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README.md

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-license: cc0-1.0
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+---
+license: cc0-1.0
+---
+# CHEBI Chemical Classification Program Ontology (C3PO) Benchmark
+
+Name: C3PO-v237
+
+A benchmark for chemical classification, derived from v237 of the CHEBI ontology.
+
+The benchmark consists of
+
+- 177,875 *Structures*, each represented by a SMILES string
+- 1364 *Classes*, each of which classify (directly or indirectly) between 25 and 5000 Structures
+
+The CHEBI smiles property (obo:chebi/smiles) is used to derive
+structures. Only SMILES strings that lacked a `*` wildcard are
+used. If multiple CHEBI entries have the same SMILES, they are
+collapsed.
+
+The benchmark can be further partitioned based on different properties.
+
+C3PO-Slim is the subset of structures that have at least one xref
+(mapping), representing the set of classes that are more commonly used
+in the biological literature and in other databases.
+
+20% of the structures are designated as being for *validation*
+purposes. The remaining 80% can be used for training and testing.
+
+The benchmark can be downloaded as either a single JSON file, or
+separate CSVs for classes and structures. Summary stats files are also
+provided:
+
+- [dataset.json](dataset.json) - the complete benchmark
+- [classes.csv](classes.csv) - all classes
+- [classes_slim.csv](classes_slim.csv) - slim classes (any with an xref)
+- [structures.csv](structures.csv) - all structures
+- [classes_summary.csv](classes_summary.csv) - summary statistics for classes
+- [classes_slim_summary.csv](classes_slim_summary.csv) - summary statistics for classes
+- [structures_summary.csv](structures_summary.csv) - summary statistics for structures
+- [metadata.csv](metadata.csv) - metadata about how this was derived.
+
+For a description of all fields, see:
+
+- [datamodel](https://github.com/cmungall/c3p/blob/main/c3p/datamodel.py)
+
+For the code that extracts the benchmark from CHEBI, see:
+
+- [extractor](https://github.com/cmungall/c3p/blob/main/c3p/extractor.py)
+
+
+