monarch-py is a Python library for interacting with and querying the Monarch knowledge graph, with implementations for Solr and SQLite backends.
This means the same API methods can be used regardless of the implementation.
This library provides a collection of interfaces for graph operations such as retrieving entities and browsing associations.
"},{"location":"#installation","title":"Installation","text":"Requires Python 3.8 or higher
This library is available via pip or pipx:
pip install monarch-py\nFull usage instructions here
"},{"location":"#basic-example-cli","title":"Basic Example - CLI","text":"$ monarch sql entity MONDO:0012933\n{\n \"id\": \"MONDO:0012933\",\n \"category\": [\n \"biolink:Disease\"\n ],\n \"name\": \"breast-ovarian cancer, familial, susceptibility to, 2\",\n \"description\": \"Any hereditary breast ovarian cancer syndrome in which the cause of the disease is a mutation in the BRCA2 gene.\",\n \"xref\": [],\n \"provided_by\": \"phenio_nodes\",\n \"in_taxon\": null,\n \"source\": null,\n \"symbol\": null,\n \"type\": null,\n \"synonym\": []\n}\n$ monarch associations --subject MONDO:0012933 --limit 5\n{\n \"limit\": 5,\n \"offset\": 0,\n \"total\": 5,\n \"associations\": [\n ... # List of Associations\n ]\n}\n>>> from monarch_py.implementations.solr.solr_implementation import SolrImplementation\n>>> si = SolrImplementation()\n>>> entity = si.get_entity(\"MONDO:0007947\")\n>>> print(entity.name)\n\"Marfan syndrome\"\n\n>>> response = si.get_associations(predicate=\"biolink:has_phenotype\")\n>>> print(response.total > 600000)\nTrue\n>>> print(\"biolink:has_phenotype\" in response.associations[0].predicate)\nTrue\nThis document describes the steps required to create a new Monarch release.
These releases consist primarily of the following components:
Monarch Mapping Commons is a repository that contains code used to generate the mapping files used in the creation of the Monarch knowledge graph. The nodes and edges in the knowledge graph come from a variety of sources, and have varying IDs and prefixes. The mapping files are used to map these IDs to IDs in Monarch's preferred namespaces.
These mapping files are generated via a Jenkins job on a weekly basis, and are stored in the Monarch Data Bucket.
"},{"location":"release-process/#monarch-ingest-knowledge-graph","title":"Monarch Ingest (Knowledge Graph)","text":"Monarch's knowledge graph is built using the Monarch Ingest pipeline. The pipeline is run on a Jenkins server, and the resulting knowledge graph is uploaded to both Monarch's data bucket on Google Cloud, as well as the KG-Hub AWS S3 bucket.
Changes to the Monarch Ingest pipeline are made in the Monarch Ingest repository.
After the knowledge graph has been built, the QC Dashboard is used to verify the difference between the new build of the knowledge graph and the previous build.
Once the knowledge graph has been verified, additional steps are required to make the new knowledge graph available to the dev, beta, and production versions of the Monarch website.
"},{"location":"release-process/#deploying-the-knowledge-graph","title":"Deploying the Knowledge Graph","text":""},{"location":"release-process/#deploying-to-dev","title":"Deploying to dev","text":"While the Github Actions workflow for Monarch App will automatically update and deploy API & UI code to the dev environment, the knowledge graph must be manually deployed to the dev environment.
Preparing the environment for deployment:
To deploy the knowledge graph to the dev environment, follow these steps:
cd deployment && source site-envs/monarch-dev.env./provision.shgcloud compute ssh --zone us-central1-a monarch-v3-${TF_VAR_env}-manager -- sudo docker service update --force monarch-v3_solr\nFrom this point forward, code updates on the dev environment will be automatically deployed and additional work will happen to finish the work planned for the milestone. Ideally changes to the graph will happen early in the release cycle.
"},{"location":"release-process/#deploying-to-beta","title":"Deploying to beta","text":"Once work on the milestone is complete, we need to tag the release in GitHub then we can deploy to the beta environment.
To tag the release, go to the Monarch App and click on releases. Create a new release with the new version number and click generate release notes. Make any changes to the release notes that are necessary (generally none) and click publish release.
You may want to set an environment variable for the release version to make it easier to copy and paste the version number in the following steps (update for your current version):
RELEASE=\"2024-02-13\"\nFirst, copy the KG release from monarch-kg-dev to monarch-kg:
gsutil cp -r gs://data-public-monarchinitiative/monarch-kg-dev/${RELEASE} gs://data-public-monarchinitiative/monarch-kg/${RELEASE}\ngsutil cp -r gs://monarch-archive/monarch-kg-dev/${RELEASE} gs://monarch-archive/monarch-kg/${RELEASE}\nWithin monarch-stack-v3, copy the latest release env file to a new env, for example: cp site-envs/monarch-2023-10-11.env site-envs/monarch-${RELEASE}.env The date for the environment file name should match the KG release version, rather than today's date. Edit the top two lines in new env to match the latest KG & API versions:
export MONARCH_KG_VERSION=\"2023-11-16\"\nexport MONARCH_API_VERSION=\"0.18.1\"\nThen source the new environment and run provision.sh to create the new VM stack, paying attention to the terrform output to make sure that it's creating VMs with a version name you expect:
source site-envs/monarch-2023-11-16.env\n./provision.sh\nOutput for the provision script should look something like this:
...\nChanges to Outputs:\n + api_image_tag = \"1.0.0\"\n + env = \"2024-02-13\"\n + full_prefix = \"monarch-v3-2024-02-13-\"\n + neo4j_archive_url = \"https://data.monarchinitiative.org/monarch-kg-dev/latest/monarch-kg.neo4j.dump\"\n + phenio_archive_url = \"https://data.monarchinitiative.org/monarch-kg/2024-02-13/phenio.db.gz\"\n + project = \"monarch-initiative\"\n + semsimian_image_tag = \"latest\"\n + solr_archive_url = \"https://data.monarchinitiative.org/monarch-kg/2024-02-13/solr.tar.gz\"\n + sqlite_archive_url = \"https://data.monarchinitiative.org/monarch-kg/2024-02-13/monarch-kg.db.gz\"\n + stack = \"monarch-v3\"\n + ui_image_tag = \"latest\"\n + vm_svc_acct_email = \"terraform@monarch-initiative.iam.gserviceaccount.com\"\n\nDo you want to perform these actions?\n Terraform will perform the actions described above.\n Only 'yes' will be accepted to approve.\nAt the end of the run you should see a message like this:
PLAY RECAP ***************************************************************************************************\nmonarch-v3-2024-02-13-api : ok=11 changed=3 unreachable=0 failed=0 skipped=2 rescued=0 ignored=0\nmonarch-v3-2024-02-13-manager : ok=12 changed=3 unreachable=0 failed=0 skipped=2 rescued=0 ignored=0\nmonarch-v3-2024-02-13-neo4j : ok=11 changed=3 unreachable=0 failed=0 skipped=2 rescued=0 ignored=0\nmonarch-v3-2024-02-13-solr : ok=11 changed=3 unreachable=0 failed=0 skipped=2 rescued=0 ignored=0\nOnce this completes, open the GCP load balancer configuration.
monarch-v3-{release}-api-backend & monarch-v3-{release}-nginx-backend, leave the other boxes checked, and click ok.Host and path rules section to point beta.monarchinitiative.org to the nginx backend, api-beta.monarchinitiative.org to the api backend, and neo4j-beta.monarchinitiative.org to the neo4j backend./* to the path matcher, and click update.If you get a pop-up window error, you may have forgotten to delete one of the old routes when pointing to the new backend. You will need to redo the configuration if this happens.
The load balancer will automatically restart with the new configuration. Then we'll need to confirm that the site is up and running.
Get yourself a cup of hot chocolate / ice cold lemonade (season dependent) and settle in to go through the issues in the milestone. Make sure that each issue appears to actually be fixed, and close them with a note that they're confirmed to be working on beta.monarchinitiative.org. (with some additional explanation for externally submitted issues about when the change is expected to be visible on the production site)
"},{"location":"release-process/#deploying-to-production","title":"Deploying to production","text":"Edit the load balancer 1. Remove the nginx and api backends from the last release 2. Point api-beta.monarchinitiative.org, api-v3.monarchinitiative.org, and api-next.monarchinitiative.org to monarch-v3-{release}-api-backend 3. Point next.monarchinitiative.org and monarchinitiative.org to monarch-v3-{release}-nginx-backend 4. At the top of the host and path rules seciton, change the default backend (\"Backend 1\") to point to monarch-v3-{release}-nginx-backend as well
Then turn off the former production VMs (but keep them around for disaster recovery) by going to the GCP console VM listings and just clicking stop on each VM.
Source the former former env in v3 stack to delete it (say yes to deleting, and no to creating in the terraform dialogs)
source site-envs/monarch-2023-10-17.env\n./provision.sh -d\nHere are some known issues that we have seen before:
In ./provision.sh you may see an error like this:
fatal: [monarch-v3-2024-02-13-api]: UNREACHABLE! => changed=false\n msg: |-\n Data could not be sent to remote host \"monarch-v3-2024-02-13-api\". Make sure this host can be reached over ssh: Pseudo-terminal will not be allocated because stdin is not a terminal.\n sa_116692422516913491665@34.42.108.156: Permission denied (publickey).\n\n Recommendation: To check for possible causes of SSH connectivity issues and get\n recommendations, rerun the ssh command with the --troubleshoot option.\n\n gcloud compute ssh monarch-v3-2024-02-13-api --project=monarch-initiative --zone=us-central1-a --troubleshoot\n\n Or, to investigate an IAP tunneling issue:\n\n gcloud compute ssh monarch-v3-2024-02-13-api --project=monarch-initiative --zone=us-central1-a --troubleshoot --tunnel-through-iap\n\n ERROR: (gcloud.compute.ssh) [/usr/bin/ssh] exited with return code [255].\n unreachable: true\nIf so you may want to run the stated command (update to your version):
gcloud compute ssh monarch-v3-2024-02-13-api --project=monarch-initiative --zone=us-central1-a --troubleshoot\nData models for the Monarch Initiative data access library
URI: https://w3id.org/monarch/monarch-py
Name: monarch-py
"},{"location":"Data-Model/#classes","title":"Classes","text":"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"},{"location":"Data-Model/#slots","title":"Slots","text":"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_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_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_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_label The name of the sex_qualifier entity sex_qualifier_namespace The namespace/prefix of the sex_qualifier entity similarity solr species_context_qualifier A context qualifier representing a species in which a relationship expressed ... species_context_qualifier_category The category of the species_context_qualifier entity species_context_qualifier_label The name of the species_context_qualifier entity species_context_qualifier_namespace The namespace/prefix of the species_context_qualifier entity sqlite stage_qualifier stage_qualifier_category The category of the stage_qualifier entity 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"},{"location":"Data-Model/#enumerations","title":"Enumerations","text":"Enumeration Description AssociationDirectionEnum The directionality of an association as it relates to a specified entity, wit..."},{"location":"Data-Model/#types","title":"Types","text":"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"},{"location":"Data-Model/#subsets","title":"Subsets","text":"Subset Description"},{"location":"Data-Model/Association/","title":"Class: Association","text":"URI: https://w3id.org/monarch/monarch-py/:Association
classDiagram\n class Association\n click Association href \"../Association\"\n Association <|-- DirectionalAssociation\n click DirectionalAssociation href \"../DirectionalAssociation\"\n\n Association : agent_type\n\n Association : aggregator_knowledge_source\n\n Association : category\n\n Association : disease_context_qualifier\n\n Association : disease_context_qualifier_category\n\n Association : disease_context_qualifier_closure\n\n Association : disease_context_qualifier_closure_label\n\n Association : disease_context_qualifier_label\n\n Association : disease_context_qualifier_namespace\n\n Association : evidence_count\n\n Association : frequency_qualifier\n\n Association : frequency_qualifier_category\n\n Association : frequency_qualifier_label\n\n Association : frequency_qualifier_namespace\n\n Association : grouping_key\n\n Association : has_count\n\n Association : has_evidence\n\n Association : has_evidence_links\n\n\n\n\n Association --> \"*\" ExpandedCurie : has_evidence_links\n click ExpandedCurie href \"../ExpandedCurie\"\n\n\n Association : has_percentage\n\n Association : has_quotient\n\n Association : has_total\n\n Association : id\n\n Association : knowledge_level\n\n Association : negated\n\n Association : object\n\n Association : object_category\n\n Association : object_closure\n\n Association : object_closure_label\n\n Association : object_label\n\n Association : object_namespace\n\n Association : object_taxon\n\n Association : object_taxon_label\n\n Association : onset_qualifier\n\n Association : onset_qualifier_category\n\n Association : onset_qualifier_label\n\n Association : onset_qualifier_namespace\n\n Association : original_object\n\n Association : original_subject\n\n Association : pathway\n\n Association : predicate\n\n Association : primary_knowledge_source\n\n Association : provided_by\n\n Association : provided_by_link\n\n\n\n\n Association --> \"0..1\" ExpandedCurie : provided_by_link\n click ExpandedCurie href \"../ExpandedCurie\"\n\n\n Association : publications\n\n Association : publications_links\n\n\n\n\n Association --> \"*\" ExpandedCurie : publications_links\n click ExpandedCurie href \"../ExpandedCurie\"\n\n\n Association : qualifier\n\n Association : qualifier_category\n\n Association : qualifier_label\n\n Association : qualifier_namespace\n\n Association : qualifiers\n\n Association : qualifiers_category\n\n Association : qualifiers_label\n\n Association : qualifiers_namespace\n\n Association : sex_qualifier\n\n Association : sex_qualifier_category\n\n Association : sex_qualifier_label\n\n Association : sex_qualifier_namespace\n\n Association : species_context_qualifier\n\n Association : species_context_qualifier_category\n\n Association : species_context_qualifier_label\n\n Association : species_context_qualifier_namespace\n\n Association : stage_qualifier\n\n Association : stage_qualifier_category\n\n Association : stage_qualifier_label\n\n Association : stage_qualifier_namespace\n\n Association : subject\n\n Association : subject_category\n\n Association : subject_closure\n\n Association : subject_closure_label\n\n Association : subject_label\n\n Association : subject_namespace\n\n Association : subject_taxon\n\n Association : subject_taxon_label\nname: Association\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- id\n- category\n- subject\n- original_subject\n- subject_namespace\n- subject_category\n- subject_closure\n- subject_label\n- subject_closure_label\n- subject_taxon\n- subject_taxon_label\n- predicate\n- object\n- original_object\n- object_namespace\n- object_category\n- object_closure\n- object_label\n- object_closure_label\n- object_taxon\n- object_taxon_label\n- primary_knowledge_source\n- aggregator_knowledge_source\n- negated\n- pathway\n- evidence_count\n- knowledge_level\n- agent_type\n- has_evidence\n- has_evidence_links\n- has_count\n- has_total\n- has_percentage\n- has_quotient\n- grouping_key\n- provided_by\n- provided_by_link\n- publications\n- publications_links\n- frequency_qualifier\n- onset_qualifier\n- sex_qualifier\n- stage_qualifier\n- qualifiers\n- qualifiers_label\n- qualifiers_namespace\n- qualifiers_category\n- qualifier\n- qualifier_label\n- qualifier_namespace\n- qualifier_category\n- frequency_qualifier_label\n- frequency_qualifier_namespace\n- frequency_qualifier_category\n- onset_qualifier_label\n- onset_qualifier_namespace\n- onset_qualifier_category\n- sex_qualifier_label\n- sex_qualifier_namespace\n- sex_qualifier_category\n- stage_qualifier_label\n- stage_qualifier_namespace\n- stage_qualifier_category\n- disease_context_qualifier\n- disease_context_qualifier_label\n- disease_context_qualifier_namespace\n- disease_context_qualifier_category\n- disease_context_qualifier_closure\n- disease_context_qualifier_closure_label\n- species_context_qualifier\n- species_context_qualifier_label\n- species_context_qualifier_namespace\n- species_context_qualifier_category\nname: Association\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n id:\n name: id\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n identifier: true\n alias: id\n owner: Association\n domain_of:\n - Association\n - ExpandedCurie\n - Entity\n - HistoPheno\n - HistoBin\n - Mapping\n - MultiEntityAssociationResults\n - TermInfo\n range: string\n required: true\n category:\n name: category\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: category\n owner: Association\n domain_of:\n - Association\n - AssociationCount\n - CompactAssociation\n - AssociationTypeMapping\n - Entity\n range: string\n multivalued: false\n subject:\n name: subject\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: subject\n owner: Association\n domain_of:\n - Association\n - CompactAssociation\n - SemsimSearchResult\n range: string\n required: true\n original_subject:\n name: original_subject\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: original_subject\n owner: Association\n domain_of:\n - Association\n range: string\n subject_namespace:\n name: subject_namespace\n description: The namespace/prefix of the subject entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: subject_namespace\n owner: Association\n domain_of:\n - Association\n range: string\n subject_category:\n name: subject_category\n description: The category of the subject entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: category\n alias: subject_category\n owner: Association\n domain_of:\n - Association\n range: string\n subject_closure:\n name: subject_closure\n description: Field containing subject id and the ids of all of it's ancestors\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: subject_closure\n owner: Association\n domain_of:\n - Association\n range: string\n multivalued: true\n subject_label:\n name: subject_label\n description: The name of the subject entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: subject_label\n owner: Association\n domain_of:\n - Association\n - CompactAssociation\n - AssociationTypeMapping\n - Mapping\n - TermPairwiseSimilarity\n range: string\n subject_closure_label:\n name: subject_closure_label\n description: Field containing subject name and the names of all of it's ancestors\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: subject_closure_label\n owner: Association\n domain_of:\n - Association\n range: string\n multivalued: true\n subject_taxon:\n name: subject_taxon\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: in_taxon\n alias: subject_taxon\n owner: Association\n domain_of:\n - Association\n range: string\n subject_taxon_label:\n name: subject_taxon_label\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: in_taxon_label\n alias: subject_taxon_label\n owner: Association\n domain_of:\n - Association\n range: string\n predicate:\n name: predicate\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: predicate\n owner: Association\n domain_of:\n - Association\n - CompactAssociation\n range: string\n required: true\n multivalued: false\n object:\n name: object\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: object\n owner: Association\n domain_of:\n - Association\n - CompactAssociation\n range: string\n required: true\n original_object:\n name: original_object\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: original_object\n owner: Association\n domain_of:\n - Association\n range: string\n object_namespace:\n name: object_namespace\n description: The namespace/prefix of the object entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: object_namespace\n owner: Association\n domain_of:\n - Association\n range: string\n object_category:\n name: object_category\n description: The category of the object entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: category\n alias: object_category\n owner: Association\n domain_of:\n - Association\n range: string\n object_closure:\n name: object_closure\n description: Field containing object id and the ids of all of it's ancestors\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: object_closure\n owner: Association\n domain_of:\n - Association\n range: string\n multivalued: true\n object_label:\n name: object_label\n description: The name of the object entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: object_label\n owner: Association\n domain_of:\n - Association\n - CompactAssociation\n - AssociationTypeMapping\n - Mapping\n - TermPairwiseSimilarity\n range: string\n object_closure_label:\n name: object_closure_label\n description: Field containing object name and the names of all of it's ancestors\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: object_closure_label\n owner: Association\n domain_of:\n - Association\n range: string\n multivalued: true\n object_taxon:\n name: object_taxon\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: in_taxon\n alias: object_taxon\n owner: Association\n domain_of:\n - Association\n range: string\n object_taxon_label:\n name: object_taxon_label\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: in_taxon_label\n alias: object_taxon_label\n owner: Association\n domain_of:\n - Association\n range: string\n primary_knowledge_source:\n name: primary_knowledge_source\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: primary_knowledge_source\n owner: Association\n domain_of:\n - Association\n range: string\n aggregator_knowledge_source:\n name: aggregator_knowledge_source\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: aggregator_knowledge_source\n owner: Association\n domain_of:\n - Association\n range: string\n multivalued: true\n negated:\n name: negated\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: negated\n owner: Association\n domain_of:\n - Association\n - CompactAssociation\n range: boolean\n pathway:\n name: pathway\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: pathway\n owner: Association\n domain_of:\n - Association\n range: string\n evidence_count:\n name: evidence_count\n description: count of supporting documents, evidence codes, and sources supplying\n evidence\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: evidence_count\n owner: Association\n domain_of:\n - Association\n range: integer\n knowledge_level:\n name: knowledge_level\n description: Describes the level of knowledge expressed in a statement, based\n on the reasoning or analysis methods used to generate the statement, or the\n scope or specificity of what the statement expresses to be true.\n notes:\n - The range in this schema is represented as a string, but is constrained to\n values from biolink:KnowledgeLevelEnum at ingest time\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n slot_uri: biolink:knowledge_level\n alias: knowledge_level\n owner: Association\n domain_of:\n - Association\n range: string\n required: true\n multivalued: false\n agent_type:\n name: agent_type\n description: Describes the high-level category of agent who originally generated\n a statement of knowledge or other type of information.\n notes:\n - The range in this schema is represented as a string, but is constrained to\n values from biolink:AgentTypeEnum at ingest time\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n slot_uri: biolink:agent_type\n alias: agent_type\n owner: Association\n domain_of:\n - Association\n range: string\n required: true\n multivalued: false\n has_evidence:\n name: has_evidence\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_evidence\n owner: Association\n domain_of:\n - Association\n range: string\n multivalued: true\n has_evidence_links:\n name: has_evidence_links\n description: List of ExpandedCuries with id and url for evidence\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_evidence_links\n owner: Association\n domain_of:\n - Association\n range: ExpandedCurie\n multivalued: true\n inlined: true\n inlined_as_list: true\n has_count:\n name: has_count\n description: count of out of has_total representing a frequency\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_count\n owner: Association\n domain_of:\n - Association\n range: integer\n has_total:\n name: has_total\n description: total, devided by has_count, representing a frequency\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_total\n owner: Association\n domain_of:\n - Association\n range: integer\n has_percentage:\n name: has_percentage\n description: percentage, which may be calculated from has_count and has_total,\n as 100 * quotient or provided directly, rounded to the integer level\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_percentage\n owner: Association\n domain_of:\n - Association\n range: float\n has_quotient:\n name: has_quotient\n description: quotient, which should be 1/100 of has_percentage\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_quotient\n owner: Association\n domain_of:\n - Association\n range: float\n grouping_key:\n name: grouping_key\n description: A concatenation of fields used to group associations with the same\n essential/defining properties\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: grouping_key\n owner: Association\n domain_of:\n - Association\n range: string\n provided_by:\n name: provided_by\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: provided_by\n owner: Association\n domain_of:\n - Association\n - Entity\n range: string\n provided_by_link:\n name: provided_by_link\n description: A link to the docs for the knowledge source that provided the node/edge.\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: provided_by_link\n owner: Association\n domain_of:\n - Association\n - Node\n range: ExpandedCurie\n inlined: true\n publications:\n name: publications\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: publications\n owner: Association\n domain_of:\n - Association\n range: string\n multivalued: true\n publications_links:\n name: publications_links\n description: List of ExpandedCuries with id and url for publications\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: publications_links\n owner: Association\n domain_of:\n - Association\n range: ExpandedCurie\n multivalued: true\n inlined: true\n inlined_as_list: true\n frequency_qualifier:\n name: frequency_qualifier\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: frequency_qualifier\n owner: Association\n domain_of:\n - Association\n range: string\n onset_qualifier:\n name: onset_qualifier\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: onset_qualifier\n owner: Association\n domain_of:\n - Association\n range: string\n sex_qualifier:\n name: sex_qualifier\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: sex_qualifier\n owner: Association\n domain_of:\n - Association\n range: string\n stage_qualifier:\n name: stage_qualifier\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: stage_qualifier\n owner: Association\n domain_of:\n - Association\n range: string\n qualifiers:\n name: qualifiers\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: qualifiers\n owner: Association\n domain_of:\n - Association\n range: string\n multivalued: true\n qualifiers_label:\n name: qualifiers_label\n description: The name of the frequency_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: qualifiers_label\n owner: Association\n domain_of:\n - Association\n range: string\n qualifiers_namespace:\n name: qualifiers_namespace\n description: The namespace/prefix of the frequency_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: qualifiers_namespace\n owner: Association\n domain_of:\n - Association\n range: string\n qualifiers_category:\n name: qualifiers_category\n description: The category of the frequency_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: category\n alias: qualifiers_category\n owner: Association\n domain_of:\n - Association\n range: string\n qualifier:\n name: qualifier\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: qualifier\n owner: Association\n domain_of:\n - Association\n range: string\n multivalued: true\n qualifier_label:\n name: qualifier_label\n description: The name of the frequency_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: qualifier_label\n owner: Association\n domain_of:\n - Association\n range: string\n qualifier_namespace:\n name: qualifier_namespace\n description: The namespace/prefix of the frequency_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: qualifier_namespace\n owner: Association\n domain_of:\n - Association\n range: string\n qualifier_category:\n name: qualifier_category\n description: The category of the frequency_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: category\n alias: qualifier_category\n owner: Association\n domain_of:\n - Association\n range: string\n frequency_qualifier_label:\n name: frequency_qualifier_label\n description: The name of the frequency_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: frequency_qualifier_label\n owner: Association\n domain_of:\n - Association\n range: string\n frequency_qualifier_namespace:\n name: frequency_qualifier_namespace\n description: The namespace/prefix of the frequency_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: frequency_qualifier_namespace\n owner: Association\n domain_of:\n - Association\n range: string\n frequency_qualifier_category:\n name: frequency_qualifier_category\n description: The category of the frequency_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: category\n alias: frequency_qualifier_category\n owner: Association\n domain_of:\n - Association\n range: string\n onset_qualifier_label:\n name: onset_qualifier_label\n description: The name of the onset_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: onset_qualifier_label\n owner: Association\n domain_of:\n - Association\n range: string\n onset_qualifier_namespace:\n name: onset_qualifier_namespace\n description: The namespace/prefix of the onset_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: onset_qualifier_namespace\n owner: Association\n domain_of:\n - Association\n range: string\n onset_qualifier_category:\n name: onset_qualifier_category\n description: The category of the onset_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: category\n alias: onset_qualifier_category\n owner: Association\n domain_of:\n - Association\n range: string\n sex_qualifier_label:\n name: sex_qualifier_label\n description: The name of the sex_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: sex_qualifier_label\n owner: Association\n domain_of:\n - Association\n range: string\n sex_qualifier_namespace:\n name: sex_qualifier_namespace\n description: The namespace/prefix of the sex_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: sex_qualifier_namespace\n owner: Association\n domain_of:\n - Association\n range: string\n sex_qualifier_category:\n name: sex_qualifier_category\n description: The category of the sex_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: category\n alias: sex_qualifier_category\n owner: Association\n domain_of:\n - Association\n range: string\n stage_qualifier_label:\n name: stage_qualifier_label\n description: The name of the stage_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: stage_qualifier_label\n owner: Association\n domain_of:\n - Association\n range: string\n stage_qualifier_namespace:\n name: stage_qualifier_namespace\n description: The namespace/prefix of the stage_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: stage_qualifier_namespace\n owner: Association\n domain_of:\n - Association\n range: string\n stage_qualifier_category:\n name: stage_qualifier_category\n description: The category of the stage_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: category\n alias: stage_qualifier_category\n owner: Association\n domain_of:\n - Association\n range: string\n disease_context_qualifier:\n name: disease_context_qualifier\n description: A context qualifier representing a disease or condition in which\n a relationship expressed in an association took place.\n examples:\n - value: MONDO:0004979\n - value: MONDO:0005148\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: disease_context_qualifier\n owner: Association\n domain_of:\n - Association\n range: string\n disease_context_qualifier_label:\n name: disease_context_qualifier_label\n description: The name of the disease_context_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: disease_context_qualifier_label\n owner: Association\n domain_of:\n - Association\n range: string\n disease_context_qualifier_namespace:\n name: disease_context_qualifier_namespace\n description: The namespace/prefix of the disease_context_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: disease_context_qualifier_namespace\n owner: Association\n domain_of:\n - Association\n range: string\n disease_context_qualifier_category:\n name: disease_context_qualifier_category\n description: The category of the disease_context_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: category\n alias: disease_context_qualifier_category\n owner: Association\n domain_of:\n - Association\n range: string\n disease_context_qualifier_closure:\n name: disease_context_qualifier_closure\n description: Field containing disease_context_qualifier id and the ids of all\n of it's ancestors\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: disease_context_qualifier_closure\n owner: Association\n domain_of:\n - Association\n range: string\n multivalued: true\n disease_context_qualifier_closure_label:\n name: disease_context_qualifier_closure_label\n description: Field containing disease_context_qualifier name and the names of\n all of it's ancestors\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: disease_context_qualifier_closure_label\n owner: Association\n domain_of:\n - Association\n range: string\n multivalued: true\n species_context_qualifier:\n name: species_context_qualifier\n description: A context qualifier representing a species in which a relationship\n expressed in an association took place.\n examples:\n - value: NCBITaxon:9606\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: species_context_qualifier\n owner: Association\n domain_of:\n - Association\n range: string\n species_context_qualifier_label:\n name: species_context_qualifier_label\n description: The name of the species_context_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: species_context_qualifier_label\n owner: Association\n domain_of:\n - Association\n range: string\n species_context_qualifier_namespace:\n name: species_context_qualifier_namespace\n description: The namespace/prefix of the species_context_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: species_context_qualifier_namespace\n owner: Association\n domain_of:\n - Association\n range: string\n species_context_qualifier_category:\n name: species_context_qualifier_category\n description: The category of the species_context_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: category\n alias: species_context_qualifier_category\n owner: Association\n domain_of:\n - Association\n range: string\nURI: https://w3id.org/monarch/monarch-py/:AssociationCount
classDiagram\n class AssociationCount\n click AssociationCount href \"../AssociationCount\"\n FacetValue <|-- AssociationCount\n click FacetValue href \"../FacetValue\"\n\n AssociationCount : category\n\n AssociationCount : count\n\n AssociationCount : label\nname: AssociationCount\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: FacetValue\nslots:\n- category\nslot_usage:\n category:\n name: category\n multivalued: false\nname: AssociationCount\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: FacetValue\nslot_usage:\n category:\n name: category\n multivalued: false\nattributes:\n category:\n name: category\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: category\n owner: AssociationCount\n domain_of:\n - Association\n - AssociationCount\n - CompactAssociation\n - AssociationTypeMapping\n - Entity\n range: string\n multivalued: false\n label:\n name: label\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: label\n owner: AssociationCount\n domain_of:\n - FacetValue\n - FacetField\n - TermInfo\n range: string\n required: true\n count:\n name: count\n description: count of documents\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: count\n owner: AssociationCount\n domain_of:\n - FacetValue\n range: integer\nContainer class for a list of association counts
URI: https://w3id.org/monarch/monarch-py/:AssociationCountList
classDiagram\n class AssociationCountList\n click AssociationCountList href \"../AssociationCountList\"\n AssociationCountList : items\n\n\n\n\n AssociationCountList --> \"1..*\" AssociationCount : items\n click AssociationCount href \"../AssociationCount\"\nname: AssociationCountList\ndescription: Container class for a list of association counts\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- items\nslot_usage:\n items:\n name: items\n range: AssociationCount\nname: AssociationCountList\ndescription: Container class for a list of association counts\nfrom_schema: https://w3id.org/monarch/monarch-py\nslot_usage:\n items:\n name: items\n range: AssociationCount\nattributes:\n items:\n name: items\n description: A collection of items, with the type to be overriden by slot_usage\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: items\n owner: AssociationCountList\n domain_of:\n - AssociationCountList\n - AssociationResults\n - CompactAssociationResults\n - AssociationTableResults\n - CategoryGroupedAssociationResults\n - EntityResults\n - HistoPheno\n - MappingResults\n - SearchResults\n range: AssociationCount\n required: true\n multivalued: true\n inlined: true\n inlined_as_list: true\nThe directionality of an association as it relates to a specified entity, with edges being categorized as incoming or outgoing
URI: AssociationDirectionEnum
"},{"location":"Data-Model/AssociationDirectionEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description incoming None An association for which a specified entity is the object or part of the obje... outgoing None An association for which a specified entity is the subject or part of the sub..."},{"location":"Data-Model/AssociationDirectionEnum/#slots","title":"Slots","text":"Name Description direction The directionality of the association relative to a given entity for an assoc..."},{"location":"Data-Model/AssociationDirectionEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/AssociationDirectionEnum/#schema-source","title":"Schema Source","text":"name: AssociationDirectionEnum\ndescription: The directionality of an association as it relates to a specified entity,\n with edges being categorized as incoming or outgoing\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\npermissible_values:\n incoming:\n text: incoming\n description: An association for which a specified entity is the object or part\n of the object closure\n outgoing:\n text: outgoing\n description: An association for which a specified entity is the subject or part\n of the subject closure\nURI: https://w3id.org/monarch/monarch-py/:AssociationResults
classDiagram\n class AssociationResults\n click AssociationResults href \"../AssociationResults\"\n Results <|-- AssociationResults\n click Results href \"../Results\"\n\n AssociationResults : facet_fields\n\n\n\n\n AssociationResults --> \"*\" FacetField : facet_fields\n click FacetField href \"../FacetField\"\n\n\n AssociationResults : facet_queries\n\n\n\n\n AssociationResults --> \"*\" FacetValue : facet_queries\n click FacetValue href \"../FacetValue\"\n\n\n AssociationResults : items\n\n\n\n\n AssociationResults --> \"1..*\" Association : items\n click Association href \"../Association\"\n\n\n AssociationResults : limit\n\n AssociationResults : offset\n\n AssociationResults : total\nname: AssociationResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslots:\n- items\n- facet_fields\n- facet_queries\nslot_usage:\n items:\n name: items\n range: Association\nname: AssociationResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslot_usage:\n items:\n name: items\n range: Association\nattributes:\n items:\n name: items\n description: A collection of items, with the type to be overriden by slot_usage\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: items\n owner: AssociationResults\n domain_of:\n - AssociationCountList\n - AssociationResults\n - CompactAssociationResults\n - AssociationTableResults\n - CategoryGroupedAssociationResults\n - EntityResults\n - HistoPheno\n - MappingResults\n - SearchResults\n range: Association\n required: true\n multivalued: true\n inlined: true\n inlined_as_list: true\n facet_fields:\n name: facet_fields\n description: Collection of facet field responses with the field values and counts\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: facet_fields\n owner: AssociationResults\n domain_of:\n - AssociationResults\n - CompactAssociationResults\n - AssociationTableResults\n - SearchResults\n range: FacetField\n multivalued: true\n inlined: true\n inlined_as_list: true\n facet_queries:\n name: facet_queries\n description: Collection of facet query responses with the query string values\n and counts\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: facet_queries\n owner: AssociationResults\n domain_of:\n - AssociationResults\n - CompactAssociationResults\n - AssociationTableResults\n - SearchResults\n range: FacetValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n limit:\n name: limit\n description: number of items to return in a response\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: limit\n owner: AssociationResults\n domain_of:\n - Results\n range: integer\n required: true\n offset:\n name: offset\n description: offset into the total number of items\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: offset\n owner: AssociationResults\n domain_of:\n - Results\n range: integer\n required: true\n total:\n name: total\n description: total number of items matching a query\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: total\n owner: AssociationResults\n domain_of:\n - Results\n range: integer\n required: true\nURI: https://w3id.org/monarch/monarch-py/:AssociationTableResults
classDiagram\n class AssociationTableResults\n click AssociationTableResults href \"../AssociationTableResults\"\n Results <|-- AssociationTableResults\n click Results href \"../Results\"\n\n AssociationTableResults : facet_fields\n\n\n\n\n AssociationTableResults --> \"*\" FacetField : facet_fields\n click FacetField href \"../FacetField\"\n\n\n AssociationTableResults : facet_queries\n\n\n\n\n AssociationTableResults --> \"*\" FacetValue : facet_queries\n click FacetValue href \"../FacetValue\"\n\n\n AssociationTableResults : items\n\n\n\n\n AssociationTableResults --> \"1..*\" DirectionalAssociation : items\n click DirectionalAssociation href \"../DirectionalAssociation\"\n\n\n AssociationTableResults : limit\n\n AssociationTableResults : offset\n\n AssociationTableResults : total\nname: AssociationTableResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslots:\n- items\n- facet_fields\n- facet_queries\nslot_usage:\n items:\n name: items\n range: DirectionalAssociation\nname: AssociationTableResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslot_usage:\n items:\n name: items\n range: DirectionalAssociation\nattributes:\n items:\n name: items\n description: A collection of items, with the type to be overriden by slot_usage\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: items\n owner: AssociationTableResults\n domain_of:\n - AssociationCountList\n - AssociationResults\n - CompactAssociationResults\n - AssociationTableResults\n - CategoryGroupedAssociationResults\n - EntityResults\n - HistoPheno\n - MappingResults\n - SearchResults\n range: DirectionalAssociation\n required: true\n multivalued: true\n inlined: true\n inlined_as_list: true\n facet_fields:\n name: facet_fields\n description: Collection of facet field responses with the field values and counts\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: facet_fields\n owner: AssociationTableResults\n domain_of:\n - AssociationResults\n - CompactAssociationResults\n - AssociationTableResults\n - SearchResults\n range: FacetField\n multivalued: true\n inlined: true\n inlined_as_list: true\n facet_queries:\n name: facet_queries\n description: Collection of facet query responses with the query string values\n and counts\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: facet_queries\n owner: AssociationTableResults\n domain_of:\n - AssociationResults\n - CompactAssociationResults\n - AssociationTableResults\n - SearchResults\n range: FacetValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n limit:\n name: limit\n description: number of items to return in a response\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: limit\n owner: AssociationTableResults\n domain_of:\n - Results\n range: integer\n required: true\n offset:\n name: offset\n description: offset into the total number of items\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: offset\n owner: AssociationTableResults\n domain_of:\n - Results\n range: integer\n required: true\n total:\n name: total\n description: total number of items matching a query\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: total\n owner: AssociationTableResults\n domain_of:\n - Results\n range: integer\n required: true\nA data class to hold the necessary information to produce association type counts for given entities with appropriate directional labels
URI: https://w3id.org/monarch/monarch-py/:AssociationTypeMapping
classDiagram\n class AssociationTypeMapping\n click AssociationTypeMapping href \"../AssociationTypeMapping\"\n AssociationTypeMapping : category\n\n AssociationTypeMapping : object_label\n\n AssociationTypeMapping : subject_label\n\n AssociationTypeMapping : symmetric\nname: AssociationTypeMapping\ndescription: A data class to hold the necessary information to produce association\n type counts for given entities with appropriate directional labels\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- subject_label\n- object_label\n- symmetric\n- category\nslot_usage:\n subject_label:\n name: subject_label\n description: A label to describe the subjects of the association type as a whole\n for use in the UI\n object_label:\n name: object_label\n description: A label to describe the objects of the association type as a whole\n for use in the UI\n symmetric:\n name: symmetric\n description: Whether the association type is symmetric, meaning that the subject\n and object labels should be interchangeable\n ifabsent: 'False'\n required: true\n category:\n name: category\n description: The biolink category to use in queries for this association type\n required: true\n multivalued: false\nname: AssociationTypeMapping\ndescription: A data class to hold the necessary information to produce association\n type counts for given entities with appropriate directional labels\nfrom_schema: https://w3id.org/monarch/monarch-py\nslot_usage:\n subject_label:\n name: subject_label\n description: A label to describe the subjects of the association type as a whole\n for use in the UI\n object_label:\n name: object_label\n description: A label to describe the objects of the association type as a whole\n for use in the UI\n symmetric:\n name: symmetric\n description: Whether the association type is symmetric, meaning that the subject\n and object labels should be interchangeable\n ifabsent: 'False'\n required: true\n category:\n name: category\n description: The biolink category to use in queries for this association type\n required: true\n multivalued: false\nattributes:\n subject_label:\n name: subject_label\n description: A label to describe the subjects of the association type as a whole\n for use in the UI\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: subject_label\n owner: AssociationTypeMapping\n domain_of:\n - Association\n - CompactAssociation\n - AssociationTypeMapping\n - Mapping\n - TermPairwiseSimilarity\n range: string\n object_label:\n name: object_label\n description: A label to describe the objects of the association type as a whole\n for use in the UI\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: object_label\n owner: AssociationTypeMapping\n domain_of:\n - Association\n - CompactAssociation\n - AssociationTypeMapping\n - Mapping\n - TermPairwiseSimilarity\n range: string\n symmetric:\n name: symmetric\n description: Whether the association type is symmetric, meaning that the subject\n and object labels should be interchangeable\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n ifabsent: 'False'\n alias: symmetric\n owner: AssociationTypeMapping\n domain_of:\n - AssociationTypeMapping\n range: boolean\n required: true\n category:\n name: category\n description: The biolink category to use in queries for this association type\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: category\n owner: AssociationTypeMapping\n domain_of:\n - Association\n - AssociationCount\n - CompactAssociation\n - AssociationTypeMapping\n - Entity\n range: string\n required: true\n multivalued: false\nURI: https://w3id.org/monarch/monarch-py/:BestMatch
