic data to Chemotion. Each deposit receives its own DOI, and the paper’s data access statement simply lists them all. Splitting is better for discoverability than pooling everything in a single general-purpose archive: your crystal structure becomes part of the CSD’s searchable collection, your DFT files become findable alongside related computational datasets, and so on. Multiple DOIs in a data access statement are perfectly acceptable to funders and journals.

When a single deposit is more appropriate. There are situations where keeping data together in a general-purpose repository makes more sense:

  • No specialist repository exists for any of your data types. Zenodo or your institutional repository is the right home for all of it.
  • The relationships between data types are central to the paper for example, a dataset where computational predictions are directly compared with experimental outcomes row-by-row is more coherent and interpretable as a single structured package.
  • Complexity warrants a “front door.” A well-structured Zenodo record with a clear README can link out to specialist deposits in the CSD, ioChem-BD, and Chemotion, giving readers a single starting point without sacrificing domain-specific discoverability. This hybrid approach is increasingly common for complex multi-technique papers.

Journal policies often resolve the decision. Many journals now specify exactly where each data type should go: RSC journals require CSD deposition for crystal structures and recommend domain-specific repositories for other data. If your journal has explicit guidance, follow it. For anything not covered, apply the hierarchy of preference: domain-specific first, institutional second, general-purpose as a fallback.

Callout

Signpost Multiple DOIs in Your Data Access Statement

When data is split across repositories, mention each DOI explicitly in your data access statement, with a brief note on what each one contains. For example:

“Crystal structure data are deposited in the Cambridge Structural Database (CCDC 2345678). NMR and mass spectrometry data are available in the Chemotion Repository at https://doi.org/10.14272/xxxxx under a CC-BY 4.0 licence. DFT input and output files are deposited in ioChem-BD at https://doi.org/10.xxxxx.”

This is clearer and more useful to readers than a single catch-all reference, and it ensures each dataset is correctly attributed and independently citable.

NFDI4Chem and the German Chemistry Data Infrastructure

NFDI4Chem is Germany’s national initiative for chemistry research data infrastructure, part of the broader National Research Data Infrastructure (NFDI). Despite being German-led, its resources are freely available internationally and represent current best practice for chemistry data management. NFDI4Chem maintains the Chemotion ecosystem, working groups developing community standards for NMR and mass spectrometry, and a detailed knowledge base at knowledgebase.nfdi4chem.de covering repositories, file formats, metadata standards, and practical guidance. Whether or not you are based in Germany, the NFDI4Chem Knowledge Base is one of the best free resources for practical chemistry RDM.

Journal Policies and Mandatory Deposition

Many chemistry journals now require data deposition as a condition of publication. Requirements vary by journal and are tightening across the field:

  • Crystal structures: Deposition in the CSD is mandatory for most crystallography journals (RSC, Wiley, ACS). The CCDC reference number must be cited in the paper.
  • Spectroscopic data: RSC journals expect supporting data to be deposited in a repository rather than attached as supplementary information.
  • Computational data: Journals such as Journal of Chemical Theory and Computation encourage deposition of input and output files in a specialist repository.

Always check the specific journal’s data policy before submission.

Challenge

Challenge: Find and Evaluate a Repository

Go to re3data.org, a global registry of research data repositories, and search for repositories relevant to your own area of chemistry.

Find one repository you were not previously aware of, then note down:

  1. What is it called, and what type of data does it accept?
  2. Does it mint DOIs?
  3. Is it free to deposit?
  4. What metadata standards or controlled vocabularies does it use?
  5. What file formats does it require or recommend?

Share your findings with your neighbour.

Common finds when navigating re3data.org for chemistry include:

  • Chemotion Repository (synthetic chemistry, spectroscopy)
  • CSD/CCDC (crystal structures)
  • NOMAD or ioChem-BD (computational data)
  • MassBank (mass spectrometry reference spectra)
  • nmrXiv (NMR spectra, developed by NFDI4Chem)
  • Zenodo (general fallback for any data type)

Key things to check: persistent identifiers (DOIs), long-term preservation commitments, metadata standards enforced at upload, and whether the repository is indexed in re3data, FAIRsharing, or DataCite. A repository that appears in multiple registries with an active community is a safer long-term choice than one that is only recently established.

Key Points
  • Domain-specific repositories provide better discoverability and community-standard validation than general-purpose alternatives – use them as your first choice.
  • Key repositories for chemistry include Chemotion (synthetic/spectroscopic), CSD (crystal structures), NOMAD and ioChem-BD (computational), and Zenodo (general fallback).
  • When a paper involves multiple data types, split the deposit across appropriate repositories – each with its own DOI – rather than pooling everything in a general-purpose archive. List all DOIs in the data access statement.
  • Crystal structure deposition in the CSD is mandatory for most crystallography journals.
  • re3data.org and FAIRsharing.org are the best starting points for finding a repository appropriate for your data type.
  • NFDI4Chem provides freely accessible guidance and tools for chemistry data management regardless of where you are based.