.. How to explore Schema classes and properties
Explore Classes and Properties Defined in Schema
************************************************
biothings_schema pyton package allows you to explore the classes (e.g. ancestors, descendants, associated properties, etc.) as well as the properties defined within the schema.
.. _list_all_classes:
List all classes defined in schema
-----------------------------------
.. code-block:: python
In [1]: from biothings_schema import Schema
In [2]: schema_url = 'https://raw.githubusercontent.com/data2health/schemas/biothings/biothings/biothings_curie_kevin.jsonld'
In [3]: se = Schema(schema=schema_url)
In [4]: se.list_all_classes()
Out [4]: [SchemaClass(name=BiologicalEntity),
SchemaClass(name=Thing),
SchemaClass(name=OntologyClass),
SchemaClass(name=RelationshipType),
SchemaClass(name=GeneOntologyClass),
......
SchemaClass(name=CellLine),
SchemaClass(name=GrossAnatomicalStructure),
SchemaClass(name=ProteinStructure)]
.. _find_parent_classes:
Find all parents of a specific class
------------------------------------
.. code-block:: python
In [1]: from biothings_schema import Schema
In [2]: schema_url = 'https://raw.githubusercontent.com/data2health/schemas/biothings/biothings/biothings_curie_kevin.jsonld'
In [3]: se = Schema(schema=schema_url)
In [4]: scls = se.get_class("Gene")
In [5]: scls.parent_classes
Out [5]: [[SchemaClass(name=Thing),
SchemaClass(name=BiologicalEntity),
SchemaClass(name=MolecularEntity),
SchemaClass(name=GenomicEntity),
SchemaClass(name=MacromolecularMachine),
SchemaClass(name=GeneOrGeneProduct)]]
.. _find_child_classes:
Find all children of a specific class
-------------------------------------
.. code-block:: python
In [1]: from biothings_schema import Schema
In [2]: schema_url = 'https://raw.githubusercontent.com/data2health/schemas/biothings/biothings/biothings_curie_kevin.jsonld'
In [3]: se = Schema(schema=schema_url)
In [4]: scls = se.get_class("MolecularEntity")
In [5]: scls.child_classes
Out [5]: [SchemaClass(name=ChemicalSubstance),
SchemaClass(name=GenomicEntity),
SchemaClass(name=GeneFamily)]
.. _find_descendant_classes:
Find all descendants of a specific class
----------------------------------------
.. code-block:: python
In [1]: from biothings_schema import Schema
In [2]: schema_url = 'https://raw.githubusercontent.com/data2health/schemas/biothings/biothings/biothings_curie_kevin.jsonld'
In [3]: se = Schema(schema=schema_url)
In [4]: scls = se.get_class("MolecularEntity")
In [5]: scls.descendant_classes
Out [5]: [SchemaClass(name=Metabolite),
SchemaClass(name=ProteinIsoform),
SchemaClass(name=GeneProduct),
SchemaClass(name=GeneProductIsoform),
SchemaClass(name=Genome),
SchemaClass(name=Haplotype),
SchemaClass(name=Transcript),
SchemaClass(name=GeneOrGeneProduct),
SchemaClass(name=RnaProductIsoform),
SchemaClass(name=GeneFamily),
SchemaClass(name=Drug),
SchemaClass(name=RnaProduct),
SchemaClass(name=Protein),
SchemaClass(name=Gene),
SchemaClass(name=GenomicEntity),
SchemaClass(name=Microrna),
SchemaClass(name=CodingSequence),
SchemaClass(name=MacromolecularMachine),
SchemaClass(name=Exon),
SchemaClass(name=SequenceVariant),
SchemaClass(name=MacromolecularComplex),
SchemaClass(name=Genotype),
SchemaClass(name=NoncodingRnaProduct),
SchemaClass(name=ChemicalSubstance)]