classDiagram\n class BestMatch\n click BestMatch href \"../BestMatch\"\n BestMatch : match_source\n\n BestMatch : match_source_label\n\n BestMatch : match_subsumer\n\n BestMatch : match_subsumer_label\n\n BestMatch : match_target\n\n BestMatch : match_target_label\n\n BestMatch : score\n\n BestMatch : similarity\n\n\n\n\n BestMatch --> \"1\" TermPairwiseSimilarity : similarity\n click TermPairwiseSimilarity href \"../TermPairwiseSimilarity\"\nname: BestMatch\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n match_source:\n name: match_source\n comments:\n - note that the match_source is either the subject or the object\n from_schema: https://w3id.org/monarch/monarch-py-similarity\n rank: 1000\n identifier: true\n domain_of:\n - BestMatch\n required: true\n match_source_label:\n name: match_source_label\n from_schema: https://w3id.org/monarch/monarch-py-similarity\n rank: 1000\n domain_of:\n - BestMatch\n match_target:\n name: match_target\n description: the entity matches\n from_schema: https://w3id.org/monarch/monarch-py-similarity\n rank: 1000\n domain_of:\n - BestMatch\n match_target_label:\n name: match_target_label\n from_schema: https://w3id.org/monarch/monarch-py-similarity\n rank: 1000\n domain_of:\n - BestMatch\n score:\n name: score\n from_schema: https://w3id.org/monarch/monarch-py-similarity\n domain_of:\n - SearchResult\n - BestMatch\n - SemsimSearchResult\n range: float\n required: true\n match_subsumer:\n name: match_subsumer\n from_schema: https://w3id.org/monarch/monarch-py-similarity\n rank: 1000\n domain_of:\n - BestMatch\n range: uriorcurie\n match_subsumer_label:\n name: match_subsumer_label\n from_schema: https://w3id.org/monarch/monarch-py-similarity\n rank: 1000\n domain_of:\n - BestMatch\n similarity:\n name: similarity\n from_schema: https://w3id.org/monarch/monarch-py-similarity\n domain_of:\n - BestMatch\n - SemsimSearchResult\n range: TermPairwiseSimilarity\n required: true\nname: BestMatch\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n match_source:\n name: match_source\n comments:\n - note that the match_source is either the subject or the object\n from_schema: https://w3id.org/monarch/monarch-py-similarity\n rank: 1000\n identifier: true\n alias: match_source\n owner: BestMatch\n domain_of:\n - BestMatch\n range: string\n required: true\n match_source_label:\n name: match_source_label\n from_schema: https://w3id.org/monarch/monarch-py-similarity\n rank: 1000\n alias: match_source_label\n owner: BestMatch\n domain_of:\n - BestMatch\n range: string\n match_target:\n name: match_target\n description: the entity matches\n from_schema: https://w3id.org/monarch/monarch-py-similarity\n rank: 1000\n alias: match_target\n owner: BestMatch\n domain_of:\n - BestMatch\n range: string\n match_target_label:\n name: match_target_label\n from_schema: https://w3id.org/monarch/monarch-py-similarity\n rank: 1000\n alias: match_target_label\n owner: BestMatch\n domain_of:\n - BestMatch\n range: string\n score:\n name: score\n from_schema: https://w3id.org/monarch/monarch-py-similarity\n alias: score\n owner: BestMatch\n domain_of:\n - SearchResult\n - BestMatch\n - SemsimSearchResult\n range: float\n required: true\n match_subsumer:\n name: match_subsumer\n from_schema: https://w3id.org/monarch/monarch-py-similarity\n rank: 1000\n alias: match_subsumer\n owner: BestMatch\n domain_of:\n - BestMatch\n range: uriorcurie\n match_subsumer_label:\n name: match_subsumer_label\n from_schema: https://w3id.org/monarch/monarch-py-similarity\n rank: 1000\n alias: match_subsumer_label\n owner: BestMatch\n domain_of:\n - BestMatch\n range: string\n similarity:\n name: similarity\n from_schema: https://w3id.org/monarch/monarch-py-similarity\n alias: similarity\n owner: BestMatch\n domain_of:\n - BestMatch\n - SemsimSearchResult\n range: TermPairwiseSimilarity\n required: true\nA binary (true or false) value
URI: xsd:boolean
base: Bool
uri: xsd:boolean
repr: bool
URI: https://w3id.org/monarch/monarch-py/:CategoryGroupedAssociationResults
classDiagram\n class CategoryGroupedAssociationResults\n click CategoryGroupedAssociationResults href \"../CategoryGroupedAssociationResults\"\n Results <|-- CategoryGroupedAssociationResults\n click Results href \"../Results\"\n\n CategoryGroupedAssociationResults : counterpart_category\n\n CategoryGroupedAssociationResults : items\n\n\n\n\n CategoryGroupedAssociationResults --> \"1..*\" Association : items\n click Association href \"../Association\"\n\n\n CategoryGroupedAssociationResults : limit\n\n CategoryGroupedAssociationResults : offset\n\n CategoryGroupedAssociationResults : total\nname: CategoryGroupedAssociationResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslots:\n- counterpart_category\n- items\nslot_usage:\n items:\n name: items\n range: Association\nname: CategoryGroupedAssociationResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslot_usage:\n items:\n name: items\n range: Association\nattributes:\n counterpart_category:\n name: counterpart_category\n description: The category of the counterpart entity in a given association, eg.\n the category of the entity that is not the subject\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: counterpart_category\n owner: CategoryGroupedAssociationResults\n domain_of:\n - CategoryGroupedAssociationResults\n range: string\n items:\n name: items\n description: A collection of items, with the type to be overriden by slot_usage\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: items\n owner: CategoryGroupedAssociationResults\n domain_of:\n - AssociationCountList\n - AssociationResults\n - CompactAssociationResults\n - AssociationTableResults\n - CategoryGroupedAssociationResults\n - EntityResults\n - HistoPheno\n - MappingResults\n - SearchResults\n range: Association\n required: true\n multivalued: true\n inlined: true\n inlined_as_list: true\n limit:\n name: limit\n description: number of items to return in a response\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: limit\n owner: CategoryGroupedAssociationResults\n domain_of:\n - Results\n range: integer\n required: true\n offset:\n name: offset\n description: offset into the total number of items\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: offset\n owner: CategoryGroupedAssociationResults\n domain_of:\n - Results\n range: integer\n required: true\n total:\n name: total\n description: total number of items matching a query\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: total\n owner: CategoryGroupedAssociationResults\n domain_of:\n - Results\n range: integer\n required: true\nURI: https://w3id.org/monarch/monarch-py/:CompactAssociation
classDiagram\n class CompactAssociation\n click CompactAssociation href \"../CompactAssociation\"\n CompactAssociation : category\n\n CompactAssociation : negated\n\n CompactAssociation : object\n\n CompactAssociation : object_label\n\n CompactAssociation : predicate\n\n CompactAssociation : subject\n\n CompactAssociation : subject_label\nname: CompactAssociation\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- category\n- subject\n- subject_label\n- predicate\n- object\n- object_label\n- negated\nname: CompactAssociation\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n category:\n name: category\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: category\n owner: CompactAssociation\n domain_of:\n - Association\n - AssociationCount\n - CompactAssociation\n - AssociationTypeMapping\n - Entity\n range: string\n multivalued: false\n subject:\n name: subject\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: subject\n owner: CompactAssociation\n domain_of:\n - Association\n - CompactAssociation\n - SemsimSearchResult\n range: string\n required: true\n subject_label:\n name: subject_label\n description: The name of the subject entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: subject_label\n owner: CompactAssociation\n domain_of:\n - Association\n - CompactAssociation\n - AssociationTypeMapping\n - Mapping\n - TermPairwiseSimilarity\n range: string\n predicate:\n name: predicate\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: predicate\n owner: CompactAssociation\n domain_of:\n - Association\n - CompactAssociation\n range: string\n required: true\n multivalued: false\n object:\n name: object\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: object\n owner: CompactAssociation\n domain_of:\n - Association\n - CompactAssociation\n range: string\n required: true\n object_label:\n name: object_label\n description: The name of the object entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: object_label\n owner: CompactAssociation\n domain_of:\n - Association\n - CompactAssociation\n - AssociationTypeMapping\n - Mapping\n - TermPairwiseSimilarity\n range: string\n negated:\n name: negated\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: negated\n owner: CompactAssociation\n domain_of:\n - Association\n - CompactAssociation\n range: boolean\nURI: https://w3id.org/monarch/monarch-py/:CompactAssociationResults
classDiagram\n class CompactAssociationResults\n click CompactAssociationResults href \"../CompactAssociationResults\"\n Results <|-- CompactAssociationResults\n click Results href \"../Results\"\n\n CompactAssociationResults : facet_fields\n\n\n\n\n CompactAssociationResults --> \"*\" FacetField : facet_fields\n click FacetField href \"../FacetField\"\n\n\n CompactAssociationResults : facet_queries\n\n\n\n\n CompactAssociationResults --> \"*\" FacetValue : facet_queries\n click FacetValue href \"../FacetValue\"\n\n\n CompactAssociationResults : items\n\n\n\n\n CompactAssociationResults --> \"1..*\" CompactAssociation : items\n click CompactAssociation href \"../CompactAssociation\"\n\n\n CompactAssociationResults : limit\n\n CompactAssociationResults : offset\n\n CompactAssociationResults : total\nname: CompactAssociationResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslots:\n- items\n- facet_fields\n- facet_queries\nslot_usage:\n items:\n name: items\n range: CompactAssociation\nname: CompactAssociationResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslot_usage:\n items:\n name: items\n range: CompactAssociation\nattributes:\n items:\n name: items\n description: A collection of items, with the type to be overriden by slot_usage\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: items\n owner: CompactAssociationResults\n domain_of:\n - AssociationCountList\n - AssociationResults\n - CompactAssociationResults\n - AssociationTableResults\n - CategoryGroupedAssociationResults\n - EntityResults\n - HistoPheno\n - MappingResults\n - SearchResults\n range: CompactAssociation\n required: true\n multivalued: true\n inlined: true\n inlined_as_list: true\n facet_fields:\n name: facet_fields\n description: Collection of facet field responses with the field values and counts\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: facet_fields\n owner: CompactAssociationResults\n domain_of:\n - AssociationResults\n - CompactAssociationResults\n - AssociationTableResults\n - SearchResults\n range: FacetField\n multivalued: true\n inlined: true\n inlined_as_list: true\n facet_queries:\n name: facet_queries\n description: Collection of facet query responses with the query string values\n and counts\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: facet_queries\n owner: CompactAssociationResults\n domain_of:\n - AssociationResults\n - CompactAssociationResults\n - AssociationTableResults\n - SearchResults\n range: FacetValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n limit:\n name: limit\n description: number of items to return in a response\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: limit\n owner: CompactAssociationResults\n domain_of:\n - Results\n range: integer\n required: true\n offset:\n name: offset\n description: offset into the total number of items\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: offset\n owner: CompactAssociationResults\n domain_of:\n - Results\n range: integer\n required: true\n total:\n name: total\n description: total number of items matching a query\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: total\n owner: CompactAssociationResults\n domain_of:\n - Results\n range: integer\n required: true\na compact URI
URI: xsd:string
base: Curie
uri: xsd:string
repr: str
a date (year, month and day) in an idealized calendar
URI: xsd:date
base: XSDDate
uri: xsd:date
repr: str
Either a date or a datetime
URI: linkml:DateOrDatetime
base: str
uri: linkml:DateOrDatetime
repr: str
The combination of a date and time
URI: xsd:dateTime
base: XSDDateTime
uri: xsd:dateTime
repr: str
A real number with arbitrary precision that conforms to the xsd:decimal specification
URI: xsd:decimal
base: Decimal
uri: xsd:decimal
An association that gives it's direction relative to a specified entity
URI: https://w3id.org/monarch/monarch-py/:DirectionalAssociation
classDiagram\n class DirectionalAssociation\n click DirectionalAssociation href \"../DirectionalAssociation\"\n Association <|-- DirectionalAssociation\n click Association href \"../Association\"\n\n DirectionalAssociation : agent_type\n\n DirectionalAssociation : aggregator_knowledge_source\n\n DirectionalAssociation : category\n\n DirectionalAssociation : direction\n\n\n\n\n DirectionalAssociation --> \"1\" AssociationDirectionEnum : direction\n click AssociationDirectionEnum href \"../AssociationDirectionEnum\"\n\n\n DirectionalAssociation : disease_context_qualifier\n\n DirectionalAssociation : disease_context_qualifier_category\n\n DirectionalAssociation : disease_context_qualifier_closure\n\n DirectionalAssociation : disease_context_qualifier_closure_label\n\n DirectionalAssociation : disease_context_qualifier_label\n\n DirectionalAssociation : disease_context_qualifier_namespace\n\n DirectionalAssociation : evidence_count\n\n DirectionalAssociation : frequency_qualifier\n\n DirectionalAssociation : frequency_qualifier_category\n\n DirectionalAssociation : frequency_qualifier_label\n\n DirectionalAssociation : frequency_qualifier_namespace\n\n DirectionalAssociation : grouping_key\n\n DirectionalAssociation : has_count\n\n DirectionalAssociation : has_evidence\n\n DirectionalAssociation : has_evidence_links\n\n\n\n\n DirectionalAssociation --> \"*\" ExpandedCurie : has_evidence_links\n click ExpandedCurie href \"../ExpandedCurie\"\n\n\n DirectionalAssociation : has_percentage\n\n DirectionalAssociation : has_quotient\n\n DirectionalAssociation : has_total\n\n DirectionalAssociation : id\n\n DirectionalAssociation : knowledge_level\n\n DirectionalAssociation : negated\n\n DirectionalAssociation : object\n\n DirectionalAssociation : object_category\n\n DirectionalAssociation : object_closure\n\n DirectionalAssociation : object_closure_label\n\n DirectionalAssociation : object_label\n\n DirectionalAssociation : object_namespace\n\n DirectionalAssociation : object_taxon\n\n DirectionalAssociation : object_taxon_label\n\n DirectionalAssociation : onset_qualifier\n\n DirectionalAssociation : onset_qualifier_category\n\n DirectionalAssociation : onset_qualifier_label\n\n DirectionalAssociation : onset_qualifier_namespace\n\n DirectionalAssociation : original_object\n\n DirectionalAssociation : original_subject\n\n DirectionalAssociation : pathway\n\n DirectionalAssociation : predicate\n\n DirectionalAssociation : primary_knowledge_source\n\n DirectionalAssociation : provided_by\n\n DirectionalAssociation : provided_by_link\n\n\n\n\n DirectionalAssociation --> \"0..1\" ExpandedCurie : provided_by_link\n click ExpandedCurie href \"../ExpandedCurie\"\n\n\n DirectionalAssociation : publications\n\n DirectionalAssociation : publications_links\n\n\n\n\n DirectionalAssociation --> \"*\" ExpandedCurie : publications_links\n click ExpandedCurie href \"../ExpandedCurie\"\n\n\n DirectionalAssociation : qualifier\n\n DirectionalAssociation : qualifier_category\n\n DirectionalAssociation : qualifier_label\n\n DirectionalAssociation : qualifier_namespace\n\n DirectionalAssociation : qualifiers\n\n DirectionalAssociation : qualifiers_category\n\n DirectionalAssociation : qualifiers_label\n\n DirectionalAssociation : qualifiers_namespace\n\n DirectionalAssociation : sex_qualifier\n\n DirectionalAssociation : sex_qualifier_category\n\n DirectionalAssociation : sex_qualifier_label\n\n DirectionalAssociation : sex_qualifier_namespace\n\n DirectionalAssociation : species_context_qualifier\n\n DirectionalAssociation : species_context_qualifier_category\n\n DirectionalAssociation : species_context_qualifier_label\n\n DirectionalAssociation : species_context_qualifier_namespace\n\n DirectionalAssociation : stage_qualifier\n\n DirectionalAssociation : stage_qualifier_category\n\n DirectionalAssociation : stage_qualifier_label\n\n DirectionalAssociation : stage_qualifier_namespace\n\n DirectionalAssociation : subject\n\n DirectionalAssociation : subject_category\n\n DirectionalAssociation : subject_closure\n\n DirectionalAssociation : subject_closure_label\n\n DirectionalAssociation : subject_label\n\n DirectionalAssociation : subject_namespace\n\n DirectionalAssociation : subject_taxon\n\n DirectionalAssociation : subject_taxon_label\nname: DirectionalAssociation\ndescription: An association that gives it's direction relative to a specified entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Association\nslots:\n- direction\nname: DirectionalAssociation\ndescription: An association that gives it's direction relative to a specified entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Association\nattributes:\n direction:\n name: direction\n description: The directionality of the association relative to a given entity\n for an association_count. If the entity is the subject or in the subject closure,\n the direction is forwards, if it is the object or in the object closure, the\n direction is backwards.\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: direction\n owner: DirectionalAssociation\n domain_of:\n - DirectionalAssociation\n range: AssociationDirectionEnum\n required: true\n id:\n name: id\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n identifier: true\n alias: id\n owner: DirectionalAssociation\n domain_of:\n - Association\n - ExpandedCurie\n - Entity\n - HistoPheno\n - HistoBin\n - Mapping\n - MultiEntityAssociationResults\n - TermInfo\n range: string\n required: true\n category:\n name: category\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: category\n owner: DirectionalAssociation\n domain_of:\n - Association\n - AssociationCount\n - CompactAssociation\n - AssociationTypeMapping\n - Entity\n range: string\n multivalued: false\n subject:\n name: subject\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: subject\n owner: DirectionalAssociation\n domain_of:\n - Association\n - CompactAssociation\n - SemsimSearchResult\n range: string\n required: true\n original_subject:\n name: original_subject\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: original_subject\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n subject_namespace:\n name: subject_namespace\n description: The namespace/prefix of the subject entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: subject_namespace\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n subject_category:\n name: subject_category\n description: The category of the subject entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: category\n alias: subject_category\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n subject_closure:\n name: subject_closure\n description: Field containing subject id and the ids of all of it's ancestors\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: subject_closure\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n multivalued: true\n subject_label:\n name: subject_label\n description: The name of the subject entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: subject_label\n owner: DirectionalAssociation\n domain_of:\n - Association\n - CompactAssociation\n - AssociationTypeMapping\n - Mapping\n - TermPairwiseSimilarity\n range: string\n subject_closure_label:\n name: subject_closure_label\n description: Field containing subject name and the names of all of it's ancestors\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: subject_closure_label\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n multivalued: true\n subject_taxon:\n name: subject_taxon\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: in_taxon\n alias: subject_taxon\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n subject_taxon_label:\n name: subject_taxon_label\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: in_taxon_label\n alias: subject_taxon_label\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n predicate:\n name: predicate\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: predicate\n owner: DirectionalAssociation\n domain_of:\n - Association\n - CompactAssociation\n range: string\n required: true\n multivalued: false\n object:\n name: object\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: object\n owner: DirectionalAssociation\n domain_of:\n - Association\n - CompactAssociation\n range: string\n required: true\n original_object:\n name: original_object\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: original_object\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n object_namespace:\n name: object_namespace\n description: The namespace/prefix of the object entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: object_namespace\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n object_category:\n name: object_category\n description: The category of the object entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: category\n alias: object_category\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n object_closure:\n name: object_closure\n description: Field containing object id and the ids of all of it's ancestors\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: object_closure\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n multivalued: true\n object_label:\n name: object_label\n description: The name of the object entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: object_label\n owner: DirectionalAssociation\n domain_of:\n - Association\n - CompactAssociation\n - AssociationTypeMapping\n - Mapping\n - TermPairwiseSimilarity\n range: string\n object_closure_label:\n name: object_closure_label\n description: Field containing object name and the names of all of it's ancestors\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: object_closure_label\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n multivalued: true\n object_taxon:\n name: object_taxon\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: in_taxon\n alias: object_taxon\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n object_taxon_label:\n name: object_taxon_label\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: in_taxon_label\n alias: object_taxon_label\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n primary_knowledge_source:\n name: primary_knowledge_source\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: primary_knowledge_source\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n aggregator_knowledge_source:\n name: aggregator_knowledge_source\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: aggregator_knowledge_source\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n multivalued: true\n negated:\n name: negated\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: negated\n owner: DirectionalAssociation\n domain_of:\n - Association\n - CompactAssociation\n range: boolean\n pathway:\n name: pathway\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: pathway\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n evidence_count:\n name: evidence_count\n description: count of supporting documents, evidence codes, and sources supplying\n evidence\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: evidence_count\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: integer\n knowledge_level:\n name: knowledge_level\n description: Describes the level of knowledge expressed in a statement, based\n on the reasoning or analysis methods used to generate the statement, or the\n scope or specificity of what the statement expresses to be true.\n notes:\n - The range in this schema is represented as a string, but is constrained to\n values from biolink:KnowledgeLevelEnum at ingest time\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n slot_uri: biolink:knowledge_level\n alias: knowledge_level\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n required: true\n multivalued: false\n agent_type:\n name: agent_type\n description: Describes the high-level category of agent who originally generated\n a statement of knowledge or other type of information.\n notes:\n - The range in this schema is represented as a string, but is constrained to\n values from biolink:AgentTypeEnum at ingest time\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n slot_uri: biolink:agent_type\n alias: agent_type\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n required: true\n multivalued: false\n has_evidence:\n name: has_evidence\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_evidence\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n multivalued: true\n has_evidence_links:\n name: has_evidence_links\n description: List of ExpandedCuries with id and url for evidence\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_evidence_links\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: ExpandedCurie\n multivalued: true\n inlined: true\n inlined_as_list: true\n has_count:\n name: has_count\n description: count of out of has_total representing a frequency\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_count\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: integer\n has_total:\n name: has_total\n description: total, devided by has_count, representing a frequency\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_total\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: integer\n has_percentage:\n name: has_percentage\n description: percentage, which may be calculated from has_count and has_total,\n as 100 * quotient or provided directly, rounded to the integer level\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_percentage\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: float\n has_quotient:\n name: has_quotient\n description: quotient, which should be 1/100 of has_percentage\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_quotient\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: float\n grouping_key:\n name: grouping_key\n description: A concatenation of fields used to group associations with the same\n essential/defining properties\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: grouping_key\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n provided_by:\n name: provided_by\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: provided_by\n owner: DirectionalAssociation\n domain_of:\n - Association\n - Entity\n range: string\n provided_by_link:\n name: provided_by_link\n description: A link to the docs for the knowledge source that provided the node/edge.\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: provided_by_link\n owner: DirectionalAssociation\n domain_of:\n - Association\n - Node\n range: ExpandedCurie\n inlined: true\n publications:\n name: publications\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: publications\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n multivalued: true\n publications_links:\n name: publications_links\n description: List of ExpandedCuries with id and url for publications\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: publications_links\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: ExpandedCurie\n multivalued: true\n inlined: true\n inlined_as_list: true\n frequency_qualifier:\n name: frequency_qualifier\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: frequency_qualifier\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n onset_qualifier:\n name: onset_qualifier\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: onset_qualifier\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n sex_qualifier:\n name: sex_qualifier\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: sex_qualifier\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n stage_qualifier:\n name: stage_qualifier\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: stage_qualifier\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n qualifiers:\n name: qualifiers\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: qualifiers\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n multivalued: true\n qualifiers_label:\n name: qualifiers_label\n description: The name of the frequency_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: qualifiers_label\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n qualifiers_namespace:\n name: qualifiers_namespace\n description: The namespace/prefix of the frequency_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: qualifiers_namespace\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n qualifiers_category:\n name: qualifiers_category\n description: The category of the frequency_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: category\n alias: qualifiers_category\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n qualifier:\n name: qualifier\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: qualifier\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n multivalued: true\n qualifier_label:\n name: qualifier_label\n description: The name of the frequency_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: qualifier_label\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n qualifier_namespace:\n name: qualifier_namespace\n description: The namespace/prefix of the frequency_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: qualifier_namespace\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n qualifier_category:\n name: qualifier_category\n description: The category of the frequency_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: category\n alias: qualifier_category\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n frequency_qualifier_label:\n name: frequency_qualifier_label\n description: The name of the frequency_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: frequency_qualifier_label\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n frequency_qualifier_namespace:\n name: frequency_qualifier_namespace\n description: The namespace/prefix of the frequency_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: frequency_qualifier_namespace\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n frequency_qualifier_category:\n name: frequency_qualifier_category\n description: The category of the frequency_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: category\n alias: frequency_qualifier_category\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n onset_qualifier_label:\n name: onset_qualifier_label\n description: The name of the onset_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: onset_qualifier_label\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n onset_qualifier_namespace:\n name: onset_qualifier_namespace\n description: The namespace/prefix of the onset_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: onset_qualifier_namespace\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n onset_qualifier_category:\n name: onset_qualifier_category\n description: The category of the onset_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: category\n alias: onset_qualifier_category\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n sex_qualifier_label:\n name: sex_qualifier_label\n description: The name of the sex_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: sex_qualifier_label\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n sex_qualifier_namespace:\n name: sex_qualifier_namespace\n description: The namespace/prefix of the sex_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: sex_qualifier_namespace\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n sex_qualifier_category:\n name: sex_qualifier_category\n description: The category of the sex_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: category\n alias: sex_qualifier_category\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n stage_qualifier_label:\n name: stage_qualifier_label\n description: The name of the stage_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: stage_qualifier_label\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n stage_qualifier_namespace:\n name: stage_qualifier_namespace\n description: The namespace/prefix of the stage_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: stage_qualifier_namespace\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n stage_qualifier_category:\n name: stage_qualifier_category\n description: The category of the stage_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: category\n alias: stage_qualifier_category\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n disease_context_qualifier:\n name: disease_context_qualifier\n description: A context qualifier representing a disease or condition in which\n a relationship expressed in an association took place.\n examples:\n - value: MONDO:0004979\n - value: MONDO:0005148\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: disease_context_qualifier\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n disease_context_qualifier_label:\n name: disease_context_qualifier_label\n description: The name of the disease_context_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: disease_context_qualifier_label\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n disease_context_qualifier_namespace:\n name: disease_context_qualifier_namespace\n description: The namespace/prefix of the disease_context_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: disease_context_qualifier_namespace\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n disease_context_qualifier_category:\n name: disease_context_qualifier_category\n description: The category of the disease_context_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: category\n alias: disease_context_qualifier_category\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n disease_context_qualifier_closure:\n name: disease_context_qualifier_closure\n description: Field containing disease_context_qualifier id and the ids of all\n of it's ancestors\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: disease_context_qualifier_closure\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n multivalued: true\n disease_context_qualifier_closure_label:\n name: disease_context_qualifier_closure_label\n description: Field containing disease_context_qualifier name and the names of\n all of it's ancestors\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: disease_context_qualifier_closure_label\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n multivalued: true\n species_context_qualifier:\n name: species_context_qualifier\n description: A context qualifier representing a species in which a relationship\n expressed in an association took place.\n examples:\n - value: NCBITaxon:9606\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: species_context_qualifier\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n species_context_qualifier_label:\n name: species_context_qualifier_label\n description: The name of the species_context_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: species_context_qualifier_label\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n species_context_qualifier_namespace:\n name: species_context_qualifier_namespace\n description: The namespace/prefix of the species_context_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: species_context_qualifier_namespace\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n species_context_qualifier_category:\n name: species_context_qualifier_category\n description: The category of the species_context_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: category\n alias: species_context_qualifier_category\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\nA real number that conforms to the xsd:double specification
URI: xsd:double
base: float
uri: xsd:double
Represents an Entity in the Monarch KG data model
URI: https://w3id.org/monarch/monarch-py/:Entity
classDiagram\n class Entity\n click Entity href \"../Entity\"\n Entity <|-- Node\n click Node href \"../Node\"\n Entity <|-- SearchResult\n click SearchResult href \"../SearchResult\"\n\n Entity : category\n\n Entity : deprecated\n\n Entity : description\n\n Entity : full_name\n\n Entity : has_phenotype\n\n Entity : has_phenotype_closure\n\n Entity : has_phenotype_closure_label\n\n Entity : has_phenotype_count\n\n Entity : has_phenotype_label\n\n Entity : id\n\n Entity : in_taxon\n\n Entity : in_taxon_label\n\n Entity : iri\n\n Entity : name\n\n Entity : namespace\n\n Entity : provided_by\n\n Entity : symbol\n\n Entity : synonym\n\n Entity : uri\n\n Entity : xref\nname: Entity\ndescription: Represents an Entity in the Monarch KG data model\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- id\n- category\n- name\n- full_name\n- deprecated\n- description\n- xref\n- provided_by\n- in_taxon\n- in_taxon_label\n- symbol\n- synonym\n- uri\n- iri\n- namespace\n- has_phenotype\n- has_phenotype_label\n- has_phenotype_closure\n- has_phenotype_closure_label\n- has_phenotype_count\nname: Entity\ndescription: Represents an Entity in the Monarch KG data model\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n id:\n name: id\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n identifier: true\n alias: id\n owner: Entity\n domain_of:\n - Association\n - ExpandedCurie\n - Entity\n - HistoPheno\n - HistoBin\n - Mapping\n - MultiEntityAssociationResults\n - TermInfo\n range: string\n required: true\n category:\n name: category\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: category\n owner: Entity\n domain_of:\n - Association\n - AssociationCount\n - CompactAssociation\n - AssociationTypeMapping\n - Entity\n range: string\n multivalued: false\n name:\n name: name\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: name\n owner: Entity\n domain_of:\n - Entity\n - MultiEntityAssociationResults\n range: string\n full_name:\n name: full_name\n description: The long form name of an entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: full_name\n owner: Entity\n domain_of:\n - Entity\n range: string\n deprecated:\n name: deprecated\n description: A boolean flag indicating that an entity is no longer considered\n current or valid.\n from_schema: https://w3id.org/monarch/monarch-py\n exact_mappings:\n - oboInOwl:ObsoleteClass\n rank: 1000\n alias: deprecated\n owner: Entity\n domain_of:\n - Entity\n range: boolean\n description:\n name: description\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: description\n owner: Entity\n domain_of:\n - Entity\n range: string\n xref:\n name: xref\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: xref\n owner: Entity\n domain_of:\n - Entity\n range: string\n multivalued: true\n provided_by:\n name: provided_by\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: provided_by\n owner: Entity\n domain_of:\n - Association\n - Entity\n range: string\n in_taxon:\n name: in_taxon\n description: The biolink taxon that the entity is in the closure of.\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: in_taxon\n owner: Entity\n domain_of:\n - Entity\n - Node\n range: string\n in_taxon_label:\n name: in_taxon_label\n description: The label of the biolink taxon that the entity is in the closure\n of.\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: in_taxon_label\n owner: Entity\n domain_of:\n - Entity\n - Node\n range: string\n symbol:\n name: symbol\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: symbol\n owner: Entity\n domain_of:\n - Entity\n range: string\n synonym:\n name: synonym\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: synonym\n owner: Entity\n domain_of:\n - Entity\n range: string\n multivalued: true\n uri:\n name: uri\n description: The URI of the entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: uri\n owner: Entity\n domain_of:\n - Entity\n range: string\n iri:\n name: iri\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: iri\n owner: Entity\n domain_of:\n - Entity\n range: string\n namespace:\n name: namespace\n description: The namespace/prefix portion of this entity's identifier\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: namespace\n owner: Entity\n domain_of:\n - Entity\n range: string\n has_phenotype:\n name: has_phenotype\n description: A list of phenotype identifiers that are known to be associated with\n this entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_phenotype\n owner: Entity\n domain_of:\n - Entity\n range: string\n multivalued: true\n inlined: true\n inlined_as_list: true\n has_phenotype_label:\n name: has_phenotype_label\n description: A list of phenotype labels that are known to be associated with this\n entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_phenotype_label\n owner: Entity\n domain_of:\n - Entity\n range: string\n multivalued: true\n inlined: true\n inlined_as_list: true\n has_phenotype_closure:\n name: has_phenotype_closure\n description: A list of phenotype identifiers that are known to be associated with\n this entity expanded to include all ancestors\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_phenotype_closure\n owner: Entity\n domain_of:\n - Entity\n range: string\n multivalued: true\n inlined: true\n inlined_as_list: true\n has_phenotype_closure_label:\n name: has_phenotype_closure_label\n description: A list of phenotype labels that are known to be associated with this\n entity expanded to include all ancestors\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_phenotype_closure_label\n owner: Entity\n domain_of:\n - Entity\n range: string\n multivalued: true\n inlined: true\n inlined_as_list: true\n has_phenotype_count:\n name: has_phenotype_count\n description: A count of the number of phenotypes that are known to be associated\n with this entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_phenotype_count\n owner: Entity\n domain_of:\n - Entity\n range: integer\nURI: https://w3id.org/monarch/monarch-py/:EntityResults
classDiagram\n class EntityResults\n click EntityResults href \"../EntityResults\"\n Results <|-- EntityResults\n click Results href \"../Results\"\n\n EntityResults : items\n\n\n\n\n EntityResults --> \"1..*\" Entity : items\n click Entity href \"../Entity\"\n\n\n EntityResults : limit\n\n EntityResults : offset\n\n EntityResults : total\nname: EntityResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslots:\n- items\nslot_usage:\n items:\n name: items\n range: Entity\nname: EntityResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslot_usage:\n items:\n name: items\n range: Entity\nattributes:\n items:\n name: items\n description: A collection of items, with the type to be overriden by slot_usage\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: items\n owner: EntityResults\n domain_of:\n - AssociationCountList\n - AssociationResults\n - CompactAssociationResults\n - AssociationTableResults\n - CategoryGroupedAssociationResults\n - EntityResults\n - HistoPheno\n - MappingResults\n - SearchResults\n range: Entity\n required: true\n multivalued: true\n inlined: true\n inlined_as_list: true\n limit:\n name: limit\n description: number of items to return in a response\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: limit\n owner: EntityResults\n domain_of:\n - Results\n range: integer\n required: true\n offset:\n name: offset\n description: offset into the total number of items\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: offset\n owner: EntityResults\n domain_of:\n - Results\n range: integer\n required: true\n total:\n name: total\n description: total number of items matching a query\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: total\n owner: EntityResults\n domain_of:\n - Results\n range: integer\n required: true\nA curie bundled along with its expanded url
URI: https://w3id.org/monarch/monarch-py/:ExpandedCurie
classDiagram\n class ExpandedCurie\n click ExpandedCurie href \"../ExpandedCurie\"\n ExpandedCurie : id\n\n ExpandedCurie : url\nname: ExpandedCurie\ndescription: A curie bundled along with its expanded url\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- id\n- url\nname: ExpandedCurie\ndescription: A curie bundled along with its expanded url\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n id:\n name: id\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n identifier: true\n alias: id\n owner: ExpandedCurie\n domain_of:\n - Association\n - ExpandedCurie\n - Entity\n - HistoPheno\n - HistoBin\n - Mapping\n - MultiEntityAssociationResults\n - TermInfo\n range: string\n required: true\n url:\n name: url\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: url\n owner: ExpandedCurie\n domain_of:\n - ExpandedCurie\n - Release\n range: string\nURI: https://w3id.org/monarch/monarch-py/:FacetField
classDiagram\n class FacetField\n click FacetField href \"../FacetField\"\n FacetField : facet_values\n\n\n\n\n FacetField --> \"*\" FacetValue : facet_values\n click FacetValue href \"../FacetValue\"\n\n\n FacetField : label\nname: FacetField\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- label\n- facet_values\nname: FacetField\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n label:\n name: label\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: label\n owner: FacetField\n domain_of:\n - FacetValue\n - FacetField\n - TermInfo\n range: string\n required: true\n facet_values:\n name: facet_values\n description: Collection of FacetValue label/value instances belonging to a FacetField\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: facet_values\n owner: FacetField\n domain_of:\n - FacetField\n range: FacetValue\n multivalued: true\n inlined: true\n inlined_as_list: true\nURI: https://w3id.org/monarch/monarch-py/:FacetValue
classDiagram\n class FacetValue\n click FacetValue href \"../FacetValue\"\n FacetValue <|-- AssociationCount\n click AssociationCount href \"../AssociationCount\"\n FacetValue <|-- HistoBin\n click HistoBin href \"../HistoBin\"\n\n FacetValue : count\n\n FacetValue : label\nname: FacetValue\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- label\n- count\nname: FacetValue\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n label:\n name: label\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: label\n owner: FacetValue\n domain_of:\n - FacetValue\n - FacetField\n - TermInfo\n range: string\n required: true\n count:\n name: count\n description: count of documents\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: count\n owner: FacetValue\n domain_of:\n - FacetValue\n range: integer\nA real number that conforms to the xsd:float specification
URI: xsd:float
base: float
uri: xsd:float
URI: https://w3id.org/monarch/monarch-py/:HistoBin
classDiagram\n class HistoBin\n click HistoBin href \"../HistoBin\"\n FacetValue <|-- HistoBin\n click FacetValue href \"../FacetValue\"\n\n HistoBin : count\n\n HistoBin : id\n\n HistoBin : label\nname: HistoBin\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: FacetValue\nslots:\n- id\nname: HistoBin\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: FacetValue\nattributes:\n id:\n name: id\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n identifier: true\n alias: id\n owner: HistoBin\n domain_of:\n - Association\n - ExpandedCurie\n - Entity\n - HistoPheno\n - HistoBin\n - Mapping\n - MultiEntityAssociationResults\n - TermInfo\n range: string\n required: true\n label:\n name: label\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: label\n owner: HistoBin\n domain_of:\n - FacetValue\n - FacetField\n - TermInfo\n range: string\n required: true\n count:\n name: count\n description: count of documents\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: count\n owner: HistoBin\n domain_of:\n - FacetValue\n range: integer\nURI: https://w3id.org/monarch/monarch-py/:HistoPheno
classDiagram\n class HistoPheno\n click HistoPheno href \"../HistoPheno\"\n HistoPheno : id\n\n HistoPheno : items\n\n\n\n\n HistoPheno --> \"1..*\" HistoBin : items\n click HistoBin href \"../HistoBin\"\nname: HistoPheno\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- id\n- items\nslot_usage:\n items:\n name: items\n range: HistoBin\nname: HistoPheno\nfrom_schema: https://w3id.org/monarch/monarch-py\nslot_usage:\n items:\n name: items\n range: HistoBin\nattributes:\n id:\n name: id\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n identifier: true\n alias: id\n owner: HistoPheno\n domain_of:\n - Association\n - ExpandedCurie\n - Entity\n - HistoPheno\n - HistoBin\n - Mapping\n - MultiEntityAssociationResults\n - TermInfo\n range: string\n required: true\n items:\n name: items\n description: A collection of items, with the type to be overriden by slot_usage\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: items\n owner: HistoPheno\n domain_of:\n - AssociationCountList\n - AssociationResults\n - CompactAssociationResults\n - AssociationTableResults\n - CategoryGroupedAssociationResults\n - EntityResults\n - HistoPheno\n - MappingResults\n - SearchResults\n range: HistoBin\n required: true\n multivalued: true\n inlined: true\n inlined_as_list: true\nAn integer
URI: xsd:integer
base: int
uri: xsd:integer
URI: xsd:integer
base: int
uri: xsd:integer
typeof: integer
A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.
URI: xsd:string
base: str
uri: xsd:string
repr: str
A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.
