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Parts copied from the neo-chem compilation.


Schemas, Ontologies & Vocabulariesโ€‹


See also the Semantic Python Overview list.


Data formats and modelsโ€‹

  • JCAMP - IUPAC recommended data exchange format with standardized vocabularies for some fields
  • FAIRSpec - standard for sharing spectroscopic data
  • DataCite metadata schema - A set of mandatory metadata that must be registered with the DataCite Metadata Store when minting a DOI persistent identifier for a dataset
  • AniML - Analytical Information Markup Language (AnIML) is an open ASTM XML standard for storing and sharing any analytical chemistry data.
  • Chemical Markup Language CML - is an approach to managing molecular information using XML
  • NeXus format - common data format for neutron, x-ray, and muon science
  • JSON-LD - publishing linked data as JSON files on the Web
  • GEMD data model - Graphical Expression of Materials Data that links together materials, the processes that produced them, and the measurements that characterize them
  • chemrof - data model for managing information about chemical entities, ranging from atoms through molecules to complex mixtures.


  • MOP - Molecular process ontology
  • RXNO - name reaction ontology
  • OWL - Web ontology language
  • ChEBI - Chemical Entities of Biological Interest is a chemical database and ontology of molecular entities


  • PyStow - for reproducible downloading of data in various computational Workflows in Python
  • Chemotion - Electronic lab notebook, focussed on organic chemistry, developed at KIT
  • rdflib - Python libary to deal with RDF
  • LinkML -- see above
  • Ontology Development Kit - a toolbox of various ontology related tools such as ROBOT, owltools, dosdp-tools and many more, bundled as a docker image, a set of executable workflows for managing your ontologies continuous integration, quality control, releases and dynamic imports
  • iochem-bd - The Computational Chemistry Results Repository, using CML as internal data format
  • Wikidata - a collaboratively edited multilingual knowledge graph
  • Pipeline Pilot - Proprietary software to build ETL, data science/analytics workflows in a graphical user interface
  • OPTIMADE - consortium that aims to make materials databases interoperable by developing a specification for a common REST API