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[DATALAD RUNCMD] run codespell throughout fixing typo automagically
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=== Do not change lines below ===
{
 "chain": [],
 "cmd": "codespell -w",
 "exit": 0,
 "extra_inputs": [],
 "inputs": [],
 "outputs": [],
 "pwd": "."
}
^^^ Do not change lines above ^^^
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yarikoptic committed Oct 24, 2023
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2 changes: 1 addition & 1 deletion docs/datamodels/cross-ontology-diff/Objectidentifier.md
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Expand Up @@ -21,7 +21,7 @@ URI: [shex:iri](http://www.w3.org/ns/shex#iri)

## Comments

* Used for inheritence and type checking
* Used for inheritance and type checking

## Identifier and Mapping Information

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2 changes: 1 addition & 1 deletion docs/datamodels/lexical-index/Objectidentifier.md
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Expand Up @@ -21,7 +21,7 @@ URI: [shex:iri](http://www.w3.org/ns/shex#iri)

## Comments

* Used for inheritence and type checking
* Used for inheritance and type checking

## Identifier and Mapping Information

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2 changes: 1 addition & 1 deletion docs/datamodels/mapping-rules/Objectidentifier.md
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Expand Up @@ -21,7 +21,7 @@ URI: [shex:iri](http://www.w3.org/ns/shex#iri)

## Comments

* Used for inheritence and type checking
* Used for inheritance and type checking

## Identifier and Mapping Information

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2 changes: 1 addition & 1 deletion docs/datamodels/obograph/Graph.md
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Expand Up @@ -266,7 +266,7 @@ attributes:
name: nodes
description: All nodes present in a graph. This includes class nodes as well as
supporting nodes, including nodes representing relationship types, subsets,
annotation proeprties, etc
annotation properties, etc
from_schema: https://github.com/geneontology/obographs
rank: 1000
multivalued: true
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2 changes: 1 addition & 1 deletion docs/datamodels/obograph/Objectidentifier.md
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Expand Up @@ -21,7 +21,7 @@ URI: [shex:iri](http://www.w3.org/ns/shex#iri)

## Comments

* Used for inheritence and type checking
* Used for inheritance and type checking

## Identifier and Mapping Information

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4 changes: 2 additions & 2 deletions docs/datamodels/obograph/nodes.md
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@@ -1,5 +1,5 @@
# Slot: nodes
_All nodes present in a graph. This includes class nodes as well as supporting nodes, including nodes representing relationship types, subsets, annotation proeprties, etc_
_All nodes present in a graph. This includes class nodes as well as supporting nodes, including nodes representing relationship types, subsets, annotation properties, etc_