.. _find_associated_properties:
Find properties associated to a specific class
----------------------------------------------
Only fetch properties specifically defined for this class
.. code-block:: python
In [1]: from biothings_schema import Schema
In [2]: schema_url = 'https://raw.githubusercontent.com/data2health/schemas/biothings/biothings/biothings_curie_kevin.jsonld'
In [3]: se = Schema(schema=schema_url)
In [4]: scls = se.get_class("Gene")
In [5]: scls.list_properties()
Out [5]: [{'class': 'Gene',
'properties': [SchemaProperty(name=hgnc),
SchemaProperty(name=mgi),
SchemaProperty(name=rgd),
SchemaProperty(name=zfin),
SchemaProperty(name=flybase),
SchemaProperty(name=sgd),
SchemaProperty(name=pombase),
SchemaProperty(name=dictybase),
SchemaProperty(name=tair),
SchemaProperty(name=inTaxon),
SchemaProperty(name=entrez),
SchemaProperty(name=pharos),
SchemaProperty(name=pharmgkb),
SchemaProperty(name=symbol),
SchemaProperty(name=omim),
SchemaProperty(name=umls),
SchemaProperty(name=unigene),
SchemaProperty(name=geneticallyInteractsWith),
SchemaProperty(name=hasGeneProduct),
SchemaProperty(name=hasTranscript),
SchemaProperty(name=geneAssociatedWithCondition)]}]
List all properties associated with a class (include properties for its ancestors)
.. code-block:: python
In [1]: from biothings_schema import Schema
In [2]: schema_url = 'https://raw.githubusercontent.com/data2health/schemas/biothings/biothings/biothings_curie_kevin.jsonld'
In [3]: se = Schema(schema=schema_url)
In [4]: scls = se.get_class("Gene")
In [5]: scls.list_properties(class_specific=False)
Out [5]: [{'class': 'Gene',
'properties': SchemaProperty(name=hgnc),
SchemaProperty(name=mgi),
SchemaProperty(name=rgd),
SchemaProperty(name=zfin),
SchemaProperty(name=flybase),
SchemaProperty(name=sgd),
SchemaProperty(name=pombase),
SchemaProperty(name=dictybase),
SchemaProperty(name=tair),
SchemaProperty(name=inTaxon),
SchemaProperty(name=entrez),
SchemaProperty(name=pharos),
SchemaProperty(name=pharmgkb),
SchemaProperty(name=symbol),
SchemaProperty(name=omim),
SchemaProperty(name=umls),
SchemaProperty(name=unigene),
SchemaProperty(name=geneticallyInteractsWith),
SchemaProperty(name=hasGeneProduct),
SchemaProperty(name=hasTranscript),
SchemaProperty(name=geneAssociatedWithCondition)]}]},
{'class': 'GeneOrGeneProduct',
'properties': [SchemaProperty(name=ensembl),
SchemaProperty(name=refseq),
SchemaProperty(name=metabolize),
SchemaProperty(name=targetedBy),
SchemaProperty(name=enablesMF),
SchemaProperty(name=involvedInBP),
SchemaProperty(name=involvedInPathway),
SchemaProperty(name=involvedInWikipathway),
SchemaProperty(name=involvedInReactomePathway),
SchemaProperty(name=hasHomolog),
SchemaProperty(name=orthologousTo),
SchemaProperty(name=hasProteinStructure),
SchemaProperty(name=inPathwayWith),
SchemaProperty(name=inComplexWith),
SchemaProperty(name=inCellPopulationWith),
SchemaProperty(name=expressedIn)]},
{'class': 'MacromolecularMachine', 'properties': []},
{'class': 'GenomicEntity', 'properties': []},
{'class': 'MolecularEntity',
'properties': [SchemaProperty(name=molecularlyInteractsWith),
SchemaProperty(name=affectsAbundanceOf),
SchemaProperty(name=increasesAbundanceOf),
SchemaProperty(name=decreasesAbundanceOf),
SchemaProperty(name=affectsActivityOf),
.....