URI: xsd:string
base: str
uri: xsd:string
repr: str
A minimal class to hold a SSSOM mapping
URI: https://w3id.org/monarch/monarch-py/:Mapping
classDiagram\n class Mapping\n click Mapping href \"../Mapping\"\n Mapping : id\n\n Mapping : mapping_justification\n\n Mapping : object_id\n\n Mapping : object_label\n\n Mapping : predicate_id\n\n Mapping : subject_id\n\n Mapping : subject_label\nname: Mapping\ndescription: A minimal class to hold a SSSOM mapping\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- subject_id\n- subject_label\n- predicate_id\n- object_id\n- object_label\n- mapping_justification\n- id\nname: Mapping\ndescription: A minimal class to hold a SSSOM mapping\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n subject_id:\n name: subject_id\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: subject_id\n owner: Mapping\n domain_of:\n - Mapping\n - TermPairwiseSimilarity\n range: string\n required: true\n subject_label:\n name: subject_label\n description: The name of the subject entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: subject_label\n owner: Mapping\n domain_of:\n - Association\n - CompactAssociation\n - AssociationTypeMapping\n - Mapping\n - TermPairwiseSimilarity\n range: string\n predicate_id:\n name: predicate_id\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: predicate_id\n owner: Mapping\n domain_of:\n - Mapping\n range: string\n required: true\n object_id:\n name: object_id\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: object_id\n owner: Mapping\n domain_of:\n - Mapping\n - TermPairwiseSimilarity\n range: string\n required: true\n object_label:\n name: object_label\n description: The name of the object entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: object_label\n owner: Mapping\n domain_of:\n - Association\n - CompactAssociation\n - AssociationTypeMapping\n - Mapping\n - TermPairwiseSimilarity\n range: string\n mapping_justification:\n name: mapping_justification\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: mapping_justification\n owner: Mapping\n domain_of:\n - Mapping\n range: string\n id:\n name: id\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n identifier: true\n alias: id\n owner: Mapping\n domain_of:\n - Association\n - ExpandedCurie\n - Entity\n - HistoPheno\n - HistoBin\n - Mapping\n - MultiEntityAssociationResults\n - TermInfo\n range: string\n required: true\nSSSOM Mappings returned as a results collection
URI: https://w3id.org/monarch/monarch-py/:MappingResults
classDiagram\n class MappingResults\n click MappingResults href \"../MappingResults\"\n Results <|-- MappingResults\n click Results href \"../Results\"\n\n MappingResults : items\n\n\n\n\n MappingResults --> \"1..*\" Mapping : items\n click Mapping href \"../Mapping\"\n\n\n MappingResults : limit\n\n MappingResults : offset\n\n MappingResults : total\nname: MappingResults\ndescription: SSSOM Mappings returned as a results collection\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslots:\n- items\nslot_usage:\n items:\n name: items\n range: Mapping\nname: MappingResults\ndescription: SSSOM Mappings returned as a results collection\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslot_usage:\n items:\n name: items\n range: Mapping\nattributes:\n items:\n name: items\n description: A collection of items, with the type to be overriden by slot_usage\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: items\n owner: MappingResults\n domain_of:\n - AssociationCountList\n - AssociationResults\n - CompactAssociationResults\n - AssociationTableResults\n - CategoryGroupedAssociationResults\n - EntityResults\n - HistoPheno\n - MappingResults\n - SearchResults\n range: Mapping\n required: true\n multivalued: true\n inlined: true\n inlined_as_list: true\n limit:\n name: limit\n description: number of items to return in a response\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: limit\n owner: MappingResults\n domain_of:\n - Results\n range: integer\n required: true\n offset:\n name: offset\n description: offset into the total number of items\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: offset\n owner: MappingResults\n domain_of:\n - Results\n range: integer\n required: true\n total:\n name: total\n description: total number of items matching a query\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: total\n owner: MappingResults\n domain_of:\n - Results\n range: integer\n required: true\nURI: https://w3id.org/monarch/monarch-py/:MultiEntityAssociationResults
classDiagram\n class MultiEntityAssociationResults\n click MultiEntityAssociationResults href \"../MultiEntityAssociationResults\"\n Results <|-- MultiEntityAssociationResults\n click Results href \"../Results\"\n\n MultiEntityAssociationResults : associated_categories\n\n\n\n\n MultiEntityAssociationResults --> \"1..*\" CategoryGroupedAssociationResults : associated_categories\n click CategoryGroupedAssociationResults href \"../CategoryGroupedAssociationResults\"\n\n\n MultiEntityAssociationResults : id\n\n MultiEntityAssociationResults : limit\n\n MultiEntityAssociationResults : name\n\n MultiEntityAssociationResults : offset\n\n MultiEntityAssociationResults : total\nname: MultiEntityAssociationResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslots:\n- id\n- name\n- associated_categories\nname: MultiEntityAssociationResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nattributes:\n id:\n name: id\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n identifier: true\n alias: id\n owner: MultiEntityAssociationResults\n domain_of:\n - Association\n - ExpandedCurie\n - Entity\n - HistoPheno\n - HistoBin\n - Mapping\n - MultiEntityAssociationResults\n - TermInfo\n range: string\n required: true\n name:\n name: name\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: name\n owner: MultiEntityAssociationResults\n domain_of:\n - Entity\n - MultiEntityAssociationResults\n range: string\n associated_categories:\n name: associated_categories\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: associated_categories\n owner: MultiEntityAssociationResults\n domain_of:\n - MultiEntityAssociationResults\n range: CategoryGroupedAssociationResults\n required: true\n multivalued: true\n inlined: true\n inlined_as_list: true\n limit:\n name: limit\n description: number of items to return in a response\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: limit\n owner: MultiEntityAssociationResults\n domain_of:\n - Results\n range: integer\n required: true\n offset:\n name: offset\n description: offset into the total number of items\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: offset\n owner: MultiEntityAssociationResults\n domain_of:\n - Results\n range: integer\n required: true\n total:\n name: total\n description: total number of items matching a query\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: total\n owner: MultiEntityAssociationResults\n domain_of:\n - Results\n range: integer\n required: true\nPrefix part of CURIE
URI: xsd:string
base: NCName
uri: xsd:string
repr: str
URI: xsd:float
base: float
uri: xsd:float
typeof: float
UI container class extending Entity with additional information
URI: https://w3id.org/monarch/monarch-py/:Node
classDiagram\n class Node\n click Node href \"../Node\"\n Entity <|-- Node\n click Entity href \"../Entity\"\n\n Node : association_counts\n\n\n\n\n Node --> \"1..*\" AssociationCount : association_counts\n click AssociationCount href \"../AssociationCount\"\n\n\n Node : category\n\n Node : causal_gene\n\n\n\n\n Node --> \"*\" Entity : causal_gene\n click Entity href \"../Entity\"\n\n\n Node : causes_disease\n\n\n\n\n Node --> \"*\" Entity : causes_disease\n click Entity href \"../Entity\"\n\n\n Node : deprecated\n\n Node : description\n\n Node : external_links\n\n\n\n\n Node --> \"*\" ExpandedCurie : external_links\n click ExpandedCurie href \"../ExpandedCurie\"\n\n\n Node : full_name\n\n Node : has_phenotype\n\n Node : has_phenotype_closure\n\n Node : has_phenotype_closure_label\n\n Node : has_phenotype_count\n\n Node : has_phenotype_label\n\n Node : id\n\n Node : in_taxon\n\n Node : in_taxon_label\n\n Node : inheritance\n\n\n\n\n Node --> \"0..1\" Entity : inheritance\n click Entity href \"../Entity\"\n\n\n Node : iri\n\n Node : mappings\n\n\n\n\n Node --> \"*\" ExpandedCurie : mappings\n click ExpandedCurie href \"../ExpandedCurie\"\n\n\n Node : name\n\n Node : namespace\n\n Node : node_hierarchy\n\n\n\n\n Node --> \"0..1\" NodeHierarchy : node_hierarchy\n click NodeHierarchy href \"../NodeHierarchy\"\n\n\n Node : provided_by\n\n Node : provided_by_link\n\n\n\n\n Node --> \"0..1\" ExpandedCurie : provided_by_link\n click ExpandedCurie href \"../ExpandedCurie\"\n\n\n Node : symbol\n\n Node : synonym\n\n Node : uri\n\n Node : xref\nname: Node\ndescription: UI container class extending Entity with additional information\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Entity\nslots:\n- in_taxon\n- in_taxon_label\n- inheritance\n- causal_gene\n- causes_disease\n- mappings\n- external_links\n- provided_by_link\n- association_counts\n- node_hierarchy\nname: Node\ndescription: UI container class extending Entity with additional information\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Entity\nattributes:\n in_taxon:\n name: in_taxon\n description: The biolink taxon that the entity is in the closure of.\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: in_taxon\n owner: Node\n domain_of:\n - Entity\n - Node\n range: string\n in_taxon_label:\n name: in_taxon_label\n description: The label of the biolink taxon that the entity is in the closure\n of.\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: in_taxon_label\n owner: Node\n domain_of:\n - Entity\n - Node\n range: string\n inheritance:\n name: inheritance\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: inheritance\n owner: Node\n domain_of:\n - Node\n range: Entity\n inlined: true\n causal_gene:\n name: causal_gene\n description: A list of genes that are known to be causally associated with a disease\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: causal_gene\n owner: Node\n domain_of:\n - Node\n range: Entity\n multivalued: true\n inlined: true\n inlined_as_list: true\n causes_disease:\n name: causes_disease\n description: A list of diseases that are known to be causally associated with\n a gene\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: causes_disease\n owner: Node\n domain_of:\n - Node\n range: Entity\n multivalued: true\n inlined: true\n inlined_as_list: true\n mappings:\n name: mappings\n description: List of ExpandedCuries with id and url for mapped entities\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: mappings\n owner: Node\n domain_of:\n - Node\n range: ExpandedCurie\n multivalued: true\n inlined: true\n inlined_as_list: true\n external_links:\n name: external_links\n description: ExpandedCurie with id and url for xrefs\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: external_links\n owner: Node\n domain_of:\n - Node\n range: ExpandedCurie\n multivalued: true\n inlined: true\n inlined_as_list: true\n provided_by_link:\n name: provided_by_link\n description: A link to the docs for the knowledge source that provided the node/edge.\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: provided_by_link\n owner: Node\n domain_of:\n - Association\n - Node\n range: ExpandedCurie\n inlined: true\n association_counts:\n name: association_counts\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: association_counts\n owner: Node\n domain_of:\n - Node\n range: AssociationCount\n required: true\n multivalued: true\n inlined: true\n inlined_as_list: true\n node_hierarchy:\n name: node_hierarchy\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: node_hierarchy\n owner: Node\n domain_of:\n - Node\n range: NodeHierarchy\n inlined: true\n id:\n name: id\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n identifier: true\n alias: id\n owner: Node\n domain_of:\n - Association\n - ExpandedCurie\n - Entity\n - HistoPheno\n - HistoBin\n - Mapping\n - MultiEntityAssociationResults\n - TermInfo\n range: string\n required: true\n category:\n name: category\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: category\n owner: Node\n domain_of:\n - Association\n - AssociationCount\n - CompactAssociation\n - AssociationTypeMapping\n - Entity\n range: string\n multivalued: false\n name:\n name: name\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: name\n owner: Node\n domain_of:\n - Entity\n - MultiEntityAssociationResults\n range: string\n full_name:\n name: full_name\n description: The long form name of an entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: full_name\n owner: Node\n domain_of:\n - Entity\n range: string\n deprecated:\n name: deprecated\n description: A boolean flag indicating that an entity is no longer considered\n current or valid.\n from_schema: https://w3id.org/monarch/monarch-py\n exact_mappings:\n - oboInOwl:ObsoleteClass\n rank: 1000\n alias: deprecated\n owner: Node\n domain_of:\n - Entity\n range: boolean\n description:\n name: description\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: description\n owner: Node\n domain_of:\n - Entity\n range: string\n xref:\n name: xref\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: xref\n owner: Node\n domain_of:\n - Entity\n range: string\n multivalued: true\n provided_by:\n name: provided_by\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: provided_by\n owner: Node\n domain_of:\n - Association\n - Entity\n range: string\n symbol:\n name: symbol\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: symbol\n owner: Node\n domain_of:\n - Entity\n range: string\n synonym:\n name: synonym\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: synonym\n owner: Node\n domain_of:\n - Entity\n range: string\n multivalued: true\n uri:\n name: uri\n description: The URI of the entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: uri\n owner: Node\n domain_of:\n - Entity\n range: string\n iri:\n name: iri\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: iri\n owner: Node\n domain_of:\n - Entity\n range: string\n namespace:\n name: namespace\n description: The namespace/prefix portion of this entity's identifier\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: namespace\n owner: Node\n domain_of:\n - Entity\n range: string\n has_phenotype:\n name: has_phenotype\n description: A list of phenotype identifiers that are known to be associated with\n this entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_phenotype\n owner: Node\n domain_of:\n - Entity\n range: string\n multivalued: true\n inlined: true\n inlined_as_list: true\n has_phenotype_label:\n name: has_phenotype_label\n description: A list of phenotype labels that are known to be associated with this\n entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_phenotype_label\n owner: Node\n domain_of:\n - Entity\n range: string\n multivalued: true\n inlined: true\n inlined_as_list: true\n has_phenotype_closure:\n name: has_phenotype_closure\n description: A list of phenotype identifiers that are known to be associated with\n this entity expanded to include all ancestors\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_phenotype_closure\n owner: Node\n domain_of:\n - Entity\n range: string\n multivalued: true\n inlined: true\n inlined_as_list: true\n has_phenotype_closure_label:\n name: has_phenotype_closure_label\n description: A list of phenotype labels that are known to be associated with this\n entity expanded to include all ancestors\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_phenotype_closure_label\n owner: Node\n domain_of:\n - Entity\n range: string\n multivalued: true\n inlined: true\n inlined_as_list: true\n has_phenotype_count:\n name: has_phenotype_count\n description: A count of the number of phenotypes that are known to be associated\n with this entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_phenotype_count\n owner: Node\n domain_of:\n - Entity\n range: integer\nURI: https://w3id.org/monarch/monarch-py/:NodeHierarchy
classDiagram\n class NodeHierarchy\n click NodeHierarchy href \"../NodeHierarchy\"\n NodeHierarchy : sub_classes\n\n\n\n\n NodeHierarchy --> \"1..*\" Entity : sub_classes\n click Entity href \"../Entity\"\n\n\n NodeHierarchy : super_classes\n\n\n\n\n NodeHierarchy --> \"1..*\" Entity : super_classes\n click Entity href \"../Entity\"\nname: NodeHierarchy\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- super_classes\n- sub_classes\nname: NodeHierarchy\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n super_classes:\n name: super_classes\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: super_classes\n owner: NodeHierarchy\n domain_of:\n - NodeHierarchy\n range: Entity\n required: true\n multivalued: true\n inlined: true\n inlined_as_list: true\n sub_classes:\n name: sub_classes\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: sub_classes\n owner: NodeHierarchy\n domain_of:\n - NodeHierarchy\n range: Entity\n required: true\n multivalued: true\n inlined: true\n inlined_as_list: true\nA URI, CURIE or BNODE that represents a node in a model.
URI: shex:nonLiteral
base: NodeIdentifier
uri: shex:nonLiteral
repr: str
URI: xsd:float
base: float
uri: xsd:float
typeof: float
A URI or CURIE that represents an object in the model.
URI: shex:iri
base: ElementIdentifier
uri: shex:iri
repr: str
Abstract grouping for representing individual pairwise similarities
URI: https://w3id.org/monarch/monarch-py/:PairwiseSimilarity
classDiagram\n class PairwiseSimilarity\n click PairwiseSimilarity href \"../PairwiseSimilarity\"\n PairwiseSimilarity <|-- TermPairwiseSimilarity\n click TermPairwiseSimilarity href \"../TermPairwiseSimilarity\"\n PairwiseSimilarity <|-- TermSetPairwiseSimilarity\n click TermSetPairwiseSimilarity href \"../TermSetPairwiseSimilarity\"\nname: PairwiseSimilarity\ndescription: Abstract grouping for representing individual pairwise similarities\nfrom_schema: https://w3id.org/monarch/monarch-py\nabstract: true\nname: PairwiseSimilarity\ndescription: Abstract grouping for representing individual pairwise similarities\nfrom_schema: https://w3id.org/monarch/monarch-py\nabstract: true\nA class to hold information about a release of the Monarch KG
URI: https://w3id.org/monarch/monarch-py/:Release
classDiagram\n class Release\n click Release href \"../Release\"\n Release : graph_stats\n\n Release : kg\n\n Release : metadata\n\n Release : neo4j\n\n Release : qc_report\n\n Release : solr\n\n Release : sqlite\n\n Release : url\n\n Release : version\nname: Release\ndescription: A class to hold information about a release of the Monarch KG\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- version\n- url\n- kg\n- sqlite\n- solr\n- neo4j\n- metadata\n- graph_stats\n- qc_report\nname: Release\ndescription: A class to hold information about a release of the Monarch KG\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n version:\n name: version\n id_prefixes:\n - string\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: version\n owner: Release\n domain_of:\n - Release\n range: string\n url:\n name: url\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: url\n owner: Release\n domain_of:\n - ExpandedCurie\n - Release\n range: string\n kg:\n name: kg\n id_prefixes:\n - string\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: kg\n owner: Release\n domain_of:\n - Release\n range: string\n sqlite:\n name: sqlite\n id_prefixes:\n - string\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: sqlite\n owner: Release\n domain_of:\n - Release\n range: string\n solr:\n name: solr\n id_prefixes:\n - string\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: solr\n owner: Release\n domain_of:\n - Release\n range: string\n neo4j:\n name: neo4j\n id_prefixes:\n - string\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: neo4j\n owner: Release\n domain_of:\n - Release\n range: string\n metadata:\n name: metadata\n id_prefixes:\n - string\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: metadata\n owner: Release\n domain_of:\n - Release\n range: string\n graph_stats:\n name: graph_stats\n id_prefixes:\n - string\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: graph_stats\n owner: Release\n domain_of:\n - Release\n range: string\n qc_report:\n name: qc_report\n id_prefixes:\n - string\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: qc_report\n owner: Release\n domain_of:\n - Release\n range: string\nURI: https://w3id.org/monarch/monarch-py/:Results
classDiagram\n class Results\n click Results href \"../Results\"\n Results <|-- AssociationResults\n click AssociationResults href \"../AssociationResults\"\n Results <|-- CompactAssociationResults\n click CompactAssociationResults href \"../CompactAssociationResults\"\n Results <|-- AssociationTableResults\n click AssociationTableResults href \"../AssociationTableResults\"\n Results <|-- CategoryGroupedAssociationResults\n click CategoryGroupedAssociationResults href \"../CategoryGroupedAssociationResults\"\n Results <|-- EntityResults\n click EntityResults href \"../EntityResults\"\n Results <|-- MappingResults\n click MappingResults href \"../MappingResults\"\n Results <|-- MultiEntityAssociationResults\n click MultiEntityAssociationResults href \"../MultiEntityAssociationResults\"\n Results <|-- SearchResults\n click SearchResults href \"../SearchResults\"\n\n Results : limit\n\n Results : offset\n\n Results : total\nname: Results\nfrom_schema: https://w3id.org/monarch/monarch-py\nabstract: true\nslots:\n- limit\n- offset\n- total\nname: Results\nfrom_schema: https://w3id.org/monarch/monarch-py\nabstract: true\nattributes:\n limit:\n name: limit\n description: number of items to return in a response\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: limit\n owner: Results\n domain_of:\n - Results\n range: integer\n required: true\n offset:\n name: offset\n description: offset into the total number of items\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: offset\n owner: Results\n domain_of:\n - Results\n range: integer\n required: true\n total:\n name: total\n description: total number of items matching a query\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: total\n owner: Results\n domain_of:\n - Results\n range: integer\n required: true\nURI: https://w3id.org/monarch/monarch-py/:SearchResult
classDiagram\n class SearchResult\n click SearchResult href \"../SearchResult\"\n Entity <|-- SearchResult\n click Entity href \"../Entity\"\n\n SearchResult : category\n\n SearchResult : deprecated\n\n SearchResult : description\n\n SearchResult : full_name\n\n SearchResult : has_phenotype\n\n SearchResult : has_phenotype_closure\n\n SearchResult : has_phenotype_closure_label\n\n SearchResult : has_phenotype_count\n\n SearchResult : has_phenotype_label\n\n SearchResult : highlight\n\n SearchResult : id\n\n SearchResult : in_taxon\n\n SearchResult : in_taxon_label\n\n SearchResult : iri\n\n SearchResult : name\n\n SearchResult : namespace\n\n SearchResult : provided_by\n\n SearchResult : score\n\n SearchResult : symbol\n\n SearchResult : synonym\n\n SearchResult : uri\n\n SearchResult : xref\nname: SearchResult\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Entity\nslots:\n- highlight\n- score\nslot_usage:\n category:\n name: category\n required: true\n name:\n name: name\n required: true\nname: SearchResult\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Entity\nslot_usage:\n category:\n name: category\n required: true\n name:\n name: name\n required: true\nattributes:\n highlight:\n name: highlight\n description: matching text snippet containing html tags\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: highlight\n owner: SearchResult\n domain_of:\n - SearchResult\n range: string\n score:\n name: score\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: score\n owner: SearchResult\n domain_of:\n - SearchResult\n - BestMatch\n - SemsimSearchResult\n range: float\n id:\n name: id\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n identifier: true\n alias: id\n owner: SearchResult\n domain_of:\n - Association\n - ExpandedCurie\n - Entity\n - HistoPheno\n - HistoBin\n - Mapping\n - MultiEntityAssociationResults\n - TermInfo\n range: string\n required: true\n category:\n name: category\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: category\n owner: SearchResult\n domain_of:\n - Association\n - AssociationCount\n - CompactAssociation\n - AssociationTypeMapping\n - Entity\n range: string\n required: true\n multivalued: false\n name:\n name: name\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: name\n owner: SearchResult\n domain_of:\n - Entity\n - MultiEntityAssociationResults\n range: string\n required: true\n full_name:\n name: full_name\n description: The long form name of an entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: full_name\n owner: SearchResult\n domain_of:\n - Entity\n range: string\n deprecated:\n name: deprecated\n description: A boolean flag indicating that an entity is no longer considered\n current or valid.\n from_schema: https://w3id.org/monarch/monarch-py\n exact_mappings:\n - oboInOwl:ObsoleteClass\n rank: 1000\n alias: deprecated\n owner: SearchResult\n domain_of:\n - Entity\n range: boolean\n description:\n name: description\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: description\n owner: SearchResult\n domain_of:\n - Entity\n range: string\n xref:\n name: xref\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: xref\n owner: SearchResult\n domain_of:\n - Entity\n range: string\n multivalued: true\n provided_by:\n name: provided_by\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: provided_by\n owner: SearchResult\n domain_of:\n - Association\n - Entity\n range: string\n in_taxon:\n name: in_taxon\n description: The biolink taxon that the entity is in the closure of.\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: in_taxon\n owner: SearchResult\n domain_of:\n - Entity\n - Node\n range: string\n in_taxon_label:\n name: in_taxon_label\n description: The label of the biolink taxon that the entity is in the closure\n of.\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: in_taxon_label\n owner: SearchResult\n domain_of:\n - Entity\n - Node\n range: string\n symbol:\n name: symbol\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: symbol\n owner: SearchResult\n domain_of:\n - Entity\n range: string\n synonym:\n name: synonym\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: synonym\n owner: SearchResult\n domain_of:\n - Entity\n range: string\n multivalued: true\n uri:\n name: uri\n description: The URI of the entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: uri\n owner: SearchResult\n domain_of:\n - Entity\n range: string\n iri:\n name: iri\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: iri\n owner: SearchResult\n domain_of:\n - Entity\n range: string\n namespace:\n name: namespace\n description: The namespace/prefix portion of this entity's identifier\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: namespace\n owner: SearchResult\n domain_of:\n - Entity\n range: string\n has_phenotype:\n name: has_phenotype\n description: A list of phenotype identifiers that are known to be associated with\n this entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_phenotype\n owner: SearchResult\n domain_of:\n - Entity\n range: string\n multivalued: true\n inlined: true\n inlined_as_list: true\n has_phenotype_label:\n name: has_phenotype_label\n description: A list of phenotype labels that are known to be associated with this\n entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_phenotype_label\n owner: SearchResult\n domain_of:\n - Entity\n range: string\n multivalued: true\n inlined: true\n inlined_as_list: true\n has_phenotype_closure:\n name: has_phenotype_closure\n description: A list of phenotype identifiers that are known to be associated with\n this entity expanded to include all ancestors\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_phenotype_closure\n owner: SearchResult\n domain_of:\n - Entity\n range: string\n multivalued: true\n inlined: true\n inlined_as_list: true\n has_phenotype_closure_label:\n name: has_phenotype_closure_label\n description: A list of phenotype labels that are known to be associated with this\n entity expanded to include all ancestors\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_phenotype_closure_label\n owner: SearchResult\n domain_of:\n - Entity\n range: string\n multivalued: true\n inlined: true\n inlined_as_list: true\n has_phenotype_count:\n name: has_phenotype_count\n description: A count of the number of phenotypes that are known to be associated\n with this entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_phenotype_count\n owner: SearchResult\n domain_of:\n - Entity\n range: integer\nURI: https://w3id.org/monarch/monarch-py/:SearchResults
classDiagram\n class SearchResults\n click SearchResults href \"../SearchResults\"\n Results <|-- SearchResults\n click Results href \"../Results\"\n\n SearchResults : facet_fields\n\n\n\n\n SearchResults --> \"*\" FacetField : facet_fields\n click FacetField href \"../FacetField\"\n\n\n SearchResults : facet_queries\n\n\n\n\n SearchResults --> \"*\" FacetValue : facet_queries\n click FacetValue href \"../FacetValue\"\n\n\n SearchResults : items\n\n\n\n\n SearchResults --> \"1..*\" SearchResult : items\n click SearchResult href \"../SearchResult\"\n\n\n SearchResults : limit\n\n SearchResults : offset\n\n SearchResults : total\nname: SearchResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslots:\n- items\n- facet_fields\n- facet_queries\nslot_usage:\n items:\n name: items\n range: SearchResult\nname: SearchResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslot_usage:\n items:\n name: items\n range: SearchResult\nattributes:\n items:\n name: items\n description: A collection of items, with the type to be overriden by slot_usage\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: items\n owner: SearchResults\n domain_of:\n - AssociationCountList\n - AssociationResults\n - CompactAssociationResults\n - AssociationTableResults\n - CategoryGroupedAssociationResults\n - EntityResults\n - HistoPheno\n - MappingResults\n - SearchResults\n range: SearchResult\n required: true\n multivalued: true\n inlined: true\n inlined_as_list: true\n facet_fields:\n name: facet_fields\n description: Collection of facet field responses with the field values and counts\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: facet_fields\n owner: SearchResults\n domain_of:\n - AssociationResults\n - CompactAssociationResults\n - AssociationTableResults\n - SearchResults\n range: FacetField\n multivalued: true\n inlined: true\n inlined_as_list: true\n facet_queries:\n name: facet_queries\n description: Collection of facet query responses with the query string values\n and counts\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: facet_queries\n owner: SearchResults\n domain_of:\n - AssociationResults\n - CompactAssociationResults\n - AssociationTableResults\n - SearchResults\n range: FacetValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n limit:\n name: limit\n description: number of items to return in a response\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: limit\n owner: SearchResults\n domain_of:\n - Results\n range: integer\n required: true\n offset:\n name: offset\n description: offset into the total number of items\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: offset\n owner: SearchResults\n domain_of:\n - Results\n range: integer\n required: true\n total:\n name: total\n description: total number of items matching a query\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: total\n owner: SearchResults\n domain_of:\n - Results\n range: integer\n required: true\nURI: https://w3id.org/monarch/monarch-py/:SemsimSearchResult
classDiagram\n class SemsimSearchResult\n click SemsimSearchResult href \"../SemsimSearchResult\"\n SemsimSearchResult : score\n\n SemsimSearchResult : similarity\n\n\n\n\n SemsimSearchResult --> \"0..1\" TermSetPairwiseSimilarity : similarity\n click TermSetPairwiseSimilarity href \"../TermSetPairwiseSimilarity\"\n\n\n SemsimSearchResult : subject\n\n\n\n\n SemsimSearchResult --> \"1\" Entity : subject\n click Entity href \"../Entity\"\nname: SemsimSearchResult\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- subject\n- score\n- similarity\nslot_usage:\n subject:\n name: subject\n range: Entity\n inlined: true\nname: SemsimSearchResult\nfrom_schema: https://w3id.org/monarch/monarch-py\nslot_usage:\n subject:\n name: subject\n range: Entity\n inlined: true\nattributes:\n subject:\n name: subject\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: subject\n owner: SemsimSearchResult\n domain_of:\n - Association\n - CompactAssociation\n - SemsimSearchResult\n range: Entity\n required: true\n inlined: true\n score:\n name: score\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: score\n owner: SemsimSearchResult\n domain_of:\n - SearchResult\n - BestMatch\n - SemsimSearchResult\n range: float\n similarity:\n name: similarity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: similarity\n owner: SemsimSearchResult\n domain_of:\n - BestMatch\n - SemsimSearchResult\n range: TermSetPairwiseSimilarity\nA string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.
URI: xsd:string
base: str
uri: xsd:string
repr: str
A character string
URI: xsd:string
base: str
uri: xsd:string
URI: https://w3id.org/monarch/monarch-py/:TermInfo
classDiagram\n class TermInfo\n click TermInfo href \"../TermInfo\"\n TermInfo : id\n\n TermInfo : label\nname: TermInfo\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n id:\n name: id\n from_schema: https://w3id.org/monarch/monarch-py-similarity\n identifier: true\n domain_of:\n - Association\n - ExpandedCurie\n - Entity\n - HistoPheno\n - HistoBin\n - Mapping\n - MultiEntityAssociationResults\n - TermInfo\n required: true\n label:\n name: label\n from_schema: https://w3id.org/monarch/monarch-py-similarity\n slot_uri: rdfs:label\n domain_of:\n - FacetValue\n - FacetField\n - TermInfo\nname: TermInfo\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n id:\n name: id\n from_schema: https://w3id.org/monarch/monarch-py-similarity\n identifier: true\n alias: id\n owner: TermInfo\n domain_of:\n - Association\n - ExpandedCurie\n - Entity\n - HistoPheno\n - HistoBin\n - Mapping\n - MultiEntityAssociationResults\n - TermInfo\n range: string\n required: true\n label:\n name: label\n from_schema: https://w3id.org/monarch/monarch-py-similarity\n slot_uri: rdfs:label\n alias: label\n owner: TermInfo\n domain_of:\n - FacetValue\n - FacetField\n - TermInfo\n range: string\nA simple pairwise similarity between two atomic concepts/terms
URI: https://w3id.org/monarch/monarch-py/:TermPairwiseSimilarity
classDiagram\n class TermPairwiseSimilarity\n click TermPairwiseSimilarity href \"../TermPairwiseSimilarity\"\n PairwiseSimilarity <|-- TermPairwiseSimilarity\n click PairwiseSimilarity href \"../PairwiseSimilarity\"\n\n TermPairwiseSimilarity : ancestor_id\n\n TermPairwiseSimilarity : ancestor_information_content\n\n TermPairwiseSimilarity : ancestor_label\n\n TermPairwiseSimilarity : ancestor_source\n\n TermPairwiseSimilarity : cosine_similarity\n\n TermPairwiseSimilarity : dice_similarity\n\n TermPairwiseSimilarity : jaccard_similarity\n\n TermPairwiseSimilarity : object_id\n\n TermPairwiseSimilarity : object_information_content\n\n TermPairwiseSimilarity : object_label\n\n TermPairwiseSimilarity : object_source\n\n TermPairwiseSimilarity : phenodigm_score\n\n TermPairwiseSimilarity : subject_id\n\n TermPairwiseSimilarity : subject_information_content\n\n TermPairwiseSimilarity : subject_label\n\n TermPairwiseSimilarity : subject_source\nname: TermPairwiseSimilarity\ndescription: A simple pairwise similarity between two atomic concepts/terms\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: PairwiseSimilarity\nslots:\n- subject_id\n- subject_label\n- subject_source\n- object_id\n- object_label\n- object_source\n- ancestor_id\n- ancestor_label\n- ancestor_source\n- object_information_content\n- subject_information_content\n- ancestor_information_content\n- jaccard_similarity\n- cosine_similarity\n- dice_similarity\n- phenodigm_score\nname: TermPairwiseSimilarity\ndescription: A simple pairwise similarity between two atomic concepts/terms\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: PairwiseSimilarity\nattributes:\n subject_id:\n name: subject_id\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: subject_id\n owner: TermPairwiseSimilarity\n domain_of:\n - Mapping\n - TermPairwiseSimilarity\n range: string\n required: true\n subject_label:\n name: subject_label\n description: The name of the subject entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: subject_label\n owner: TermPairwiseSimilarity\n domain_of:\n - Association\n - CompactAssociation\n - AssociationTypeMapping\n - Mapping\n - TermPairwiseSimilarity\n range: string\n subject_source:\n name: subject_source\n description: the source for the first entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n slot_uri: sssom:subject_source\n alias: subject_source\n owner: TermPairwiseSimilarity\n domain_of:\n - TermPairwiseSimilarity\n range: string\n object_id:\n name: object_id\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: object_id\n owner: TermPairwiseSimilarity\n domain_of:\n - Mapping\n - TermPairwiseSimilarity\n range: string\n required: true\n object_label:\n name: object_label\n description: The name of the object entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: object_label\n owner: TermPairwiseSimilarity\n domain_of:\n - Association\n - CompactAssociation\n - AssociationTypeMapping\n - Mapping\n - TermPairwiseSimilarity\n range: string\n object_source:\n name: object_source\n description: the source for the second entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n slot_uri: sssom:object_source\n alias: object_source\n owner: TermPairwiseSimilarity\n domain_of:\n - TermPairwiseSimilarity\n range: string\n ancestor_id:\n name: ancestor_id\n description: the most recent common ancestor of the two compared entities. If\n there are multiple MRCAs then the most informative one is selected\n todos:\n - decide on what to do when there are multiple possible ancestos\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: ancestor_id\n owner: TermPairwiseSimilarity\n domain_of:\n - TermPairwiseSimilarity\n range: uriorcurie\n ancestor_label:\n name: ancestor_label\n description: the name or label of the ancestor concept\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: ancestor_label\n owner: TermPairwiseSimilarity\n domain_of:\n - TermPairwiseSimilarity\n range: string\n ancestor_source:\n name: ancestor_source\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: ancestor_source\n owner: TermPairwiseSimilarity\n domain_of:\n - TermPairwiseSimilarity\n range: string\n object_information_content:\n name: object_information_content\n description: The IC of the object\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: information_content\n alias: object_information_content\n owner: TermPairwiseSimilarity\n domain_of:\n - TermPairwiseSimilarity\n range: NegativeLogValue\n subject_information_content:\n name: subject_information_content\n description: The IC of the subject\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: information_content\n alias: subject_information_content\n owner: TermPairwiseSimilarity\n domain_of:\n - TermPairwiseSimilarity\n range: NegativeLogValue\n ancestor_information_content:\n name: ancestor_information_content\n description: The IC of the object\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: information_content\n alias: ancestor_information_content\n owner: TermPairwiseSimilarity\n domain_of:\n - TermPairwiseSimilarity\n range: NegativeLogValue\n jaccard_similarity:\n name: jaccard_similarity\n description: The number of concepts in the intersection divided by the number\n in the union\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: score\n alias: jaccard_similarity\n owner: TermPairwiseSimilarity\n domain_of:\n - TermPairwiseSimilarity\n range: ZeroToOne\n cosine_similarity:\n name: cosine_similarity\n description: the dot product of two node embeddings divided by the product of\n their lengths\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: score\n alias: cosine_similarity\n owner: TermPairwiseSimilarity\n domain_of:\n - TermPairwiseSimilarity\n range: float\n dice_similarity:\n name: dice_similarity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: score\n alias: dice_similarity\n owner: TermPairwiseSimilarity\n domain_of:\n - TermPairwiseSimilarity\n range: ZeroToOne\n phenodigm_score:\n name: phenodigm_score\n description: the geometric mean of the jaccard similarity and the information\n content\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: score\n alias: phenodigm_score\n owner: TermPairwiseSimilarity\n domain_of:\n - TermPairwiseSimilarity\n range: NonNegativeFloat\n equals_expression: sqrt({jaccard_similarity} * {information_content})\nA simple pairwise similarity between two sets of concepts/terms
URI: https://w3id.org/monarch/monarch-py/:TermSetPairwiseSimilarity
classDiagram\n class TermSetPairwiseSimilarity\n click TermSetPairwiseSimilarity href \"../TermSetPairwiseSimilarity\"\n PairwiseSimilarity <|-- TermSetPairwiseSimilarity\n click PairwiseSimilarity href \"../PairwiseSimilarity\"\n\n TermSetPairwiseSimilarity : average_score\n\n TermSetPairwiseSimilarity : best_score\n\n TermSetPairwiseSimilarity : metric\n\n TermSetPairwiseSimilarity : object_best_matches\n\n\n\n\n TermSetPairwiseSimilarity --> \"*\" BestMatch : object_best_matches\n click BestMatch href \"../BestMatch\"\n\n\n TermSetPairwiseSimilarity : object_termset\n\n\n\n\n TermSetPairwiseSimilarity --> \"*\" TermInfo : object_termset\n click TermInfo href \"../TermInfo\"\n\n\n TermSetPairwiseSimilarity : subject_best_matches\n\n\n\n\n TermSetPairwiseSimilarity --> \"*\" BestMatch : subject_best_matches\n click BestMatch href \"../BestMatch\"\n\n\n TermSetPairwiseSimilarity : subject_termset\n\n\n\n\n TermSetPairwiseSimilarity --> \"*\" TermInfo : subject_termset\n click TermInfo href \"../TermInfo\"\nname: TermSetPairwiseSimilarity\ndescription: A simple pairwise similarity between two sets of concepts/terms\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: PairwiseSimilarity\nslots:\n- subject_termset\n- object_termset\n- subject_best_matches\n- object_best_matches\n- average_score\n- best_score\n- metric\nname: TermSetPairwiseSimilarity\ndescription: A simple pairwise similarity between two sets of concepts/terms\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: PairwiseSimilarity\nattributes:\n subject_termset:\n name: subject_termset\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: subject_termset\n owner: TermSetPairwiseSimilarity\n domain_of:\n - TermSetPairwiseSimilarity\n range: TermInfo\n multivalued: true\n inlined: true\n object_termset:\n name: object_termset\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: object_termset\n owner: TermSetPairwiseSimilarity\n domain_of:\n - TermSetPairwiseSimilarity\n range: TermInfo\n multivalued: true\n inlined: true\n subject_best_matches:\n name: subject_best_matches\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: subject_best_matches\n owner: TermSetPairwiseSimilarity\n domain_of:\n - TermSetPairwiseSimilarity\n range: BestMatch\n multivalued: true\n inlined: true\n object_best_matches:\n name: object_best_matches\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: object_best_matches\n owner: TermSetPairwiseSimilarity\n domain_of:\n - TermSetPairwiseSimilarity\n range: BestMatch\n multivalued: true\n inlined: true\n average_score:\n name: average_score\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: average_score\n owner: TermSetPairwiseSimilarity\n domain_of:\n - TermSetPairwiseSimilarity\n range: float\n required: false\n best_score:\n name: best_score\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: best_score\n owner: TermSetPairwiseSimilarity\n domain_of:\n - TermSetPairwiseSimilarity\n range: float\n required: false\n metric:\n name: metric\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: metric\n owner: TermSetPairwiseSimilarity\n domain_of:\n - TermSetPairwiseSimilarity\n range: uriorcurie\nURI: https://w3id.org/monarch/monarch-py/:TextAnnotationResult
classDiagram\n class TextAnnotationResult\n click TextAnnotationResult href \"../TextAnnotationResult\"\n TextAnnotationResult : end\n\n TextAnnotationResult : start\n\n TextAnnotationResult : text\n\n TextAnnotationResult : tokens\n\n\n\n\n TextAnnotationResult --> \"*\" Entity : tokens\n click Entity href \"../Entity\"\nname: TextAnnotationResult\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- text\n- tokens\n- start\n- end\nname: TextAnnotationResult\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n text:\n name: text\n description: text without tokens\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: text\n owner: TextAnnotationResult\n domain_of:\n - TextAnnotationResult\n range: string\n inlined: true\n tokens:\n name: tokens\n description: A collection of entities or concepts\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: tokens\n owner: TextAnnotationResult\n domain_of:\n - TextAnnotationResult\n range: Entity\n multivalued: true\n inlined: true\n inlined_as_list: true\n start:\n name: start\n description: start position of the annotation\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: start\n owner: TextAnnotationResult\n domain_of:\n - TextAnnotationResult\n range: integer\n end:\n name: end\n description: end position of the annotation\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: end\n owner: TextAnnotationResult\n domain_of:\n - TextAnnotationResult\n range: integer\nA time object represents a (local) time of day, independent of any particular day
URI: xsd:time
base: XSDTime
uri: xsd:time
repr: str
a complete URI
URI: xsd:anyURI
base: URI
uri: xsd:anyURI
repr: str
a URI or a CURIE
URI: xsd:anyURI
base: URIorCURIE
uri: xsd:anyURI
repr: str
URI: xsd:float
base: float
uri: xsd:float
typeof: float
Describes the high-level category of agent who originally generated a statement of knowledge or other type of information.
URI: biolink:agent_type
"},{"location":"Data-Model/agent_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/agent_type/#properties","title":"Properties","text":"Range: String
Required: True
name: agent_type\ndescription: Describes the high-level category of agent who originally generated a statement\n of knowledge or other type of information.\nnotes:\n- The range in this schema is represented as a string, but is constrained to values\n from biolink:AgentTypeEnum at ingest time\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nslot_uri: biolink:agent_type\nalias: agent_type\ndomain_of:\n- Association\nrange: string\nrequired: true\nmultivalued: false\nURI: https://w3id.org/monarch/monarch-py/:aggregator_knowledge_source
"},{"location":"Data-Model/aggregator_knowledge_source/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/aggregator_knowledge_source/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: aggregator_knowledge_source\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: aggregator_knowledge_source\ndomain_of:\n- Association\nrange: string\nmultivalued: true\nthe most recent common ancestor of the two compared entities. If there are multiple MRCAs then the most informative one is selected
URI: https://w3id.org/monarch/monarch-py/:ancestor_id
"},{"location":"Data-Model/ancestor_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms no"},{"location":"Data-Model/ancestor_id/#properties","title":"Properties","text":"name: ancestor_id\ndescription: the most recent common ancestor of the two compared entities. If there\n are multiple MRCAs then the most informative one is selected\ntodos:\n- decide on what to do when there are multiple possible ancestos\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: ancestor_id\ndomain_of:\n- TermPairwiseSimilarity\nrange: uriorcurie\nThe IC of the object
URI: https://w3id.org/monarch/monarch-py/:ancestor_information_content
"},{"location":"Data-Model/ancestor_information_content/#inheritance","title":"Inheritance","text":"name: ancestor_information_content\ndescription: The IC of the object\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: information_content\nalias: ancestor_information_content\ndomain_of:\n- TermPairwiseSimilarity\nrange: NegativeLogValue\nthe name or label of the ancestor concept
URI: https://w3id.org/monarch/monarch-py/:ancestor_label
"},{"location":"Data-Model/ancestor_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms no"},{"location":"Data-Model/ancestor_label/#properties","title":"Properties","text":"name: ancestor_label\ndescription: the name or label of the ancestor concept\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: ancestor_label\ndomain_of:\n- TermPairwiseSimilarity\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:ancestor_source
"},{"location":"Data-Model/ancestor_source/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms no"},{"location":"Data-Model/ancestor_source/#properties","title":"Properties","text":"name: ancestor_source\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: ancestor_source\ndomain_of:\n- TermPairwiseSimilarity\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:associated_categories
"},{"location":"Data-Model/associated_categories/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MultiEntityAssociationResults no"},{"location":"Data-Model/associated_categories/#properties","title":"Properties","text":"Range: CategoryGroupedAssociationResults
Multivalued: True
Required: True
name: associated_categories\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: associated_categories\ndomain_of:\n- MultiEntityAssociationResults\nrange: CategoryGroupedAssociationResults\nrequired: true\nmultivalued: true\ninlined: true\ninlined_as_list: true\nURI: https://w3id.org/monarch/monarch-py/:association_counts
"},{"location":"Data-Model/association_counts/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Node UI container class extending Entity with additional information no"},{"location":"Data-Model/association_counts/#properties","title":"Properties","text":"Range: AssociationCount
Multivalued: True
Required: True
name: association_counts\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: association_counts\ndomain_of:\n- Node\nrange: AssociationCount\nrequired: true\nmultivalued: true\ninlined: true\ninlined_as_list: true\nURI: https://w3id.org/monarch/monarch-py/:average_score
"},{"location":"Data-Model/average_score/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermSetPairwiseSimilarity A simple pairwise similarity between two sets of concepts/terms no"},{"location":"Data-Model/average_score/#properties","title":"Properties","text":"name: average_score\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: average_score\ndomain_of:\n- TermSetPairwiseSimilarity\nrange: float\nrequired: false\nURI: https://w3id.org/monarch/monarch-py/:best_score
"},{"location":"Data-Model/best_score/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermSetPairwiseSimilarity A simple pairwise similarity between two sets of concepts/terms no"},{"location":"Data-Model/best_score/#properties","title":"Properties","text":"name: best_score\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: best_score\ndomain_of:\n- TermSetPairwiseSimilarity\nrange: float\nrequired: false\nURI: https://w3id.org/monarch/monarch-py/:category
"},{"location":"Data-Model/category/#inheritance","title":"Inheritance","text":"name: category\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: category\ndomain_of:\n- Association\n- AssociationCount\n- CompactAssociation\n- AssociationTypeMapping\n- Entity\nrange: string\nmultivalued: false\nA list of genes that are known to be causally associated with a disease
URI: https://w3id.org/monarch/monarch-py/:causal_gene
"},{"location":"Data-Model/causal_gene/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Node UI container class extending Entity with additional information no"},{"location":"Data-Model/causal_gene/#properties","title":"Properties","text":"Range: Entity
Multivalued: True
name: causal_gene\ndescription: A list of genes that are known to be causally associated with a disease\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: causal_gene\ndomain_of:\n- Node\nrange: Entity\nmultivalued: true\ninlined: true\ninlined_as_list: true\nA list of diseases that are known to be causally associated with a gene
URI: https://w3id.org/monarch/monarch-py/:causes_disease
"},{"location":"Data-Model/causes_disease/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Node UI container class extending Entity with additional information no"},{"location":"Data-Model/causes_disease/#properties","title":"Properties","text":"Range: Entity
Multivalued: True
name: causes_disease\ndescription: A list of diseases that are known to be causally associated with a gene\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: causes_disease\ndomain_of:\n- Node\nrange: Entity\nmultivalued: true\ninlined: true\ninlined_as_list: true\nthe dot product of two node embeddings divided by the product of their lengths
URI: https://w3id.org/monarch/monarch-py/:cosine_similarity
"},{"location":"Data-Model/cosine_similarity/#inheritance","title":"Inheritance","text":"name: cosine_similarity\ndescription: the dot product of two node embeddings divided by the product of their\n lengths\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: score\nalias: cosine_similarity\ndomain_of:\n- TermPairwiseSimilarity\nrange: float\ncount of documents
URI: https://w3id.org/monarch/monarch-py/:count
"},{"location":"Data-Model/count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FacetValue no HistoBin no AssociationCount no"},{"location":"Data-Model/count/#properties","title":"Properties","text":"name: count\ndescription: count of documents\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: count\ndomain_of:\n- FacetValue\nrange: integer\nThe category of the counterpart entity in a given association, eg. the category of the entity that is not the subject
URI: https://w3id.org/monarch/monarch-py/:counterpart_category
"},{"location":"Data-Model/counterpart_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CategoryGroupedAssociationResults no"},{"location":"Data-Model/counterpart_category/#properties","title":"Properties","text":"name: counterpart_category\ndescription: The category of the counterpart entity in a given association, eg. the\n category of the entity that is not the subject\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: counterpart_category\ndomain_of:\n- CategoryGroupedAssociationResults\nrange: string\nA boolean flag indicating that an entity is no longer considered current or valid.