URI: [obographs:nodes](https://github.com/geneontology/obographs/nodes)
Expand Down Expand Up @@ -56,7 +56,7 @@ URI: [obographs:nodes](https://github.com/geneontology/obographs/nodes)
```yaml
name: nodes
description: All nodes present in a graph. This includes class nodes as well as supporting
nodes, including nodes representing relationship types, subsets, annotation proeprties,
nodes, including nodes representing relationship types, subsets, annotation properties,
etc
from_schema: https://github.com/geneontology/obographs
rank: 1000
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2 changes: 1 addition & 1 deletion docs/datamodels/ontology-metadata/Objectidentifier.md
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Expand Up @@ -21,7 +21,7 @@ URI: [shex:iri](http://www.w3.org/ns/shex#iri)

## Comments

* Used for inheritence and type checking
* Used for inheritance and type checking

## Identifier and Mapping Information

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2 changes: 1 addition & 1 deletion docs/datamodels/search/Objectidentifier.md
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Expand Up @@ -21,7 +21,7 @@ URI: [shex:iri](http://www.w3.org/ns/shex#iri)

## Comments

* Used for inheritence and type checking
* Used for inheritance and type checking

## Identifier and Mapping Information

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4 changes: 2 additions & 2 deletions docs/datamodels/search/SearchBaseConfiguration.md
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Expand Up @@ -132,7 +132,7 @@ attributes:
description: An individual search term. The syntax is determined by the syntax
slot
comments:
- This slot is optional when the configuration is used to paramterize multiple
- This slot is optional when the configuration is used to parameterize multiple
searches
- If multiple terms are provided this is treated as a union query
from_schema: https://w3id.org/oak/search-datamodel
Expand Down Expand Up @@ -222,7 +222,7 @@ attributes:
description: An individual search term. The syntax is determined by the syntax
slot
comments:
- This slot is optional when the configuration is used to paramterize multiple
- This slot is optional when the configuration is used to parameterize multiple
searches
- If multiple terms are provided this is treated as a union query
from_schema: https://w3id.org/oak/search-datamodel
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4 changes: 2 additions & 2 deletions docs/datamodels/search/search_terms.md
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Expand Up @@ -36,7 +36,7 @@ URI: [ontosearch:search_terms](https://w3id.org/oak/search-datamodel/search_term

## Comments

* This slot is optional when the configuration is used to paramterize multiple searches
* This slot is optional when the configuration is used to parameterize multiple searches
* If multiple terms are provided this is treated as a union query

## Identifier and Mapping Information
Expand All @@ -62,7 +62,7 @@ URI: [ontosearch:search_terms](https://w3id.org/oak/search-datamodel/search_term
name: search_terms
description: An individual search term. The syntax is determined by the syntax slot
comments:
- This slot is optional when the configuration is used to paramterize multiple searches
- This slot is optional when the configuration is used to parameterize multiple searches
- If multiple terms are provided this is treated as a union query
from_schema: https://w3id.org/oak/search-datamodel
rank: 1000
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2 changes: 1 addition & 1 deletion docs/datamodels/summary-statistics/Objectidentifier.md
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Expand Up @@ -21,7 +21,7 @@ URI: [shex:iri](http://www.w3.org/ns/shex#iri)

## Comments

* Used for inheritence and type checking
* Used for inheritance and type checking

## Identifier and Mapping Information

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2 changes: 1 addition & 1 deletion docs/datamodels/text-annotator/Objectidentifier.md
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Expand Up @@ -21,7 +21,7 @@ URI: [shex:iri](http://www.w3.org/ns/shex#iri)

## Comments

* Used for inheritence and type checking
* Used for inheritance and type checking

## Identifier and Mapping Information

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2 changes: 1 addition & 1 deletion docs/datamodels/validation/Objectidentifier.md
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Expand Up @@ -21,7 +21,7 @@ URI: [shex:iri](http://www.w3.org/ns/shex#iri)

## Comments

* Used for inheritence and type checking
* Used for inheritance and type checking

## Identifier and Mapping Information

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2 changes: 1 addition & 1 deletion docs/faq/architecture.rst
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Expand Up @@ -67,7 +67,7 @@ OAK uses a mixture of native an external data models.

Native data models have the OAK w3id namespace - for example, `<https://w3id.org/oak/class-enrichment>`_.

What is an interator and why does OAK use them so much?
What is an iterator and why does OAK use them so much?
---------------------

OAK uses iterators in place of lists in a lot of places, in order to make the
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2 changes: 1 addition & 1 deletion docs/guide/curies-and-uris.rst
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Expand Up @@ -117,7 +117,7 @@ can understand. These can be used in the same way:
subject subject_label predicate predicate_label object object_label
