owmeta.evidence module

exception owmeta.evidence.EvidenceError

Bases: Exception

class owmeta.evidence.Evidence(*args, no_type_decl=False, **kwargs)

Bases: DataObject

A representation which provides evidence, for a group of statements.

Attaching evidence to an set of statements is done like this:

>>> from owmeta.connection import Connection
>>> from owmeta.evidence import Evidence
>>> from owmeta_core.context import Context

Declare contexts:

>>> ACTX = Context(ident="http://example.org/data/some_statements")
>>> BCTX = Context(ident="http://example.org/data/some_other_statements")
>>> EVCTX = Context(ident="http://example.org/data/some_statements#evidence")

Make statements in ACTX and BCTX contexts:

>>> ACTX(Connection)(pre_cell="VA11", post_cell="VD12", number=3)
>>> BCTX(Connection)(pre_cell="VA11", post_cell="VD12", number=2)

In EVCTX, state that a that a certain document supports the set of statements in ACTX, but refutes the set of statements in BCTX:

>>> doc = EVCTX(Document)(author='White et al.', date='1986')
>>> EVCTX(Evidence)(reference=doc, supports=ACTX.rdf_object)
>>> EVCTX(Evidence)(reference=doc, refutes=BCTX.rdf_object)

Finally, save the contexts:

>>> ACTX.save_context()
>>> BCTX.save_context()
>>> EVCTX.save_context()

One note about the reference predicate: the reference should, ideally, be an unambiguous link to a peer-reviewed piece of scientific literature detailing methods and data analysis that supports the set of statements. However, in gather data from pre-existing sources, going to that level of specificity may be difficult due to deficient query capability at the data source. In such cases, a broader reference, such as a Website with information which guides readers to a peer-reviewed article supporting the statement is sufficient.

defined_augment()

This fuction must return False if identifier_augment() would raise an IdentifierMissingException. Override it when defining a non-standard identifier for subclasses of DataObjects.

identifier_augment()

Override this method to define an identifier in lieu of one explicity set.

One must also override defined_augment() to return True whenever this method could return a valid identifier. IdentifierMissingException should be raised if an identifier cannot be generated by this method.

Raises

IdentifierMissingException

class_context = owmeta_core.context.ClassContext(ident="http://schema.openworm.org/2020/07/sci")

property reference

The resource providing evidence supporting/refuting the attached context

property refutes

A context naming a set of statements which are refuted by the attached reference

property supports

A context naming a set of statements which are supported by the attached reference

owmeta.evidence.evidence_for(qctx, ctx, evctx=None)

Returns an iterable of Evidence

Parameters

qctxobject

an object supported by evidence. If the object is a Context with no identifier, then the query considers statements ‘staged’ (rather than stored) in the context

ctxContext

Context that bounds where we look for statements about qctx. The contexts for statements found in this context are the actual targets of Evidence.supports statements.

evctxContext

if the Evidence.supports statements should be looked for somewhere other than ctx, that can be specified in evctx. optional

owmeta.evidence.query_context(graph, qctx)

graphrdflib.graph.Graph

Graph where we can find the contexts for statements in qctx

qctxowmeta.context.Context

Container for statements