URI: https://w3id.org/monarch/monarch-py/:deprecated
"},{"location":"Data-Model/deprecated/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Node UI container class extending Entity with additional information no Entity Represents an Entity in the Monarch KG data model no SearchResult no"},{"location":"Data-Model/deprecated/#properties","title":"Properties","text":"name: deprecated\ndescription: A boolean flag indicating that an entity is no longer considered current\n or valid.\nfrom_schema: https://w3id.org/monarch/monarch-py\nexact_mappings:\n- oboInOwl:ObsoleteClass\nrank: 1000\nalias: deprecated\ndomain_of:\n- Entity\nrange: boolean\nURI: https://w3id.org/monarch/monarch-py/:description
"},{"location":"Data-Model/description/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Node UI container class extending Entity with additional information no Entity Represents an Entity in the Monarch KG data model no SearchResult no"},{"location":"Data-Model/description/#properties","title":"Properties","text":"name: description\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: description\ndomain_of:\n- Entity\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:dice_similarity
"},{"location":"Data-Model/dice_similarity/#inheritance","title":"Inheritance","text":"name: dice_similarity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: score\nalias: dice_similarity\ndomain_of:\n- TermPairwiseSimilarity\nrange: ZeroToOne\nThe directionality of the association relative to a given entity for an association_count. If the entity is the subject or in the subject closure, the direction is forwards, if it is the object or in the object closure, the direction is backwards.
URI: https://w3id.org/monarch/monarch-py/:direction
"},{"location":"Data-Model/direction/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/direction/#properties","title":"Properties","text":"Range: AssociationDirectionEnum
Required: True
name: direction\ndescription: The directionality of the association relative to a given entity for\n an association_count. If the entity is the subject or in the subject closure, the\n direction is forwards, if it is the object or in the object closure, the direction\n is backwards.\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: direction\ndomain_of:\n- DirectionalAssociation\nrange: AssociationDirectionEnum\nrequired: true\nA context qualifier representing a disease or condition in which a relationship expressed in an association took place.
URI: https://w3id.org/monarch/monarch-py/:disease_context_qualifier
"},{"location":"Data-Model/disease_context_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/disease_context_qualifier/#properties","title":"Properties","text":"name: disease_context_qualifier\ndescription: A context qualifier representing a disease or condition in which a relationship\n expressed in an association took place.\nexamples:\n- value: MONDO:0004979\n- value: MONDO:0005148\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: disease_context_qualifier\ndomain_of:\n- Association\nrange: string\nThe category of the disease_context_qualifier entity
URI: https://w3id.org/monarch/monarch-py/:disease_context_qualifier_category
"},{"location":"Data-Model/disease_context_qualifier_category/#inheritance","title":"Inheritance","text":"name: disease_context_qualifier_category\ndescription: The category of the disease_context_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: category\nalias: disease_context_qualifier_category\ndomain_of:\n- Association\nrange: string\nField containing disease_context_qualifier id and the ids of all of it's ancestors
URI: https://w3id.org/monarch/monarch-py/:disease_context_qualifier_closure
"},{"location":"Data-Model/disease_context_qualifier_closure/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/disease_context_qualifier_closure/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: disease_context_qualifier_closure\ndescription: Field containing disease_context_qualifier id and the ids of all of it's\n ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: disease_context_qualifier_closure\ndomain_of:\n- Association\nrange: string\nmultivalued: true\nField containing disease_context_qualifier name and the names of all of it's ancestors
URI: https://w3id.org/monarch/monarch-py/:disease_context_qualifier_closure_label
"},{"location":"Data-Model/disease_context_qualifier_closure_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/disease_context_qualifier_closure_label/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: disease_context_qualifier_closure_label\ndescription: Field containing disease_context_qualifier name and the names of all\n of it's ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: disease_context_qualifier_closure_label\ndomain_of:\n- Association\nrange: string\nmultivalued: true\nThe name of the disease_context_qualifier entity
URI: https://w3id.org/monarch/monarch-py/:disease_context_qualifier_label
"},{"location":"Data-Model/disease_context_qualifier_label/#inheritance","title":"Inheritance","text":"name: disease_context_qualifier_label\ndescription: The name of the disease_context_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: name\nalias: disease_context_qualifier_label\ndomain_of:\n- Association\nrange: string\nThe namespace/prefix of the disease_context_qualifier entity
URI: https://w3id.org/monarch/monarch-py/:disease_context_qualifier_namespace
"},{"location":"Data-Model/disease_context_qualifier_namespace/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/disease_context_qualifier_namespace/#properties","title":"Properties","text":"name: disease_context_qualifier_namespace\ndescription: The namespace/prefix of the disease_context_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: disease_context_qualifier_namespace\ndomain_of:\n- Association\nrange: string\nend position of the annotation
URI: https://w3id.org/monarch/monarch-py/:end
"},{"location":"Data-Model/end/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextAnnotationResult no"},{"location":"Data-Model/end/#properties","title":"Properties","text":"name: end\ndescription: end position of the annotation\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: end\ndomain_of:\n- TextAnnotationResult\nrange: integer\ncount of supporting documents, evidence codes, and sources supplying evidence
URI: https://w3id.org/monarch/monarch-py/:evidence_count
"},{"location":"Data-Model/evidence_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/evidence_count/#properties","title":"Properties","text":"name: evidence_count\ndescription: count of supporting documents, evidence codes, and sources supplying\n evidence\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: evidence_count\ndomain_of:\n- Association\nrange: integer\nExpandedCurie with id and url for xrefs
URI: https://w3id.org/monarch/monarch-py/:external_links
"},{"location":"Data-Model/external_links/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Node UI container class extending Entity with additional information no"},{"location":"Data-Model/external_links/#properties","title":"Properties","text":"Range: ExpandedCurie
Multivalued: True
name: external_links\ndescription: ExpandedCurie with id and url for xrefs\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: external_links\ndomain_of:\n- Node\nrange: ExpandedCurie\nmultivalued: true\ninlined: true\ninlined_as_list: true\nCollection of facet field responses with the field values and counts
URI: https://w3id.org/monarch/monarch-py/:facet_fields
"},{"location":"Data-Model/facet_fields/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AssociationTableResults no CompactAssociationResults no SearchResults no AssociationResults no"},{"location":"Data-Model/facet_fields/#properties","title":"Properties","text":"Range: FacetField
Multivalued: True
name: facet_fields\ndescription: Collection of facet field responses with the field values and counts\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: facet_fields\ndomain_of:\n- AssociationResults\n- CompactAssociationResults\n- AssociationTableResults\n- SearchResults\nrange: FacetField\nmultivalued: true\ninlined: true\ninlined_as_list: true\nCollection of facet query responses with the query string values and counts
URI: https://w3id.org/monarch/monarch-py/:facet_queries
"},{"location":"Data-Model/facet_queries/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AssociationTableResults no CompactAssociationResults no SearchResults no AssociationResults no"},{"location":"Data-Model/facet_queries/#properties","title":"Properties","text":"Range: FacetValue
Multivalued: True
name: facet_queries\ndescription: Collection of facet query responses with the query string values and\n counts\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: facet_queries\ndomain_of:\n- AssociationResults\n- CompactAssociationResults\n- AssociationTableResults\n- SearchResults\nrange: FacetValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\nCollection of FacetValue label/value instances belonging to a FacetField
URI: https://w3id.org/monarch/monarch-py/:facet_values
"},{"location":"Data-Model/facet_values/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FacetField no"},{"location":"Data-Model/facet_values/#properties","title":"Properties","text":"Range: FacetValue
Multivalued: True
name: facet_values\ndescription: Collection of FacetValue label/value instances belonging to a FacetField\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: facet_values\ndomain_of:\n- FacetField\nrange: FacetValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\nURI: https://w3id.org/monarch/monarch-py/:frequency_qualifier
"},{"location":"Data-Model/frequency_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/frequency_qualifier/#properties","title":"Properties","text":"name: frequency_qualifier\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: frequency_qualifier\ndomain_of:\n- Association\nrange: string\nThe category of the frequency_qualifier entity
URI: https://w3id.org/monarch/monarch-py/:frequency_qualifier_category
"},{"location":"Data-Model/frequency_qualifier_category/#inheritance","title":"Inheritance","text":"name: frequency_qualifier_category\ndescription: The category of the frequency_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: category\nalias: frequency_qualifier_category\ndomain_of:\n- Association\nrange: string\nThe name of the frequency_qualifier entity
URI: https://w3id.org/monarch/monarch-py/:frequency_qualifier_label
"},{"location":"Data-Model/frequency_qualifier_label/#inheritance","title":"Inheritance","text":"name: frequency_qualifier_label\ndescription: The name of the frequency_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: name\nalias: frequency_qualifier_label\ndomain_of:\n- Association\nrange: string\nThe namespace/prefix of the frequency_qualifier entity
URI: https://w3id.org/monarch/monarch-py/:frequency_qualifier_namespace
"},{"location":"Data-Model/frequency_qualifier_namespace/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/frequency_qualifier_namespace/#properties","title":"Properties","text":"name: frequency_qualifier_namespace\ndescription: The namespace/prefix of the frequency_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: frequency_qualifier_namespace\ndomain_of:\n- Association\nrange: string\nThe long form name of an entity
URI: https://w3id.org/monarch/monarch-py/:full_name
"},{"location":"Data-Model/full_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Node UI container class extending Entity with additional information no Entity Represents an Entity in the Monarch KG data model no SearchResult no"},{"location":"Data-Model/full_name/#properties","title":"Properties","text":"name: full_name\ndescription: The long form name of an entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: full_name\ndomain_of:\n- Entity\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:graph_stats
"},{"location":"Data-Model/graph_stats/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Release A class to hold information about a release of the Monarch KG no"},{"location":"Data-Model/graph_stats/#properties","title":"Properties","text":"Instances of this class should have identifiers with one of the following prefixes:
name: graph_stats\nid_prefixes:\n- string\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: graph_stats\ndomain_of:\n- Release\nrange: string\nA concatenation of fields used to group associations with the same essential/defining properties
URI: https://w3id.org/monarch/monarch-py/:grouping_key
"},{"location":"Data-Model/grouping_key/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/grouping_key/#properties","title":"Properties","text":"name: grouping_key\ndescription: A concatenation of fields used to group associations with the same essential/defining\n properties\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: grouping_key\ndomain_of:\n- Association\nrange: string\ncount of out of has_total representing a frequency
URI: https://w3id.org/monarch/monarch-py/:has_count
"},{"location":"Data-Model/has_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/has_count/#properties","title":"Properties","text":"name: has_count\ndescription: count of out of has_total representing a frequency\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: has_count\ndomain_of:\n- Association\nrange: integer\nURI: https://w3id.org/monarch/monarch-py/:has_evidence
"},{"location":"Data-Model/has_evidence/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/has_evidence/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: has_evidence\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: has_evidence\ndomain_of:\n- Association\nrange: string\nmultivalued: true\nList of ExpandedCuries with id and url for evidence
URI: https://w3id.org/monarch/monarch-py/:has_evidence_links
"},{"location":"Data-Model/has_evidence_links/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/has_evidence_links/#properties","title":"Properties","text":"Range: ExpandedCurie
Multivalued: True
name: has_evidence_links\ndescription: List of ExpandedCuries with id and url for evidence\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: has_evidence_links\ndomain_of:\n- Association\nrange: ExpandedCurie\nmultivalued: true\ninlined: true\ninlined_as_list: true\npercentage, which may be calculated from has_count and has_total, as 100 * quotient or provided directly, rounded to the integer level
URI: https://w3id.org/monarch/monarch-py/:has_percentage
"},{"location":"Data-Model/has_percentage/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/has_percentage/#properties","title":"Properties","text":"name: has_percentage\ndescription: percentage, which may be calculated from has_count and has_total, as\n 100 * quotient or provided directly, rounded to the integer level\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: has_percentage\ndomain_of:\n- Association\nrange: float\nA list of phenotype identifiers that are known to be associated with this entity
URI: https://w3id.org/monarch/monarch-py/:has_phenotype
"},{"location":"Data-Model/has_phenotype/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Node UI container class extending Entity with additional information no Entity Represents an Entity in the Monarch KG data model no SearchResult no"},{"location":"Data-Model/has_phenotype/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: has_phenotype\ndescription: A list of phenotype identifiers that are known to be associated with\n this entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: has_phenotype\ndomain_of:\n- Entity\nrange: string\nmultivalued: true\ninlined: true\ninlined_as_list: true\nA list of phenotype identifiers that are known to be associated with this entity expanded to include all ancestors
URI: https://w3id.org/monarch/monarch-py/:has_phenotype_closure
"},{"location":"Data-Model/has_phenotype_closure/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Node UI container class extending Entity with additional information no Entity Represents an Entity in the Monarch KG data model no SearchResult no"},{"location":"Data-Model/has_phenotype_closure/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: has_phenotype_closure\ndescription: A list of phenotype identifiers that are known to be associated with\n this entity expanded to include all ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: has_phenotype_closure\ndomain_of:\n- Entity\nrange: string\nmultivalued: true\ninlined: true\ninlined_as_list: true\nA list of phenotype labels that are known to be associated with this entity expanded to include all ancestors
URI: https://w3id.org/monarch/monarch-py/:has_phenotype_closure_label
"},{"location":"Data-Model/has_phenotype_closure_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Node UI container class extending Entity with additional information no Entity Represents an Entity in the Monarch KG data model no SearchResult no"},{"location":"Data-Model/has_phenotype_closure_label/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: has_phenotype_closure_label\ndescription: A list of phenotype labels that are known to be associated with this\n entity expanded to include all ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: has_phenotype_closure_label\ndomain_of:\n- Entity\nrange: string\nmultivalued: true\ninlined: true\ninlined_as_list: true\nA count of the number of phenotypes that are known to be associated with this entity
URI: https://w3id.org/monarch/monarch-py/:has_phenotype_count
"},{"location":"Data-Model/has_phenotype_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Node UI container class extending Entity with additional information no Entity Represents an Entity in the Monarch KG data model no SearchResult no"},{"location":"Data-Model/has_phenotype_count/#properties","title":"Properties","text":"name: has_phenotype_count\ndescription: A count of the number of phenotypes that are known to be associated with\n this entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: has_phenotype_count\ndomain_of:\n- Entity\nrange: integer\nA list of phenotype labels that are known to be associated with this entity
URI: https://w3id.org/monarch/monarch-py/:has_phenotype_label
"},{"location":"Data-Model/has_phenotype_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Node UI container class extending Entity with additional information no Entity Represents an Entity in the Monarch KG data model no SearchResult no"},{"location":"Data-Model/has_phenotype_label/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: has_phenotype_label\ndescription: A list of phenotype labels that are known to be associated with this\n entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: has_phenotype_label\ndomain_of:\n- Entity\nrange: string\nmultivalued: true\ninlined: true\ninlined_as_list: true\nquotient, which should be 1/100 of has_percentage
URI: https://w3id.org/monarch/monarch-py/:has_quotient
"},{"location":"Data-Model/has_quotient/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/has_quotient/#properties","title":"Properties","text":"name: has_quotient\ndescription: quotient, which should be 1/100 of has_percentage\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: has_quotient\ndomain_of:\n- Association\nrange: float\ntotal, devided by has_count, representing a frequency
URI: https://w3id.org/monarch/monarch-py/:has_total
"},{"location":"Data-Model/has_total/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/has_total/#properties","title":"Properties","text":"name: has_total\ndescription: total, devided by has_count, representing a frequency\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: has_total\ndomain_of:\n- Association\nrange: integer\nmatching text snippet containing html tags
URI: https://w3id.org/monarch/monarch-py/:highlight
"},{"location":"Data-Model/highlight/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SearchResult no"},{"location":"Data-Model/highlight/#properties","title":"Properties","text":"name: highlight\ndescription: matching text snippet containing html tags\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: highlight\ndomain_of:\n- SearchResult\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:id
"},{"location":"Data-Model/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Entity Represents an Entity in the Monarch KG data model no ExpandedCurie A curie bundled along with its expanded url no MultiEntityAssociationResults no Node UI container class extending Entity with additional information no SearchResult no HistoPheno no Mapping A minimal class to hold a SSSOM mapping no HistoBin no TermInfo no Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/id/#properties","title":"Properties","text":"Range: String
Required: True
name: id\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nidentifier: true\nalias: id\ndomain_of:\n- Association\n- ExpandedCurie\n- Entity\n- HistoPheno\n- HistoBin\n- Mapping\n- MultiEntityAssociationResults\n- TermInfo\nrange: string\nrequired: true\nThe biolink taxon that the entity is in the closure of.
URI: https://w3id.org/monarch/monarch-py/:in_taxon
"},{"location":"Data-Model/in_taxon/#inheritance","title":"Inheritance","text":"name: in_taxon\ndescription: The biolink taxon that the entity is in the closure of.\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: in_taxon\ndomain_of:\n- Entity\n- Node\nrange: string\nThe label of the biolink taxon that the entity is in the closure of.
URI: https://w3id.org/monarch/monarch-py/:in_taxon_label
"},{"location":"Data-Model/in_taxon_label/#inheritance","title":"Inheritance","text":"name: in_taxon_label\ndescription: The label of the biolink taxon that the entity is in the closure of.\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: in_taxon_label\ndomain_of:\n- Entity\n- Node\nrange: string\nThe IC is the negative log of the probability of the concept
URI: https://w3id.org/monarch/monarch-py/:information_content
"},{"location":"Data-Model/information_content/#inheritance","title":"Inheritance","text":"name: information_content\ndescription: The IC is the negative log of the probability of the concept\nfrom_schema: https://w3id.org/monarch/monarch-py\naliases:\n- IC\nrank: 1000\nis_a: score\nabstract: true\nalias: information_content\nrange: NegativeLogValue\nURI: https://w3id.org/monarch/monarch-py/:inheritance
"},{"location":"Data-Model/inheritance/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Node UI container class extending Entity with additional information no"},{"location":"Data-Model/inheritance/#properties","title":"Properties","text":"name: inheritance\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: inheritance\ndomain_of:\n- Node\nrange: Entity\ninlined: true\nURI: https://w3id.org/monarch/monarch-py/:intersection_count
"},{"location":"Data-Model/intersection_count/#inheritance","title":"Inheritance","text":"name: intersection_count\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: score\nalias: intersection_count\nrange: ItemCount\nURI: https://w3id.org/monarch/monarch-py/:iri
"},{"location":"Data-Model/iri/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Node UI container class extending Entity with additional information no Entity Represents an Entity in the Monarch KG data model no SearchResult no"},{"location":"Data-Model/iri/#properties","title":"Properties","text":"name: iri\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: iri\ndomain_of:\n- Entity\nrange: string\nA collection of items, with the type to be overriden by slot_usage
URI: https://w3id.org/monarch/monarch-py/:items
"},{"location":"Data-Model/items/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AssociationCountList Container class for a list of association counts yes EntityResults yes CompactAssociationResults yes AssociationTableResults yes HistoPheno yes MappingResults SSSOM Mappings returned as a results collection yes CategoryGroupedAssociationResults yes SearchResults yes AssociationResults yes"},{"location":"Data-Model/items/#properties","title":"Properties","text":"Range: String
Multivalued: True
Required: True
name: items\ndescription: A collection of items, with the type to be overriden by slot_usage\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: items\ndomain_of:\n- AssociationCountList\n- AssociationResults\n- CompactAssociationResults\n- AssociationTableResults\n- CategoryGroupedAssociationResults\n- EntityResults\n- HistoPheno\n- MappingResults\n- SearchResults\nrange: string\nrequired: true\nmultivalued: true\ninlined: true\ninlined_as_list: true\nThe number of concepts in the intersection divided by the number in the union
URI: https://w3id.org/monarch/monarch-py/:jaccard_similarity
"},{"location":"Data-Model/jaccard_similarity/#inheritance","title":"Inheritance","text":"name: jaccard_similarity\ndescription: The number of concepts in the intersection divided by the number in the\n union\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: score\nalias: jaccard_similarity\ndomain_of:\n- TermPairwiseSimilarity\nrange: ZeroToOne\nURI: https://w3id.org/monarch/monarch-py/:kg
"},{"location":"Data-Model/kg/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Release A class to hold information about a release of the Monarch KG no"},{"location":"Data-Model/kg/#properties","title":"Properties","text":"Instances of this class should have identifiers with one of the following prefixes:
name: kg\nid_prefixes:\n- string\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: kg\ndomain_of:\n- Release\nrange: string\nDescribes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true.
URI: biolink:knowledge_level
"},{"location":"Data-Model/knowledge_level/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/knowledge_level/#properties","title":"Properties","text":"Range: String
Required: True
name: knowledge_level\ndescription: Describes the level of knowledge expressed in a statement, based on the\n reasoning or analysis methods used to generate the statement, or the scope or specificity\n of what the statement expresses to be true.\nnotes:\n- The range in this schema is represented as a string, but is constrained to values\n from biolink:KnowledgeLevelEnum at ingest time\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nslot_uri: biolink:knowledge_level\nalias: knowledge_level\ndomain_of:\n- Association\nrange: string\nrequired: true\nmultivalued: false\nURI: https://w3id.org/monarch/monarch-py/:knowledge_source
"},{"location":"Data-Model/knowledge_source/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: knowledge_source\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: knowledge_source\nrange: string\nmultivalued: true\nURI: https://w3id.org/monarch/monarch-py/:label
"},{"location":"Data-Model/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AssociationCount no FacetValue no HistoBin no TermInfo no FacetField no"},{"location":"Data-Model/label/#properties","title":"Properties","text":"Range: String
Required: True
name: label\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: label\ndomain_of:\n- FacetValue\n- FacetField\n- TermInfo\nrange: string\nrequired: true\nnumber of items to return in a response
URI: https://w3id.org/monarch/monarch-py/:limit
"},{"location":"Data-Model/limit/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot EntityResults no CompactAssociationResults no MultiEntityAssociationResults no AssociationTableResults no MappingResults SSSOM Mappings returned as a results collection no CategoryGroupedAssociationResults no Results no SearchResults no AssociationResults no"},{"location":"Data-Model/limit/#properties","title":"Properties","text":"Range: Integer
Required: True
name: limit\ndescription: number of items to return in a response\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: limit\ndomain_of:\n- Results\nrange: integer\nrequired: true\nURI: https://w3id.org/monarch/monarch-py/:mapping_justification
"},{"location":"Data-Model/mapping_justification/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Mapping A minimal class to hold a SSSOM mapping no"},{"location":"Data-Model/mapping_justification/#properties","title":"Properties","text":"name: mapping_justification\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: mapping_justification\ndomain_of:\n- Mapping\nrange: string\nList of ExpandedCuries with id and url for mapped entities
URI: https://w3id.org/monarch/monarch-py/:mappings
"},{"location":"Data-Model/mappings/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Node UI container class extending Entity with additional information no"},{"location":"Data-Model/mappings/#properties","title":"Properties","text":"Range: ExpandedCurie
Multivalued: True
name: mappings\ndescription: List of ExpandedCuries with id and url for mapped entities\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: mappings\ndomain_of:\n- Node\nrange: ExpandedCurie\nmultivalued: true\ninlined: true\ninlined_as_list: true\nURI: https://w3id.org/monarch/monarch-py/:match_source
"},{"location":"Data-Model/match_source/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BestMatch no"},{"location":"Data-Model/match_source/#properties","title":"Properties","text":"Range: String
Required: True
name: match_source\ncomments:\n- note that the match_source is either the subject or the object\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nidentifier: true\nalias: match_source\nowner: BestMatch\ndomain_of:\n- BestMatch\nrange: string\nrequired: true\nURI: https://w3id.org/monarch/monarch-py/:match_source_label
"},{"location":"Data-Model/match_source_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BestMatch no"},{"location":"Data-Model/match_source_label/#properties","title":"Properties","text":"name: match_source_label\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: match_source_label\nowner: BestMatch\ndomain_of:\n- BestMatch\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:match_subsumer
"},{"location":"Data-Model/match_subsumer/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BestMatch no"},{"location":"Data-Model/match_subsumer/#properties","title":"Properties","text":"name: match_subsumer\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: match_subsumer\nowner: BestMatch\ndomain_of:\n- BestMatch\nrange: uriorcurie\nURI: https://w3id.org/monarch/monarch-py/:match_subsumer_label
"},{"location":"Data-Model/match_subsumer_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BestMatch no"},{"location":"Data-Model/match_subsumer_label/#properties","title":"Properties","text":"name: match_subsumer_label\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: match_subsumer_label\nowner: BestMatch\ndomain_of:\n- BestMatch\nrange: string\nthe entity matches
URI: https://w3id.org/monarch/monarch-py/:match_target
"},{"location":"Data-Model/match_target/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BestMatch no"},{"location":"Data-Model/match_target/#properties","title":"Properties","text":"name: match_target\ndescription: the entity matches\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: match_target\nowner: BestMatch\ndomain_of:\n- BestMatch\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:match_target_label
"},{"location":"Data-Model/match_target_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BestMatch no"},{"location":"Data-Model/match_target_label/#properties","title":"Properties","text":"name: match_target_label\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: match_target_label\nowner: BestMatch\ndomain_of:\n- BestMatch\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:metadata
"},{"location":"Data-Model/metadata/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Release A class to hold information about a release of the Monarch KG no"},{"location":"Data-Model/metadata/#properties","title":"Properties","text":"Instances of this class should have identifiers with one of the following prefixes:
name: metadata\nid_prefixes:\n- string\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: metadata\ndomain_of:\n- Release\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:metric
"},{"location":"Data-Model/metric/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermSetPairwiseSimilarity A simple pairwise similarity between two sets of concepts/terms no"},{"location":"Data-Model/metric/#properties","title":"Properties","text":"name: metric\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: metric\ndomain_of:\n- TermSetPairwiseSimilarity\nrange: uriorcurie\nData models for the Monarch Initiative data access library
URI: https://w3id.org/monarch/monarch-py
"},{"location":"Data-Model/name/","title":"Slot: name","text":"URI: https://w3id.org/monarch/monarch-py/:name
"},{"location":"Data-Model/name/#inheritance","title":"Inheritance","text":"name: name\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: name\ndomain_of:\n- Entity\n- MultiEntityAssociationResults\nrange: string\nThe namespace/prefix portion of this entity's identifier
URI: https://w3id.org/monarch/monarch-py/:namespace
"},{"location":"Data-Model/namespace/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Node UI container class extending Entity with additional information no Entity Represents an Entity in the Monarch KG data model no SearchResult no"},{"location":"Data-Model/namespace/#properties","title":"Properties","text":"name: namespace\ndescription: The namespace/prefix portion of this entity's identifier\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: namespace\ndomain_of:\n- Entity\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:negated
"},{"location":"Data-Model/negated/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no CompactAssociation no"},{"location":"Data-Model/negated/#properties","title":"Properties","text":"name: negated\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: negated\ndomain_of:\n- Association\n- CompactAssociation\nrange: boolean\nURI: https://w3id.org/monarch/monarch-py/:neo4j
"},{"location":"Data-Model/neo4j/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Release A class to hold information about a release of the Monarch KG no"},{"location":"Data-Model/neo4j/#properties","title":"Properties","text":"Instances of this class should have identifiers with one of the following prefixes:
name: neo4j\nid_prefixes:\n- string\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: neo4j\ndomain_of:\n- Release\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:node_hierarchy
"},{"location":"Data-Model/node_hierarchy/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Node UI container class extending Entity with additional information no"},{"location":"Data-Model/node_hierarchy/#properties","title":"Properties","text":"name: node_hierarchy\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: node_hierarchy\ndomain_of:\n- Node\nrange: NodeHierarchy\ninlined: true\nURI: https://w3id.org/monarch/monarch-py/:object
"},{"location":"Data-Model/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no CompactAssociation no"},{"location":"Data-Model/object/#properties","title":"Properties","text":"Range: String
Required: True
name: object\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: object\ndomain_of:\n- Association\n- CompactAssociation\nrange: string\nrequired: true\nURI: https://w3id.org/monarch/monarch-py/:object_best_matches
"},{"location":"Data-Model/object_best_matches/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermSetPairwiseSimilarity A simple pairwise similarity between two sets of concepts/terms no"},{"location":"Data-Model/object_best_matches/#properties","title":"Properties","text":"Range: BestMatch
Multivalued: True
name: object_best_matches\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: object_best_matches\ndomain_of:\n- TermSetPairwiseSimilarity\nrange: BestMatch\nmultivalued: true\ninlined: true\nThe category of the object entity
URI: https://w3id.org/monarch/monarch-py/:object_category
"},{"location":"Data-Model/object_category/#inheritance","title":"Inheritance","text":"name: object_category\ndescription: The category of the object entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: category\nalias: object_category\ndomain_of:\n- Association\nrange: string\nField containing object id and the ids of all of it's ancestors
URI: https://w3id.org/monarch/monarch-py/:object_closure
"},{"location":"Data-Model/object_closure/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/object_closure/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: object_closure\ndescription: Field containing object id and the ids of all of it's ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: object_closure\ndomain_of:\n- Association\nrange: string\nmultivalued: true\nField containing object name and the names of all of it's ancestors
URI: https://w3id.org/monarch/monarch-py/:object_closure_label
"},{"location":"Data-Model/object_closure_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/object_closure_label/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: object_closure_label\ndescription: Field containing object name and the names of all of it's ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: object_closure_label\ndomain_of:\n- Association\nrange: string\nmultivalued: true\nURI: https://w3id.org/monarch/monarch-py/:object_id
"},{"location":"Data-Model/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms no Mapping A minimal class to hold a SSSOM mapping no"},{"location":"Data-Model/object_id/#properties","title":"Properties","text":"Range: String
Required: True
name: object_id\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: object_id\ndomain_of:\n- Mapping\n- TermPairwiseSimilarity\nrange: string\nrequired: true\nThe IC of the object
URI: https://w3id.org/monarch/monarch-py/:object_information_content
"},{"location":"Data-Model/object_information_content/#inheritance","title":"Inheritance","text":"name: object_information_content\ndescription: The IC of the object\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: information_content\nalias: object_information_content\ndomain_of:\n- TermPairwiseSimilarity\nrange: NegativeLogValue\nThe name of the object entity
URI: https://w3id.org/monarch/monarch-py/:object_label
"},{"location":"Data-Model/object_label/#inheritance","title":"Inheritance","text":"name: object_label\ndescription: The name of the object entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: name\nalias: object_label\ndomain_of:\n- Association\n- CompactAssociation\n- AssociationTypeMapping\n- Mapping\n- TermPairwiseSimilarity\nrange: string\nThe namespace/prefix of the object entity
URI: https://w3id.org/monarch/monarch-py/:object_namespace
"},{"location":"Data-Model/object_namespace/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/object_namespace/#properties","title":"Properties","text":"name: object_namespace\ndescription: The namespace/prefix of the object entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: object_namespace\ndomain_of:\n- Association\nrange: string\nthe source for the second entity
URI: sssom:object_source
"},{"location":"Data-Model/object_source/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms no"},{"location":"Data-Model/object_source/#properties","title":"Properties","text":"name: object_source\ndescription: the source for the second entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nslot_uri: sssom:object_source\nalias: object_source\ndomain_of:\n- TermPairwiseSimilarity\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:object_taxon
"},{"location":"Data-Model/object_taxon/#inheritance","title":"Inheritance","text":"name: object_taxon\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: in_taxon\nalias: object_taxon\ndomain_of:\n- Association\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:object_taxon_label
"},{"location":"Data-Model/object_taxon_label/#inheritance","title":"Inheritance","text":"name: object_taxon_label\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: in_taxon_label\nalias: object_taxon_label\ndomain_of:\n- Association\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:object_termset
"},{"location":"Data-Model/object_termset/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermSetPairwiseSimilarity A simple pairwise similarity between two sets of concepts/terms no"},{"location":"Data-Model/object_termset/#properties","title":"Properties","text":"Range: TermInfo
Multivalued: True
name: object_termset\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: object_termset\ndomain_of:\n- TermSetPairwiseSimilarity\nrange: TermInfo\nmultivalued: true\ninlined: true\noffset into the total number of items
URI: https://w3id.org/monarch/monarch-py/:offset
"},{"location":"Data-Model/offset/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot EntityResults no CompactAssociationResults no MultiEntityAssociationResults no AssociationTableResults no MappingResults SSSOM Mappings returned as a results collection no CategoryGroupedAssociationResults no Results no SearchResults no AssociationResults no"},{"location":"Data-Model/offset/#properties","title":"Properties","text":"Range: Integer
Required: True
name: offset\ndescription: offset into the total number of items\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: offset\ndomain_of:\n- Results\nrange: integer\nrequired: true\nURI: https://w3id.org/monarch/monarch-py/:onset_qualifier
"},{"location":"Data-Model/onset_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/onset_qualifier/#properties","title":"Properties","text":"name: onset_qualifier\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: onset_qualifier\ndomain_of:\n- Association\nrange: string\nThe category of the onset_qualifier entity
URI: https://w3id.org/monarch/monarch-py/:onset_qualifier_category
"},{"location":"Data-Model/onset_qualifier_category/#inheritance","title":"Inheritance","text":"name: onset_qualifier_category\ndescription: The category of the onset_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: category\nalias: onset_qualifier_category\ndomain_of:\n- Association\nrange: string\nThe name of the onset_qualifier entity
URI: https://w3id.org/monarch/monarch-py/:onset_qualifier_label
"},{"location":"Data-Model/onset_qualifier_label/#inheritance","title":"Inheritance","text":"name: onset_qualifier_label\ndescription: The name of the onset_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: name\nalias: onset_qualifier_label\ndomain_of:\n- Association\nrange: string\nThe namespace/prefix of the onset_qualifier entity
URI: https://w3id.org/monarch/monarch-py/:onset_qualifier_namespace
"},{"location":"Data-Model/onset_qualifier_namespace/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/onset_qualifier_namespace/#properties","title":"Properties","text":"name: onset_qualifier_namespace\ndescription: The namespace/prefix of the onset_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: onset_qualifier_namespace\ndomain_of:\n- Association\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:original_object
"},{"location":"Data-Model/original_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/original_object/#properties","title":"Properties","text":"name: original_object\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: original_object\ndomain_of:\n- Association\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:original_subject
"},{"location":"Data-Model/original_subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/original_subject/#properties","title":"Properties","text":"name: original_subject\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: original_subject\ndomain_of:\n- Association\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:overlap_coefficient
"},{"location":"Data-Model/overlap_coefficient/#inheritance","title":"Inheritance","text":"name: overlap_coefficient\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: score\nalias: overlap_coefficient\nrange: ZeroToOne\nURI: https://w3id.org/monarch/monarch-py/:pathway
"},{"location":"Data-Model/pathway/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/pathway/#properties","title":"Properties","text":"name: pathway\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: pathway\ndomain_of:\n- Association\nrange: string\nthe geometric mean of the jaccard similarity and the information content
URI: https://w3id.org/monarch/monarch-py/:phenodigm_score
"},{"location":"Data-Model/phenodigm_score/#inheritance","title":"Inheritance","text":"name: phenodigm_score\ndescription: the geometric mean of the jaccard similarity and the information content\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: score\nalias: phenodigm_score\ndomain_of:\n- TermPairwiseSimilarity\nrange: NonNegativeFloat\nequals_expression: sqrt({jaccard_similarity} * {information_content})\nURI: https://w3id.org/monarch/monarch-py/:predicate
"},{"location":"Data-Model/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no CompactAssociation no"},{"location":"Data-Model/predicate/#properties","title":"Properties","text":"Range: String
Required: True
name: predicate\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: predicate\ndomain_of:\n- Association\n- CompactAssociation\nrange: string\nrequired: true\nmultivalued: false\nURI: https://w3id.org/monarch/monarch-py/:predicate_id
"},{"location":"Data-Model/predicate_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Mapping A minimal class to hold a SSSOM mapping no"},{"location":"Data-Model/predicate_id/#properties","title":"Properties","text":"Range: String
Required: True
name: predicate_id\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: predicate_id\ndomain_of:\n- Mapping\nrange: string\nrequired: true\nURI: https://w3id.org/monarch/monarch-py/:primary_knowledge_source
"},{"location":"Data-Model/primary_knowledge_source/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/primary_knowledge_source/#properties","title":"Properties","text":"name: primary_knowledge_source\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: primary_knowledge_source\ndomain_of:\n- Association\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:provided_by
"},{"location":"Data-Model/provided_by/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Entity Represents an Entity in the Monarch KG data model no Node UI container class extending Entity with additional information no SearchResult no Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/provided_by/#properties","title":"Properties","text":"name: provided_by\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: provided_by\ndomain_of:\n- Association\n- Entity\nrange: string\nA link to the docs for the knowledge source that provided the node/edge.
URI: https://w3id.org/monarch/monarch-py/:provided_by_link
"},{"location":"Data-Model/provided_by_link/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Node UI container class extending Entity with additional information no Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/provided_by_link/#properties","title":"Properties","text":"name: provided_by_link\ndescription: A link to the docs for the knowledge source that provided the node/edge.\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: provided_by_link\ndomain_of:\n- Association\n- Node\nrange: ExpandedCurie\ninlined: true\nURI: https://w3id.org/monarch/monarch-py/:publications
"},{"location":"Data-Model/publications/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/publications/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: publications\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: publications\ndomain_of:\n- Association\nrange: string\nmultivalued: true\nList of ExpandedCuries with id and url for publications
URI: https://w3id.org/monarch/monarch-py/:publications_links
"},{"location":"Data-Model/publications_links/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/publications_links/#properties","title":"Properties","text":"Range: ExpandedCurie
Multivalued: True
name: publications_links\ndescription: List of ExpandedCuries with id and url for publications\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: publications_links\ndomain_of:\n- Association\nrange: ExpandedCurie\nmultivalued: true\ninlined: true\ninlined_as_list: true\nURI: https://w3id.org/monarch/monarch-py/:qc_report
"},{"location":"Data-Model/qc_report/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Release A class to hold information about a release of the Monarch KG no"},{"location":"Data-Model/qc_report/#properties","title":"Properties","text":"Instances of this class should have identifiers with one of the following prefixes:
name: qc_report\nid_prefixes:\n- string\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: qc_report\ndomain_of:\n- Release\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:qualifier
"},{"location":"Data-Model/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/qualifier/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: qualifier\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: qualifier\ndomain_of:\n- Association\nrange: string\nmultivalued: true\nThe category of the frequency_qualifier entity
URI: https://w3id.org/monarch/monarch-py/:qualifier_category
"},{"location":"Data-Model/qualifier_category/#inheritance","title":"Inheritance","text":"name: qualifier_category\ndescription: The category of the frequency_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: category\nalias: qualifier_category\ndomain_of:\n- Association\nrange: string\nThe name of the frequency_qualifier entity
URI: https://w3id.org/monarch/monarch-py/:qualifier_label
"},{"location":"Data-Model/qualifier_label/#inheritance","title":"Inheritance","text":"name: qualifier_label\ndescription: The name of the frequency_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: name\nalias: qualifier_label\ndomain_of:\n- Association\nrange: string\nThe namespace/prefix of the frequency_qualifier entity
URI: https://w3id.org/monarch/monarch-py/:qualifier_namespace
"},{"location":"Data-Model/qualifier_namespace/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/qualifier_namespace/#properties","title":"Properties","text":"name: qualifier_namespace\ndescription: The namespace/prefix of the frequency_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: qualifier_namespace\ndomain_of:\n- Association\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:qualifiers
"},{"location":"Data-Model/qualifiers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/qualifiers/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: qualifiers\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: qualifiers\ndomain_of:\n- Association\nrange: string\nmultivalued: true\nThe category of the frequency_qualifier entity
URI: https://w3id.org/monarch/monarch-py/:qualifiers_category
"},{"location":"Data-Model/qualifiers_category/#inheritance","title":"Inheritance","text":"name: qualifiers_category\ndescription: The category of the frequency_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: category\nalias: qualifiers_category\ndomain_of:\n- Association\nrange: string\nField containing frequency_qualifier id and the ids of all of it's ancestors
URI: https://w3id.org/monarch/monarch-py/:qualifiers_closure
"},{"location":"Data-Model/qualifiers_closure/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: qualifiers_closure\ndescription: Field containing frequency_qualifier id and the ids of all of it's ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: qualifiers_closure\nrange: string\nmultivalued: true\nField containing frequency_qualifier name and the names of all of it's ancestors
URI: https://w3id.org/monarch/monarch-py/:qualifiers_closure_label
"},{"location":"Data-Model/qualifiers_closure_label/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: qualifiers_closure_label\ndescription: Field containing frequency_qualifier name and the names of all of it's\n ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: qualifiers_closure_label\nrange: string\nmultivalued: true\nThe name of the frequency_qualifier entity
URI: https://w3id.org/monarch/monarch-py/:qualifiers_label
"},{"location":"Data-Model/qualifiers_label/#inheritance","title":"Inheritance","text":"name: qualifiers_label\ndescription: The name of the frequency_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: name\nalias: qualifiers_label\ndomain_of:\n- Association\nrange: string\nThe namespace/prefix of the frequency_qualifier entity
URI: https://w3id.org/monarch/monarch-py/:qualifiers_namespace
"},{"location":"Data-Model/qualifiers_namespace/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/qualifiers_namespace/#properties","title":"Properties","text":"name: qualifiers_namespace\ndescription: The namespace/prefix of the frequency_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: qualifiers_namespace\ndomain_of:\n- Association\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:score
"},{"location":"Data-Model/score/#inheritance","title":"Inheritance","text":"name: score\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: score\ndomain_of:\n- SearchResult\n- BestMatch\n- SemsimSearchResult\nrange: float\nURI: https://w3id.org/monarch/monarch-py/:sex_qualifier
"},{"location":"Data-Model/sex_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/sex_qualifier/#properties","title":"Properties","text":"name: sex_qualifier\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: sex_qualifier\ndomain_of:\n- Association\nrange: string\nThe category of the sex_qualifier entity
URI: https://w3id.org/monarch/monarch-py/:sex_qualifier_category
"},{"location":"Data-Model/sex_qualifier_category/#inheritance","title":"Inheritance","text":"name: sex_qualifier_category\ndescription: The category of the sex_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: category\nalias: sex_qualifier_category\ndomain_of:\n- Association\nrange: string\nThe name of the sex_qualifier entity
URI: https://w3id.org/monarch/monarch-py/:sex_qualifier_label
"},{"location":"Data-Model/sex_qualifier_label/#inheritance","title":"Inheritance","text":"name: sex_qualifier_label\ndescription: The name of the sex_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: name\nalias: sex_qualifier_label\ndomain_of:\n- Association\nrange: string\nThe namespace/prefix of the sex_qualifier entity
URI: https://w3id.org/monarch/monarch-py/:sex_qualifier_namespace
"},{"location":"Data-Model/sex_qualifier_namespace/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/sex_qualifier_namespace/#properties","title":"Properties","text":"name: sex_qualifier_namespace\ndescription: The namespace/prefix of the sex_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: sex_qualifier_namespace\ndomain_of:\n- Association\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:similarity
"},{"location":"Data-Model/similarity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BestMatch no SemsimSearchResult no"},{"location":"Data-Model/similarity/#properties","title":"Properties","text":"name: similarity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: similarity\ndomain_of:\n- BestMatch\n- SemsimSearchResult\nrange: TermSetPairwiseSimilarity\nURI: https://w3id.org/monarch/monarch-py/:solr
"},{"location":"Data-Model/solr/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Release A class to hold information about a release of the Monarch KG no"},{"location":"Data-Model/solr/#properties","title":"Properties","text":"Instances of this class should have identifiers with one of the following prefixes:
name: solr\nid_prefixes:\n- string\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: solr\ndomain_of:\n- Release\nrange: string\nA context qualifier representing a species in which a relationship expressed in an association took place.