schema:Person Person rdfs:subClassOf None schema:Thing Thing
Futher reading
Further reading
--------------

* `OBO Foundry Identifiers <https://obofoundry.org/id-policy>`_
2 changes: 1 addition & 1 deletion docs/howtos/fhir-conversions.rst
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Expand Up @@ -67,7 +67,7 @@ concepts that are not native to that CodeSystem. In cases where they do appear,
references, unless this flag is present, in which case the converter will attempt to construct CURIEs.

predicate_period_replacement (default=False): _Predicates URIs populated into `CodeSystem.
concept.property.code` and `CodeSystem.concept.property.code`, but the popular FHIR server "HAPI" has a bug in whih
concept.property.code` and `CodeSystem.concept.property.code`, but the popular FHIR server "HAPI" has a bug in which
periods '.' cause errors. If this flag is present, periods will be replaced with underscores '_'.

Example:
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2 changes: 1 addition & 1 deletion docs/intro/tutorial07.rst
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Expand Up @@ -14,7 +14,7 @@ The :ref:`sql_implementation` wraps SQLite or any relational database.
Download a SQLite file
----------------

You can download ready made SQLite files for any :term:`OBO` Libray ontology
You can download ready made SQLite files for any :term:`OBO` Library ontology

For example: the Cell Ontology (CL) is available from https://s3.amazonaws.com/bbop-sqlite/cl.db.gz

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2 changes: 1 addition & 1 deletion notebooks/Commands/DiffViaMappings.ipynb
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Expand Up @@ -690,7 +690,7 @@
"\n",
"### Non-entailed relationships\n",
"\n",
"i.e. this is an edge in UBERON that corresonds to a different kind of edge in ZFA (or vice versa), where the former\n",
"i.e. this is an edge in UBERON that corresponds to a different kind of edge in ZFA (or vice versa), where the former\n",
"doesn't subsume the latter.\n",
"\n",
"For example, in UBERON PNS *part_of* NS; in ZFA PNS *is_a* NS"
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2 changes: 1 addition & 1 deletion notebooks/Commands/TaxonConstraints.ipynb
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Expand Up @@ -311,7 +311,7 @@
"source": [
"## Evaluating Candidate taxon constraints\n",
"\n",
"The related `apply-taxon-constraints` commmand can be used to test taxon constraints\n",
"The related `apply-taxon-constraints` command can be used to test taxon constraints\n",
"\n"
]
},
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2 changes: 1 addition & 1 deletion notebooks/Developers-Tutorial.ipynb
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Expand Up @@ -125,7 +125,7 @@
"![images/oak-docs-code.png](images/oak-docs-code.png)\n",
"\n",
"If you click the \"copy\" button it will copy the code only (no `>>>`s, and no output) such that you\n",
"can paste directly into a Pythin REPL or a notebook (provided the paths are preserved).\n",
"can paste directly into a Python REPL or a notebook (provided the paths are preserved).\n",
"\n",
"E.g. try copying this section from the docs\n",
"\n",
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2 changes: 1 addition & 1 deletion notebooks/Lessons/PrefixMaps.ipynb
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Expand Up @@ -869,7 +869,7 @@
"ERROR:root:Multiple labels for OAE:0000352 = ['a pain AE that occurs in shoulder', 'shoulder pain is a pain iin or around the shoulder joint']\n",
"WARNING:root:Multiple labels for OAE:0001610 = abdomen crushing AE != blood folate level abnormal AE\n",
"\n",
"ERROR:root:Multiple labels for OAE:0001610 = ['a metabolic and nutritional investigation result abnormal AE that is charaterized by an abnormal blood folate level', 'This is an AE which is a symptom associated with both non-serious and serious medical issues.']\n",
"ERROR:root:Multiple labels for OAE:0001610 = ['a metabolic and nutritional investigation result abnormal AE that is characterized by an abnormal blood folate level', 'This is an AE which is a symptom associated with both non-serious and serious medical issues.']\n",
"WARNING:root:Multiple labels for OAE:0001628 = blood pH decreased AE\n",
" != hernial eventration AE\n",
"ERROR:root:Multiple labels for OAE:0001628 = ['This is an AE which is the protrusion of contents of the abdomen through a defect or weakness in the abdominal wall.', 'a blood pH abnormal AE that is characterized by a decreased blood pH']\n",
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2 changes: 1 addition & 1 deletion notebooks/Lessons/Why-predicates-are-important.ipynb
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Expand Up @@ -563,7 +563,7 @@
"\n",
"## So how do we handle these?\n",
"\n",
"At this point you might be thinking it makes no sense to use measures like semantic similarity over cyclic graphs. Or that it may be necessary to include ad-hoc measures like maximim distance. _But this isn't the case_\n",
"At this point you might be thinking it makes no sense to use measures like semantic similarity over cyclic graphs. Or that it may be necessary to include ad-hoc measures like maximum distance. _But this isn't the case_\n",
"\n",
"Because ontology graphs are _existential graphs_ over concepts, where the existence of the subject depends on the existence of the object, you can still use algorithms designed with concepts of \"ancestors\" and \"descendants\". The overall structure of the relation graph will still (in general) follow a pattern of narrowing down to more general concepts.\n",