SchemaProperty(name=decreasesUptakeOf),
SchemaProperty(name=regulates,EntityToEntity),
SchemaProperty(name=biomarkerFor)]},
{'class': 'BiologicalEntity',
'properties': [SchemaProperty(name=hasPhenotype)]},
{'class': 'Thing',
'properties': [SchemaProperty(name=sameAs),
SchemaProperty(name=alternateName),
SchemaProperty(name=image),
SchemaProperty(name=additionalType),
SchemaProperty(name=name),
SchemaProperty(name=identifier),
SchemaProperty(name=subjectOf),
SchemaProperty(name=mainEntityOfPage),
SchemaProperty(name=url),
SchemaProperty(name=potentialAction),
SchemaProperty(name=description),
SchemaProperty(name=disambiguatingDescription)]}]
.. _find_class_usage:
Find class usage
-------------------
Find where this class has been used in the schema
.. code-block:: python
In [1]: from biothings_schema import Schema
In [2]: schema_url = 'https://raw.githubusercontent.com/data2health/schemas/biothings/biothings/biothings_curie_kevin.jsonld'
In [3]: se = Schema(schema=schema_url)
In [4]: scls = se.get_class("GenomicEntity")
In [5]: scls.used_by()
Out [5]: [{'property': SchemaProperty(name=affectsExpressionOf),
'property_used_on_class': SchemaClass(name=MolecularEntity),
'description': 'holds between two molecular entities where the action or effect of one changes the level of expression of the other within a system of interest'},
{'property': SchemaProperty(name=increasesExpressionOf),
'property_used_on_class': SchemaClass(name=MolecularEntity),
'description': 'holds between two molecular entities where the action or effect of one increases the level of expression of the other within a system of interest'},
{'property': SchemaProperty(name=decreasesExpressionOf),
'property_used_on_class': SchemaClass(name=MolecularEntity),
'description': 'holds between two molecular entities where the action or effect of one decreases the level of expression of the other within a system of interest'},
{'property': SchemaProperty(name=affectsMutationRateOf),
'property_used_on_class': SchemaClass(name=MolecularEntity),
'description': 'holds between a molecular entity and a genomic entity where the action or effect of the molecular entity impacts the rate of mutation of the genomic entity within a system of interest'},
{'property': SchemaProperty(name=increasesMutationRateOf),
'property_used_on_class': SchemaClass(name=MolecularEntity),
'description': 'holds between a molecular entity and a genomic entity where the action or effect of the molecular entity increases the rate of mutation of the genomic entity within a system of interest'},
{'property': SchemaProperty(name=decreasesMutationRateOf),
'property_used_on_class': SchemaClass(name=MolecularEntity),
'description': 'holds between a molecular entity and a genomic entity where the action or effect of the molecular entity decreases the rate of mutation of the genomic entity within a system of interest'}]
.. _explore_class:
Explore everything related to a class
-------------------------------------
Find all information related to a specific class, including its ancestors, descendants, associated properties as well as its usage
.. code-block:: python
In [1]: from biothings_schema import Schema
In [2]: schema_url = 'https://raw.githubusercontent.com/data2health/schemas/biothings/biothings/biothings_curie_kevin.jsonld'
In [3]: se = Schema(schema=schema_url)
In [4]: scls = se.get_class("GenomicEntity")
In [5]: scls.describe()
Out [5]:{'properties': [{'class': 'GenomicEntity', 'properties': []},
{'class': 'MolecularEntity',
'properties': [SchemaProperty( name=molecularlyInteractsWith),
SchemaProperty(name=affectsAbundanceOf),
SchemaProperty(name=increasesAbundanceOf),
SchemaProperty(name=decreasesAbundanceOf),
......