URI: https://w3id.org/monarch/monarch-py/:species_context_qualifier
"},{"location":"Data-Model/species_context_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/species_context_qualifier/#properties","title":"Properties","text":"name: species_context_qualifier\ndescription: A context qualifier representing a species in which a relationship expressed\n in an association took place.\nexamples:\n- value: NCBITaxon:9606\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: species_context_qualifier\ndomain_of:\n- Association\nrange: string\nThe category of the species_context_qualifier entity
URI: https://w3id.org/monarch/monarch-py/:species_context_qualifier_category
"},{"location":"Data-Model/species_context_qualifier_category/#inheritance","title":"Inheritance","text":"name: species_context_qualifier_category\ndescription: The category of the species_context_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: category\nalias: species_context_qualifier_category\ndomain_of:\n- Association\nrange: string\nThe name of the species_context_qualifier entity
URI: https://w3id.org/monarch/monarch-py/:species_context_qualifier_label
"},{"location":"Data-Model/species_context_qualifier_label/#inheritance","title":"Inheritance","text":"name: species_context_qualifier_label\ndescription: The name of the species_context_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: name\nalias: species_context_qualifier_label\ndomain_of:\n- Association\nrange: string\nThe namespace/prefix of the species_context_qualifier entity
URI: https://w3id.org/monarch/monarch-py/:species_context_qualifier_namespace
"},{"location":"Data-Model/species_context_qualifier_namespace/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/species_context_qualifier_namespace/#properties","title":"Properties","text":"name: species_context_qualifier_namespace\ndescription: The namespace/prefix of the species_context_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: species_context_qualifier_namespace\ndomain_of:\n- Association\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:sqlite
"},{"location":"Data-Model/sqlite/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Release A class to hold information about a release of the Monarch KG no"},{"location":"Data-Model/sqlite/#properties","title":"Properties","text":"Instances of this class should have identifiers with one of the following prefixes:
name: sqlite\nid_prefixes:\n- string\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: sqlite\ndomain_of:\n- Release\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:stage_qualifier
"},{"location":"Data-Model/stage_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/stage_qualifier/#properties","title":"Properties","text":"name: stage_qualifier\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: stage_qualifier\ndomain_of:\n- Association\nrange: string\nThe category of the stage_qualifier entity
URI: https://w3id.org/monarch/monarch-py/:stage_qualifier_category
"},{"location":"Data-Model/stage_qualifier_category/#inheritance","title":"Inheritance","text":"name: stage_qualifier_category\ndescription: The category of the stage_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: category\nalias: stage_qualifier_category\ndomain_of:\n- Association\nrange: string\nThe name of the stage_qualifier entity
URI: https://w3id.org/monarch/monarch-py/:stage_qualifier_label
"},{"location":"Data-Model/stage_qualifier_label/#inheritance","title":"Inheritance","text":"name: stage_qualifier_label\ndescription: The name of the stage_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: name\nalias: stage_qualifier_label\ndomain_of:\n- Association\nrange: string\nThe namespace/prefix of the stage_qualifier entity
URI: https://w3id.org/monarch/monarch-py/:stage_qualifier_namespace
"},{"location":"Data-Model/stage_qualifier_namespace/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/stage_qualifier_namespace/#properties","title":"Properties","text":"name: stage_qualifier_namespace\ndescription: The namespace/prefix of the stage_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: stage_qualifier_namespace\ndomain_of:\n- Association\nrange: string\nstart position of the annotation
URI: https://w3id.org/monarch/monarch-py/:start
"},{"location":"Data-Model/start/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextAnnotationResult no"},{"location":"Data-Model/start/#properties","title":"Properties","text":"name: start\ndescription: start position of the annotation\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: start\ndomain_of:\n- TextAnnotationResult\nrange: integer\nURI: https://w3id.org/monarch/monarch-py/:sub_classes
"},{"location":"Data-Model/sub_classes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot NodeHierarchy no"},{"location":"Data-Model/sub_classes/#properties","title":"Properties","text":"Range: Entity
Multivalued: True
Required: True
name: sub_classes\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: sub_classes\ndomain_of:\n- NodeHierarchy\nrange: Entity\nrequired: true\nmultivalued: true\ninlined: true\ninlined_as_list: true\nURI: https://w3id.org/monarch/monarch-py/:subject
"},{"location":"Data-Model/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SemsimSearchResult yes Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no CompactAssociation no"},{"location":"Data-Model/subject/#properties","title":"Properties","text":"Range: String
Required: True
name: subject\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: subject\ndomain_of:\n- Association\n- CompactAssociation\n- SemsimSearchResult\nrange: string\nrequired: true\nURI: https://w3id.org/monarch/monarch-py/:subject_best_matches
"},{"location":"Data-Model/subject_best_matches/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermSetPairwiseSimilarity A simple pairwise similarity between two sets of concepts/terms no"},{"location":"Data-Model/subject_best_matches/#properties","title":"Properties","text":"Range: BestMatch
Multivalued: True
name: subject_best_matches\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: subject_best_matches\ndomain_of:\n- TermSetPairwiseSimilarity\nrange: BestMatch\nmultivalued: true\ninlined: true\nThe category of the subject entity
URI: https://w3id.org/monarch/monarch-py/:subject_category
"},{"location":"Data-Model/subject_category/#inheritance","title":"Inheritance","text":"name: subject_category\ndescription: The category of the subject entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: category\nalias: subject_category\ndomain_of:\n- Association\nrange: string\nField containing subject id and the ids of all of it's ancestors
URI: https://w3id.org/monarch/monarch-py/:subject_closure
"},{"location":"Data-Model/subject_closure/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/subject_closure/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: subject_closure\ndescription: Field containing subject id and the ids of all of it's ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: subject_closure\ndomain_of:\n- Association\nrange: string\nmultivalued: true\nField containing subject name and the names of all of it's ancestors
URI: https://w3id.org/monarch/monarch-py/:subject_closure_label
"},{"location":"Data-Model/subject_closure_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/subject_closure_label/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: subject_closure_label\ndescription: Field containing subject name and the names of all of it's ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: subject_closure_label\ndomain_of:\n- Association\nrange: string\nmultivalued: true\nURI: https://w3id.org/monarch/monarch-py/:subject_id
"},{"location":"Data-Model/subject_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms no Mapping A minimal class to hold a SSSOM mapping no"},{"location":"Data-Model/subject_id/#properties","title":"Properties","text":"Range: String
Required: True
name: subject_id\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: subject_id\ndomain_of:\n- Mapping\n- TermPairwiseSimilarity\nrange: string\nrequired: true\nThe IC of the subject
URI: https://w3id.org/monarch/monarch-py/:subject_information_content
"},{"location":"Data-Model/subject_information_content/#inheritance","title":"Inheritance","text":"name: subject_information_content\ndescription: The IC of the subject\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: information_content\nalias: subject_information_content\ndomain_of:\n- TermPairwiseSimilarity\nrange: NegativeLogValue\nThe name of the subject entity
URI: https://w3id.org/monarch/monarch-py/:subject_label
"},{"location":"Data-Model/subject_label/#inheritance","title":"Inheritance","text":"name: subject_label\ndescription: The name of the subject entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: name\nalias: subject_label\ndomain_of:\n- Association\n- CompactAssociation\n- AssociationTypeMapping\n- Mapping\n- TermPairwiseSimilarity\nrange: string\nThe namespace/prefix of the subject entity
URI: https://w3id.org/monarch/monarch-py/:subject_namespace
"},{"location":"Data-Model/subject_namespace/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/subject_namespace/#properties","title":"Properties","text":"name: subject_namespace\ndescription: The namespace/prefix of the subject entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: subject_namespace\ndomain_of:\n- Association\nrange: string\nthe source for the first entity
URI: sssom:subject_source
"},{"location":"Data-Model/subject_source/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms no"},{"location":"Data-Model/subject_source/#properties","title":"Properties","text":"name: subject_source\ndescription: the source for the first entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nslot_uri: sssom:subject_source\nalias: subject_source\ndomain_of:\n- TermPairwiseSimilarity\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:subject_taxon
"},{"location":"Data-Model/subject_taxon/#inheritance","title":"Inheritance","text":"name: subject_taxon\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: in_taxon\nalias: subject_taxon\ndomain_of:\n- Association\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:subject_taxon_label
"},{"location":"Data-Model/subject_taxon_label/#inheritance","title":"Inheritance","text":"name: subject_taxon_label\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: in_taxon_label\nalias: subject_taxon_label\ndomain_of:\n- Association\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:subject_termset
"},{"location":"Data-Model/subject_termset/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermSetPairwiseSimilarity A simple pairwise similarity between two sets of concepts/terms no"},{"location":"Data-Model/subject_termset/#properties","title":"Properties","text":"Range: TermInfo
Multivalued: True
name: subject_termset\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: subject_termset\ndomain_of:\n- TermSetPairwiseSimilarity\nrange: TermInfo\nmultivalued: true\ninlined: true\nURI: https://w3id.org/monarch/monarch-py/:subsumed_by_score
"},{"location":"Data-Model/subsumed_by_score/#inheritance","title":"Inheritance","text":"name: subsumed_by_score\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: score\nalias: subsumed_by_score\nrange: ZeroToOne\nURI: https://w3id.org/monarch/monarch-py/:subsumes_score
"},{"location":"Data-Model/subsumes_score/#inheritance","title":"Inheritance","text":"name: subsumes_score\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: score\nalias: subsumes_score\nrange: ZeroToOne\nURI: https://w3id.org/monarch/monarch-py/:super_classes
"},{"location":"Data-Model/super_classes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot NodeHierarchy no"},{"location":"Data-Model/super_classes/#properties","title":"Properties","text":"Range: Entity
Multivalued: True
Required: True
name: super_classes\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: super_classes\ndomain_of:\n- NodeHierarchy\nrange: Entity\nrequired: true\nmultivalued: true\ninlined: true\ninlined_as_list: true\nURI: https://w3id.org/monarch/monarch-py/:symbol
"},{"location":"Data-Model/symbol/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Node UI container class extending Entity with additional information no Entity Represents an Entity in the Monarch KG data model no SearchResult no"},{"location":"Data-Model/symbol/#properties","title":"Properties","text":"name: symbol\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: symbol\ndomain_of:\n- Entity\nrange: string\nWhether the association type is symmetric, i.e. the subject and object labels are interchangeable.
URI: https://w3id.org/monarch/monarch-py/:symmetric
"},{"location":"Data-Model/symmetric/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AssociationTypeMapping A data class to hold the necessary information to produce association type co... yes"},{"location":"Data-Model/symmetric/#properties","title":"Properties","text":"name: symmetric\ndescription: Whether the association type is symmetric, i.e. the subject and object\n labels are interchangeable.\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: symmetric\ndomain_of:\n- AssociationTypeMapping\nrange: boolean\nURI: https://w3id.org/monarch/monarch-py/:synonym
"},{"location":"Data-Model/synonym/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Node UI container class extending Entity with additional information no Entity Represents an Entity in the Monarch KG data model no SearchResult no"},{"location":"Data-Model/synonym/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: synonym\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: synonym\ndomain_of:\n- Entity\nrange: string\nmultivalued: true\ntext without tokens
URI: https://w3id.org/monarch/monarch-py/:text
"},{"location":"Data-Model/text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextAnnotationResult no"},{"location":"Data-Model/text/#properties","title":"Properties","text":"name: text\ndescription: text without tokens\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: text\ndomain_of:\n- TextAnnotationResult\nrange: string\ninlined: true\nA collection of entities or concepts
URI: https://w3id.org/monarch/monarch-py/:tokens
"},{"location":"Data-Model/tokens/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextAnnotationResult no"},{"location":"Data-Model/tokens/#properties","title":"Properties","text":"Range: Entity
Multivalued: True
name: tokens\ndescription: A collection of entities or concepts\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: tokens\ndomain_of:\n- TextAnnotationResult\nrange: Entity\nmultivalued: true\ninlined: true\ninlined_as_list: true\ntotal number of items matching a query
URI: https://w3id.org/monarch/monarch-py/:total
"},{"location":"Data-Model/total/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot EntityResults no CompactAssociationResults no MultiEntityAssociationResults no AssociationTableResults no MappingResults SSSOM Mappings returned as a results collection no CategoryGroupedAssociationResults no Results no SearchResults no AssociationResults no"},{"location":"Data-Model/total/#properties","title":"Properties","text":"Range: Integer
Required: True
name: total\ndescription: total number of items matching a query\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: total\ndomain_of:\n- Results\nrange: integer\nrequired: true\nURI: https://w3id.org/monarch/monarch-py/:union_count
"},{"location":"Data-Model/union_count/#inheritance","title":"Inheritance","text":"name: union_count\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: score\nalias: union_count\nrange: ItemCount\nThe URI of the entity
URI: https://w3id.org/monarch/monarch-py/:uri
"},{"location":"Data-Model/uri/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Node UI container class extending Entity with additional information no Entity Represents an Entity in the Monarch KG data model no SearchResult no"},{"location":"Data-Model/uri/#properties","title":"Properties","text":"name: uri\ndescription: The URI of the entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: uri\ndomain_of:\n- Entity\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:url
"},{"location":"Data-Model/url/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Release A class to hold information about a release of the Monarch KG no ExpandedCurie A curie bundled along with its expanded url no"},{"location":"Data-Model/url/#properties","title":"Properties","text":"name: url\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: url\ndomain_of:\n- ExpandedCurie\n- Release\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:version
"},{"location":"Data-Model/version/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Release A class to hold information about a release of the Monarch KG no"},{"location":"Data-Model/version/#properties","title":"Properties","text":"Instances of this class should have identifiers with one of the following prefixes:
name: version\nid_prefixes:\n- string\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: version\ndomain_of:\n- Release\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:xref
"},{"location":"Data-Model/xref/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Node UI container class extending Entity with additional information no Entity Represents an Entity in the Monarch KG data model no SearchResult no"},{"location":"Data-Model/xref/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: xref\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: xref\ndomain_of:\n- Entity\nrange: string\nmultivalued: true\nA FastAPI is also available for browsing the knowledge graph produced by the Monarch Initiative, which wraps the monarch-py library.
It is included automatically as part of monarch-py when installed via pip or pipx.
A local development server can be started with the command:
monarch-api\nor using uvicorn:
# Using uvicorn directly:\npoetry run uvicorn src.monarch_py.api.main:app --reload\n\n# Using the Makefile shortcut:\ncd <path-to>/monarch-app\nmake dev-api\nThe API is then available at http://127.0.0.1:8000/v3/api.
Swagger documentation is available at http://127.0.0.1:8000/v3/docs, and a ReDoc interface at http://127.0.0.1:8000/v3/redoc.
API Reference
Data Response Model
"},{"location":"FastAPI/Endpoints/","title":"Monarch API Endpoints","text":"This section contains API reference for the various endpoints provided by monarch-api.
autocomplete","text":"Autocomplete for semantic similarity lookups, prioritizes entities which have direct phenotype associations. Note: This API endpoint is experimental and may evolve or disappear over time.
Parameters:
Name Type Description Defaultq str Query string to autocomplete against
Query(default='*:*', title='Query string to autocomplete against', examples=['fanc', 'ehler']) Returns:
Type DescriptionSearchResults SearchResults
"},{"location":"Usage/","title":"Usage","text":"monarch-py can be used via command line, or as a Python module.
"},{"location":"Usage/#cli","title":"CLI","text":""},{"location":"Usage/#overview","title":"Overview","text":"monarch-py can be used to query various implementations of the Monarch knowledge graph. The default, and more feature-rich, implementation is Solr, and is the default.
Subcommands are available to specify the backend.
For example:
# The following two commands are equivalent,\n# as both query the Solr KG\n$ monarch entity MONDO:0012933 \n$ monarch solr entity MONDO:0012933\n\n# Whereas the following specifies the SQL implementation\n$ monarch sql entity MONDO:0012933\nYou can also use an environment variable to specify a Solr URL to query a different Solr instance. monarch-py checks for the MONARCH_SOLR_URL environment variable, and uses it if it exists. If not, it uses the default Solr URL of http://localhost:8983/solr.
CLI commands are listed here, or can be found by running monarch --help.
TBD
"},{"location":"Usage/CLI/","title":"monarch","text":"Usage:
$ monarch [OPTIONS] COMMAND [ARGS]...\nOptions:
-v, --version: Show the currently installed version-q, --quiet: Set log level to warning-d, --debug: Set log level to debug--install-completion: Install completion for the current shell.--show-completion: Show completion for the current shell, to copy it or customize the installation.--help: Show this message and exit.Commands:
association-counts: Retrieve the association counts for a...association-tableassociations: Paginate through associationsautocomplete: Return entity autcomplete matches for a...compare: Compare two sets of phenotypes using...entity: Retrieve an entity by IDhistopheno: Retrieve the histopheno associations for a...mappingsmulti-entity-associations: Paginate through associations for multiple...release: Retrieve metadata for a specific releasereleases: List all available releases of the Monarch...schema: Print the linkml schema for the data modelsearch: Search for entitiessolrsqltest: Test the CLImonarch association-counts","text":"Retrieve the association counts for a given entity
Usage:
$ monarch association-counts [OPTIONS] ENTITY_ID\nArguments:
ENTITY_ID: The entity to get association counts for [required]Options:
-f, --format [json|yaml|tsv|table]: The format of the output (json, yaml, tsv, table) [default: json]-O, --output TEXT: Path to file to write command output (stdout if not specified)--help: Show this message and exit.monarch association-table","text":"Usage:
$ monarch association-table [OPTIONS] ENTITY_ID CATEGORY:{biolink:PairwiseGeneToGeneInteraction|biolink:GeneToExpressionSiteAssociation|biolink:VariantToGeneAssociation|biolink:MacromolecularMachineToBiologicalProcessAssociation|biolink:GeneToPhenotypicFeatureAssociation|biolink:MacromolecularMachineToMolecularActivityAssociation|biolink:MacromolecularMachineToCellularComponentAssociation|biolink:Association|biolink:GeneToGeneHomologyAssociation|biolink:GenotypeToPhenotypicFeatureAssociation|biolink:DiseaseToPhenotypicFeatureAssociation|biolink:GeneToPathwayAssociation|biolink:DiseaseOrPhenotypicFeatureToLocationAssociation|biolink:ChemicalToPathwayAssociation|biolink:GenotypeToDiseaseAssociation|biolink:CorrelatedGeneToDiseaseAssociation|biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation|biolink:VariantToDiseaseAssociation|biolink:CausalGeneToDiseaseAssociation|biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation}\nArguments:
ENTITY_ID: The entity to get associations for [required]CATEGORY:{biolink:PairwiseGeneToGeneInteraction|biolink:GeneToExpressionSiteAssociation|biolink:VariantToGeneAssociation|biolink:MacromolecularMachineToBiologicalProcessAssociation|biolink:GeneToPhenotypicFeatureAssociation|biolink:MacromolecularMachineToMolecularActivityAssociation|biolink:MacromolecularMachineToCellularComponentAssociation|biolink:Association|biolink:GeneToGeneHomologyAssociation|biolink:GenotypeToPhenotypicFeatureAssociation|biolink:DiseaseToPhenotypicFeatureAssociation|biolink:GeneToPathwayAssociation|biolink:DiseaseOrPhenotypicFeatureToLocationAssociation|biolink:ChemicalToPathwayAssociation|biolink:GenotypeToDiseaseAssociation|biolink:CorrelatedGeneToDiseaseAssociation|biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation|biolink:VariantToDiseaseAssociation|biolink:CausalGeneToDiseaseAssociation|biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation}: The association category to get associations for, ex. biolink:GeneToPhenotypicFeatureAssociation [required]Options:
-q, --query TEXT-t, --traverse-orthologs: Whether to traverse orthologs when getting associations-s, --sort TEXT-l, --limit INTEGER: The number of results to return [default: 20]--offset INTEGER: The offset of the first result to be retrieved [default: 0]-f, --format [json|yaml|tsv|table]: The format of the output (json, yaml, tsv, table) [default: json]-O, --output TEXT: Path to file to write command output (stdout if not specified)--help: Show this message and exit.monarch associations","text":"Paginate through associations
Usage:
$ monarch associations [OPTIONS]\nOptions:
-c, --category [biolink:PairwiseGeneToGeneInteraction|biolink:GeneToExpressionSiteAssociation|biolink:VariantToGeneAssociation|biolink:MacromolecularMachineToBiologicalProcessAssociation|biolink:GeneToPhenotypicFeatureAssociation|biolink:MacromolecularMachineToMolecularActivityAssociation|biolink:MacromolecularMachineToCellularComponentAssociation|biolink:Association|biolink:GeneToGeneHomologyAssociation|biolink:GenotypeToPhenotypicFeatureAssociation|biolink:DiseaseToPhenotypicFeatureAssociation|biolink:GeneToPathwayAssociation|biolink:DiseaseOrPhenotypicFeatureToLocationAssociation|biolink:ChemicalToPathwayAssociation|biolink:GenotypeToDiseaseAssociation|biolink:CorrelatedGeneToDiseaseAssociation|biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation|biolink:VariantToDiseaseAssociation|biolink:CausalGeneToDiseaseAssociation|biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation]: Category to get associations for-s, --subject TEXT: Subject ID to get associations for-p, --predicate [biolink:interacts_with|biolink:expressed_in|biolink:has_phenotype|biolink:is_sequence_variant_of|biolink:enables|biolink:actively_involved_in|biolink:orthologous_to|biolink:located_in|biolink:subclass_of|biolink:related_to|biolink:participates_in|biolink:acts_upstream_of_or_within|biolink:active_in|biolink:part_of|biolink:model_of|biolink:causes|biolink:acts_upstream_of|biolink:has_mode_of_inheritance|biolink:contributes_to|biolink:gene_associated_with_condition|biolink:treats_or_applied_or_studied_to_treat|biolink:colocalizes_with|biolink:acts_upstream_of_positive_effect|biolink:acts_upstream_of_or_within_positive_effect|biolink:acts_upstream_of_negative_effect|biolink:acts_upstream_of_or_within_negative_effect]: Predicate ID to get associations for-o, --object TEXT: Object ID to get associations for-e, --entity TEXT: Entity (subject or object) ID to get associations for-d, --direct: Whether to exclude associations with subject/object as ancestors-C, --compact: Whether to return a compact representation of the associations-l, --limit INTEGER: The number of results to return [default: 20]--offset INTEGER: The offset of the first result to be retrieved [default: 0]-f, --format [json|yaml|tsv|table]: The format of the output (json, yaml, tsv, table) [default: json]-O, --output TEXT: Path to file to write command output (stdout if not specified)--help: Show this message and exit.monarch autocomplete","text":"Return entity autcomplete matches for a query string
Usage:
$ monarch autocomplete [OPTIONS] Q\nArguments:
Q: Query string to autocomplete against [required]Options:
-f, --format [json|yaml|tsv|table]: The format of the output (json, yaml, tsv, table) [default: json]-O, --output TEXT: Path to file to write command output (stdout if not specified)--help: Show this message and exit.monarch compare","text":"Compare two sets of phenotypes using semantic similarity via SemSimian
Usage:
$ monarch compare [OPTIONS] SUBJECTS OBJECTS\nArguments:
SUBJECTS: Comma separated list of subjects to compare [required]OBJECTS: Comma separated list of objects to compare [required]Options:
-m, --metric [ancestor_information_content|jaccard_similarity|phenodigm_score]: The metric to use for comparison [default: ancestor_information_content]-f, --format [json|yaml|tsv|table]: The format of the output (json, yaml, tsv, table) [default: json]-O, --output TEXT: Path to file to write command output (stdout if not specified)--help: Show this message and exit.monarch entity","text":"Retrieve an entity by ID
Usage:
$ monarch entity [OPTIONS] ENTITY_ID\nArguments:
ENTITY_ID: The identifier of the entity to be retrieved [required]Options:
-e, --extra: Include extra fields in the output (association_counts and node_hierarchy)-f, --format [json|yaml|tsv|table]: The format of the output (json, yaml, tsv, table) [default: json]-O, --output TEXT: Path to file to write command output (stdout if not specified)--help: Show this message and exit.monarch histopheno","text":"Retrieve the histopheno associations for a given subject
Usage:
$ monarch histopheno [OPTIONS] SUBJECT\nArguments:
SUBJECT: The subject of the association [required]Options:
-f, --format [json|yaml|tsv|table]: The format of the output (json, yaml, tsv, table) [default: json]-O, --output TEXT: Path to file to write command output (stdout if not specified)--help: Show this message and exit.monarch mappings","text":"Usage:
$ monarch mappings [OPTIONS]\nOptions:
-e, --entity-id TEXT: entity ID to get mappings for-s, --subject-id TEXT: subject ID to get mappings for-p, --predicate-id [skos:exactMatch|skos:broadMatch]: predicate ID to get mappings for-o, --object-id TEXT: object ID to get mappings for-m, --mapping-justification TEXT: mapping justification to get mappings for-l, --limit INTEGER: The number of results to return [default: 20]--offset INTEGER: The offset of the first result to be retrieved [default: 0]-f, --format [json|yaml|tsv|table]: The format of the output (json, yaml, tsv, table) [default: json]-O, --output TEXT: Path to file to write command output (stdout if not specified)--help: Show this message and exit.monarch multi-entity-associations","text":"Paginate through associations for multiple entities
Usage:
$ monarch multi-entity-associations [OPTIONS]\nOptions:
-e, --entity TEXT: Comma-separated list of entities-c, --counterpart-category TEXT: A comma-separated list of counterpart categories-l, --limit INTEGER: The number of results to return [default: 20]--offset INTEGER: The offset of the first result to be retrieved [default: 0]-f, --format [json|yaml|tsv|table]: The format of the output (json, yaml, tsv, table) [default: json]-O, --output TEXT: Path to file to write command output (stdout if not specified)--help: Show this message and exit.monarch release","text":"Retrieve metadata for a specific release
Usage:
$ monarch release [OPTIONS] RELEASE_VER\nArguments:
RELEASE_VER: The release version to get metadata for [required]Options:
-f, --format [json|yaml|tsv|table]: The format of the output (json, yaml, tsv, table) [default: json]-O, --output TEXT: Path to file to write command output (stdout if not specified)--help: Show this message and exit.monarch releases","text":"List all available releases of the Monarch Knowledge Graph
Usage:
$ monarch releases [OPTIONS]\nOptions:
--dev: Get dev releases of the KG (default is False)-l, --limit INTEGER: The number of results to return [default: 0]--help: Show this message and exit.monarch schema","text":"Print the linkml schema for the data model
Usage:
$ monarch schema [OPTIONS]\nOptions:
--help: Show this message and exit.monarch search","text":"Search for entities
Usage:
$ monarch search [OPTIONS]\nOptions:
-q, --query TEXT: [default: :*]-c, --category [biolink:SequenceVariant|biolink:Gene|biolink:Genotype|biolink:PhenotypicFeature|biolink:BiologicalProcessOrActivity|biolink:Disease|biolink:GrossAnatomicalStructure|biolink:Cell|biolink:Pathway|biolink:NamedThing|biolink:AnatomicalEntity|biolink:CellularComponent|biolink:MolecularEntity|biolink:BiologicalProcess|biolink:MacromolecularComplex|biolink:MolecularActivity|biolink:Protein|biolink:CellularOrganism|biolink:Vertebrate|biolink:Virus|biolink:BehavioralFeature|biolink:ChemicalEntity|biolink:LifeStage|biolink:PathologicalProcess|biolink:Drug|biolink:SmallMolecule|biolink:OrganismTaxon|biolink:InformationContentEntity|biolink:NucleicAcidEntity|biolink:EvidenceType|biolink:RNAProduct|biolink:Transcript|biolink:Fungus|biolink:Plant|biolink:ProcessedMaterial|biolink:Activity|biolink:Agent|biolink:ConfidenceLevel|biolink:Dataset|biolink:EnvironmentalFeature|biolink:GeneticInheritance|biolink:Haplotype|biolink:Invertebrate|biolink:Mammal|biolink:PopulationOfIndividualOrganisms|biolink:ProteinFamily|biolink:Publication|biolink:AccessibleDnaRegion|biolink:Bacterium|biolink:BiologicalSex|biolink:CellLine|biolink:ChemicalExposure|biolink:ChemicalMixture|biolink:DatasetDistribution|biolink:DiagnosticAid|biolink:DrugExposure|biolink:EnvironmentalProcess|biolink:Event|biolink:Exon|biolink:Genome|biolink:GenotypicSex|biolink:Human|biolink:IndividualOrganism|biolink:MaterialSample|biolink:MicroRNA|biolink:OrganismalEntity|biolink:Patent|biolink:PhenotypicSex|biolink:Polypeptide|biolink:ProteinDomain|biolink:ReagentTargetedGene|biolink:RegulatoryRegion|biolink:SiRNA|biolink:Snv|biolink:Study|biolink:StudyVariable|biolink:TranscriptionFactorBindingSite|biolink:Treatment|biolink:WebPage|biolink:Zygosity]-t, --in-taxon-label TEXT-ff, --facet-fields TEXT-fq, --facet-queries TEXT-l, --limit INTEGER: The number of results to return [default: 20]--offset INTEGER: The offset of the first result to be retrieved [default: 0]-f, --format [json|yaml|tsv|table]: The format of the output (json, yaml, tsv, table) [default: json]-O, --output TEXT: Path to file to write command output (stdout if not specified)--help: Show this message and exit.monarch solr","text":"Usage:
$ monarch solr [OPTIONS] COMMAND [ARGS]...\nOptions:
-q, --quiet: Set log level to warning-d, --debug: Set log level to debug--help: Show this message and exit.Commands:
association-counts: Retrieve the association counts for a...association-tableassociations: Paginate through associationsautocomplete: Return entity autcomplete matches for a...download: Download the Monarch Solr KG.entity: Retrieve an entity by IDhistopheno: Retrieve the histopheno associations for a...mappingsmulti-entity-associations: Paginate through associations for multiple...search: Search for entitiesstart: Starts a local Solr container.status: Checks the status of the local Solr...stop: Stops the local Solr container.monarch solr association-counts","text":"Retrieve the association counts for a given entity
Usage:
$ monarch solr association-counts [OPTIONS] ENTITY_ID\nArguments:
ENTITY_ID: The entity to get association counts for [required]Options:
-f, --format [json|yaml|tsv|table]: The format of the output (json, yaml, tsv, table) [default: json]-O, --output TEXT: Path to file to write command output (stdout if not specified)--help: Show this message and exit.monarch solr association-table","text":"Usage:
$ monarch solr association-table [OPTIONS] ENTITY_ID CATEGORY:{biolink:PairwiseGeneToGeneInteraction|biolink:GeneToExpressionSiteAssociation|biolink:VariantToGeneAssociation|biolink:MacromolecularMachineToBiologicalProcessAssociation|biolink:GeneToPhenotypicFeatureAssociation|biolink:MacromolecularMachineToMolecularActivityAssociation|biolink:MacromolecularMachineToCellularComponentAssociation|biolink:Association|biolink:GeneToGeneHomologyAssociation|biolink:GenotypeToPhenotypicFeatureAssociation|biolink:DiseaseToPhenotypicFeatureAssociation|biolink:GeneToPathwayAssociation|biolink:DiseaseOrPhenotypicFeatureToLocationAssociation|biolink:ChemicalToPathwayAssociation|biolink:GenotypeToDiseaseAssociation|biolink:CorrelatedGeneToDiseaseAssociation|biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation|biolink:VariantToDiseaseAssociation|biolink:CausalGeneToDiseaseAssociation|biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation}\nArguments:
ENTITY_ID: The entity to get associations for [required]CATEGORY:{biolink:PairwiseGeneToGeneInteraction|biolink:GeneToExpressionSiteAssociation|biolink:VariantToGeneAssociation|biolink:MacromolecularMachineToBiologicalProcessAssociation|biolink:GeneToPhenotypicFeatureAssociation|biolink:MacromolecularMachineToMolecularActivityAssociation|biolink:MacromolecularMachineToCellularComponentAssociation|biolink:Association|biolink:GeneToGeneHomologyAssociation|biolink:GenotypeToPhenotypicFeatureAssociation|biolink:DiseaseToPhenotypicFeatureAssociation|biolink:GeneToPathwayAssociation|biolink:DiseaseOrPhenotypicFeatureToLocationAssociation|biolink:ChemicalToPathwayAssociation|biolink:GenotypeToDiseaseAssociation|biolink:CorrelatedGeneToDiseaseAssociation|biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation|biolink:VariantToDiseaseAssociation|biolink:CausalGeneToDiseaseAssociation|biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation}: The association category to get associations for, ex. biolink:GeneToPhenotypicFeatureAssociation [required]Options:
-q, --query TEXT-t, --traverse-orthologs: Whether to traverse orthologs when getting associations-s, --sort TEXT-l, --limit INTEGER: The number of results to return [default: 20]--offset INTEGER: The offset of the first result to be retrieved [default: 0]-f, --format [json|yaml|tsv|table]: The format of the output (json, yaml, tsv, table) [default: json]-O, --output TEXT: Path to file to write command output (stdout if not specified)--help: Show this message and exit.monarch solr associations","text":"Paginate through associations
Usage:
$ monarch solr associations [OPTIONS]\nOptions:
-c, --category [biolink:PairwiseGeneToGeneInteraction|biolink:GeneToExpressionSiteAssociation|biolink:VariantToGeneAssociation|biolink:MacromolecularMachineToBiologicalProcessAssociation|biolink:GeneToPhenotypicFeatureAssociation|biolink:MacromolecularMachineToMolecularActivityAssociation|biolink:MacromolecularMachineToCellularComponentAssociation|biolink:Association|biolink:GeneToGeneHomologyAssociation|biolink:GenotypeToPhenotypicFeatureAssociation|biolink:DiseaseToPhenotypicFeatureAssociation|biolink:GeneToPathwayAssociation|biolink:DiseaseOrPhenotypicFeatureToLocationAssociation|biolink:ChemicalToPathwayAssociation|biolink:GenotypeToDiseaseAssociation|biolink:CorrelatedGeneToDiseaseAssociation|biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation|biolink:VariantToDiseaseAssociation|biolink:CausalGeneToDiseaseAssociation|biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation]: Category to get associations for-s, --subject TEXT: Subject ID to get associations for-p, --predicate [biolink:interacts_with|biolink:expressed_in|biolink:has_phenotype|biolink:is_sequence_variant_of|biolink:enables|biolink:actively_involved_in|biolink:orthologous_to|biolink:located_in|biolink:subclass_of|biolink:related_to|biolink:participates_in|biolink:acts_upstream_of_or_within|biolink:active_in|biolink:part_of|biolink:model_of|biolink:causes|biolink:acts_upstream_of|biolink:has_mode_of_inheritance|biolink:contributes_to|biolink:gene_associated_with_condition|biolink:treats_or_applied_or_studied_to_treat|biolink:colocalizes_with|biolink:acts_upstream_of_positive_effect|biolink:acts_upstream_of_or_within_positive_effect|biolink:acts_upstream_of_negative_effect|biolink:acts_upstream_of_or_within_negative_effect]: Predicate ID to get associations for-o, --object TEXT: Object ID to get associations for-e, --entity TEXT: Entity (subject or object) ID to get associations for-d, --direct: Whether to exclude associations with subject/object as ancestors-C, --compact: Whether to return a compact representation of the associations-l, --limit INTEGER: The number of results to return [default: 20]--offset INTEGER: The offset of the first result to be retrieved [default: 0]-f, --format [json|yaml|tsv|table]: The format of the output (json, yaml, tsv, table) [default: json]-O, --output TEXT: Path to file to write command output (stdout if not specified)--help: Show this message and exit.monarch solr autocomplete","text":"Return entity autcomplete matches for a query string
Usage:
$ monarch solr autocomplete [OPTIONS] Q\nArguments:
Q: Query string to autocomplete against [required]Options:
-f, --format [json|yaml|tsv|table]: The format of the output (json, yaml, tsv, table) [default: json]-O, --output TEXT: Path to file to write command output (stdout if not specified)--help: Show this message and exit.monarch solr download","text":"Download the Monarch Solr KG.
Usage:
$ monarch solr download [OPTIONS] [VERSION]\nArguments:
[VERSION]: The version of the Solr KG to download (latest, dev, or a specific version) [default: latest]Options:
--overwrite: Overwrite the existing Solr KG if it exists--help: Show this message and exit.monarch solr entity","text":"Retrieve an entity by ID
Usage:
$ monarch solr entity [OPTIONS] ENTITY_ID\nArguments:
ENTITY_ID: The identifier of the entity to be retrieved [required]Options:
-e, --extra: Include extra fields in the output (association_counts and node_hierarchy)-f, --format [json|yaml|tsv|table]: The format of the output (json, yaml, tsv, table) [default: json]-O, --output TEXT: Path to file to write command output (stdout if not specified)--help: Show this message and exit.monarch solr histopheno","text":"Retrieve the histopheno associations for a given subject
Usage:
$ monarch solr histopheno [OPTIONS] SUBJECT\nArguments:
SUBJECT: The subject of the association [required]Options:
-f, --format [json|yaml|tsv|table]: The format of the output (json, yaml, tsv, table) [default: json]-O, --output TEXT: Path to file to write command output (stdout if not specified)--help: Show this message and exit.monarch solr mappings","text":"Usage:
$ monarch solr mappings [OPTIONS]\nOptions:
-e, --entity-id TEXT: entity ID to get mappings for-s, --subject-id TEXT: subject ID to get mappings for-p, --predicate-id [skos:exactMatch|skos:broadMatch]: predicate ID to get mappings for-o, --object-id TEXT: object ID to get mappings for-m, --mapping-justification TEXT: mapping justification to get mappings for-l, --limit INTEGER: The number of results to return [default: 20]--offset INTEGER: The offset of the first result to be retrieved [default: 0]-f, --format [json|yaml|tsv|table]: The format of the output (json, yaml, tsv, table) [default: json]-O, --output TEXT: Path to file to write command output (stdout if not specified)--help: Show this message and exit.monarch solr multi-entity-associations","text":"Paginate through associations for multiple entities
Usage:
$ monarch solr multi-entity-associations [OPTIONS]\nOptions:
-e, --entity TEXT: Comma-separated list of entities-c, --counterpart-category TEXT: A comma-separated list of counterpart categories-l, --limit INTEGER: The number of results to return [default: 20]--offset INTEGER: The offset of the first result to be retrieved [default: 0]-f, --format [json|yaml|tsv|table]: The format of the output (json, yaml, tsv, table) [default: json]-O, --output TEXT: Path to file to write command output (stdout if not specified)--help: Show this message and exit.monarch solr search","text":"Search for entities
Usage:
$ monarch solr search [OPTIONS]\nOptions:
-q, --query TEXT: [default: :*]-c, --category [biolink:SequenceVariant|biolink:Gene|biolink:Genotype|biolink:PhenotypicFeature|biolink:BiologicalProcessOrActivity|biolink:Disease|biolink:GrossAnatomicalStructure|biolink:Cell|biolink:Pathway|biolink:NamedThing|biolink:AnatomicalEntity|biolink:CellularComponent|biolink:MolecularEntity|biolink:BiologicalProcess|biolink:MacromolecularComplex|biolink:MolecularActivity|biolink:Protein|biolink:CellularOrganism|biolink:Vertebrate|biolink:Virus|biolink:BehavioralFeature|biolink:ChemicalEntity|biolink:LifeStage|biolink:PathologicalProcess|biolink:Drug|biolink:SmallMolecule|biolink:OrganismTaxon|biolink:InformationContentEntity|biolink:NucleicAcidEntity|biolink:EvidenceType|biolink:RNAProduct|biolink:Transcript|biolink:Fungus|biolink:Plant|biolink:ProcessedMaterial|biolink:Activity|biolink:Agent|biolink:ConfidenceLevel|biolink:Dataset|biolink:EnvironmentalFeature|biolink:GeneticInheritance|biolink:Haplotype|biolink:Invertebrate|biolink:Mammal|biolink:PopulationOfIndividualOrganisms|biolink:ProteinFamily|biolink:Publication|biolink:AccessibleDnaRegion|biolink:Bacterium|biolink:BiologicalSex|biolink:CellLine|biolink:ChemicalExposure|biolink:ChemicalMixture|biolink:DatasetDistribution|biolink:DiagnosticAid|biolink:DrugExposure|biolink:EnvironmentalProcess|biolink:Event|biolink:Exon|biolink:Genome|biolink:GenotypicSex|biolink:Human|biolink:IndividualOrganism|biolink:MaterialSample|biolink:MicroRNA|biolink:OrganismalEntity|biolink:Patent|biolink:PhenotypicSex|biolink:Polypeptide|biolink:ProteinDomain|biolink:ReagentTargetedGene|biolink:RegulatoryRegion|biolink:SiRNA|biolink:Snv|biolink:Study|biolink:StudyVariable|biolink:TranscriptionFactorBindingSite|biolink:Treatment|biolink:WebPage|biolink:Zygosity]-t, --in-taxon-label TEXT-ff, --facet-fields TEXT-fq, --facet-queries TEXT-l, --limit INTEGER: The number of results to return [default: 20]--offset INTEGER: The offset of the first result to be retrieved [default: 0]-f, --format [json|yaml|tsv|table]: The format of the output (json, yaml, tsv, table) [default: json]-O, --output TEXT: Path to file to write command output (stdout if not specified)--help: Show this message and exit.monarch solr start","text":"Starts a local Solr container.
Usage:
$ monarch solr start [OPTIONS]\nOptions:
--update / --no-update: [default: no-update]--help: Show this message and exit.monarch solr status","text":"Checks the status of the local Solr container.
Usage:
$ monarch solr status [OPTIONS]\nOptions:
--help: Show this message and exit.monarch solr stop","text":"Stops the local Solr container.