"\n",
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2 changes: 1 addition & 1 deletion notebooks/Neuro/CL-Neuro-Tutorial.ipynb
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Expand Up @@ -1379,7 +1379,7 @@
"source": [
"### Complex queries\n",
"\n",
"We can also make use of entailed egdes in complex boolean queries.\n",
"We can also make use of entailed edges in complex boolean queries.\n",
"\n",
"The following query is an *intersection* (using `and`) syntax of\n",
"\n",
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2 changes: 1 addition & 1 deletion notebooks/input/go-nucleus.owl
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Expand Up @@ -639,7 +639,7 @@
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002211"/>
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002305"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002335"/>
<obo1:IAO_0000115>Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2.</obo1:IAO_0000115>
<obo1:IAO_0000115>Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 decreases the the frequency of initiation of P2 or the magnitude or rate of output of P2.</obo1:IAO_0000115>
<oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RO:0002212</oboInOwl:hasDbXref>
<oboInOwl:hasOBONamespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">external</oboInOwl:hasOBONamespace>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">negatively_regulates</oboInOwl:id>
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4 changes: 2 additions & 2 deletions src/oaklib/cli.py
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Expand Up @@ -1251,7 +1251,7 @@ def statistics(
For bundled ontologies, we recommend some kind of partitioning, such as via
defined roots, or via the CURIE prefix, using the ``--group-by-prefix`` option.
Ouput formats:
Output formats:
The recommended output types for this command are yaml, json, or csv.
The default output type is yaml, following the SummaryStatistics data model.
Expand Down Expand Up @@ -2020,7 +2020,7 @@ def ancestors(
This will show ancestry over the full relationship graph. Like any relational
OAK command, this can be filtered by relationship type (predicate), using --predicate (-p).
For exampple, constrained to is-a and part-of:
For example, constrained to is-a and part-of:
runoak -i cl.owl ancestors CL:4023094 -p i,BFO:0000050
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2 changes: 1 addition & 1 deletion src/oaklib/converters/obo_graph_to_fhir_converter.py
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Expand Up @@ -158,7 +158,7 @@ def convert(
will attempt to construct CURIEs. (not implemented)
:param predicate_period_replacement: Predicates URIs populated into `CodeSystem.concept.property.packages`
and `CodeSystem.concept.property.packages`, but the HAPI FHIR server
has a bug in whih periods '.' cause errors. If this flag is present,
has a bug in which periods '.' cause errors. If this flag is present,
periods will be replaced with underscores '_'.
:return: FHIR CodeSystem object
"""
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2 changes: 1 addition & 1 deletion src/oaklib/datamodels/obograph.yaml
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Expand Up @@ -228,7 +228,7 @@ slots:
inlined_as_list: true
description: >-
All nodes present in a graph. This includes class nodes as well as supporting nodes, including
nodes representing relationship types, subsets, annotation proeprties, etc
nodes representing relationship types, subsets, annotation properties, etc
edges:
multivalued: true
range: Edge
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2 changes: 1 addition & 1 deletion src/oaklib/datamodels/search_datamodel.yaml
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Expand Up @@ -56,7 +56,7 @@ classes:
description: >-
An individual search term. The syntax is determined by the syntax slot
comments:
- This slot is optional when the configuration is used to paramterize multiple searches
- This slot is optional when the configuration is used to parameterize multiple searches
- If multiple terms are provided this is treated as a union query
syntax:
range: SearchTermSyntax
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2 changes: 1 addition & 1 deletion src/oaklib/datamodels/taxon_constraints.yaml
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Expand Up @@ -113,7 +113,7 @@ classes:
predicate:
slot_uri: rdf:predicate
range: PredicateTerm
description: The relationship type for the contraint (e.g. in_taxon, never_in taxon)
description: The relationship type for the constraint (e.g. in_taxon, never_in taxon)
todos:
- define a value set of this
asserted:
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2 changes: 1 addition & 1 deletion src/oaklib/interfaces/association_provider_interface.py
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Expand Up @@ -170,7 +170,7 @@ def associations(
PomBase:SPAC1142.02c sgt2
...
When determinining a match on `objects`, the predicates in ``object_closure_predicates`` is used.
When determining a match on `objects`, the predicates in ``object_closure_predicates`` is used.
We recommend you always explicitly provide this. A good choice is typically IS_A and PART_OF for
ontologies like GO, Uberon, CL, ENVO.
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2 changes: 1 addition & 1 deletion src/oaklib/interfaces/basic_ontology_interface.py
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Expand Up @@ -90,7 +90,7 @@ class BasicOntologyInterface(OntologyInterface, ABC):
horsetail nucleus
