Skip to content

monarch-py

Data models for the Monarch Initiative data access library

URI: https://w3id.org/monarch/monarch-py

Name: monarch-py

Classes

Class Description
Association None
        DirectionalAssociation An association that gives it's direction relative to a specified entity
AssociationCountList Container class for a list of association counts
AssociationTypeMapping A data class to hold the necessary information to produce association type counts for given entities with appropriate directional labels
BestMatch None
CompactAssociation None
Entity Represents an Entity in the Monarch KG data model
        Node UI container class extending Entity with additional information
        SearchResult None
ExpandedCurie A curie bundled along with its expanded url
FacetField None
FacetValue None
        AssociationCount None
        HistoBin None
HistoPheno None
Mapping A minimal class to hold a SSSOM mapping
NodeHierarchy None
PairwiseSimilarity Abstract grouping for representing individual pairwise similarities
        TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms
        TermSetPairwiseSimilarity A simple pairwise similarity between two sets of concepts/terms
Release A class to hold information about a release of the Monarch KG
Results None
        AssociationResults None
        AssociationTableResults None
        CategoryGroupedAssociationResults None
        CompactAssociationResults None
        EntityResults None
        MappingResults SSSOM Mappings returned as a results collection
        MultiEntityAssociationResults None
        SearchResults None
SemsimSearchResult None
TermInfo None
TextAnnotationResult None