Usage:
$ monarch solr stop [OPTIONS]\nOptions:
--help: Show this message and exit.monarch sql","text":"Usage:
$ monarch sql [OPTIONS] COMMAND [ARGS]...\nOptions:
-q, --quiet: Set log level to warning-d, --debug: Set log level to debug--help: Show this message and exit.Commands:
associations: Paginate through associationsentity: Retrieve an entity by IDmonarch sql associations","text":"Paginate through associations
Usage:
$ monarch sql associations [OPTIONS]\nOptions:
-c, --category [biolink:PairwiseGeneToGeneInteraction|biolink:GeneToExpressionSiteAssociation|biolink:VariantToGeneAssociation|biolink:MacromolecularMachineToBiologicalProcessAssociation|biolink:GeneToPhenotypicFeatureAssociation|biolink:MacromolecularMachineToMolecularActivityAssociation|biolink:MacromolecularMachineToCellularComponentAssociation|biolink:Association|biolink:GeneToGeneHomologyAssociation|biolink:GenotypeToPhenotypicFeatureAssociation|biolink:DiseaseToPhenotypicFeatureAssociation|biolink:GeneToPathwayAssociation|biolink:DiseaseOrPhenotypicFeatureToLocationAssociation|biolink:ChemicalToPathwayAssociation|biolink:GenotypeToDiseaseAssociation|biolink:CorrelatedGeneToDiseaseAssociation|biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation|biolink:VariantToDiseaseAssociation|biolink:CausalGeneToDiseaseAssociation|biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation]: Category to get associations for-s, --subject TEXT: Subject ID to get associations for-p, --predicate [biolink:interacts_with|biolink:expressed_in|biolink:has_phenotype|biolink:is_sequence_variant_of|biolink:enables|biolink:actively_involved_in|biolink:orthologous_to|biolink:located_in|biolink:subclass_of|biolink:related_to|biolink:participates_in|biolink:acts_upstream_of_or_within|biolink:active_in|biolink:part_of|biolink:model_of|biolink:causes|biolink:acts_upstream_of|biolink:has_mode_of_inheritance|biolink:contributes_to|biolink:gene_associated_with_condition|biolink:treats_or_applied_or_studied_to_treat|biolink:colocalizes_with|biolink:acts_upstream_of_positive_effect|biolink:acts_upstream_of_or_within_positive_effect|biolink:acts_upstream_of_negative_effect|biolink:acts_upstream_of_or_within_negative_effect]: Predicate ID to get associations for-o, --object TEXT: Object ID to get associations for-e, --entity TEXT: Entity (subject or object) ID to get associations for-d, --direct: Whether to exclude associations with subject/object as ancestors-C, --compact: Whether to return a compact representation of the associations-l, --limit INTEGER: The number of results to return [default: 20]--offset INTEGER: The offset of the first result to be retrieved [default: 0]-f, --format [json|yaml|tsv|table]: The format of the output (json, yaml, tsv, table) [default: json]-O, --output TEXT: Path to file to write command output (stdout if not specified)--help: Show this message and exit.monarch sql entity","text":"Retrieve an entity by ID
Usage:
$ monarch sql entity [OPTIONS] ENTITY_ID\nArguments:
ENTITY_ID: The identifier of the entity to be retrieved [required]Options:
-e, --extra: Include extra fields in the output (association_counts and node_hierarchy) [required]-u, --update: Whether to re-download the Monarch KG [required]-f, --format [json|yaml|tsv|table]: The format of the output (json, yaml, tsv, table) [default: json]-O, --output TEXT: Path to file to write command output (stdout if not specified)--help: Show this message and exit.monarch test","text":"Test the CLI
Usage:
$ monarch test [OPTIONS]\nOptions:
--help: Show this message and exit.monarch-py provides implementations of the abstract Interfaces for different Monarch KG endpoints/backends.
SQLImplementation dataclass","text":" Bases: EntityInterface, AssociationInterface
Implementation of Monarch Interfaces for SQL endpoint
"},{"location":"Usage/Implementations/SQL/#src.monarch_py.implementations.sql.sql_implementation.SQLImplementation.get_associations","title":"get_associations","text":"Retrieve paginated association records, with filter options
Parameters:
Name Type Description Defaultcategory str Filter to only associations matching the specified category. Defaults to None.
None predicate str Filter to only associations matching the specified predicate. Defaults to None.
None subject str Filter to only associations matching the specified subject. Defaults to None.
None object str Filter to only associations matching the specified object. Defaults to None.
None subject_closure str Filter to only associations with the specified term ID as an ancestor of the subject. Defaults to None.
None object_closure str Filter to only associations the specified term ID as an ancestor of the object. Defaults to None.
None entity str Filter to only associations where the specified entity is the subject or the object. Defaults to None.
None association_type str Filter to only associations matching the specified association label. Defaults to None.
requiredcompact bool Whether to return compact or full association records. Defaults to False.
False offset int Result offset, for pagination. Defaults to 0.
0 limit int Limit results to specified number. Defaults to 20.
20 Returns:
Name Type DescriptionAssociationResults Union[AssociationResults, CompactAssociationResults] Dataclass representing results of an association search.
"},{"location":"Usage/Implementations/SQL/#src.monarch_py.implementations.sql.sql_implementation.SQLImplementation.get_entity","title":"get_entity","text":"Retrieve a specific entity by exact ID match, writh optional extras
Parameters:
Name Type Description Defaultid str id of the entity to search for.
requiredget_association_counts bool Whether to get association counts. Defaults to False.
requiredget_hierarchy bool Whether to get the entity hierarchy. Defaults to False.
requiredReturns:
Name Type DescriptionEntity Entity Dataclass representing results of an entity search.
"},{"location":"Usage/Implementations/Solr/","title":"Solr","text":""},{"location":"Usage/Implementations/Solr/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation","title":"SolrImplementation dataclass","text":" Bases: EntityInterface, AssociationInterface, SearchInterface, GroundingInterface
Implementation of Monarch Interfaces for Solr endpoint
"},{"location":"Usage/Implementations/Solr/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.get_association_counts","title":"get_association_counts","text":"Get list of association counts for a given entity
"},{"location":"Usage/Implementations/Solr/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.get_associations","title":"get_associations","text":"Retrieve paginated association records, with filter options
Parameters:
Name Type Description Defaultcategory List[AssociationCategory] Filter to only associations matching the specified categories. Defaults to None.
None predicate List[AssociationPredicate] Filter to only associations matching the specified predicates. Defaults to None.
None subject Optional[List[str]] Filter to only associations matching the specified subjects. Defaults to None.
None object Optional[List[str]] Filter to only associations matching the specified objects. Defaults to None.
None subject_closure Optional[str] Filter to only associations with the specified term ID as an ancestor of the subject. Defaults to None
None object_closure Optional[str] Filter to only associations with the specified term ID as an ancestor of the object. Defaults to None
None entity Optional[List[str]] Filter to only associations where the specified entities are the subject or the object. Defaults to None.
None q Optional[str] Query string to search within matches. Defaults to None.
None facet_fields Optional[List[str]] List of fields to include facet counts for. Defaults to None.
None facet_queries Optional[List[str]] List of queries to include facet counts for. Defaults to None.
None filter_queries Optional[List[str]] List of queries to filter results by. Defaults to None.
None compact bool Return compact results with fewer fields. Defaults to False.
False offset int Result offset, for pagination. Defaults to 0.
0 limit int Limit results to specified number. Defaults to 20.
20 Returns:
Name Type DescriptionAssociationResults Union[AssociationResults, CompactAssociation] Dataclass representing results of an association search.
"},{"location":"Usage/Implementations/Solr/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.get_counterpart_entities","title":"get_counterpart_entities","text":"Get a list of entities directly associated with this_entity fetched from associations in the Solr index
Parameters:
Name Type Description Defaultthis_entity Entity The entity to get associations for
requiredentity str an entity ID occurring in either the subject or object. Defaults to None.
None subject str an entity ID occurring in the subject. Defaults to None.
None predicate str a predicate value. Defaults to None.
None object str an entity ID occurring in the object. Defaults to None.
None"},{"location":"Usage/Implementations/Solr/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.get_entity","title":"get_entity","text":"Retrieve a specific entity by exact ID match, with optional extras
Parameters:
Name Type Description Defaultid str id of the entity to search for.
requiredextra bool Whether to include association counts and hierarchy in the response.
requiredReturns:
Name Type DescriptionEntity Optional[Union[Node, Entity]] Dataclass representing results of an entity search.
Node Optional[Union[Node, Entity]] Dataclass representing results of an entity search with extra=True.
"},{"location":"Usage/Implementations/Solr/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.get_histopheno","title":"get_histopheno","text":"Get histopheno counts for a given subject_closure
"},{"location":"Usage/Implementations/Solr/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.get_multi_entity_associations","title":"get_multi_entity_associations","text":"Get associations between multiple entities and counterparts of a given category
Parameters:
Name Type Description Defaultentity List[str] List of entity IDs to get associations for
requiredcounterpart_category List[str] List of categories of counterpart entity to get associations for. Defaults to None.
None offset int Result offset, for pagination. Defaults to 0.
0 limit int Limit results to specified number. Defaults to 20.
requiredlimit_per_group int Limit results to specified number per group. Defaults to 20.
20"},{"location":"Usage/Implementations/Solr/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.ground_entity","title":"ground_entity","text":"Grounds a single entity
Parameters:
Name Type Description Defaulttext str Text to ground
requiredReturns:
Name Type DescriptionEntity List[Entity] Dataclass representing a single entity
"},{"location":"Usage/Implementations/Solr/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.search","title":"search","text":"Search for entities by label, with optional filters
Parameters:
Name Type Description Defaultq str Query string. Defaults to \":\".
'*:*' offset int Result offset, for pagination. Defaults to 0.
0 limit int Limit results to specified number. Defaults to 20.
20 category List[str] Filter to only entities matching the specified categories. Defaults to None.
None in_taxon_label List[str] Filter to only entities matching the specified taxon label. Defaults to None.
None facet_fields List[str] List of fields to include facet counts for. Defaults to None.
None facet_queries List[str] List of queries to include facet counts for. Defaults to None.
None filter_queries List[str] List of queries to filter results by. Defaults to None.
None sort str Sort results by the specified field. Defaults to None.
None Returns:
Name Type DescriptionSearchResults SearchResults Dataclass representing results of a search.
"},{"location":"Usage/Implementations/Solr/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.solr_is_available","title":"solr_is_available","text":"Check if the Solr instance is available
"},{"location":"Usage/Interfaces/","title":"Interfaces","text":"monarch-py provides a collection of interfaces that abstractify implementation details, and provide a coherent set of graph operations.
Developers can code according to the interface, mostly ignoring whether the implementation is a relational database, a local file, etc.
"},{"location":"Usage/Interfaces/#interface","title":"Interface","text":"AssociationInterface","text":" Bases: ABC
Abstract interface for associations in the Monarch KG
"},{"location":"Usage/Interfaces/Association/#src.monarch_py.interfaces.association_interface.AssociationInterface.get_associations","title":"get_associations abstractmethod","text":"Retrieve paginated association records, with filter options
Parameters:
Name Type Description Defaultcategory str Filter to only associations matching the specified category. Defaults to None.
None predicate str Filter to only associations matching the specified predicate. Defaults to None.
None subject str Filter to only associations matching the specified subject. Defaults to None.
None subject_closure str Filter to only associations with the specified term ID as an ancestor of the subject. Defaults to None
None object str Filter to only associations matching the specified object. Defaults to None.
None object_closure str Filter to only associations with the specified term ID as an ancestor of the object. Defaults to None
None entity str Filter to only associations where the specified entity is the subject or the object. Defaults to None.
None offset int Result offset, for pagination. Defaults to 0.
0 limit int Limit results to specified number. Defaults to 20.
20 Raises:
Type DescriptionNotImplementedError Use a specific implementation (see the documentation for a list of implementations)
Returns:
Type DescriptionAssociationResults AssociationResults: Dataclass representing results of an association search.
"},{"location":"Usage/Interfaces/Entity/","title":"Entity","text":""},{"location":"Usage/Interfaces/Entity/#src.monarch_py.interfaces.entity_interface.EntityInterface","title":"EntityInterface","text":" Bases: ABC
Abstract interface for entities in the Monarch KG
"},{"location":"Usage/Interfaces/Entity/#src.monarch_py.interfaces.entity_interface.EntityInterface.get_entity","title":"get_entity abstractmethod","text":"Retrieve a specific entity by exact ID match, with optional extras
Parameters:
Name Type Description Defaultid str id of the entity to search for.
requiredget_association_counts bool Whether to get a count of associations for the entity. Defaults to False.
False get_hierarchy bool Whether to get the entity's heirarchy in the data model. Defaults to False.
False Raises:
Type DescriptionNotImplementedError Use a specific implementation (see the documentation for a list of implementations)
Returns:
Name Type DescriptionEntity Entity Dataclass representing results of an entity search.
"},{"location":"Usage/Interfaces/Query/","title":"Query","text":""},{"location":"Usage/Interfaces/Query/#src.monarch_py.interfaces.query_interface.QueryInterface","title":"QueryInterface","text":" Bases: ABC
Abstract interface for querying the Monarch KG in a SQL way
"},{"location":"Usage/Interfaces/Query/#src.monarch_py.interfaces.query_interface.QueryInterface.query","title":"query abstractmethod","text":"Parameters:
Name Type Description Defaultq str Query string to match against
requiredcategory str Limit results to only this category
requiredtaxon str Limit results to only this taxon
requiredoffset int Offset of the first result to return, defaults to 0
requiredlimit int Limit the number of results to return, defaults to 20
requiredRaises:
Type DescriptionNotImplementedError Use a specific implementation (see the documentation for a list of implementations)
Returns:
Name Type DescriptionEntityResults EntityResults Dataclass representing results of a generic entity search.
"},{"location":"Usage/Interfaces/Search/","title":"Search","text":""},{"location":"Usage/Interfaces/Search/#src.monarch_py.interfaces.search_interface.SearchInterface","title":"SearchInterface","text":" Bases: ABC
Abstract interface for searching the Monarch KG in a Lucene way
"},{"location":"Usage/Interfaces/Search/#src.monarch_py.interfaces.search_interface.SearchInterface.autocomplete","title":"autocomplete","text":"Parameters:
Name Type Description Defaultq str Query string to match against
requiredRaises:
Type DescriptionNotImplementedError Use a specific implementation (see the documentation for a list of implementations)
Returns:
Name Type DescriptionSearchResults SearchResults Dataclass representing results of a generic entity search.
"},{"location":"Usage/Interfaces/Search/#src.monarch_py.interfaces.search_interface.SearchInterface.get_association_counts","title":"get_association_counts","text":"Get counts of associations for a given entity Args: entity (str): Entity to get association counts for Returns: List[FacetValue]: List of FacetValue objects representing the counts of associations for the given entity
"},{"location":"Usage/Interfaces/Search/#src.monarch_py.interfaces.search_interface.SearchInterface.get_association_facets","title":"get_association_facets","text":"Get facet counts and facet query counts for associations Args: facet_fields (List[str]): Facet fields to return counts for facet_queries (List[str]): Facet queries to return counts for category (str): Filter to only associations matching the specified category predicate (str): Filter to only associations matching the specified predicate subject (str): Filter to only associations matching the specified subject subject_closure (str): Filter to only associations with the specified term ID as an ancestor of the subject object (str): Filter to only associations matching the specified object object_closure (str): Filter to only associations with the specified term ID as an ancestor of the object entity (str): Filter to only associations where the specified entity is the subject or the object Returns: SearchResults: Dataclass representing results of a search, with zero rows returned but total count and faceting information populated
"},{"location":"Usage/Interfaces/Search/#src.monarch_py.interfaces.search_interface.SearchInterface.get_association_table","title":"get_association_table","text":"Get associations for an entity matching a specified type, with optional search and sort parameters
Parameters:
Name Type Description Defaultentity str Entity to get associations for
requiredcategory str Category of associations to return
requiredquery str Query string to match against
None sort str Sort order, defaults to None
None offset int Offset of the first result to return, defaults to 0
0 limit int Limit the number of results to return, defaults to 20
5 Returns:
Name Type DescriptionAssociationResults AssociationTableResults Dataclass representing results of an association search.
"},{"location":"Usage/Interfaces/Search/#src.monarch_py.interfaces.search_interface.SearchInterface.search","title":"search abstractmethod","text":"Parameters:
Name Type Description Defaultq str Query string to match against
requiredcategory str Limit results to only this category
None taxon str Limit results to only this taxon
requiredoffset int Offset of the first result to return, defaults to 0
0 limit int Limit the number of results to return, defaults to 20
20 Raises:
Type DescriptionNotImplementedError Use a specific implementation (see the documentation for a list of implementations)
Returns:
Name Type DescriptionEntityResults SearchResults Dataclass representing results of a generic entity search.
"}]} \ No newline at end of file +{"config":{"lang":["en"],"separator":"[\\s\\-]+","pipeline":["stopWordFilter"]},"docs":[{"location":"","title":"monarch-py","text":""},{"location":"#introduction","title":"Introduction","text":"monarch-py is a Python library for interacting with and querying the Monarch knowledge graph, with implementations for Solr and SQLite backends.
This means the same API methods can be used regardless of the implementation.
This library provides a collection of interfaces for graph operations such as retrieving entities and browsing associations.
"},{"location":"#installation","title":"Installation","text":"Requires Python 3.8 or higher
This library is available via pip or pipx:
pip install monarch-py\nFull usage instructions here
"},{"location":"#basic-example-cli","title":"Basic Example - CLI","text":"$ monarch sql entity MONDO:0012933\n{\n \"id\": \"MONDO:0012933\",\n \"category\": [\n \"biolink:Disease\"\n ],\n \"name\": \"breast-ovarian cancer, familial, susceptibility to, 2\",\n \"description\": \"Any hereditary breast ovarian cancer syndrome in which the cause of the disease is a mutation in the BRCA2 gene.\",\n \"xref\": [],\n \"provided_by\": \"phenio_nodes\",\n \"in_taxon\": null,\n \"source\": null,\n \"symbol\": null,\n \"type\": null,\n \"synonym\": []\n}\n$ monarch associations --subject MONDO:0012933 --limit 5\n{\n \"limit\": 5,\n \"offset\": 0,\n \"total\": 5,\n \"associations\": [\n ... # List of Associations\n ]\n}\n>>> from monarch_py.implementations.solr.solr_implementation import SolrImplementation\n>>> si = SolrImplementation()\n>>> entity = si.get_entity(\"MONDO:0007947\")\n>>> print(entity.name)\n\"Marfan syndrome\"\n\n>>> response = si.get_associations(predicate=\"biolink:has_phenotype\")\n>>> print(response.total > 600000)\nTrue\n>>> print(\"biolink:has_phenotype\" in response.associations[0].predicate)\nTrue\nThis document describes the steps required to create a new Monarch release.
These releases consist primarily of the following components:
Monarch Mapping Commons is a repository that contains code used to generate the mapping files used in the creation of the Monarch knowledge graph. The nodes and edges in the knowledge graph come from a variety of sources, and have varying IDs and prefixes. The mapping files are used to map these IDs to IDs in Monarch's preferred namespaces.
These mapping files are generated via a Jenkins job on a weekly basis, and are stored in the Monarch Data Bucket.
"},{"location":"release-process/#monarch-ingest-knowledge-graph","title":"Monarch Ingest (Knowledge Graph)","text":"Monarch's knowledge graph is built using the Monarch Ingest pipeline. The pipeline is run on a Jenkins server, and the resulting knowledge graph is uploaded to both Monarch's data bucket on Google Cloud, as well as the KG-Hub AWS S3 bucket.
Changes to the Monarch Ingest pipeline are made in the Monarch Ingest repository.
After the knowledge graph has been built, the QC Dashboard is used to verify the difference between the new build of the knowledge graph and the previous build.
Once the knowledge graph has been verified, additional steps are required to make the new knowledge graph available to the dev, beta, and production versions of the Monarch website.
"},{"location":"release-process/#deploying-the-knowledge-graph","title":"Deploying the Knowledge Graph","text":""},{"location":"release-process/#deploying-to-dev","title":"Deploying to dev","text":"While the Github Actions workflow for Monarch App will automatically update and deploy API & UI code to the dev environment, the knowledge graph must be manually deployed to the dev environment.
Preparing the environment for deployment:
To deploy the knowledge graph to the dev environment, follow these steps:
cd deployment && source site-envs/monarch-dev.env./provision.shgcloud compute ssh --zone us-central1-a monarch-v3-${TF_VAR_env}-manager -- sudo docker service update --force monarch-v3_solr\nFrom this point forward, code updates on the dev environment will be automatically deployed and additional work will happen to finish the work planned for the milestone. Ideally changes to the graph will happen early in the release cycle.
"},{"location":"release-process/#deploying-to-beta","title":"Deploying to beta","text":"Once work on the milestone is complete, we need to tag the release in GitHub then we can deploy to the beta environment.
To tag the release, go to the Monarch App and click on releases. Create a new release with the new version number and click generate release notes. Make any changes to the release notes that are necessary (generally none) and click publish release.
You may want to set an environment variable for the release version to make it easier to copy and paste the version number in the following steps (update for your current version):
RELEASE=\"2024-02-13\"\nFirst, copy the KG release from monarch-kg-dev to monarch-kg:
gsutil cp -r gs://data-public-monarchinitiative/monarch-kg-dev/${RELEASE} gs://data-public-monarchinitiative/monarch-kg/${RELEASE}\ngsutil cp -r gs://monarch-archive/monarch-kg-dev/${RELEASE} gs://monarch-archive/monarch-kg/${RELEASE}\nWithin monarch-stack-v3, copy the latest release env file to a new env, for example: cp site-envs/monarch-2023-10-11.env site-envs/monarch-${RELEASE}.env The date for the environment file name should match the KG release version, rather than today's date. Edit the top two lines in new env to match the latest KG & API versions:
export MONARCH_KG_VERSION=\"2023-11-16\"\nexport MONARCH_API_VERSION=\"0.18.1\"\nThen source the new environment and run provision.sh to create the new VM stack, paying attention to the terrform output to make sure that it's creating VMs with a version name you expect:
source site-envs/monarch-2023-11-16.env\n./provision.sh\nOutput for the provision script should look something like this:
...\nChanges to Outputs:\n + api_image_tag = \"1.0.0\"\n + env = \"2024-02-13\"\n + full_prefix = \"monarch-v3-2024-02-13-\"\n + neo4j_archive_url = \"https://data.monarchinitiative.org/monarch-kg-dev/latest/monarch-kg.neo4j.dump\"\n + phenio_archive_url = \"https://data.monarchinitiative.org/monarch-kg/2024-02-13/phenio.db.gz\"\n + project = \"monarch-initiative\"\n + semsimian_image_tag = \"latest\"\n + solr_archive_url = \"https://data.monarchinitiative.org/monarch-kg/2024-02-13/solr.tar.gz\"\n + sqlite_archive_url = \"https://data.monarchinitiative.org/monarch-kg/2024-02-13/monarch-kg.db.gz\"\n + stack = \"monarch-v3\"\n + ui_image_tag = \"latest\"\n + vm_svc_acct_email = \"terraform@monarch-initiative.iam.gserviceaccount.com\"\n\nDo you want to perform these actions?\n Terraform will perform the actions described above.\n Only 'yes' will be accepted to approve.\nAt the end of the run you should see a message like this:
PLAY RECAP ***************************************************************************************************\nmonarch-v3-2024-02-13-api : ok=11 changed=3 unreachable=0 failed=0 skipped=2 rescued=0 ignored=0\nmonarch-v3-2024-02-13-manager : ok=12 changed=3 unreachable=0 failed=0 skipped=2 rescued=0 ignored=0\nmonarch-v3-2024-02-13-neo4j : ok=11 changed=3 unreachable=0 failed=0 skipped=2 rescued=0 ignored=0\nmonarch-v3-2024-02-13-solr : ok=11 changed=3 unreachable=0 failed=0 skipped=2 rescued=0 ignored=0\nOnce this completes, open the GCP load balancer configuration.
monarch-v3-{release}-api-backend & monarch-v3-{release}-nginx-backend, leave the other boxes checked, and click ok.Host and path rules section to point beta.monarchinitiative.org to the nginx backend, api-beta.monarchinitiative.org to the api backend, and neo4j-beta.monarchinitiative.org to the neo4j backend./* to the path matcher, and click update.If you get a pop-up window error, you may have forgotten to delete one of the old routes when pointing to the new backend. You will need to redo the configuration if this happens.
The load balancer will automatically restart with the new configuration. Then we'll need to confirm that the site is up and running.
Get yourself a cup of hot chocolate / ice cold lemonade (season dependent) and settle in to go through the issues in the milestone. Make sure that each issue appears to actually be fixed, and close them with a note that they're confirmed to be working on beta.monarchinitiative.org. (with some additional explanation for externally submitted issues about when the change is expected to be visible on the production site)
"},{"location":"release-process/#deploying-to-production","title":"Deploying to production","text":"Edit the load balancer 1. Remove the nginx and api backends from the last release 2. Point api-beta.monarchinitiative.org, api-v3.monarchinitiative.org, and api-next.monarchinitiative.org to monarch-v3-{release}-api-backend 3. Point next.monarchinitiative.org and monarchinitiative.org to monarch-v3-{release}-nginx-backend 4. At the top of the host and path rules seciton, change the default backend (\"Backend 1\") to point to monarch-v3-{release}-nginx-backend as well
Then turn off the former production VMs (but keep them around for disaster recovery) by going to the GCP console VM listings and just clicking stop on each VM.
Source the former former env in v3 stack to delete it (say yes to deleting, and no to creating in the terraform dialogs)
source site-envs/monarch-2023-10-17.env\n./provision.sh -d\nHere are some known issues that we have seen before:
In ./provision.sh you may see an error like this:
fatal: [monarch-v3-2024-02-13-api]: UNREACHABLE! => changed=false\n msg: |-\n Data could not be sent to remote host \"monarch-v3-2024-02-13-api\". Make sure this host can be reached over ssh: Pseudo-terminal will not be allocated because stdin is not a terminal.\n sa_116692422516913491665@34.42.108.156: Permission denied (publickey).\n\n Recommendation: To check for possible causes of SSH connectivity issues and get\n recommendations, rerun the ssh command with the --troubleshoot option.\n\n gcloud compute ssh monarch-v3-2024-02-13-api --project=monarch-initiative --zone=us-central1-a --troubleshoot\n\n Or, to investigate an IAP tunneling issue:\n\n gcloud compute ssh monarch-v3-2024-02-13-api --project=monarch-initiative --zone=us-central1-a --troubleshoot --tunnel-through-iap\n\n ERROR: (gcloud.compute.ssh) [/usr/bin/ssh] exited with return code [255].\n unreachable: true\nIf so you may want to run the stated command (update to your version):
gcloud compute ssh monarch-v3-2024-02-13-api --project=monarch-initiative --zone=us-central1-a --troubleshoot\nData models for the Monarch Initiative data access library
URI: https://w3id.org/monarch/monarch-py
Name: monarch-py
"},{"location":"Data-Model/#classes","title":"Classes","text":"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"},{"location":"Data-Model/#slots","title":"Slots","text":"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_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_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_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_label The name of the sex_qualifier entity sex_qualifier_namespace The namespace/prefix of the sex_qualifier entity similarity solr species_context_qualifier A context qualifier representing a species in which a relationship expressed ... species_context_qualifier_category The category of the species_context_qualifier entity species_context_qualifier_label The name of the species_context_qualifier entity species_context_qualifier_namespace The namespace/prefix of the species_context_qualifier entity sqlite stage_qualifier stage_qualifier_category The category of the stage_qualifier entity 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"},{"location":"Data-Model/#enumerations","title":"Enumerations","text":"Enumeration Description AssociationDirectionEnum The directionality of an association as it relates to a specified entity, wit..."},{"location":"Data-Model/#types","title":"Types","text":"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"},{"location":"Data-Model/#subsets","title":"Subsets","text":"Subset Description"},{"location":"Data-Model/Association/","title":"Class: Association","text":"URI: https://w3id.org/monarch/monarch-py/:Association
classDiagram\n class Association\n click Association href \"../Association\"\n Association <|-- DirectionalAssociation\n click DirectionalAssociation href \"../DirectionalAssociation\"\n\n Association : agent_type\n\n Association : aggregator_knowledge_source\n\n Association : category\n\n Association : disease_context_qualifier\n\n Association : disease_context_qualifier_category\n\n Association : disease_context_qualifier_closure\n\n Association : disease_context_qualifier_closure_label\n\n Association : disease_context_qualifier_label\n\n Association : disease_context_qualifier_namespace\n\n Association : evidence_count\n\n Association : frequency_qualifier\n\n Association : frequency_qualifier_category\n\n Association : frequency_qualifier_label\n\n Association : frequency_qualifier_namespace\n\n Association : grouping_key\n\n Association : has_count\n\n Association : has_evidence\n\n Association : has_evidence_links\n\n\n\n\n Association --> \"*\" ExpandedCurie : has_evidence_links\n click ExpandedCurie href \"../ExpandedCurie\"\n\n\n Association : has_percentage\n\n Association : has_quotient\n\n Association : has_total\n\n Association : id\n\n Association : knowledge_level\n\n Association : negated\n\n Association : object\n\n Association : object_category\n\n Association : object_closure\n\n Association : object_closure_label\n\n Association : object_label\n\n Association : object_namespace\n\n Association : object_taxon\n\n Association : object_taxon_label\n\n Association : onset_qualifier\n\n Association : onset_qualifier_category\n\n Association : onset_qualifier_label\n\n Association : onset_qualifier_namespace\n\n Association : original_object\n\n Association : original_subject\n\n Association : pathway\n\n Association : predicate\n\n Association : primary_knowledge_source\n\n Association : provided_by\n\n Association : provided_by_link\n\n\n\n\n Association --> \"0..1\" ExpandedCurie : provided_by_link\n click ExpandedCurie href \"../ExpandedCurie\"\n\n\n Association : publications\n\n Association : publications_links\n\n\n\n\n Association --> \"*\" ExpandedCurie : publications_links\n click ExpandedCurie href \"../ExpandedCurie\"\n\n\n Association : qualifier\n\n Association : qualifier_category\n\n Association : qualifier_label\n\n Association : qualifier_namespace\n\n Association : qualifiers\n\n Association : qualifiers_category\n\n Association : qualifiers_label\n\n Association : qualifiers_namespace\n\n Association : sex_qualifier\n\n Association : sex_qualifier_category\n\n Association : sex_qualifier_label\n\n Association : sex_qualifier_namespace\n\n Association : species_context_qualifier\n\n Association : species_context_qualifier_category\n\n Association : species_context_qualifier_label\n\n Association : species_context_qualifier_namespace\n\n Association : stage_qualifier\n\n Association : stage_qualifier_category\n\n Association : stage_qualifier_label\n\n Association : stage_qualifier_namespace\n\n Association : subject\n\n Association : subject_category\n\n Association : subject_closure\n\n Association : subject_closure_label\n\n Association : subject_label\n\n Association : subject_namespace\n\n Association : subject_taxon\n\n Association : subject_taxon_label\nname: Association\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- id\n- category\n- subject\n- original_subject\n- subject_namespace\n- subject_category\n- subject_closure\n- subject_label\n- subject_closure_label\n- subject_taxon\n- subject_taxon_label\n- predicate\n- object\n- original_object\n- object_namespace\n- object_category\n- object_closure\n- object_label\n- object_closure_label\n- object_taxon\n- object_taxon_label\n- primary_knowledge_source\n- aggregator_knowledge_source\n- negated\n- pathway\n- evidence_count\n- knowledge_level\n- agent_type\n- has_evidence\n- has_evidence_links\n- has_count\n- has_total\n- has_percentage\n- has_quotient\n- grouping_key\n- provided_by\n- provided_by_link\n- publications\n- publications_links\n- frequency_qualifier\n- onset_qualifier\n- sex_qualifier\n- stage_qualifier\n- qualifiers\n- qualifiers_label\n- qualifiers_namespace\n- qualifiers_category\n- qualifier\n- qualifier_label\n- qualifier_namespace\n- qualifier_category\n- frequency_qualifier_label\n- frequency_qualifier_namespace\n- frequency_qualifier_category\n- onset_qualifier_label\n- onset_qualifier_namespace\n- onset_qualifier_category\n- sex_qualifier_label\n- sex_qualifier_namespace\n- sex_qualifier_category\n- stage_qualifier_label\n- stage_qualifier_namespace\n- stage_qualifier_category\n- disease_context_qualifier\n- disease_context_qualifier_label\n- disease_context_qualifier_namespace\n- disease_context_qualifier_category\n- disease_context_qualifier_closure\n- disease_context_qualifier_closure_label\n- species_context_qualifier\n- species_context_qualifier_label\n- species_context_qualifier_namespace\n- species_context_qualifier_category\nname: Association\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n id:\n name: id\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n identifier: true\n alias: id\n owner: Association\n domain_of:\n - Association\n - ExpandedCurie\n - Entity\n - HistoPheno\n - HistoBin\n - Mapping\n - MultiEntityAssociationResults\n - TermInfo\n range: string\n required: true\n category:\n name: category\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: category\n owner: Association\n domain_of:\n - Association\n - AssociationCount\n - CompactAssociation\n - AssociationTypeMapping\n - Entity\n range: string\n multivalued: false\n subject:\n name: subject\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: subject\n owner: Association\n domain_of:\n - Association\n - CompactAssociation\n - SemsimSearchResult\n range: string\n required: true\n original_subject:\n name: original_subject\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: original_subject\n owner: Association\n domain_of:\n - Association\n range: string\n subject_namespace:\n name: subject_namespace\n description: The namespace/prefix of the subject entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: subject_namespace\n owner: Association\n domain_of:\n - Association\n range: string\n subject_category:\n name: subject_category\n description: The category of the subject entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: category\n alias: subject_category\n owner: Association\n domain_of:\n - Association\n range: string\n subject_closure:\n name: subject_closure\n description: Field containing subject id and the ids of all of it's ancestors\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: subject_closure\n owner: Association\n domain_of:\n - Association\n range: string\n multivalued: true\n subject_label:\n name: subject_label\n description: The name of the subject entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: subject_label\n owner: Association\n domain_of:\n - Association\n - CompactAssociation\n - AssociationTypeMapping\n - Mapping\n - TermPairwiseSimilarity\n range: string\n subject_closure_label:\n name: subject_closure_label\n description: Field containing subject name and the names of all of it's ancestors\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: subject_closure_label\n owner: Association\n domain_of:\n - Association\n range: string\n multivalued: true\n subject_taxon:\n name: subject_taxon\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: in_taxon\n alias: subject_taxon\n owner: Association\n domain_of:\n - Association\n range: string\n subject_taxon_label:\n name: subject_taxon_label\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: in_taxon_label\n alias: subject_taxon_label\n owner: Association\n domain_of:\n - Association\n range: string\n predicate:\n name: predicate\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: predicate\n owner: Association\n domain_of:\n - Association\n - CompactAssociation\n range: string\n required: true\n multivalued: false\n object:\n name: object\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: object\n owner: Association\n domain_of:\n - Association\n - CompactAssociation\n range: string\n required: true\n original_object:\n name: original_object\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: original_object\n owner: Association\n domain_of:\n - Association\n range: string\n object_namespace:\n name: object_namespace\n description: The namespace/prefix of the object entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: object_namespace\n owner: Association\n domain_of:\n - Association\n range: string\n object_category:\n name: object_category\n description: The category of the object entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: category\n alias: object_category\n owner: Association\n domain_of:\n - Association\n range: string\n object_closure:\n name: object_closure\n description: Field containing object id and the ids of all of it's ancestors\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: object_closure\n owner: Association\n domain_of:\n - Association\n range: string\n multivalued: true\n object_label:\n name: object_label\n description: The name of the object entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: object_label\n owner: Association\n domain_of:\n - Association\n - CompactAssociation\n - AssociationTypeMapping\n - Mapping\n - TermPairwiseSimilarity\n range: string\n object_closure_label:\n name: object_closure_label\n description: Field containing object name and the names of all of it's ancestors\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: object_closure_label\n owner: Association\n domain_of:\n - Association\n range: string\n multivalued: true\n object_taxon:\n name: object_taxon\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: in_taxon\n alias: object_taxon\n owner: Association\n domain_of:\n - Association\n range: string\n object_taxon_label:\n name: object_taxon_label\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: in_taxon_label\n alias: object_taxon_label\n owner: Association\n domain_of:\n - Association\n range: string\n primary_knowledge_source:\n name: primary_knowledge_source\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: primary_knowledge_source\n owner: Association\n domain_of:\n - Association\n range: string\n aggregator_knowledge_source:\n name: aggregator_knowledge_source\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: aggregator_knowledge_source\n owner: Association\n domain_of:\n - Association\n range: string\n multivalued: true\n negated:\n name: negated\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: negated\n owner: Association\n domain_of:\n - Association\n - CompactAssociation\n range: boolean\n pathway:\n name: pathway\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: pathway\n owner: Association\n domain_of:\n - Association\n range: string\n evidence_count:\n name: evidence_count\n description: count of supporting documents, evidence codes, and sources supplying\n evidence\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: evidence_count\n owner: Association\n domain_of:\n - Association\n range: integer\n knowledge_level:\n name: knowledge_level\n description: Describes the level of knowledge expressed in a statement, based\n on the reasoning or analysis methods used to generate the statement, or the\n scope or specificity of what the statement expresses to be true.\n notes:\n - The range in this schema is represented as a string, but is constrained to\n values from biolink:KnowledgeLevelEnum at ingest time\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n slot_uri: biolink:knowledge_level\n alias: knowledge_level\n owner: Association\n domain_of:\n - Association\n range: string\n required: true\n multivalued: false\n agent_type:\n name: agent_type\n description: Describes the high-level category of agent who originally generated\n a statement of knowledge or other type of information.\n notes:\n - The range in this schema is represented as a string, but is constrained to\n values from biolink:AgentTypeEnum at ingest time\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n slot_uri: biolink:agent_type\n alias: agent_type\n owner: Association\n domain_of:\n - Association\n range: string\n required: true\n multivalued: false\n has_evidence:\n name: has_evidence\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_evidence\n owner: Association\n domain_of:\n - Association\n range: string\n multivalued: true\n has_evidence_links:\n name: has_evidence_links\n description: List of ExpandedCuries with id and url for evidence\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_evidence_links\n owner: Association\n domain_of:\n - Association\n range: ExpandedCurie\n multivalued: true\n inlined: true\n inlined_as_list: true\n has_count:\n name: has_count\n description: count of out of has_total representing a frequency\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_count\n owner: Association\n domain_of:\n - Association\n range: integer\n has_total:\n name: has_total\n description: total, devided by has_count, representing a frequency\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_total\n owner: Association\n domain_of:\n - Association\n range: integer\n has_percentage:\n name: has_percentage\n description: percentage, which may be calculated from has_count and has_total,\n as 100 * quotient or provided directly, rounded to the integer level\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_percentage\n owner: Association\n domain_of:\n - Association\n range: float\n has_quotient:\n name: has_quotient\n description: quotient, which should be 1/100 of has_percentage\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_quotient\n owner: Association\n domain_of:\n - Association\n range: float\n grouping_key:\n name: grouping_key\n description: A concatenation of fields used to group associations with the same\n essential/defining properties\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: grouping_key\n owner: Association\n domain_of:\n - Association\n range: string\n provided_by:\n name: provided_by\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: provided_by\n owner: Association\n domain_of:\n - Association\n - Entity\n range: string\n provided_by_link:\n name: provided_by_link\n description: A link to the docs for the knowledge source that provided the node/edge.\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: provided_by_link\n owner: Association\n domain_of:\n - Association\n - Node\n range: ExpandedCurie\n inlined: true\n publications:\n name: publications\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: publications\n owner: Association\n domain_of:\n - Association\n range: string\n multivalued: true\n publications_links:\n name: publications_links\n description: List of ExpandedCuries with id and url for publications\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: publications_links\n owner: Association\n domain_of:\n - Association\n range: ExpandedCurie\n multivalued: true\n inlined: true\n inlined_as_list: true\n frequency_qualifier:\n name: frequency_qualifier\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: frequency_qualifier\n owner: Association\n domain_of:\n - Association\n range: string\n onset_qualifier:\n name: onset_qualifier\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: onset_qualifier\n owner: Association\n domain_of:\n - Association\n range: string\n sex_qualifier:\n name: sex_qualifier\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: sex_qualifier\n owner: Association\n domain_of:\n - Association\n range: string\n stage_qualifier:\n name: stage_qualifier\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: stage_qualifier\n owner: Association\n domain_of:\n - Association\n range: string\n qualifiers:\n name: qualifiers\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: qualifiers\n owner: Association\n domain_of:\n - Association\n range: string\n multivalued: true\n qualifiers_label:\n name: qualifiers_label\n description: The name of the frequency_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: qualifiers_label\n owner: Association\n domain_of:\n - Association\n range: string\n qualifiers_namespace:\n name: qualifiers_namespace\n description: The namespace/prefix of the frequency_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: qualifiers_namespace\n owner: Association\n domain_of:\n - Association\n range: string\n qualifiers_category:\n name: qualifiers_category\n description: The category of the frequency_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: category\n alias: qualifiers_category\n owner: Association\n domain_of:\n - Association\n range: string\n qualifier:\n name: qualifier\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: qualifier\n owner: Association\n domain_of:\n - Association\n range: string\n multivalued: true\n qualifier_label:\n name: qualifier_label\n description: The name of the frequency_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: qualifier_label\n owner: Association\n domain_of:\n - Association\n range: string\n qualifier_namespace:\n name: qualifier_namespace\n description: The namespace/prefix of the frequency_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: qualifier_namespace\n owner: Association\n domain_of:\n - Association\n range: string\n qualifier_category:\n name: qualifier_category\n description: The category of the frequency_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: category\n alias: qualifier_category\n owner: Association\n domain_of:\n - Association\n range: string\n frequency_qualifier_label:\n name: frequency_qualifier_label\n description: The name of the frequency_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: frequency_qualifier_label\n owner: Association\n domain_of:\n - Association\n range: string\n frequency_qualifier_namespace:\n name: frequency_qualifier_namespace\n description: The namespace/prefix of the frequency_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: frequency_qualifier_namespace\n owner: Association\n domain_of:\n - Association\n range: string\n frequency_qualifier_category:\n name: frequency_qualifier_category\n description: The category of the frequency_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: category\n alias: frequency_qualifier_category\n owner: Association\n domain_of:\n - Association\n range: string\n onset_qualifier_label:\n name: onset_qualifier_label\n description: The name of the onset_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: onset_qualifier_label\n owner: Association\n domain_of:\n - Association\n range: string\n onset_qualifier_namespace:\n name: onset_qualifier_namespace\n description: The namespace/prefix of the onset_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: onset_qualifier_namespace\n owner: Association\n domain_of:\n - Association\n range: string\n onset_qualifier_category:\n name: onset_qualifier_category\n description: The category of the onset_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: category\n alias: onset_qualifier_category\n owner: Association\n domain_of:\n - Association\n range: string\n sex_qualifier_label:\n name: sex_qualifier_label\n description: The name of the sex_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: sex_qualifier_label\n owner: Association\n domain_of:\n - Association\n range: string\n sex_qualifier_namespace:\n name: sex_qualifier_namespace\n description: The namespace/prefix of the sex_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: sex_qualifier_namespace\n owner: Association\n domain_of:\n - Association\n range: string\n sex_qualifier_category:\n name: sex_qualifier_category\n description: The category of the sex_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: category\n alias: sex_qualifier_category\n owner: Association\n domain_of:\n - Association\n range: string\n stage_qualifier_label:\n name: stage_qualifier_label\n description: The name of the stage_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: stage_qualifier_label\n owner: Association\n domain_of:\n - Association\n range: string\n stage_qualifier_namespace:\n name: stage_qualifier_namespace\n description: The namespace/prefix of the stage_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: stage_qualifier_namespace\n owner: Association\n domain_of:\n - Association\n range: string\n stage_qualifier_category:\n name: stage_qualifier_category\n description: The category of the stage_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: category\n alias: stage_qualifier_category\n owner: Association\n domain_of:\n - Association\n range: string\n disease_context_qualifier:\n name: disease_context_qualifier\n description: A context qualifier representing a disease or condition in which\n a relationship expressed in an association took place.\n examples:\n - value: MONDO:0004979\n - value: MONDO:0005148\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: disease_context_qualifier\n owner: Association\n domain_of:\n - Association\n range: string\n disease_context_qualifier_label:\n name: disease_context_qualifier_label\n description: The name of the disease_context_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: disease_context_qualifier_label\n owner: Association\n domain_of:\n - Association\n range: string\n disease_context_qualifier_namespace:\n name: disease_context_qualifier_namespace\n description: The namespace/prefix of the disease_context_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: disease_context_qualifier_namespace\n owner: Association\n domain_of:\n - Association\n range: string\n disease_context_qualifier_category:\n name: disease_context_qualifier_category\n description: The category of the disease_context_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: category\n alias: disease_context_qualifier_category\n owner: Association\n domain_of:\n - Association\n range: string\n disease_context_qualifier_closure:\n name: disease_context_qualifier_closure\n description: Field containing disease_context_qualifier id and the ids of all\n of it's ancestors\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: disease_context_qualifier_closure\n owner: Association\n domain_of:\n - Association\n range: string\n multivalued: true\n disease_context_qualifier_closure_label:\n name: disease_context_qualifier_closure_label\n description: Field containing disease_context_qualifier name and the names of\n all of it's ancestors\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: disease_context_qualifier_closure_label\n owner: Association\n domain_of:\n - Association\n range: string\n multivalued: true\n species_context_qualifier:\n name: species_context_qualifier\n description: A context qualifier representing a species in which a relationship\n expressed in an association took place.\n examples:\n - value: NCBITaxon:9606\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: species_context_qualifier\n owner: Association\n domain_of:\n - Association\n range: string\n species_context_qualifier_label:\n name: species_context_qualifier_label\n description: The name of the species_context_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: species_context_qualifier_label\n owner: Association\n domain_of:\n - Association\n range: string\n species_context_qualifier_namespace:\n name: species_context_qualifier_namespace\n description: The namespace/prefix of the species_context_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: species_context_qualifier_namespace\n owner: Association\n domain_of:\n - Association\n range: string\n species_context_qualifier_category:\n name: species_context_qualifier_category\n description: The category of the species_context_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: category\n alias: species_context_qualifier_category\n owner: Association\n domain_of:\n - Association\n range: string\nURI: https://w3id.org/monarch/monarch-py/:AssociationCount
classDiagram\n class AssociationCount\n click AssociationCount href \"../AssociationCount\"\n FacetValue <|-- AssociationCount\n click FacetValue href \"../FacetValue\"\n\n AssociationCount : category\n\n AssociationCount : count\n\n AssociationCount : label\nname: AssociationCount\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: FacetValue\nslots:\n- category\nslot_usage:\n category:\n name: category\n multivalued: false\nname: AssociationCount\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: FacetValue\nslot_usage:\n category:\n name: category\n multivalued: false\nattributes:\n category:\n name: category\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: category\n owner: AssociationCount\n domain_of:\n - Association\n - AssociationCount\n - CompactAssociation\n - AssociationTypeMapping\n - Entity\n range: string\n multivalued: false\n label:\n name: label\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: label\n owner: AssociationCount\n domain_of:\n - FacetValue\n - FacetField\n - TermInfo\n range: string\n required: true\n count:\n name: count\n description: count of documents\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: count\n owner: AssociationCount\n domain_of:\n - FacetValue\n range: integer\nContainer class for a list of association counts
URI: https://w3id.org/monarch/monarch-py/:AssociationCountList
classDiagram\n class AssociationCountList\n click AssociationCountList href \"../AssociationCountList\"\n AssociationCountList : items\n\n\n\n\n AssociationCountList --> \"1..*\" AssociationCount : items\n click AssociationCount href \"../AssociationCount\"\nname: AssociationCountList\ndescription: Container class for a list of association counts\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- items\nslot_usage:\n items:\n name: items\n range: AssociationCount\nname: AssociationCountList\ndescription: Container class for a list of association counts\nfrom_schema: https://w3id.org/monarch/monarch-py\nslot_usage:\n items:\n name: items\n range: AssociationCount\nattributes:\n items:\n name: items\n description: A collection of items, with the type to be overriden by slot_usage\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: items\n owner: AssociationCountList\n domain_of:\n - AssociationCountList\n - AssociationResults\n - CompactAssociationResults\n - AssociationTableResults\n - CategoryGroupedAssociationResults\n - EntityResults\n - HistoPheno\n - MappingResults\n - SearchResults\n range: AssociationCount\n required: true\n multivalued: true\n inlined: true\n inlined_as_list: true\nThe directionality of an association as it relates to a specified entity, with edges being categorized as incoming or outgoing
URI: AssociationDirectionEnum
"},{"location":"Data-Model/AssociationDirectionEnum/#permissible-values","title":"Permissible Values","text":"Value Meaning Description incoming None An association for which a specified entity is the object or part of the obje... outgoing None An association for which a specified entity is the subject or part of the sub..."},{"location":"Data-Model/AssociationDirectionEnum/#slots","title":"Slots","text":"Name Description direction The directionality of the association relative to a given entity for an assoc..."},{"location":"Data-Model/AssociationDirectionEnum/#identifier-and-mapping-information","title":"Identifier and Mapping Information","text":""},{"location":"Data-Model/AssociationDirectionEnum/#schema-source","title":"Schema Source","text":"name: AssociationDirectionEnum\ndescription: The directionality of an association as it relates to a specified entity,\n with edges being categorized as incoming or outgoing\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\npermissible_values:\n incoming:\n text: incoming\n description: An association for which a specified entity is the object or part\n of the object closure\n outgoing:\n text: outgoing\n description: An association for which a specified entity is the subject or part\n of the subject closure\nURI: https://w3id.org/monarch/monarch-py/:AssociationResults