SchemaProperty(name=decreasesUptakeOf),
SchemaProperty(name=regulates,EntityToEntity),
SchemaProperty(name=biomarkerFor)]},
{'class': 'BiologicalEntity',
'properties': [SchemaProperty(name=hasPhenotype)]},
{'class': 'Thing',
'properties': [SchemaProperty(name=sameAs),
SchemaProperty(name=alternateName),
SchemaProperty(name=image),
SchemaProperty(name=additionalType),
SchemaProperty(name=name),
SchemaProperty(name=identifier),
SchemaProperty(name=subjectOf),
SchemaProperty(name=mainEntityOfPage),
SchemaProperty(name=url),
SchemaProperty(name=potentialAction),
SchemaProperty(name=description),
SchemaProperty(name=disambiguatingDescription)]}],
'description': 'an entity that can either be directly located on a genome (gene, transcript, exon, regulatory region) or is encoded in a genome (protein)',
'uri': 'http://schema.biothings.io/GenomicEntity',
'usage': [{'property': SchemaProperty(name=affectsExpressionOf),
'property_used_on_class': SchemaClass(name=MolecularEntity),
'description': 'holds between two molecular entities where the action or effect of one changes the level of expression of the other within a system of interest'},
{'property': SchemaProperty(name=increasesExpressionOf),
'property_used_on_class': SchemaClass(name=MolecularEntity),
'description': 'holds between two molecular entities where the action or effect of one increases the level of expression of the other within a system of interest'},
{'property': SchemaProperty(name=decreasesExpressionOf),
'property_used_on_class': SchemaClass(name=MolecularEntity),
'description': 'holds between two molecular entities where the action or effect of one decreases the level of expression of the other within a system of interest'},
{'property': SchemaProperty(name=affectsMutationRateOf),
'property_used_on_class': SchemaClass(name=MolecularEntity),
'description': 'holds between a molecular entity and a genomic entity where the action or effect of the molecular entity impacts the rate of mutation of the genomic entity within a system of interest'},
{'property': SchemaProperty(name=increasesMutationRateOf),
'property_used_on_class': SchemaClass(name=MolecularEntity),
'description': 'holds between a molecular entity and a genomic entity where the action or effect of the molecular entity increases the rate of mutation of the genomic entity within a system of interest'},
{'property': SchemaProperty(name=decreasesMutationRateOf),
'property_used_on_class': SchemaClass(name=MolecularEntity),
'description': 'holds between a molecular entity and a genomic entity where the action or effect of the molecular entity decreases the rate of mutation of the genomic entity within a system of interest'}],
'child_classes': [SchemaClass(name=Genome),
SchemaClass(name=Transcript),
SchemaClass(name=Exon),
SchemaClass(name=CodingSequence),
SchemaClass(name=MacromolecularMachine),
SchemaClass(name=Genotype),
SchemaClass(name=Haplotype),
SchemaClass(name=SequenceVariant)],
'parent_classes': [[SchemaClass(name=Thing),
SchemaClass(name=BiologicalEntity),
SchemaClass(name=MolecularEntity)]]}
.. _find_parent_properties:
Find all parents of a specific property
---------------------------------------
.. code-block:: python
In [1]: from biothings_schema import Schema
In [2]: schema_url = 'https://raw.githubusercontent.com/data2health/schemas/biothings/biothings/biothings_curie_kevin.jsonld'
In [3]: se = Schema(schema=schema_url)
In [4]: sp = se.get_property("ensembl")
In [5]: sp.parent_properties
Out [5]: [SchemaClass(name=identifier)]
.. _find_child_properties:
Find all children of a specific property
----------------------------------------
.. code-block:: python
In [1]: from biothings_schema import Schema
In [2]: schema_url = 'https://raw.githubusercontent.com/data2health/schemas/biothings/biothings/biothings_curie_kevin.jsonld'
In [3]: se = Schema(schema=schema_url)
In [4]: sp = se.get_property("ensembl")
In [5]: sp.child_properties
Out [5]: [SchemaClass(name=ensembl),
SchemaClass(name=hgnc),
SchemaClass(name=mgi),
SchemaClass(name=rgd),
SchemaClass(name=zfin),
SchemaClass(name=flybase),
......,
SchemaClass(name=unigene),
SchemaClass(name=inchi),
SchemaClass(name=inchikey),
SchemaClass(name=rxcui),
SchemaClass(name=smiles),
SchemaClass(name=pubchem),
SchemaClass(name=chembl),
SchemaClass(name=drugbank),
SchemaClass(name=unii)]
.. _explore_property:
Explore everything related to a property
----------------------------------------
Find all information related to a specific property, including its ancestors, descendants, etc.
.. code-block:: python
In [1]: from biothings_schema import Schema
In [2]: schema_url = 'https://raw.githubusercontent.com/data2health/schemas/biothings/biothings/biothings_curie_kevin.jsonld'
In [3]: se = Schema(schema=schema_url)
In [4]: sp = se.get_property("ensembl")
In [5]: sp.describe()
Out [5]: {'child_properties': [],
'descendant_properties': [],
'parent_properties': [SchemaClass(name=identifier)],
'id': 'ensembl',
'description': 'Ensembl ID for gene, protein or transcript',
'domain': [SchemaClass(name=GeneOrGeneProduct),
SchemaClass(name=Transcript)],
'range': SchemaClass(name=Text)}