The methods and codes in this repository are described in more detail here: Behr, A.S., Borgelt, H. & Kockmann, N. Ontologies4Cat: investigating the landscape of ontologies for catalysis research data management. J Cheminform 16, 16 (2024).https://doi.org/10.1186/s13321-024-00807-2
Repository which lists ontologies relevant for catalysis research.
For remarks, additions, or general questions either use the issues or contact the responsible person (see below). A condensed view on the data provided in the markdown-files is given in master_table. For contributions please either refer to the entries in this table or download and fill in the markdown file called General Template and contact us either via mail, issue or pull request. The respective markdown files for each ontology listed in the table below are located in ontology_metadata. In the subdirectory json, the information contained for each ontology is stored in json-format for an ease in access of the data presented in markdown.
Contact: [email protected]
To obtain the radar plots and interactive markdown files from the Excel file contained in the subdirectory ./master_table/ one has to run the convert.py code located in the main directory and execute the run() function. Make sure to have the latest name of the master table listed in the function call ConvertExcelToMD().
To reproduce the mappings, run the similarities.py code located in the main directory and execute the run() function.
For runtime performance reasons, IRIs and labels from the classes of all ontologies are stored in iriDictionary.json, which is loaded by the function called with run().
If you want to reproduce (or update) this .json file, please execute class_description_loader().
The ontologies are classified with regards to their research domain in a list here.
Here you can find the radar plot shown below as interactive plot (download html file and open it locally).
These are the ontologies and links to the ontology markdown files, NFDI4Cat deems as relevant:
| Link to Markdown | Ontology Name |
|---|---|
| AFO | Allotrope Foundation Ontology |
| BAO | BioAssay Ontology |
| BFO | Basic Formal Ontology |
| CAO | Chemical Analysis Ontology |
| ChEBI | Chemical Entities of Biological Interest |
| CHEMINF | Chemical Information Ontology |
| CHMO | Chemical Methods Ontology |
| CIF | Crystallographic Information Framework Ontology |
| EDAM | EDAM - Bioscientific data analysis ontology |
| EMMO | Elementary Multiperspective Material Ontology |
| ENMO | eNanoMapper Ontology |
| ENVO | Environmental Ontology |
| M3 | Machine to Machine Measurements Ontology |
| metadata4ing | Metadata4Ing: An ontology for describing the generation of research data within a scientific activity. |
| MOP | Molecular Process Ontology |
| MS | Mass Spectrometry Ontology |
| OBI | Ontology for Biomedical Investigations |
| OEO | Open Energy Ontology |
| OM | Ontology of units of Measure |
| OntoCAPE | Ontology for the domain of Computer Aided Process Engineering |
| OSMO | Ontology for Simulation, Modelling, and Optimization |
| REX | Physico-chemical process |
| RO | OBO Relations Ontology |
| RXNO | RXNO: name reaction ontology |
| SBO | Systems Biology Ontology |
| VIMMP | Virtual Materials Marketplace Ontology |
Here, you can see a mapping that lists the amount of common ontology classes for each ontology, focusing on IRI, label, prefLabel, altLabel and name of the classes.
| AFO | BAO | BFO | CAO | ChEBI | CHEMINF | CHMO | CIF | EDAM | EMMO | ENVO | M3 | metadata4ing | MOP | MS | OBI | OM | OSMO | REX | RXNO | SBO | VIMMP | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| AFO | 2876 | |||||||||||||||||||||
| BAO | 107 | 7512 | ||||||||||||||||||||
| BFO | 36 | 4 | 35 | |||||||||||||||||||
| CAO | 121 | 25 | 14 | 445 | ||||||||||||||||||
| ChEBI | 58 | 1678 | 1 | 45 | 176873 | |||||||||||||||||
| CHEMINF | 92 | 14 | 35 | 42 | 2 | 850 | ||||||||||||||||
| CHMO | 249 | 39 | 12 | 69 | 23 | 19 | 3101 | |||||||||||||||
| CIF | 128 | 24 | 4 | 19 | 12 | 37 | 6 | 32 | ||||||||||||||
| EDAM | 50 | 35 | 0 | 12 | 3 | 19 | 9 | 15 | 3473 | |||||||||||||
| EMMO | 144 | 21 | 4 | 22 | 23 | 36 | 10 | 502 | 14 | 935 | ||||||||||||
| ENVO | 248 | 212 | 26 | 84 | 939 | 63 | 36 | 62 | 21 | 64 | 6566 | |||||||||||
| M3 | 88 | 27 | 0 | 19 | 9 | 8 | 6 | 67 | 2 | 65 | 389 | 761 | ||||||||||
| metadata4ing | 18 | 2 | 3 | 7 | 1 | 4 | 3 | 7 | 1 | 13 | 5 | 10 | 32 | |||||||||
| MOP | 6 | 7 | 3 | 8 | 58 | 3 | 3 | 3 | 0 | 3 | 25 | 0 | 1 | 3686 | ||||||||
| MS | 140 | 47 | 0 | 26 | 20 | 28 | 30 | 35 | 26 | 31 | 75 | 61 | 1 | 1 | 14989 | |||||||
| OBI | 289 | 172 | 35 | 82 | 136 | 236 | 77 | 61 | 48 | 54 | 399 | 97 | 6 | 6 | 55 | 4866 | ||||||
| OM | 100 | 21 | 1 | 17 | 11 | 21 | 2 | 80 | 5 | 78 | 226 | 131 | 4 | 0 | 24 | 81 | 815 | |||||
| OSMO | 8 | 1 | 0 | 2 | 0 | 8 | 0 | 5 | 4 | 4 | 13 | 4 | 1 | 0 | 3 | 19 | 5 | 173 | ||||
| REX | 9 | 7 | 0 | 2 | 0 | 0 | 18 | 0 | 0 | 1 | 16 | 6 | 1 | 23 | 2 | 7 | 1 | 0 | 552 | |||
| RXNO | 14 | 8 | 2 | 17 | 230 | 5 | 10 | 5 | 0 | 4 | 95 | 1 | 1 | 123 | 3 | 16 | 0 | 0 | 12 | 1019 | ||
| SBO | 41 | 27 | 2 | 7 | 13 | 9 | 3 | 14 | 7 | 17 | 62 | 11 | 1 | 20 | 9 | 31 | 31 | 1 | 11 | 8 | 694 | |
| VIMMP | 83 | 13 | 3 | 19 | 3 | 33 | 5 | 83 | 15 | 90 | 74 | 37 | 8 | 1 | 12 | 96 | 72 | 172 | 0 | 2 | 9 | 1082 |