classDiagram\n class AssociationResults\n click AssociationResults href \"../AssociationResults\"\n Results <|-- AssociationResults\n click Results href \"../Results\"\n\n AssociationResults : facet_fields\n\n\n\n\n AssociationResults --> \"*\" FacetField : facet_fields\n click FacetField href \"../FacetField\"\n\n\n AssociationResults : facet_queries\n\n\n\n\n AssociationResults --> \"*\" FacetValue : facet_queries\n click FacetValue href \"../FacetValue\"\n\n\n AssociationResults : items\n\n\n\n\n AssociationResults --> \"1..*\" Association : items\n click Association href \"../Association\"\n\n\n AssociationResults : limit\n\n AssociationResults : offset\n\n AssociationResults : total\nname: AssociationResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslots:\n- items\n- facet_fields\n- facet_queries\nslot_usage:\n items:\n name: items\n range: Association\nname: AssociationResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslot_usage:\n items:\n name: items\n range: Association\nattributes:\n items:\n name: items\n description: A collection of items, with the type to be overriden by slot_usage\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: items\n owner: AssociationResults\n domain_of:\n - AssociationCountList\n - AssociationResults\n - CompactAssociationResults\n - AssociationTableResults\n - CategoryGroupedAssociationResults\n - EntityResults\n - HistoPheno\n - MappingResults\n - SearchResults\n range: Association\n required: true\n multivalued: true\n inlined: true\n inlined_as_list: true\n facet_fields:\n name: facet_fields\n description: Collection of facet field responses with the field values and counts\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: facet_fields\n owner: AssociationResults\n domain_of:\n - AssociationResults\n - CompactAssociationResults\n - AssociationTableResults\n - SearchResults\n range: FacetField\n multivalued: true\n inlined: true\n inlined_as_list: true\n facet_queries:\n name: facet_queries\n description: Collection of facet query responses with the query string values\n and counts\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: facet_queries\n owner: AssociationResults\n domain_of:\n - AssociationResults\n - CompactAssociationResults\n - AssociationTableResults\n - SearchResults\n range: FacetValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n limit:\n name: limit\n description: number of items to return in a response\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: limit\n owner: AssociationResults\n domain_of:\n - Results\n range: integer\n required: true\n offset:\n name: offset\n description: offset into the total number of items\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: offset\n owner: AssociationResults\n domain_of:\n - Results\n range: integer\n required: true\n total:\n name: total\n description: total number of items matching a query\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: total\n owner: AssociationResults\n domain_of:\n - Results\n range: integer\n required: true\nURI: https://w3id.org/monarch/monarch-py/:AssociationTableResults
classDiagram\n class AssociationTableResults\n click AssociationTableResults href \"../AssociationTableResults\"\n Results <|-- AssociationTableResults\n click Results href \"../Results\"\n\n AssociationTableResults : facet_fields\n\n\n\n\n AssociationTableResults --> \"*\" FacetField : facet_fields\n click FacetField href \"../FacetField\"\n\n\n AssociationTableResults : facet_queries\n\n\n\n\n AssociationTableResults --> \"*\" FacetValue : facet_queries\n click FacetValue href \"../FacetValue\"\n\n\n AssociationTableResults : items\n\n\n\n\n AssociationTableResults --> \"1..*\" DirectionalAssociation : items\n click DirectionalAssociation href \"../DirectionalAssociation\"\n\n\n AssociationTableResults : limit\n\n AssociationTableResults : offset\n\n AssociationTableResults : total\nname: AssociationTableResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslots:\n- items\n- facet_fields\n- facet_queries\nslot_usage:\n items:\n name: items\n range: DirectionalAssociation\nname: AssociationTableResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslot_usage:\n items:\n name: items\n range: DirectionalAssociation\nattributes:\n items:\n name: items\n description: A collection of items, with the type to be overriden by slot_usage\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: items\n owner: AssociationTableResults\n domain_of:\n - AssociationCountList\n - AssociationResults\n - CompactAssociationResults\n - AssociationTableResults\n - CategoryGroupedAssociationResults\n - EntityResults\n - HistoPheno\n - MappingResults\n - SearchResults\n range: DirectionalAssociation\n required: true\n multivalued: true\n inlined: true\n inlined_as_list: true\n facet_fields:\n name: facet_fields\n description: Collection of facet field responses with the field values and counts\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: facet_fields\n owner: AssociationTableResults\n domain_of:\n - AssociationResults\n - CompactAssociationResults\n - AssociationTableResults\n - SearchResults\n range: FacetField\n multivalued: true\n inlined: true\n inlined_as_list: true\n facet_queries:\n name: facet_queries\n description: Collection of facet query responses with the query string values\n and counts\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: facet_queries\n owner: AssociationTableResults\n domain_of:\n - AssociationResults\n - CompactAssociationResults\n - AssociationTableResults\n - SearchResults\n range: FacetValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n limit:\n name: limit\n description: number of items to return in a response\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: limit\n owner: AssociationTableResults\n domain_of:\n - Results\n range: integer\n required: true\n offset:\n name: offset\n description: offset into the total number of items\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: offset\n owner: AssociationTableResults\n domain_of:\n - Results\n range: integer\n required: true\n total:\n name: total\n description: total number of items matching a query\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: total\n owner: AssociationTableResults\n domain_of:\n - Results\n range: integer\n required: true\nA data class to hold the necessary information to produce association type counts for given entities with appropriate directional labels
URI: https://w3id.org/monarch/monarch-py/:AssociationTypeMapping
classDiagram\n class AssociationTypeMapping\n click AssociationTypeMapping href \"../AssociationTypeMapping\"\n AssociationTypeMapping : category\n\n AssociationTypeMapping : object_label\n\n AssociationTypeMapping : subject_label\n\n AssociationTypeMapping : symmetric\nname: AssociationTypeMapping\ndescription: A data class to hold the necessary information to produce association\n type counts for given entities with appropriate directional labels\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- subject_label\n- object_label\n- symmetric\n- category\nslot_usage:\n subject_label:\n name: subject_label\n description: A label to describe the subjects of the association type as a whole\n for use in the UI\n object_label:\n name: object_label\n description: A label to describe the objects of the association type as a whole\n for use in the UI\n symmetric:\n name: symmetric\n description: Whether the association type is symmetric, meaning that the subject\n and object labels should be interchangeable\n ifabsent: 'False'\n required: true\n category:\n name: category\n description: The biolink category to use in queries for this association type\n required: true\n multivalued: false\nname: AssociationTypeMapping\ndescription: A data class to hold the necessary information to produce association\n type counts for given entities with appropriate directional labels\nfrom_schema: https://w3id.org/monarch/monarch-py\nslot_usage:\n subject_label:\n name: subject_label\n description: A label to describe the subjects of the association type as a whole\n for use in the UI\n object_label:\n name: object_label\n description: A label to describe the objects of the association type as a whole\n for use in the UI\n symmetric:\n name: symmetric\n description: Whether the association type is symmetric, meaning that the subject\n and object labels should be interchangeable\n ifabsent: 'False'\n required: true\n category:\n name: category\n description: The biolink category to use in queries for this association type\n required: true\n multivalued: false\nattributes:\n subject_label:\n name: subject_label\n description: A label to describe the subjects of the association type as a whole\n for use in the UI\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: subject_label\n owner: AssociationTypeMapping\n domain_of:\n - Association\n - CompactAssociation\n - AssociationTypeMapping\n - Mapping\n - TermPairwiseSimilarity\n range: string\n object_label:\n name: object_label\n description: A label to describe the objects of the association type as a whole\n for use in the UI\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: object_label\n owner: AssociationTypeMapping\n domain_of:\n - Association\n - CompactAssociation\n - AssociationTypeMapping\n - Mapping\n - TermPairwiseSimilarity\n range: string\n symmetric:\n name: symmetric\n description: Whether the association type is symmetric, meaning that the subject\n and object labels should be interchangeable\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n ifabsent: 'False'\n alias: symmetric\n owner: AssociationTypeMapping\n domain_of:\n - AssociationTypeMapping\n range: boolean\n required: true\n category:\n name: category\n description: The biolink category to use in queries for this association type\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: category\n owner: AssociationTypeMapping\n domain_of:\n - Association\n - AssociationCount\n - CompactAssociation\n - AssociationTypeMapping\n - Entity\n range: string\n required: true\n multivalued: false\nURI: https://w3id.org/monarch/monarch-py/:BestMatch
classDiagram\n class BestMatch\n click BestMatch href \"../BestMatch\"\n BestMatch : match_source\n\n BestMatch : match_source_label\n\n BestMatch : match_subsumer\n\n BestMatch : match_subsumer_label\n\n BestMatch : match_target\n\n BestMatch : match_target_label\n\n BestMatch : score\n\n BestMatch : similarity\n\n\n\n\n BestMatch --> \"1\" TermPairwiseSimilarity : similarity\n click TermPairwiseSimilarity href \"../TermPairwiseSimilarity\"\nname: BestMatch\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n match_source:\n name: match_source\n comments:\n - note that the match_source is either the subject or the object\n from_schema: https://w3id.org/monarch/monarch-py-similarity\n rank: 1000\n identifier: true\n domain_of:\n - BestMatch\n required: true\n match_source_label:\n name: match_source_label\n from_schema: https://w3id.org/monarch/monarch-py-similarity\n rank: 1000\n domain_of:\n - BestMatch\n match_target:\n name: match_target\n description: the entity matches\n from_schema: https://w3id.org/monarch/monarch-py-similarity\n rank: 1000\n domain_of:\n - BestMatch\n match_target_label:\n name: match_target_label\n from_schema: https://w3id.org/monarch/monarch-py-similarity\n rank: 1000\n domain_of:\n - BestMatch\n score:\n name: score\n from_schema: https://w3id.org/monarch/monarch-py-similarity\n domain_of:\n - SearchResult\n - BestMatch\n - SemsimSearchResult\n range: float\n required: true\n match_subsumer:\n name: match_subsumer\n from_schema: https://w3id.org/monarch/monarch-py-similarity\n rank: 1000\n domain_of:\n - BestMatch\n range: uriorcurie\n match_subsumer_label:\n name: match_subsumer_label\n from_schema: https://w3id.org/monarch/monarch-py-similarity\n rank: 1000\n domain_of:\n - BestMatch\n similarity:\n name: similarity\n from_schema: https://w3id.org/monarch/monarch-py-similarity\n domain_of:\n - BestMatch\n - SemsimSearchResult\n range: TermPairwiseSimilarity\n required: true\nname: BestMatch\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n match_source:\n name: match_source\n comments:\n - note that the match_source is either the subject or the object\n from_schema: https://w3id.org/monarch/monarch-py-similarity\n rank: 1000\n identifier: true\n alias: match_source\n owner: BestMatch\n domain_of:\n - BestMatch\n range: string\n required: true\n match_source_label:\n name: match_source_label\n from_schema: https://w3id.org/monarch/monarch-py-similarity\n rank: 1000\n alias: match_source_label\n owner: BestMatch\n domain_of:\n - BestMatch\n range: string\n match_target:\n name: match_target\n description: the entity matches\n from_schema: https://w3id.org/monarch/monarch-py-similarity\n rank: 1000\n alias: match_target\n owner: BestMatch\n domain_of:\n - BestMatch\n range: string\n match_target_label:\n name: match_target_label\n from_schema: https://w3id.org/monarch/monarch-py-similarity\n rank: 1000\n alias: match_target_label\n owner: BestMatch\n domain_of:\n - BestMatch\n range: string\n score:\n name: score\n from_schema: https://w3id.org/monarch/monarch-py-similarity\n alias: score\n owner: BestMatch\n domain_of:\n - SearchResult\n - BestMatch\n - SemsimSearchResult\n range: float\n required: true\n match_subsumer:\n name: match_subsumer\n from_schema: https://w3id.org/monarch/monarch-py-similarity\n rank: 1000\n alias: match_subsumer\n owner: BestMatch\n domain_of:\n - BestMatch\n range: uriorcurie\n match_subsumer_label:\n name: match_subsumer_label\n from_schema: https://w3id.org/monarch/monarch-py-similarity\n rank: 1000\n alias: match_subsumer_label\n owner: BestMatch\n domain_of:\n - BestMatch\n range: string\n similarity:\n name: similarity\n from_schema: https://w3id.org/monarch/monarch-py-similarity\n alias: similarity\n owner: BestMatch\n domain_of:\n - BestMatch\n - SemsimSearchResult\n range: TermPairwiseSimilarity\n required: true\nA binary (true or false) value
URI: xsd:boolean
base: Bool
uri: xsd:boolean
repr: bool
URI: https://w3id.org/monarch/monarch-py/:CategoryGroupedAssociationResults
classDiagram\n class CategoryGroupedAssociationResults\n click CategoryGroupedAssociationResults href \"../CategoryGroupedAssociationResults\"\n Results <|-- CategoryGroupedAssociationResults\n click Results href \"../Results\"\n\n CategoryGroupedAssociationResults : counterpart_category\n\n CategoryGroupedAssociationResults : items\n\n\n\n\n CategoryGroupedAssociationResults --> \"1..*\" Association : items\n click Association href \"../Association\"\n\n\n CategoryGroupedAssociationResults : limit\n\n CategoryGroupedAssociationResults : offset\n\n CategoryGroupedAssociationResults : total\nname: CategoryGroupedAssociationResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslots:\n- counterpart_category\n- items\nslot_usage:\n items:\n name: items\n range: Association\nname: CategoryGroupedAssociationResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslot_usage:\n items:\n name: items\n range: Association\nattributes:\n counterpart_category:\n name: counterpart_category\n description: The category of the counterpart entity in a given association, eg.\n the category of the entity that is not the subject\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: counterpart_category\n owner: CategoryGroupedAssociationResults\n domain_of:\n - CategoryGroupedAssociationResults\n range: string\n items:\n name: items\n description: A collection of items, with the type to be overriden by slot_usage\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: items\n owner: CategoryGroupedAssociationResults\n domain_of:\n - AssociationCountList\n - AssociationResults\n - CompactAssociationResults\n - AssociationTableResults\n - CategoryGroupedAssociationResults\n - EntityResults\n - HistoPheno\n - MappingResults\n - SearchResults\n range: Association\n required: true\n multivalued: true\n inlined: true\n inlined_as_list: true\n limit:\n name: limit\n description: number of items to return in a response\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: limit\n owner: CategoryGroupedAssociationResults\n domain_of:\n - Results\n range: integer\n required: true\n offset:\n name: offset\n description: offset into the total number of items\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: offset\n owner: CategoryGroupedAssociationResults\n domain_of:\n - Results\n range: integer\n required: true\n total:\n name: total\n description: total number of items matching a query\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: total\n owner: CategoryGroupedAssociationResults\n domain_of:\n - Results\n range: integer\n required: true\nURI: https://w3id.org/monarch/monarch-py/:CompactAssociation
classDiagram\n class CompactAssociation\n click CompactAssociation href \"../CompactAssociation\"\n CompactAssociation : category\n\n CompactAssociation : negated\n\n CompactAssociation : object\n\n CompactAssociation : object_label\n\n CompactAssociation : predicate\n\n CompactAssociation : subject\n\n CompactAssociation : subject_label\nname: CompactAssociation\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- category\n- subject\n- subject_label\n- predicate\n- object\n- object_label\n- negated\nname: CompactAssociation\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n category:\n name: category\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: category\n owner: CompactAssociation\n domain_of:\n - Association\n - AssociationCount\n - CompactAssociation\n - AssociationTypeMapping\n - Entity\n range: string\n multivalued: false\n subject:\n name: subject\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: subject\n owner: CompactAssociation\n domain_of:\n - Association\n - CompactAssociation\n - SemsimSearchResult\n range: string\n required: true\n subject_label:\n name: subject_label\n description: The name of the subject entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: subject_label\n owner: CompactAssociation\n domain_of:\n - Association\n - CompactAssociation\n - AssociationTypeMapping\n - Mapping\n - TermPairwiseSimilarity\n range: string\n predicate:\n name: predicate\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: predicate\n owner: CompactAssociation\n domain_of:\n - Association\n - CompactAssociation\n range: string\n required: true\n multivalued: false\n object:\n name: object\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: object\n owner: CompactAssociation\n domain_of:\n - Association\n - CompactAssociation\n range: string\n required: true\n object_label:\n name: object_label\n description: The name of the object entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: object_label\n owner: CompactAssociation\n domain_of:\n - Association\n - CompactAssociation\n - AssociationTypeMapping\n - Mapping\n - TermPairwiseSimilarity\n range: string\n negated:\n name: negated\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: negated\n owner: CompactAssociation\n domain_of:\n - Association\n - CompactAssociation\n range: boolean\nURI: https://w3id.org/monarch/monarch-py/:CompactAssociationResults
classDiagram\n class CompactAssociationResults\n click CompactAssociationResults href \"../CompactAssociationResults\"\n Results <|-- CompactAssociationResults\n click Results href \"../Results\"\n\n CompactAssociationResults : facet_fields\n\n\n\n\n CompactAssociationResults --> \"*\" FacetField : facet_fields\n click FacetField href \"../FacetField\"\n\n\n CompactAssociationResults : facet_queries\n\n\n\n\n CompactAssociationResults --> \"*\" FacetValue : facet_queries\n click FacetValue href \"../FacetValue\"\n\n\n CompactAssociationResults : items\n\n\n\n\n CompactAssociationResults --> \"1..*\" CompactAssociation : items\n click CompactAssociation href \"../CompactAssociation\"\n\n\n CompactAssociationResults : limit\n\n CompactAssociationResults : offset\n\n CompactAssociationResults : total\nname: CompactAssociationResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslots:\n- items\n- facet_fields\n- facet_queries\nslot_usage:\n items:\n name: items\n range: CompactAssociation\nname: CompactAssociationResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslot_usage:\n items:\n name: items\n range: CompactAssociation\nattributes:\n items:\n name: items\n description: A collection of items, with the type to be overriden by slot_usage\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: items\n owner: CompactAssociationResults\n domain_of:\n - AssociationCountList\n - AssociationResults\n - CompactAssociationResults\n - AssociationTableResults\n - CategoryGroupedAssociationResults\n - EntityResults\n - HistoPheno\n - MappingResults\n - SearchResults\n range: CompactAssociation\n required: true\n multivalued: true\n inlined: true\n inlined_as_list: true\n facet_fields:\n name: facet_fields\n description: Collection of facet field responses with the field values and counts\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: facet_fields\n owner: CompactAssociationResults\n domain_of:\n - AssociationResults\n - CompactAssociationResults\n - AssociationTableResults\n - SearchResults\n range: FacetField\n multivalued: true\n inlined: true\n inlined_as_list: true\n facet_queries:\n name: facet_queries\n description: Collection of facet query responses with the query string values\n and counts\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: facet_queries\n owner: CompactAssociationResults\n domain_of:\n - AssociationResults\n - CompactAssociationResults\n - AssociationTableResults\n - SearchResults\n range: FacetValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n limit:\n name: limit\n description: number of items to return in a response\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: limit\n owner: CompactAssociationResults\n domain_of:\n - Results\n range: integer\n required: true\n offset:\n name: offset\n description: offset into the total number of items\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: offset\n owner: CompactAssociationResults\n domain_of:\n - Results\n range: integer\n required: true\n total:\n name: total\n description: total number of items matching a query\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: total\n owner: CompactAssociationResults\n domain_of:\n - Results\n range: integer\n required: true\na compact URI
URI: xsd:string
base: Curie
uri: xsd:string
repr: str
a date (year, month and day) in an idealized calendar
URI: xsd:date
base: XSDDate
uri: xsd:date
repr: str
Either a date or a datetime
URI: linkml:DateOrDatetime
base: str
uri: linkml:DateOrDatetime
repr: str
The combination of a date and time
URI: xsd:dateTime
base: XSDDateTime
uri: xsd:dateTime
repr: str
A real number with arbitrary precision that conforms to the xsd:decimal specification
URI: xsd:decimal
base: Decimal
uri: xsd:decimal
An association that gives it's direction relative to a specified entity
URI: https://w3id.org/monarch/monarch-py/:DirectionalAssociation
classDiagram\n class DirectionalAssociation\n click DirectionalAssociation href \"../DirectionalAssociation\"\n Association <|-- DirectionalAssociation\n click Association href \"../Association\"\n\n DirectionalAssociation : agent_type\n\n DirectionalAssociation : aggregator_knowledge_source\n\n DirectionalAssociation : category\n\n DirectionalAssociation : direction\n\n\n\n\n DirectionalAssociation --> \"1\" AssociationDirectionEnum : direction\n click AssociationDirectionEnum href \"../AssociationDirectionEnum\"\n\n\n DirectionalAssociation : disease_context_qualifier\n\n DirectionalAssociation : disease_context_qualifier_category\n\n DirectionalAssociation : disease_context_qualifier_closure\n\n DirectionalAssociation : disease_context_qualifier_closure_label\n\n DirectionalAssociation : disease_context_qualifier_label\n\n DirectionalAssociation : disease_context_qualifier_namespace\n\n DirectionalAssociation : evidence_count\n\n DirectionalAssociation : frequency_qualifier\n\n DirectionalAssociation : frequency_qualifier_category\n\n DirectionalAssociation : frequency_qualifier_label\n\n DirectionalAssociation : frequency_qualifier_namespace\n\n DirectionalAssociation : grouping_key\n\n DirectionalAssociation : has_count\n\n DirectionalAssociation : has_evidence\n\n DirectionalAssociation : has_evidence_links\n\n\n\n\n DirectionalAssociation --> \"*\" ExpandedCurie : has_evidence_links\n click ExpandedCurie href \"../ExpandedCurie\"\n\n\n DirectionalAssociation : has_percentage\n\n DirectionalAssociation : has_quotient\n\n DirectionalAssociation : has_total\n\n DirectionalAssociation : id\n\n DirectionalAssociation : knowledge_level\n\n DirectionalAssociation : negated\n\n DirectionalAssociation : object\n\n DirectionalAssociation : object_category\n\n DirectionalAssociation : object_closure\n\n DirectionalAssociation : object_closure_label\n\n DirectionalAssociation : object_label\n\n DirectionalAssociation : object_namespace\n\n DirectionalAssociation : object_taxon\n\n DirectionalAssociation : object_taxon_label\n\n DirectionalAssociation : onset_qualifier\n\n DirectionalAssociation : onset_qualifier_category\n\n DirectionalAssociation : onset_qualifier_label\n\n DirectionalAssociation : onset_qualifier_namespace\n\n DirectionalAssociation : original_object\n\n DirectionalAssociation : original_subject\n\n DirectionalAssociation : pathway\n\n DirectionalAssociation : predicate\n\n DirectionalAssociation : primary_knowledge_source\n\n DirectionalAssociation : provided_by\n\n DirectionalAssociation : provided_by_link\n\n\n\n\n DirectionalAssociation --> \"0..1\" ExpandedCurie : provided_by_link\n click ExpandedCurie href \"../ExpandedCurie\"\n\n\n DirectionalAssociation : publications\n\n DirectionalAssociation : publications_links\n\n\n\n\n DirectionalAssociation --> \"*\" ExpandedCurie : publications_links\n click ExpandedCurie href \"../ExpandedCurie\"\n\n\n DirectionalAssociation : qualifier\n\n DirectionalAssociation : qualifier_category\n\n DirectionalAssociation : qualifier_label\n\n DirectionalAssociation : qualifier_namespace\n\n DirectionalAssociation : qualifiers\n\n DirectionalAssociation : qualifiers_category\n\n DirectionalAssociation : qualifiers_label\n\n DirectionalAssociation : qualifiers_namespace\n\n DirectionalAssociation : sex_qualifier\n\n DirectionalAssociation : sex_qualifier_category\n\n DirectionalAssociation : sex_qualifier_label\n\n DirectionalAssociation : sex_qualifier_namespace\n\n DirectionalAssociation : species_context_qualifier\n\n DirectionalAssociation : species_context_qualifier_category\n\n DirectionalAssociation : species_context_qualifier_label\n\n DirectionalAssociation : species_context_qualifier_namespace\n\n DirectionalAssociation : stage_qualifier\n\n DirectionalAssociation : stage_qualifier_category\n\n DirectionalAssociation : stage_qualifier_label\n\n DirectionalAssociation : stage_qualifier_namespace\n\n DirectionalAssociation : subject\n\n DirectionalAssociation : subject_category\n\n DirectionalAssociation : subject_closure\n\n DirectionalAssociation : subject_closure_label\n\n DirectionalAssociation : subject_label\n\n DirectionalAssociation : subject_namespace\n\n DirectionalAssociation : subject_taxon\n\n DirectionalAssociation : subject_taxon_label\nname: DirectionalAssociation\ndescription: An association that gives it's direction relative to a specified entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Association\nslots:\n- direction\nname: DirectionalAssociation\ndescription: An association that gives it's direction relative to a specified entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Association\nattributes:\n direction:\n name: direction\n description: The directionality of the association relative to a given entity\n for an association_count. If the entity is the subject or in the subject closure,\n the direction is forwards, if it is the object or in the object closure, the\n direction is backwards.\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: direction\n owner: DirectionalAssociation\n domain_of:\n - DirectionalAssociation\n range: AssociationDirectionEnum\n required: true\n id:\n name: id\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n identifier: true\n alias: id\n owner: DirectionalAssociation\n domain_of:\n - Association\n - ExpandedCurie\n - Entity\n - HistoPheno\n - HistoBin\n - Mapping\n - MultiEntityAssociationResults\n - TermInfo\n range: string\n required: true\n category:\n name: category\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: category\n owner: DirectionalAssociation\n domain_of:\n - Association\n - AssociationCount\n - CompactAssociation\n - AssociationTypeMapping\n - Entity\n range: string\n multivalued: false\n subject:\n name: subject\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: subject\n owner: DirectionalAssociation\n domain_of:\n - Association\n - CompactAssociation\n - SemsimSearchResult\n range: string\n required: true\n original_subject:\n name: original_subject\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: original_subject\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n subject_namespace:\n name: subject_namespace\n description: The namespace/prefix of the subject entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: subject_namespace\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n subject_category:\n name: subject_category\n description: The category of the subject entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: category\n alias: subject_category\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n subject_closure:\n name: subject_closure\n description: Field containing subject id and the ids of all of it's ancestors\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: subject_closure\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n multivalued: true\n subject_label:\n name: subject_label\n description: The name of the subject entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: subject_label\n owner: DirectionalAssociation\n domain_of:\n - Association\n - CompactAssociation\n - AssociationTypeMapping\n - Mapping\n - TermPairwiseSimilarity\n range: string\n subject_closure_label:\n name: subject_closure_label\n description: Field containing subject name and the names of all of it's ancestors\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: subject_closure_label\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n multivalued: true\n subject_taxon:\n name: subject_taxon\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: in_taxon\n alias: subject_taxon\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n subject_taxon_label:\n name: subject_taxon_label\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: in_taxon_label\n alias: subject_taxon_label\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n predicate:\n name: predicate\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: predicate\n owner: DirectionalAssociation\n domain_of:\n - Association\n - CompactAssociation\n range: string\n required: true\n multivalued: false\n object:\n name: object\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: object\n owner: DirectionalAssociation\n domain_of:\n - Association\n - CompactAssociation\n range: string\n required: true\n original_object:\n name: original_object\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: original_object\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n object_namespace:\n name: object_namespace\n description: The namespace/prefix of the object entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: object_namespace\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n object_category:\n name: object_category\n description: The category of the object entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: category\n alias: object_category\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n object_closure:\n name: object_closure\n description: Field containing object id and the ids of all of it's ancestors\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: object_closure\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n multivalued: true\n object_label:\n name: object_label\n description: The name of the object entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: object_label\n owner: DirectionalAssociation\n domain_of:\n - Association\n - CompactAssociation\n - AssociationTypeMapping\n - Mapping\n - TermPairwiseSimilarity\n range: string\n object_closure_label:\n name: object_closure_label\n description: Field containing object name and the names of all of it's ancestors\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: object_closure_label\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n multivalued: true\n object_taxon:\n name: object_taxon\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: in_taxon\n alias: object_taxon\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n object_taxon_label:\n name: object_taxon_label\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: in_taxon_label\n alias: object_taxon_label\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n primary_knowledge_source:\n name: primary_knowledge_source\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: primary_knowledge_source\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n aggregator_knowledge_source:\n name: aggregator_knowledge_source\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: aggregator_knowledge_source\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n multivalued: true\n negated:\n name: negated\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: negated\n owner: DirectionalAssociation\n domain_of:\n - Association\n - CompactAssociation\n range: boolean\n pathway:\n name: pathway\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: pathway\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n evidence_count:\n name: evidence_count\n description: count of supporting documents, evidence codes, and sources supplying\n evidence\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: evidence_count\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: integer\n knowledge_level:\n name: knowledge_level\n description: Describes the level of knowledge expressed in a statement, based\n on the reasoning or analysis methods used to generate the statement, or the\n scope or specificity of what the statement expresses to be true.\n notes:\n - The range in this schema is represented as a string, but is constrained to\n values from biolink:KnowledgeLevelEnum at ingest time\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n slot_uri: biolink:knowledge_level\n alias: knowledge_level\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n required: true\n multivalued: false\n agent_type:\n name: agent_type\n description: Describes the high-level category of agent who originally generated\n a statement of knowledge or other type of information.\n notes:\n - The range in this schema is represented as a string, but is constrained to\n values from biolink:AgentTypeEnum at ingest time\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n slot_uri: biolink:agent_type\n alias: agent_type\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n required: true\n multivalued: false\n has_evidence:\n name: has_evidence\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_evidence\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n multivalued: true\n has_evidence_links:\n name: has_evidence_links\n description: List of ExpandedCuries with id and url for evidence\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_evidence_links\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: ExpandedCurie\n multivalued: true\n inlined: true\n inlined_as_list: true\n has_count:\n name: has_count\n description: count of out of has_total representing a frequency\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_count\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: integer\n has_total:\n name: has_total\n description: total, devided by has_count, representing a frequency\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_total\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: integer\n has_percentage:\n name: has_percentage\n description: percentage, which may be calculated from has_count and has_total,\n as 100 * quotient or provided directly, rounded to the integer level\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_percentage\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: float\n has_quotient:\n name: has_quotient\n description: quotient, which should be 1/100 of has_percentage\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_quotient\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: float\n grouping_key:\n name: grouping_key\n description: A concatenation of fields used to group associations with the same\n essential/defining properties\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: grouping_key\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n provided_by:\n name: provided_by\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: provided_by\n owner: DirectionalAssociation\n domain_of:\n - Association\n - Entity\n range: string\n provided_by_link:\n name: provided_by_link\n description: A link to the docs for the knowledge source that provided the node/edge.\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: provided_by_link\n owner: DirectionalAssociation\n domain_of:\n - Association\n - Node\n range: ExpandedCurie\n inlined: true\n publications:\n name: publications\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: publications\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n multivalued: true\n publications_links:\n name: publications_links\n description: List of ExpandedCuries with id and url for publications\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: publications_links\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: ExpandedCurie\n multivalued: true\n inlined: true\n inlined_as_list: true\n frequency_qualifier:\n name: frequency_qualifier\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: frequency_qualifier\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n onset_qualifier:\n name: onset_qualifier\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: onset_qualifier\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n sex_qualifier:\n name: sex_qualifier\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: sex_qualifier\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n stage_qualifier:\n name: stage_qualifier\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: stage_qualifier\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n qualifiers:\n name: qualifiers\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: qualifiers\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n multivalued: true\n qualifiers_label:\n name: qualifiers_label\n description: The name of the frequency_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: qualifiers_label\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n qualifiers_namespace:\n name: qualifiers_namespace\n description: The namespace/prefix of the frequency_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: qualifiers_namespace\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n qualifiers_category:\n name: qualifiers_category\n description: The category of the frequency_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: category\n alias: qualifiers_category\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n qualifier:\n name: qualifier\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: qualifier\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n multivalued: true\n qualifier_label:\n name: qualifier_label\n description: The name of the frequency_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: qualifier_label\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n qualifier_namespace:\n name: qualifier_namespace\n description: The namespace/prefix of the frequency_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: qualifier_namespace\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n qualifier_category:\n name: qualifier_category\n description: The category of the frequency_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: category\n alias: qualifier_category\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n frequency_qualifier_label:\n name: frequency_qualifier_label\n description: The name of the frequency_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: frequency_qualifier_label\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n frequency_qualifier_namespace:\n name: frequency_qualifier_namespace\n description: The namespace/prefix of the frequency_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: frequency_qualifier_namespace\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n frequency_qualifier_category:\n name: frequency_qualifier_category\n description: The category of the frequency_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: category\n alias: frequency_qualifier_category\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n onset_qualifier_label:\n name: onset_qualifier_label\n description: The name of the onset_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: onset_qualifier_label\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n onset_qualifier_namespace:\n name: onset_qualifier_namespace\n description: The namespace/prefix of the onset_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: onset_qualifier_namespace\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n onset_qualifier_category:\n name: onset_qualifier_category\n description: The category of the onset_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: category\n alias: onset_qualifier_category\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n sex_qualifier_label:\n name: sex_qualifier_label\n description: The name of the sex_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: sex_qualifier_label\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n sex_qualifier_namespace:\n name: sex_qualifier_namespace\n description: The namespace/prefix of the sex_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: sex_qualifier_namespace\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n sex_qualifier_category:\n name: sex_qualifier_category\n description: The category of the sex_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: category\n alias: sex_qualifier_category\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n stage_qualifier_label:\n name: stage_qualifier_label\n description: The name of the stage_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: stage_qualifier_label\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n stage_qualifier_namespace:\n name: stage_qualifier_namespace\n description: The namespace/prefix of the stage_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: stage_qualifier_namespace\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n stage_qualifier_category:\n name: stage_qualifier_category\n description: The category of the stage_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: category\n alias: stage_qualifier_category\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n disease_context_qualifier:\n name: disease_context_qualifier\n description: A context qualifier representing a disease or condition in which\n a relationship expressed in an association took place.\n examples:\n - value: MONDO:0004979\n - value: MONDO:0005148\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: disease_context_qualifier\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n disease_context_qualifier_label:\n name: disease_context_qualifier_label\n description: The name of the disease_context_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: disease_context_qualifier_label\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n disease_context_qualifier_namespace:\n name: disease_context_qualifier_namespace\n description: The namespace/prefix of the disease_context_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: disease_context_qualifier_namespace\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n disease_context_qualifier_category:\n name: disease_context_qualifier_category\n description: The category of the disease_context_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: category\n alias: disease_context_qualifier_category\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n disease_context_qualifier_closure:\n name: disease_context_qualifier_closure\n description: Field containing disease_context_qualifier id and the ids of all\n of it's ancestors\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: disease_context_qualifier_closure\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n multivalued: true\n disease_context_qualifier_closure_label:\n name: disease_context_qualifier_closure_label\n description: Field containing disease_context_qualifier name and the names of\n all of it's ancestors\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: disease_context_qualifier_closure_label\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n multivalued: true\n species_context_qualifier:\n name: species_context_qualifier\n description: A context qualifier representing a species in which a relationship\n expressed in an association took place.\n examples:\n - value: NCBITaxon:9606\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: species_context_qualifier\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n species_context_qualifier_label:\n name: species_context_qualifier_label\n description: The name of the species_context_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: species_context_qualifier_label\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n species_context_qualifier_namespace:\n name: species_context_qualifier_namespace\n description: The namespace/prefix of the species_context_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: species_context_qualifier_namespace\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\n species_context_qualifier_category:\n name: species_context_qualifier_category\n description: The category of the species_context_qualifier entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: category\n alias: species_context_qualifier_category\n owner: DirectionalAssociation\n domain_of:\n - Association\n range: string\nA real number that conforms to the xsd:double specification
URI: xsd:double
base: float
uri: xsd:double
Represents an Entity in the Monarch KG data model
URI: https://w3id.org/monarch/monarch-py/:Entity
classDiagram\n class Entity\n click Entity href \"../Entity\"\n Entity <|-- Node\n click Node href \"../Node\"\n Entity <|-- SearchResult\n click SearchResult href \"../SearchResult\"\n\n Entity : category\n\n Entity : deprecated\n\n Entity : description\n\n Entity : full_name\n\n Entity : has_phenotype\n\n Entity : has_phenotype_closure\n\n Entity : has_phenotype_closure_label\n\n Entity : has_phenotype_count\n\n Entity : has_phenotype_label\n\n Entity : id\n\n Entity : in_taxon\n\n Entity : in_taxon_label\n\n Entity : iri\n\n Entity : name\n\n Entity : namespace\n\n Entity : provided_by\n\n Entity : symbol\n\n Entity : synonym\n\n Entity : uri\n\n Entity : xref\nname: Entity\ndescription: Represents an Entity in the Monarch KG data model\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- id\n- category\n- name\n- full_name\n- deprecated\n- description\n- xref\n- provided_by\n- in_taxon\n- in_taxon_label\n- symbol\n- synonym\n- uri\n- iri\n- namespace\n- has_phenotype\n- has_phenotype_label\n- has_phenotype_closure\n- has_phenotype_closure_label\n- has_phenotype_count\nname: Entity\ndescription: Represents an Entity in the Monarch KG data model\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n id:\n name: id\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n identifier: true\n alias: id\n owner: Entity\n domain_of:\n - Association\n - ExpandedCurie\n - Entity\n - HistoPheno\n - HistoBin\n - Mapping\n - MultiEntityAssociationResults\n - TermInfo\n range: string\n required: true\n category:\n name: category\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: category\n owner: Entity\n domain_of:\n - Association\n - AssociationCount\n - CompactAssociation\n - AssociationTypeMapping\n - Entity\n range: string\n multivalued: false\n name:\n name: name\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: name\n owner: Entity\n domain_of:\n - Entity\n - MultiEntityAssociationResults\n range: string\n full_name:\n name: full_name\n description: The long form name of an entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: full_name\n owner: Entity\n domain_of:\n - Entity\n range: string\n deprecated:\n name: deprecated\n description: A boolean flag indicating that an entity is no longer considered\n current or valid.\n from_schema: https://w3id.org/monarch/monarch-py\n exact_mappings:\n - oboInOwl:ObsoleteClass\n rank: 1000\n alias: deprecated\n owner: Entity\n domain_of:\n - Entity\n range: boolean\n description:\n name: description\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: description\n owner: Entity\n domain_of:\n - Entity\n range: string\n xref:\n name: xref\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: xref\n owner: Entity\n domain_of:\n - Entity\n range: string\n multivalued: true\n provided_by:\n name: provided_by\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: provided_by\n owner: Entity\n domain_of:\n - Association\n - Entity\n range: string\n in_taxon:\n name: in_taxon\n description: The biolink taxon that the entity is in the closure of.\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: in_taxon\n owner: Entity\n domain_of:\n - Entity\n - Node\n range: string\n in_taxon_label:\n name: in_taxon_label\n description: The label of the biolink taxon that the entity is in the closure\n of.\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: in_taxon_label\n owner: Entity\n domain_of:\n - Entity\n - Node\n range: string\n symbol:\n name: symbol\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: symbol\n owner: Entity\n domain_of:\n - Entity\n range: string\n synonym:\n name: synonym\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: synonym\n owner: Entity\n domain_of:\n - Entity\n range: string\n multivalued: true\n uri:\n name: uri\n description: The URI of the entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: uri\n owner: Entity\n domain_of:\n - Entity\n range: string\n iri:\n name: iri\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: iri\n owner: Entity\n domain_of:\n - Entity\n range: string\n namespace:\n name: namespace\n description: The namespace/prefix portion of this entity's identifier\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: namespace\n owner: Entity\n domain_of:\n - Entity\n range: string\n has_phenotype:\n name: has_phenotype\n description: A list of phenotype identifiers that are known to be associated with\n this entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_phenotype\n owner: Entity\n domain_of:\n - Entity\n range: string\n multivalued: true\n inlined: true\n inlined_as_list: true\n has_phenotype_label:\n name: has_phenotype_label\n description: A list of phenotype labels that are known to be associated with this\n entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_phenotype_label\n owner: Entity\n domain_of:\n - Entity\n range: string\n multivalued: true\n inlined: true\n inlined_as_list: true\n has_phenotype_closure:\n name: has_phenotype_closure\n description: A list of phenotype identifiers that are known to be associated with\n this entity expanded to include all ancestors\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_phenotype_closure\n owner: Entity\n domain_of:\n - Entity\n range: string\n multivalued: true\n inlined: true\n inlined_as_list: true\n has_phenotype_closure_label:\n name: has_phenotype_closure_label\n description: A list of phenotype labels that are known to be associated with this\n entity expanded to include all ancestors\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_phenotype_closure_label\n owner: Entity\n domain_of:\n - Entity\n range: string\n multivalued: true\n inlined: true\n inlined_as_list: true\n has_phenotype_count:\n name: has_phenotype_count\n description: A count of the number of phenotypes that are known to be associated\n with this entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_phenotype_count\n owner: Entity\n domain_of:\n - Entity\n range: integer\nURI: https://w3id.org/monarch/monarch-py/:EntityResults
classDiagram\n class EntityResults\n click EntityResults href \"../EntityResults\"\n Results <|-- EntityResults\n click Results href \"../Results\"\n\n EntityResults : items\n\n\n\n\n EntityResults --> \"1..*\" Entity : items\n click Entity href \"../Entity\"\n\n\n EntityResults : limit\n\n EntityResults : offset\n\n EntityResults : total\nname: EntityResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslots:\n- items\nslot_usage:\n items:\n name: items\n range: Entity\nname: EntityResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslot_usage:\n items:\n name: items\n range: Entity\nattributes:\n items:\n name: items\n description: A collection of items, with the type to be overriden by slot_usage\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: items\n owner: EntityResults\n domain_of:\n - AssociationCountList\n - AssociationResults\n - CompactAssociationResults\n - AssociationTableResults\n - CategoryGroupedAssociationResults\n - EntityResults\n - HistoPheno\n - MappingResults\n - SearchResults\n range: Entity\n required: true\n multivalued: true\n inlined: true\n inlined_as_list: true\n limit:\n name: limit\n description: number of items to return in a response\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: limit\n owner: EntityResults\n domain_of:\n - Results\n range: integer\n required: true\n offset:\n name: offset\n description: offset into the total number of items\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: offset\n owner: EntityResults\n domain_of:\n - Results\n range: integer\n required: true\n total:\n name: total\n description: total number of items matching a query\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: total\n owner: EntityResults\n domain_of:\n - Results\n range: integer\n required: true\nA curie bundled along with its expanded url
URI: https://w3id.org/monarch/monarch-py/:ExpandedCurie
classDiagram\n class ExpandedCurie\n click ExpandedCurie href \"../ExpandedCurie\"\n ExpandedCurie : id\n\n ExpandedCurie : url\nname: ExpandedCurie\ndescription: A curie bundled along with its expanded url\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- id\n- url\nname: ExpandedCurie\ndescription: A curie bundled along with its expanded url\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n id:\n name: id\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n identifier: true\n alias: id\n owner: ExpandedCurie\n domain_of:\n - Association\n - ExpandedCurie\n - Entity\n - HistoPheno\n - HistoBin\n - Mapping\n - MultiEntityAssociationResults\n - TermInfo\n range: string\n required: true\n url:\n name: url\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: url\n owner: ExpandedCurie\n domain_of:\n - ExpandedCurie\n - Release\n range: string\nURI: https://w3id.org/monarch/monarch-py/:FacetField
classDiagram\n class FacetField\n click FacetField href \"../FacetField\"\n FacetField : facet_values\n\n\n\n\n FacetField --> \"*\" FacetValue : facet_values\n click FacetValue href \"../FacetValue\"\n\n\n FacetField : label\nname: FacetField\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- label\n- facet_values\nname: FacetField\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n label:\n name: label\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: label\n owner: FacetField\n domain_of:\n - FacetValue\n - FacetField\n - TermInfo\n range: string\n required: true\n facet_values:\n name: facet_values\n description: Collection of FacetValue label/value instances belonging to a FacetField\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: facet_values\n owner: FacetField\n domain_of:\n - FacetField\n range: FacetValue\n multivalued: true\n inlined: true\n inlined_as_list: true\nURI: https://w3id.org/monarch/monarch-py/:FacetValue
classDiagram\n class FacetValue\n click FacetValue href \"../FacetValue\"\n FacetValue <|-- AssociationCount\n click AssociationCount href \"../AssociationCount\"\n FacetValue <|-- HistoBin\n click HistoBin href \"../HistoBin\"\n\n FacetValue : count\n\n FacetValue : label\nname: FacetValue\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- label\n- count\nname: FacetValue\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n label:\n name: label\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: label\n owner: FacetValue\n domain_of:\n - FacetValue\n - FacetField\n - TermInfo\n range: string\n required: true\n count:\n name: count\n description: count of documents\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: count\n owner: FacetValue\n domain_of:\n - FacetValue\n range: integer\nA real number that conforms to the xsd:float specification
URI: xsd:float
base: float
uri: xsd:float
URI: https://w3id.org/monarch/monarch-py/:HistoBin
classDiagram\n class HistoBin\n click HistoBin href \"../HistoBin\"\n FacetValue <|-- HistoBin\n click FacetValue href \"../FacetValue\"\n\n HistoBin : count\n\n HistoBin : id\n\n HistoBin : label\nname: HistoBin\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: FacetValue\nslots:\n- id\nname: HistoBin\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: FacetValue\nattributes:\n id:\n name: id\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n identifier: true\n alias: id\n owner: HistoBin\n domain_of:\n - Association\n - ExpandedCurie\n - Entity\n - HistoPheno\n - HistoBin\n - Mapping\n - MultiEntityAssociationResults\n - TermInfo\n range: string\n required: true\n label:\n name: label\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: label\n owner: HistoBin\n domain_of:\n - FacetValue\n - FacetField\n - TermInfo\n range: string\n required: true\n count:\n name: count\n description: count of documents\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: count\n owner: HistoBin\n domain_of:\n - FacetValue\n range: integer\nURI: https://w3id.org/monarch/monarch-py/:HistoPheno
classDiagram\n class HistoPheno\n click HistoPheno href \"../HistoPheno\"\n HistoPheno : id\n\n HistoPheno : items\n\n\n\n\n HistoPheno --> \"1..*\" HistoBin : items\n click HistoBin href \"../HistoBin\"\nname: HistoPheno\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- id\n- items\nslot_usage:\n items:\n name: items\n range: HistoBin\nname: HistoPheno\nfrom_schema: https://w3id.org/monarch/monarch-py\nslot_usage:\n items:\n name: items\n range: HistoBin\nattributes:\n id:\n name: id\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n identifier: true\n alias: id\n owner: HistoPheno\n domain_of:\n - Association\n - ExpandedCurie\n - Entity\n - HistoPheno\n - HistoBin\n - Mapping\n - MultiEntityAssociationResults\n - TermInfo\n range: string\n required: true\n items:\n name: items\n description: A collection of items, with the type to be overriden by slot_usage\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: items\n owner: HistoPheno\n domain_of:\n - AssociationCountList\n - AssociationResults\n - CompactAssociationResults\n - AssociationTableResults\n - CategoryGroupedAssociationResults\n - EntityResults\n - HistoPheno\n - MappingResults\n - SearchResults\n range: HistoBin\n required: true\n multivalued: true\n inlined: true\n inlined_as_list: true\nAn integer
URI: xsd:integer
base: int
uri: xsd:integer
URI: xsd:integer
base: int
uri: xsd:integer
typeof: integer
A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.
