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biothings / biothings_schema.py

Python Package to view and analyze schemas defined in schema.org way
Apache License 2.0
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biothings_schema

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biothings_schema is a Python package for the creation, extension and exploration of the schemas defined using the schema.org standard.

Feature Support

  1. Visulize schema structure image
  2. Find ancestors/descendants of a schema class
In [1]: from biothings_schema import Schema

In [2]: schema_file_path = "https://raw.githubusercontent.com/data2health/schemas/biothings/biothings/biothings_curie_kevin.jsonld"

In [3]: se = Schema(schema_file_path)

In [4]: scls = se.get_class("Gene")

In [5]: scls.parent_classes

Out [5]:
[[<SchemaClass "Thing">,
  <SchemaClass "BiologicalEntity">,
  <SchemaClass "MolecularEntity">,
  <SchemaClass "GenomicEntity">,
  <SchemaClass "MacromolecularMachine">,
  <SchemaClass "GeneOrGeneProduct">]]

In [6]: scls = se.get_class("MolecularEntity")

In [7]: scls.descendant_classes

Out [7]:
[<SchemaClass "Genome">,
 <SchemaClass "RnaProductIsoform">,
 <SchemaClass "GeneProduct">,
 <SchemaClass "Metabolite">,
 <SchemaClass "Protein">,
 <SchemaClass "MacromolecularComplex">,
 <SchemaClass "Microrna">,
 <SchemaClass "Exon">,
 <SchemaClass "RnaProduct">,
 <SchemaClass "CodingSequence">,
 <SchemaClass "GeneProductIsoform">,
 <SchemaClass "GeneFamily">,
 <SchemaClass "Drug">,
 <SchemaClass "Haplotype">,
 <SchemaClass "ChemicalSubstance">,
 <SchemaClass "Genotype">,
 <SchemaClass "ProteinIsoform">,
 <SchemaClass "NoncodingRnaProduct">,
 <SchemaClass "GeneOrGeneProduct">,
 <SchemaClass "Gene">,
 <SchemaClass "MacromolecularMachine">,
 <SchemaClass "Transcript">,
 <SchemaClass "SequenceVariant">,
 <SchemaClass "GenomicEntity">]
  1. Find properties associated with a schema class
In [8]: scls = se.get_class("Gene")

In [9]: scls.list_properties(group_by_class=False)

Out [9]:
[<SchemaProperty "mgi"">,
 <SchemaProperty "pombase"">,
 <SchemaProperty "rgd"">,
 <SchemaProperty "umls"">,
 <SchemaProperty "omim"">,
 <SchemaProperty "hasTranscript"">,
 <SchemaProperty "dictybase"">,
 <SchemaProperty "geneAssociatedWithCondition"">,
 <SchemaProperty "flybase"">,
 <SchemaProperty "hasGeneProduct"">,
 <SchemaProperty "pharos"">,
 <SchemaProperty "pharmgkb"">,
 <SchemaProperty "unigene"">,
 <SchemaProperty "symbol"">,
 <SchemaProperty "zfin"">,
 <SchemaProperty "entrez"">,
 <SchemaProperty "inTaxon"">,
 <SchemaProperty "hgnc"">,
 <SchemaProperty "geneticallyInteractsWith"">,
 <SchemaProperty "tair"">,
 <SchemaProperty "sgd"">]

  1. Validate your schema against JSON schema

  2. Edit/Extend your schema

For all features supported by biothings_schema as well as their usage, please see detailed jupyter notebook demo.

Installation

To install biothings_schema, simply use pip:

$ pip install git+https://github.com/biothings/biothings_schema.py#egg=biothings_schema

Documentation

Fantastic documentation is available at https://biothings-schemapy.readthedocs.io/en/latest/.

The Contributor Guide

If you want to contribute to the project, please refer to the contribution guidelines here