nucleus
This omits metdata about the synonym, such as the predicate, source, and type.
This omits metadata about the synonym, such as the predicate, source, and type.
For this more granular view, the :ref:`obograph_interface` can be used.
Basic concepts:
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2 changes: 1 addition & 1 deletion src/oaklib/interfaces/mapping_provider_interface.py
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Expand Up @@ -223,7 +223,7 @@ def normalize_prefix(
"""
Normalize a CURIE to a target prefix.
If a prefix alias map is supplied, this is takes precendence:
If a prefix alias map is supplied, this is takes precedence:
>>> from oaklib import get_adapter
>>> adapter = get_adapter("tests/input/go-nucleus.obo")
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2 changes: 1 addition & 1 deletion src/oaklib/interfaces/taxon_constraint_interface.py
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Expand Up @@ -321,7 +321,7 @@ def filter_nr_never(self, taxa: Collection[TAXON_CURIE]) -> List[TAXON_CURIE]:
return list(include)

def _fill_missing(self, st: SubjectTerm):
# fills in trivial inferrable information
# fills in trivial inferable information
for tc in st.only_in:
if not tc.subject:
tc.subject = st.id
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2 changes: 1 addition & 1 deletion src/oaklib/utilities/ner_utilities.py
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@@ -1,5 +1,5 @@
"""
Utilites used for annotation and lexmatch processes.
Utilities used for annotation and lexmatch processes.
"""

from pathlib import Path
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2 changes: 1 addition & 1 deletion src/oaklib/utilities/subsets/value_set_expander.py
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Expand Up @@ -256,7 +256,7 @@ def expand(config: str, schema: str, value_set_names: List[str], output: str):
"""
Expand a value set. EXPERIMENTAL.
This will expand an *intensional value set* (aka *dynamic enum*), running a query against
This will expand an *intentional value set* (aka *dynamic enum*), running a query against
an ontology backend or backends to materialize the value set (permissible values).
Currently the value set must be specified as LinkML, but in future this will be
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2 changes: 1 addition & 1 deletion tests/__init__.py
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Expand Up @@ -140,7 +140,7 @@ def object_is_subsumed_by_member_of(obj: YAMLRoot, obj_list: List[YAMLRoot], **k


def filecmp_difflib(left_path: Path, right_path: Path) -> bool:
"""Platfom neutral filecmp.cmp(..) function for text files
"""Platform neutral filecmp.cmp(..) function for text files
Files are read in text mode to ignore newline differences.
"""
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2 changes: 1 addition & 1 deletion tests/input/AMPK-Signaling.cx
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Expand Up @@ -2065,7 +2065,7 @@
"n": "sentence",
"v": [
"<a target=\"_blank\" href=\"http://identifiers.org/pubmed/17900900\">pubmed:17900900</a> We have recently found that AMPK phosphorylates human FOXO3 in mammalian cells at novel regulatory sites that are distinct from the AKT sites",
"<a target=\"_blank\" href=\"http://identifiers.org/pubmed/17711846\">pubmed:17711846</a> Phosphorylation by AMPK leads to the activtion of FOXO3 transcriptional activity without affecting FOXO3 subcellular localization."
"<a target=\"_blank\" href=\"http://identifiers.org/pubmed/17711846\">pubmed:17711846</a> Phosphorylation by AMPK leads to the activation of FOXO3 transcriptional activity without affecting FOXO3 subcellular localization."
],
"d": "list_of_string"
},
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2 changes: 1 addition & 1 deletion tests/input/go-nucleus.owl
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Expand Up @@ -760,7 +760,7 @@
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002211"/>
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002305"/>
<owl:inverseOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002335"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2.</obo:IAO_0000115>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 decreases the the frequency of initiation of P2 or the magnitude or rate of output of P2.</obo:IAO_0000115>
<oboInOwl:hasDbXref rdf:datatype="http://www.w3.org/2001/XMLSchema#string">RO:0002212</oboInOwl:hasDbXref>
<oboInOwl:hasOBONamespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">external</oboInOwl:hasOBONamespace>
<oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">negatively_regulates</oboInOwl:id>
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@
}


@unittest.skipIf(os.name == "nt", "DB path loading inconsisent on Windows")
@unittest.skipIf(os.name == "nt", "DB path loading inconsistent on Windows")
class TestSemSimianImplementation(unittest.TestCase):
"""Implementation tests for Rust-based semantic similarity."""

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2 changes: 1 addition & 1 deletion tests/test_utilities/test_association_index.py
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Expand Up @@ -16,7 +16,7 @@ class AssociationIndexTest(unittest.TestCase):
"""Tests indexing associations in-memory."""

def test_index(self):
"""Tests in-memory index by laoding from GAF."""
"""Tests in-memory index by loading from GAF."""
parser = XafAssociationParser(
subject_column=ColumnReference(1), object_column=ColumnReference(4)
)
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