Data Structure

SeMRA implements a data structure as an extension to a simple curies.Triple that contains a list of EvidenceMixin objects, that are come as of the the following two flavors:

1. semra.struct.SimpleEvidence - simple evidence objects correspond to rows in a SSSOM file. These contain a mapping justification, optional confidence, and optional provenance for the mapping tool and/or curator that produced the mapping

2. semra.struct.ReasonedEvidence - complex evidence objects that are based on other mappings. These contain a mapping justification (typically semra.vocabulary.INVERSION_MAPPING for inversions or semra.vocabulary.CHAIN_MAPPING for graph-based inference) and a list of full mapping objects.

Here’s an example of how a mapping might look:

Note

This data structure is based on SSSOM, but is implemented such that each mapping has a full reference to the mapping set that it’s part of (while SSSOM’s data model makes the mapping set the primary object, which contains a list of mappings).

A simple evidence can be used to justify a mapping:

from semra import (
    Reference,
    Mapping,
    EXACT_MATCH,
    SimpleEvidence,
    MappingSet,
    MANUAL_MAPPING,
)

r1 = Reference(prefix="chebi", identifier="107635", name="2,3-diacetyloxybenzoic")
r2 = Reference(prefix="mesh", identifier="C011748", name="tosiben")

mapping = Mapping(
    subject=r1,
    predicate=EXACT_MATCH,
    object=r2,
    evidence=[
        SimpleEvidence(
            justification=MANUAL_MAPPING,
            confidence=0.99,
            author=Reference(
                prefix="orcid",
                identifier="0000-0003-4423-4370",
                name="Charles Tapley Hoyt",
            ),
            mapping_set=MappingSet(
                name="biomappings",
                license="CC0",
                confidence=0.90,
            ),
        )
    ],
)

A mapping that relies on another mapping can use a reasoned evidence. In the following example, we justify the inverse mapping from the first one:

from semra import ReasonedEvidence, INVERSION_MAPPING

mapping_inv = Mapping(
    subject=r2,
    predicate=EXACT_MATCH,
    object=r1,
    evidence=[
        ReasonedEvidence(
            justification=INVERSION_MAPPING,
            mappings=[mapping],
        )
    ],
)

Note

These mappings can be produced with semra.api.flip() for a single mapping or with semra.inference.infer_reversible() for a mapping set.

Classes

ConfidenceMixin()	A mixin for classes that have confidence information.
EvidenceMixin()	A class that represents evidences.
KeyedMixin()	A mixin for a class that can be hashed and CURIE-encoded.
Mapping(*, subject, predicate, object, ...)	A semantic mapping.
MappingSet(*[, purl, version, license, ...])	Represents a set of semantic mappings.
MappingSetKey(purl, name, version, license)	The key used for a mapping set.
ReasonedEvidence(*[, evidence_type, author, ...])	A complex evidence based on multiple mappings.
ReasonedEvidenceKey(evidence_type, ...)	The key used for a reasoned evidence.
SimpleEvidence(*[, evidence_type, ...])	Evidence for a mapping.

Class Inheritance Diagram

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"NamableReference" [fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",tooltip="A reference, maybe with a name."]; "Reference" -> "NamableReference" [arrowsize=0.5,style="setlinewidth(0.5)"]; "NormalizedNamableReference" [fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",tooltip="Extends :class:`curies.NamableReference` to normalize the prefix against the Bioregistry."]; "NormalizedReference" -> "NormalizedNamableReference" [arrowsize=0.5,style="setlinewidth(0.5)"]; "NamableReference" -> "NormalizedNamableReference" [arrowsize=0.5,style="setlinewidth(0.5)"]; "NormalizedReference" [fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",tooltip="Extends :class:`curies.Reference` to normalize the prefix against the Bioregistry."]; 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