Slots

Slot Description
agent_type Describes the high-level category of agent who originally generated a statem...
aggregator_knowledge_source
ancestor_id the most recent common ancestor of the two compared entities
ancestor_information_content The IC of the object
ancestor_label the name or label of the ancestor concept
ancestor_source
associated_categories
association_counts
average_score
best_score
category
causal_gene A list of genes that are known to be causally associated with a disease
causes_disease A list of diseases that are known to be causally associated with a gene
cosine_similarity the dot product of two node embeddings divided by the product of their length...
count count of documents
counterpart_category The category of the counterpart entity in a given association, eg
deprecated A boolean flag indicating that an entity is no longer considered current or v...
description
dice_similarity
direction The directionality of the association relative to a given entity for an assoc...
disease_context_qualifier A context qualifier representing a disease or condition in which a relationsh...
disease_context_qualifier_category The category of the disease_context_qualifier entity
disease_context_qualifier_closure Field containing disease_context_qualifier id and the ids of all of it's ance...
disease_context_qualifier_closure_label Field containing disease_context_qualifier name and the names of all of it's ...
disease_context_qualifier_label The name of the disease_context_qualifier entity
disease_context_qualifier_namespace The namespace/prefix of the disease_context_qualifier entity
end end position of the annotation
evidence_count count of supporting documents, evidence codes, and sources supplying evidence
external_links ExpandedCurie with id and url for xrefs
facet_fields Collection of facet field responses with the field values and counts
facet_queries Collection of facet query responses with the query string values and counts
facet_values Collection of FacetValue label/value instances belonging to a FacetField
frequency_qualifier
frequency_qualifier_category The category of the frequency_qualifier entity
frequency_qualifier_closure Field containing frequency_qualifier id and the ids of all of it's ancestors
frequency_qualifier_closure_label Field containing frequency_qualifier name and the names of all of it's ancest...
frequency_qualifier_label The name of the frequency_qualifier entity
frequency_qualifier_namespace The namespace/prefix of the frequency_qualifier entity
full_name The long form name of an entity
graph_stats
grouping_key A concatenation of fields used to group associations with the same essential/...
has_count count of out of has_total representing a frequency
has_evidence
has_evidence_links List of ExpandedCuries with id and url for evidence
has_percentage percentage, which may be calculated from has_count and has_total, as 100 * qu...
has_phenotype A list of phenotype identifiers that are known to be associated with this ent...
has_phenotype_closure A list of phenotype identifiers that are known to be associated with this ent...
has_phenotype_closure_label A list of phenotype labels that are known to be associated with this entity e...
has_phenotype_count A count of the number of phenotypes that are known to be associated with this...
has_phenotype_label A list of phenotype labels that are known to be associated with this entity
has_quotient quotient, which should be 1/100 of has_percentage
has_total total, devided by has_count, representing a frequency
highlight matching text snippet containing html tags
id
in_taxon The biolink taxon that the entity is in the closure of
in_taxon_label The label of the biolink taxon that the entity is in the closure of
information_content The IC is the negative log of the probability of the concept
inheritance
intersection_count
iri
items A collection of items, with the type to be overriden by slot_usage
jaccard_similarity The number of concepts in the intersection divided by the number in the union
kg
knowledge_level Describes the level of knowledge expressed in a statement, based on the reaso...
knowledge_source
label
limit number of items to return in a response
mapping_justification
mappings List of ExpandedCuries with id and url for mapped entities
match_source
match_source_label
match_subsumer
match_subsumer_label
match_target the entity matches
match_target_label
metadata
metric
name
namespace The namespace/prefix portion of this entity's identifier
negated
neo4j
node_hierarchy
object
object_best_matches
object_category The category of the object entity
object_closure Field containing object id and the ids of all of it's ancestors
object_closure_label Field containing object name and the names of all of it's ancestors
object_id
object_information_content The IC of the object
object_label The name of the object entity
object_namespace The namespace/prefix of the object entity
object_source the source for the second entity
object_taxon
object_taxon_label
object_termset
offset offset into the total number of items
onset_qualifier
onset_qualifier_category The category of the onset_qualifier entity
onset_qualifier_closure Field containing onset_qualifier id and the ids of all of it's ancestors
onset_qualifier_closure_label Field containing onset_qualifier name and the names of all of it's ancestors
onset_qualifier_label The name of the onset_qualifier entity
onset_qualifier_namespace The namespace/prefix of the onset_qualifier entity
original_object
original_subject
overlap_coefficient
pathway
phenodigm_score the geometric mean of the jaccard similarity and the information content
predicate
predicate_id
primary_knowledge_source
provided_by
provided_by_link A link to the docs for the knowledge source that provided the node/edge
publications
publications_links List of ExpandedCuries with id and url for publications
qc_report
qualifier
qualifier_category The category of the frequency_qualifier entity
qualifier_closure Field containing frequency_qualifier id and the ids of all of it's ancestors
qualifier_closure_label Field containing frequency_qualifier name and the names of all of it's ancest...
qualifier_label The name of the frequency_qualifier entity
qualifier_namespace The namespace/prefix of the frequency_qualifier entity
qualifiers
qualifiers_category The category of the frequency_qualifier entity
qualifiers_closure Field containing frequency_qualifier id and the ids of all of it's ancestors
qualifiers_closure_label Field containing frequency_qualifier name and the names of all of it's ancest...
qualifiers_label The name of the frequency_qualifier entity
qualifiers_namespace The namespace/prefix of the frequency_qualifier entity
score
sex_qualifier
sex_qualifier_category The category of the sex_qualifier entity
sex_qualifier_closure Field containing sex_qualifier id and the ids of all of it's ancestors
sex_qualifier_closure_label Field containing sex_qualifier name and the names of all of it's ancestors
sex_qualifier_label The name of the sex_qualifier entity
sex_qualifier_namespace The namespace/prefix of the sex_qualifier entity
similarity
solr
sqlite
stage_qualifier
stage_qualifier_category The category of the stage_qualifier entity
stage_qualifier_closure Field containing stage_qualifier id and the ids of all of it's ancestors
stage_qualifier_closure_label Field containing stage_qualifier name and the names of all of it's ancestors
stage_qualifier_label The name of the stage_qualifier entity
stage_qualifier_namespace The namespace/prefix of the stage_qualifier entity
start start position of the annotation
sub_classes
subject
subject_best_matches
subject_category The category of the subject entity
subject_closure Field containing subject id and the ids of all of it's ancestors
subject_closure_label Field containing subject name and the names of all of it's ancestors
subject_id
subject_information_content The IC of the subject
subject_label The name of the subject entity
subject_namespace The namespace/prefix of the subject entity
subject_source the source for the first entity
subject_taxon
subject_taxon_label
subject_termset
subsumed_by_score
subsumes_score
super_classes
symbol
symmetric Whether the association type is symmetric, i
synonym
text text without tokens
tokens A collection of entities or concepts
total total number of items matching a query
union_count
uri The URI of the entity
url
version
xref

Enumerations

Enumeration Description
AssociationDirectionEnum The directionality of an association as it relates to a specified entity, wit...

Types

Type Description
Boolean A binary (true or false) value
Curie a compact URI
Date a date (year, month and day) in an idealized calendar
DateOrDatetime Either a date or a datetime
Datetime The combination of a date and time
Decimal A real number with arbitrary precision that conforms to the xsd:decimal speci...
Double A real number that conforms to the xsd:double specification
Float A real number that conforms to the xsd:float specification
Integer An integer
ItemCount
Jsonpath A string encoding a JSON Path
Jsonpointer A string encoding a JSON Pointer
Ncname Prefix part of CURIE
NegativeLogValue
Nodeidentifier A URI, CURIE or BNODE that represents a node in a model
NonNegativeFloat
Objectidentifier A URI or CURIE that represents an object in the model
Sparqlpath A string encoding a SPARQL Property Path
String A character string
Time A time object represents a (local) time of day, independent of any particular...
Uri a complete URI
Uriorcurie a URI or a CURIE
ZeroToOne

Subsets

Subset Description