URI: xsd:string
base: str
uri: xsd:string
repr: str
A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.
URI: xsd:string
base: str
uri: xsd:string
repr: str
A minimal class to hold a SSSOM mapping
URI: https://w3id.org/monarch/monarch-py/:Mapping
classDiagram\n class Mapping\n click Mapping href \"../Mapping\"\n Mapping : id\n\n Mapping : mapping_justification\n\n Mapping : object_id\n\n Mapping : object_label\n\n Mapping : predicate_id\n\n Mapping : subject_id\n\n Mapping : subject_label\nname: Mapping\ndescription: A minimal class to hold a SSSOM mapping\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- subject_id\n- subject_label\n- predicate_id\n- object_id\n- object_label\n- mapping_justification\n- id\nname: Mapping\ndescription: A minimal class to hold a SSSOM mapping\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n subject_id:\n name: subject_id\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: subject_id\n owner: Mapping\n domain_of:\n - Mapping\n - TermPairwiseSimilarity\n range: string\n required: true\n subject_label:\n name: subject_label\n description: The name of the subject entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: subject_label\n owner: Mapping\n domain_of:\n - Association\n - CompactAssociation\n - AssociationTypeMapping\n - Mapping\n - TermPairwiseSimilarity\n range: string\n predicate_id:\n name: predicate_id\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: predicate_id\n owner: Mapping\n domain_of:\n - Mapping\n range: string\n required: true\n object_id:\n name: object_id\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: object_id\n owner: Mapping\n domain_of:\n - Mapping\n - TermPairwiseSimilarity\n range: string\n required: true\n object_label:\n name: object_label\n description: The name of the object entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: object_label\n owner: Mapping\n domain_of:\n - Association\n - CompactAssociation\n - AssociationTypeMapping\n - Mapping\n - TermPairwiseSimilarity\n range: string\n mapping_justification:\n name: mapping_justification\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: mapping_justification\n owner: Mapping\n domain_of:\n - Mapping\n range: string\n id:\n name: id\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n identifier: true\n alias: id\n owner: Mapping\n domain_of:\n - Association\n - ExpandedCurie\n - Entity\n - HistoPheno\n - HistoBin\n - Mapping\n - MultiEntityAssociationResults\n - TermInfo\n range: string\n required: true\nSSSOM Mappings returned as a results collection
URI: https://w3id.org/monarch/monarch-py/:MappingResults
classDiagram\n class MappingResults\n click MappingResults href \"../MappingResults\"\n Results <|-- MappingResults\n click Results href \"../Results\"\n\n MappingResults : items\n\n\n\n\n MappingResults --> \"1..*\" Mapping : items\n click Mapping href \"../Mapping\"\n\n\n MappingResults : limit\n\n MappingResults : offset\n\n MappingResults : total\nname: MappingResults\ndescription: SSSOM Mappings returned as a results collection\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslots:\n- items\nslot_usage:\n items:\n name: items\n range: Mapping\nname: MappingResults\ndescription: SSSOM Mappings returned as a results collection\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslot_usage:\n items:\n name: items\n range: Mapping\nattributes:\n items:\n name: items\n description: A collection of items, with the type to be overriden by slot_usage\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: items\n owner: MappingResults\n domain_of:\n - AssociationCountList\n - AssociationResults\n - CompactAssociationResults\n - AssociationTableResults\n - CategoryGroupedAssociationResults\n - EntityResults\n - HistoPheno\n - MappingResults\n - SearchResults\n range: Mapping\n required: true\n multivalued: true\n inlined: true\n inlined_as_list: true\n limit:\n name: limit\n description: number of items to return in a response\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: limit\n owner: MappingResults\n domain_of:\n - Results\n range: integer\n required: true\n offset:\n name: offset\n description: offset into the total number of items\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: offset\n owner: MappingResults\n domain_of:\n - Results\n range: integer\n required: true\n total:\n name: total\n description: total number of items matching a query\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: total\n owner: MappingResults\n domain_of:\n - Results\n range: integer\n required: true\nURI: https://w3id.org/monarch/monarch-py/:MultiEntityAssociationResults
classDiagram\n class MultiEntityAssociationResults\n click MultiEntityAssociationResults href \"../MultiEntityAssociationResults\"\n Results <|-- MultiEntityAssociationResults\n click Results href \"../Results\"\n\n MultiEntityAssociationResults : associated_categories\n\n\n\n\n MultiEntityAssociationResults --> \"1..*\" CategoryGroupedAssociationResults : associated_categories\n click CategoryGroupedAssociationResults href \"../CategoryGroupedAssociationResults\"\n\n\n MultiEntityAssociationResults : id\n\n MultiEntityAssociationResults : limit\n\n MultiEntityAssociationResults : name\n\n MultiEntityAssociationResults : offset\n\n MultiEntityAssociationResults : total\nname: MultiEntityAssociationResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslots:\n- id\n- name\n- associated_categories\nname: MultiEntityAssociationResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nattributes:\n id:\n name: id\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n identifier: true\n alias: id\n owner: MultiEntityAssociationResults\n domain_of:\n - Association\n - ExpandedCurie\n - Entity\n - HistoPheno\n - HistoBin\n - Mapping\n - MultiEntityAssociationResults\n - TermInfo\n range: string\n required: true\n name:\n name: name\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: name\n owner: MultiEntityAssociationResults\n domain_of:\n - Entity\n - MultiEntityAssociationResults\n range: string\n associated_categories:\n name: associated_categories\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: associated_categories\n owner: MultiEntityAssociationResults\n domain_of:\n - MultiEntityAssociationResults\n range: CategoryGroupedAssociationResults\n required: true\n multivalued: true\n inlined: true\n inlined_as_list: true\n limit:\n name: limit\n description: number of items to return in a response\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: limit\n owner: MultiEntityAssociationResults\n domain_of:\n - Results\n range: integer\n required: true\n offset:\n name: offset\n description: offset into the total number of items\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: offset\n owner: MultiEntityAssociationResults\n domain_of:\n - Results\n range: integer\n required: true\n total:\n name: total\n description: total number of items matching a query\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: total\n owner: MultiEntityAssociationResults\n domain_of:\n - Results\n range: integer\n required: true\nPrefix part of CURIE
URI: xsd:string
base: NCName
uri: xsd:string
repr: str
URI: xsd:float
base: float
uri: xsd:float
typeof: float
UI container class extending Entity with additional information
URI: https://w3id.org/monarch/monarch-py/:Node
classDiagram\n class Node\n click Node href \"../Node\"\n Entity <|-- Node\n click Entity href \"../Entity\"\n\n Node : association_counts\n\n\n\n\n Node --> \"1..*\" AssociationCount : association_counts\n click AssociationCount href \"../AssociationCount\"\n\n\n Node : category\n\n Node : causal_gene\n\n\n\n\n Node --> \"*\" Entity : causal_gene\n click Entity href \"../Entity\"\n\n\n Node : causes_disease\n\n\n\n\n Node --> \"*\" Entity : causes_disease\n click Entity href \"../Entity\"\n\n\n Node : deprecated\n\n Node : description\n\n Node : external_links\n\n\n\n\n Node --> \"*\" ExpandedCurie : external_links\n click ExpandedCurie href \"../ExpandedCurie\"\n\n\n Node : full_name\n\n Node : has_phenotype\n\n Node : has_phenotype_closure\n\n Node : has_phenotype_closure_label\n\n Node : has_phenotype_count\n\n Node : has_phenotype_label\n\n Node : id\n\n Node : in_taxon\n\n Node : in_taxon_label\n\n Node : inheritance\n\n\n\n\n Node --> \"0..1\" Entity : inheritance\n click Entity href \"../Entity\"\n\n\n Node : iri\n\n Node : mappings\n\n\n\n\n Node --> \"*\" ExpandedCurie : mappings\n click ExpandedCurie href \"../ExpandedCurie\"\n\n\n Node : name\n\n Node : namespace\n\n Node : node_hierarchy\n\n\n\n\n Node --> \"0..1\" NodeHierarchy : node_hierarchy\n click NodeHierarchy href \"../NodeHierarchy\"\n\n\n Node : provided_by\n\n Node : provided_by_link\n\n\n\n\n Node --> \"0..1\" ExpandedCurie : provided_by_link\n click ExpandedCurie href \"../ExpandedCurie\"\n\n\n Node : symbol\n\n Node : synonym\n\n Node : uri\n\n Node : xref\nname: Node\ndescription: UI container class extending Entity with additional information\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Entity\nslots:\n- in_taxon\n- in_taxon_label\n- inheritance\n- causal_gene\n- causes_disease\n- mappings\n- external_links\n- provided_by_link\n- association_counts\n- node_hierarchy\nname: Node\ndescription: UI container class extending Entity with additional information\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Entity\nattributes:\n in_taxon:\n name: in_taxon\n description: The biolink taxon that the entity is in the closure of.\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: in_taxon\n owner: Node\n domain_of:\n - Entity\n - Node\n range: string\n in_taxon_label:\n name: in_taxon_label\n description: The label of the biolink taxon that the entity is in the closure\n of.\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: in_taxon_label\n owner: Node\n domain_of:\n - Entity\n - Node\n range: string\n inheritance:\n name: inheritance\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: inheritance\n owner: Node\n domain_of:\n - Node\n range: Entity\n inlined: true\n causal_gene:\n name: causal_gene\n description: A list of genes that are known to be causally associated with a disease\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: causal_gene\n owner: Node\n domain_of:\n - Node\n range: Entity\n multivalued: true\n inlined: true\n inlined_as_list: true\n causes_disease:\n name: causes_disease\n description: A list of diseases that are known to be causally associated with\n a gene\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: causes_disease\n owner: Node\n domain_of:\n - Node\n range: Entity\n multivalued: true\n inlined: true\n inlined_as_list: true\n mappings:\n name: mappings\n description: List of ExpandedCuries with id and url for mapped entities\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: mappings\n owner: Node\n domain_of:\n - Node\n range: ExpandedCurie\n multivalued: true\n inlined: true\n inlined_as_list: true\n external_links:\n name: external_links\n description: ExpandedCurie with id and url for xrefs\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: external_links\n owner: Node\n domain_of:\n - Node\n range: ExpandedCurie\n multivalued: true\n inlined: true\n inlined_as_list: true\n provided_by_link:\n name: provided_by_link\n description: A link to the docs for the knowledge source that provided the node/edge.\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: provided_by_link\n owner: Node\n domain_of:\n - Association\n - Node\n range: ExpandedCurie\n inlined: true\n association_counts:\n name: association_counts\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: association_counts\n owner: Node\n domain_of:\n - Node\n range: AssociationCount\n required: true\n multivalued: true\n inlined: true\n inlined_as_list: true\n node_hierarchy:\n name: node_hierarchy\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: node_hierarchy\n owner: Node\n domain_of:\n - Node\n range: NodeHierarchy\n inlined: true\n id:\n name: id\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n identifier: true\n alias: id\n owner: Node\n domain_of:\n - Association\n - ExpandedCurie\n - Entity\n - HistoPheno\n - HistoBin\n - Mapping\n - MultiEntityAssociationResults\n - TermInfo\n range: string\n required: true\n category:\n name: category\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: category\n owner: Node\n domain_of:\n - Association\n - AssociationCount\n - CompactAssociation\n - AssociationTypeMapping\n - Entity\n range: string\n multivalued: false\n name:\n name: name\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: name\n owner: Node\n domain_of:\n - Entity\n - MultiEntityAssociationResults\n range: string\n full_name:\n name: full_name\n description: The long form name of an entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: full_name\n owner: Node\n domain_of:\n - Entity\n range: string\n deprecated:\n name: deprecated\n description: A boolean flag indicating that an entity is no longer considered\n current or valid.\n from_schema: https://w3id.org/monarch/monarch-py\n exact_mappings:\n - oboInOwl:ObsoleteClass\n rank: 1000\n alias: deprecated\n owner: Node\n domain_of:\n - Entity\n range: boolean\n description:\n name: description\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: description\n owner: Node\n domain_of:\n - Entity\n range: string\n xref:\n name: xref\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: xref\n owner: Node\n domain_of:\n - Entity\n range: string\n multivalued: true\n provided_by:\n name: provided_by\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: provided_by\n owner: Node\n domain_of:\n - Association\n - Entity\n range: string\n symbol:\n name: symbol\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: symbol\n owner: Node\n domain_of:\n - Entity\n range: string\n synonym:\n name: synonym\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: synonym\n owner: Node\n domain_of:\n - Entity\n range: string\n multivalued: true\n uri:\n name: uri\n description: The URI of the entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: uri\n owner: Node\n domain_of:\n - Entity\n range: string\n iri:\n name: iri\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: iri\n owner: Node\n domain_of:\n - Entity\n range: string\n namespace:\n name: namespace\n description: The namespace/prefix portion of this entity's identifier\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: namespace\n owner: Node\n domain_of:\n - Entity\n range: string\n has_phenotype:\n name: has_phenotype\n description: A list of phenotype identifiers that are known to be associated with\n this entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_phenotype\n owner: Node\n domain_of:\n - Entity\n range: string\n multivalued: true\n inlined: true\n inlined_as_list: true\n has_phenotype_label:\n name: has_phenotype_label\n description: A list of phenotype labels that are known to be associated with this\n entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_phenotype_label\n owner: Node\n domain_of:\n - Entity\n range: string\n multivalued: true\n inlined: true\n inlined_as_list: true\n has_phenotype_closure:\n name: has_phenotype_closure\n description: A list of phenotype identifiers that are known to be associated with\n this entity expanded to include all ancestors\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_phenotype_closure\n owner: Node\n domain_of:\n - Entity\n range: string\n multivalued: true\n inlined: true\n inlined_as_list: true\n has_phenotype_closure_label:\n name: has_phenotype_closure_label\n description: A list of phenotype labels that are known to be associated with this\n entity expanded to include all ancestors\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_phenotype_closure_label\n owner: Node\n domain_of:\n - Entity\n range: string\n multivalued: true\n inlined: true\n inlined_as_list: true\n has_phenotype_count:\n name: has_phenotype_count\n description: A count of the number of phenotypes that are known to be associated\n with this entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_phenotype_count\n owner: Node\n domain_of:\n - Entity\n range: integer\nURI: https://w3id.org/monarch/monarch-py/:NodeHierarchy
classDiagram\n class NodeHierarchy\n click NodeHierarchy href \"../NodeHierarchy\"\n NodeHierarchy : sub_classes\n\n\n\n\n NodeHierarchy --> \"1..*\" Entity : sub_classes\n click Entity href \"../Entity\"\n\n\n NodeHierarchy : super_classes\n\n\n\n\n NodeHierarchy --> \"1..*\" Entity : super_classes\n click Entity href \"../Entity\"\nname: NodeHierarchy\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- super_classes\n- sub_classes\nname: NodeHierarchy\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n super_classes:\n name: super_classes\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: super_classes\n owner: NodeHierarchy\n domain_of:\n - NodeHierarchy\n range: Entity\n required: true\n multivalued: true\n inlined: true\n inlined_as_list: true\n sub_classes:\n name: sub_classes\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: sub_classes\n owner: NodeHierarchy\n domain_of:\n - NodeHierarchy\n range: Entity\n required: true\n multivalued: true\n inlined: true\n inlined_as_list: true\nA URI, CURIE or BNODE that represents a node in a model.
URI: shex:nonLiteral
base: NodeIdentifier
uri: shex:nonLiteral
repr: str
URI: xsd:float
base: float
uri: xsd:float
typeof: float
A URI or CURIE that represents an object in the model.
URI: shex:iri
base: ElementIdentifier
uri: shex:iri
repr: str
Abstract grouping for representing individual pairwise similarities
URI: https://w3id.org/monarch/monarch-py/:PairwiseSimilarity
classDiagram\n class PairwiseSimilarity\n click PairwiseSimilarity href \"../PairwiseSimilarity\"\n PairwiseSimilarity <|-- TermPairwiseSimilarity\n click TermPairwiseSimilarity href \"../TermPairwiseSimilarity\"\n PairwiseSimilarity <|-- TermSetPairwiseSimilarity\n click TermSetPairwiseSimilarity href \"../TermSetPairwiseSimilarity\"\nname: PairwiseSimilarity\ndescription: Abstract grouping for representing individual pairwise similarities\nfrom_schema: https://w3id.org/monarch/monarch-py\nabstract: true\nname: PairwiseSimilarity\ndescription: Abstract grouping for representing individual pairwise similarities\nfrom_schema: https://w3id.org/monarch/monarch-py\nabstract: true\nA class to hold information about a release of the Monarch KG
URI: https://w3id.org/monarch/monarch-py/:Release
classDiagram\n class Release\n click Release href \"../Release\"\n Release : graph_stats\n\n Release : kg\n\n Release : metadata\n\n Release : neo4j\n\n Release : qc_report\n\n Release : solr\n\n Release : sqlite\n\n Release : url\n\n Release : version\nname: Release\ndescription: A class to hold information about a release of the Monarch KG\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- version\n- url\n- kg\n- sqlite\n- solr\n- neo4j\n- metadata\n- graph_stats\n- qc_report\nname: Release\ndescription: A class to hold information about a release of the Monarch KG\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n version:\n name: version\n id_prefixes:\n - string\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: version\n owner: Release\n domain_of:\n - Release\n range: string\n url:\n name: url\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: url\n owner: Release\n domain_of:\n - ExpandedCurie\n - Release\n range: string\n kg:\n name: kg\n id_prefixes:\n - string\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: kg\n owner: Release\n domain_of:\n - Release\n range: string\n sqlite:\n name: sqlite\n id_prefixes:\n - string\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: sqlite\n owner: Release\n domain_of:\n - Release\n range: string\n solr:\n name: solr\n id_prefixes:\n - string\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: solr\n owner: Release\n domain_of:\n - Release\n range: string\n neo4j:\n name: neo4j\n id_prefixes:\n - string\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: neo4j\n owner: Release\n domain_of:\n - Release\n range: string\n metadata:\n name: metadata\n id_prefixes:\n - string\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: metadata\n owner: Release\n domain_of:\n - Release\n range: string\n graph_stats:\n name: graph_stats\n id_prefixes:\n - string\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: graph_stats\n owner: Release\n domain_of:\n - Release\n range: string\n qc_report:\n name: qc_report\n id_prefixes:\n - string\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: qc_report\n owner: Release\n domain_of:\n - Release\n range: string\nURI: https://w3id.org/monarch/monarch-py/:Results
classDiagram\n class Results\n click Results href \"../Results\"\n Results <|-- AssociationResults\n click AssociationResults href \"../AssociationResults\"\n Results <|-- CompactAssociationResults\n click CompactAssociationResults href \"../CompactAssociationResults\"\n Results <|-- AssociationTableResults\n click AssociationTableResults href \"../AssociationTableResults\"\n Results <|-- CategoryGroupedAssociationResults\n click CategoryGroupedAssociationResults href \"../CategoryGroupedAssociationResults\"\n Results <|-- EntityResults\n click EntityResults href \"../EntityResults\"\n Results <|-- MappingResults\n click MappingResults href \"../MappingResults\"\n Results <|-- MultiEntityAssociationResults\n click MultiEntityAssociationResults href \"../MultiEntityAssociationResults\"\n Results <|-- SearchResults\n click SearchResults href \"../SearchResults\"\n\n Results : limit\n\n Results : offset\n\n Results : total\nname: Results\nfrom_schema: https://w3id.org/monarch/monarch-py\nabstract: true\nslots:\n- limit\n- offset\n- total\nname: Results\nfrom_schema: https://w3id.org/monarch/monarch-py\nabstract: true\nattributes:\n limit:\n name: limit\n description: number of items to return in a response\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: limit\n owner: Results\n domain_of:\n - Results\n range: integer\n required: true\n offset:\n name: offset\n description: offset into the total number of items\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: offset\n owner: Results\n domain_of:\n - Results\n range: integer\n required: true\n total:\n name: total\n description: total number of items matching a query\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: total\n owner: Results\n domain_of:\n - Results\n range: integer\n required: true\nURI: https://w3id.org/monarch/monarch-py/:SearchResult
classDiagram\n class SearchResult\n click SearchResult href \"../SearchResult\"\n Entity <|-- SearchResult\n click Entity href \"../Entity\"\n\n SearchResult : category\n\n SearchResult : deprecated\n\n SearchResult : description\n\n SearchResult : full_name\n\n SearchResult : has_phenotype\n\n SearchResult : has_phenotype_closure\n\n SearchResult : has_phenotype_closure_label\n\n SearchResult : has_phenotype_count\n\n SearchResult : has_phenotype_label\n\n SearchResult : highlight\n\n SearchResult : id\n\n SearchResult : in_taxon\n\n SearchResult : in_taxon_label\n\n SearchResult : iri\n\n SearchResult : name\n\n SearchResult : namespace\n\n SearchResult : provided_by\n\n SearchResult : score\n\n SearchResult : symbol\n\n SearchResult : synonym\n\n SearchResult : uri\n\n SearchResult : xref\nname: SearchResult\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Entity\nslots:\n- highlight\n- score\nslot_usage:\n category:\n name: category\n required: true\n name:\n name: name\n required: true\nname: SearchResult\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Entity\nslot_usage:\n category:\n name: category\n required: true\n name:\n name: name\n required: true\nattributes:\n highlight:\n name: highlight\n description: matching text snippet containing html tags\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: highlight\n owner: SearchResult\n domain_of:\n - SearchResult\n range: string\n score:\n name: score\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: score\n owner: SearchResult\n domain_of:\n - SearchResult\n - BestMatch\n - SemsimSearchResult\n range: float\n id:\n name: id\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n identifier: true\n alias: id\n owner: SearchResult\n domain_of:\n - Association\n - ExpandedCurie\n - Entity\n - HistoPheno\n - HistoBin\n - Mapping\n - MultiEntityAssociationResults\n - TermInfo\n range: string\n required: true\n category:\n name: category\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: category\n owner: SearchResult\n domain_of:\n - Association\n - AssociationCount\n - CompactAssociation\n - AssociationTypeMapping\n - Entity\n range: string\n required: true\n multivalued: false\n name:\n name: name\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: name\n owner: SearchResult\n domain_of:\n - Entity\n - MultiEntityAssociationResults\n range: string\n required: true\n full_name:\n name: full_name\n description: The long form name of an entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: full_name\n owner: SearchResult\n domain_of:\n - Entity\n range: string\n deprecated:\n name: deprecated\n description: A boolean flag indicating that an entity is no longer considered\n current or valid.\n from_schema: https://w3id.org/monarch/monarch-py\n exact_mappings:\n - oboInOwl:ObsoleteClass\n rank: 1000\n alias: deprecated\n owner: SearchResult\n domain_of:\n - Entity\n range: boolean\n description:\n name: description\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: description\n owner: SearchResult\n domain_of:\n - Entity\n range: string\n xref:\n name: xref\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: xref\n owner: SearchResult\n domain_of:\n - Entity\n range: string\n multivalued: true\n provided_by:\n name: provided_by\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: provided_by\n owner: SearchResult\n domain_of:\n - Association\n - Entity\n range: string\n in_taxon:\n name: in_taxon\n description: The biolink taxon that the entity is in the closure of.\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: in_taxon\n owner: SearchResult\n domain_of:\n - Entity\n - Node\n range: string\n in_taxon_label:\n name: in_taxon_label\n description: The label of the biolink taxon that the entity is in the closure\n of.\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: in_taxon_label\n owner: SearchResult\n domain_of:\n - Entity\n - Node\n range: string\n symbol:\n name: symbol\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: symbol\n owner: SearchResult\n domain_of:\n - Entity\n range: string\n synonym:\n name: synonym\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: synonym\n owner: SearchResult\n domain_of:\n - Entity\n range: string\n multivalued: true\n uri:\n name: uri\n description: The URI of the entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: uri\n owner: SearchResult\n domain_of:\n - Entity\n range: string\n iri:\n name: iri\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: iri\n owner: SearchResult\n domain_of:\n - Entity\n range: string\n namespace:\n name: namespace\n description: The namespace/prefix portion of this entity's identifier\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: namespace\n owner: SearchResult\n domain_of:\n - Entity\n range: string\n has_phenotype:\n name: has_phenotype\n description: A list of phenotype identifiers that are known to be associated with\n this entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_phenotype\n owner: SearchResult\n domain_of:\n - Entity\n range: string\n multivalued: true\n inlined: true\n inlined_as_list: true\n has_phenotype_label:\n name: has_phenotype_label\n description: A list of phenotype labels that are known to be associated with this\n entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_phenotype_label\n owner: SearchResult\n domain_of:\n - Entity\n range: string\n multivalued: true\n inlined: true\n inlined_as_list: true\n has_phenotype_closure:\n name: has_phenotype_closure\n description: A list of phenotype identifiers that are known to be associated with\n this entity expanded to include all ancestors\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_phenotype_closure\n owner: SearchResult\n domain_of:\n - Entity\n range: string\n multivalued: true\n inlined: true\n inlined_as_list: true\n has_phenotype_closure_label:\n name: has_phenotype_closure_label\n description: A list of phenotype labels that are known to be associated with this\n entity expanded to include all ancestors\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_phenotype_closure_label\n owner: SearchResult\n domain_of:\n - Entity\n range: string\n multivalued: true\n inlined: true\n inlined_as_list: true\n has_phenotype_count:\n name: has_phenotype_count\n description: A count of the number of phenotypes that are known to be associated\n with this entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: has_phenotype_count\n owner: SearchResult\n domain_of:\n - Entity\n range: integer\nURI: https://w3id.org/monarch/monarch-py/:SearchResults
classDiagram\n class SearchResults\n click SearchResults href \"../SearchResults\"\n Results <|-- SearchResults\n click Results href \"../Results\"\n\n SearchResults : facet_fields\n\n\n\n\n SearchResults --> \"*\" FacetField : facet_fields\n click FacetField href \"../FacetField\"\n\n\n SearchResults : facet_queries\n\n\n\n\n SearchResults --> \"*\" FacetValue : facet_queries\n click FacetValue href \"../FacetValue\"\n\n\n SearchResults : items\n\n\n\n\n SearchResults --> \"1..*\" SearchResult : items\n click SearchResult href \"../SearchResult\"\n\n\n SearchResults : limit\n\n SearchResults : offset\n\n SearchResults : total\nname: SearchResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslots:\n- items\n- facet_fields\n- facet_queries\nslot_usage:\n items:\n name: items\n range: SearchResult\nname: SearchResults\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: Results\nslot_usage:\n items:\n name: items\n range: SearchResult\nattributes:\n items:\n name: items\n description: A collection of items, with the type to be overriden by slot_usage\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: items\n owner: SearchResults\n domain_of:\n - AssociationCountList\n - AssociationResults\n - CompactAssociationResults\n - AssociationTableResults\n - CategoryGroupedAssociationResults\n - EntityResults\n - HistoPheno\n - MappingResults\n - SearchResults\n range: SearchResult\n required: true\n multivalued: true\n inlined: true\n inlined_as_list: true\n facet_fields:\n name: facet_fields\n description: Collection of facet field responses with the field values and counts\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: facet_fields\n owner: SearchResults\n domain_of:\n - AssociationResults\n - CompactAssociationResults\n - AssociationTableResults\n - SearchResults\n range: FacetField\n multivalued: true\n inlined: true\n inlined_as_list: true\n facet_queries:\n name: facet_queries\n description: Collection of facet query responses with the query string values\n and counts\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: facet_queries\n owner: SearchResults\n domain_of:\n - AssociationResults\n - CompactAssociationResults\n - AssociationTableResults\n - SearchResults\n range: FacetValue\n multivalued: true\n inlined: true\n inlined_as_list: true\n limit:\n name: limit\n description: number of items to return in a response\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: limit\n owner: SearchResults\n domain_of:\n - Results\n range: integer\n required: true\n offset:\n name: offset\n description: offset into the total number of items\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: offset\n owner: SearchResults\n domain_of:\n - Results\n range: integer\n required: true\n total:\n name: total\n description: total number of items matching a query\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: total\n owner: SearchResults\n domain_of:\n - Results\n range: integer\n required: true\nURI: https://w3id.org/monarch/monarch-py/:SemsimSearchResult
classDiagram\n class SemsimSearchResult\n click SemsimSearchResult href \"../SemsimSearchResult\"\n SemsimSearchResult : score\n\n SemsimSearchResult : similarity\n\n\n\n\n SemsimSearchResult --> \"0..1\" TermSetPairwiseSimilarity : similarity\n click TermSetPairwiseSimilarity href \"../TermSetPairwiseSimilarity\"\n\n\n SemsimSearchResult : subject\n\n\n\n\n SemsimSearchResult --> \"1\" Entity : subject\n click Entity href \"../Entity\"\nname: SemsimSearchResult\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- subject\n- score\n- similarity\nslot_usage:\n subject:\n name: subject\n range: Entity\n inlined: true\nname: SemsimSearchResult\nfrom_schema: https://w3id.org/monarch/monarch-py\nslot_usage:\n subject:\n name: subject\n range: Entity\n inlined: true\nattributes:\n subject:\n name: subject\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: subject\n owner: SemsimSearchResult\n domain_of:\n - Association\n - CompactAssociation\n - SemsimSearchResult\n range: Entity\n required: true\n inlined: true\n score:\n name: score\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: score\n owner: SemsimSearchResult\n domain_of:\n - SearchResult\n - BestMatch\n - SemsimSearchResult\n range: float\n similarity:\n name: similarity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: similarity\n owner: SemsimSearchResult\n domain_of:\n - BestMatch\n - SemsimSearchResult\n range: TermSetPairwiseSimilarity\nA string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.
URI: xsd:string
base: str
uri: xsd:string
repr: str
A character string
URI: xsd:string
base: str
uri: xsd:string
URI: https://w3id.org/monarch/monarch-py/:TermInfo
classDiagram\n class TermInfo\n click TermInfo href \"../TermInfo\"\n TermInfo : id\n\n TermInfo : label\nname: TermInfo\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n id:\n name: id\n from_schema: https://w3id.org/monarch/monarch-py-similarity\n identifier: true\n domain_of:\n - Association\n - ExpandedCurie\n - Entity\n - HistoPheno\n - HistoBin\n - Mapping\n - MultiEntityAssociationResults\n - TermInfo\n required: true\n label:\n name: label\n from_schema: https://w3id.org/monarch/monarch-py-similarity\n slot_uri: rdfs:label\n domain_of:\n - FacetValue\n - FacetField\n - TermInfo\nname: TermInfo\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n id:\n name: id\n from_schema: https://w3id.org/monarch/monarch-py-similarity\n identifier: true\n alias: id\n owner: TermInfo\n domain_of:\n - Association\n - ExpandedCurie\n - Entity\n - HistoPheno\n - HistoBin\n - Mapping\n - MultiEntityAssociationResults\n - TermInfo\n range: string\n required: true\n label:\n name: label\n from_schema: https://w3id.org/monarch/monarch-py-similarity\n slot_uri: rdfs:label\n alias: label\n owner: TermInfo\n domain_of:\n - FacetValue\n - FacetField\n - TermInfo\n range: string\nA simple pairwise similarity between two atomic concepts/terms
URI: https://w3id.org/monarch/monarch-py/:TermPairwiseSimilarity
classDiagram\n class TermPairwiseSimilarity\n click TermPairwiseSimilarity href \"../TermPairwiseSimilarity\"\n PairwiseSimilarity <|-- TermPairwiseSimilarity\n click PairwiseSimilarity href \"../PairwiseSimilarity\"\n\n TermPairwiseSimilarity : ancestor_id\n\n TermPairwiseSimilarity : ancestor_information_content\n\n TermPairwiseSimilarity : ancestor_label\n\n TermPairwiseSimilarity : ancestor_source\n\n TermPairwiseSimilarity : cosine_similarity\n\n TermPairwiseSimilarity : dice_similarity\n\n TermPairwiseSimilarity : jaccard_similarity\n\n TermPairwiseSimilarity : object_id\n\n TermPairwiseSimilarity : object_information_content\n\n TermPairwiseSimilarity : object_label\n\n TermPairwiseSimilarity : object_source\n\n TermPairwiseSimilarity : phenodigm_score\n\n TermPairwiseSimilarity : subject_id\n\n TermPairwiseSimilarity : subject_information_content\n\n TermPairwiseSimilarity : subject_label\n\n TermPairwiseSimilarity : subject_source\nname: TermPairwiseSimilarity\ndescription: A simple pairwise similarity between two atomic concepts/terms\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: PairwiseSimilarity\nslots:\n- subject_id\n- subject_label\n- subject_source\n- object_id\n- object_label\n- object_source\n- ancestor_id\n- ancestor_label\n- ancestor_source\n- object_information_content\n- subject_information_content\n- ancestor_information_content\n- jaccard_similarity\n- cosine_similarity\n- dice_similarity\n- phenodigm_score\nname: TermPairwiseSimilarity\ndescription: A simple pairwise similarity between two atomic concepts/terms\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: PairwiseSimilarity\nattributes:\n subject_id:\n name: subject_id\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: subject_id\n owner: TermPairwiseSimilarity\n domain_of:\n - Mapping\n - TermPairwiseSimilarity\n range: string\n required: true\n subject_label:\n name: subject_label\n description: The name of the subject entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: subject_label\n owner: TermPairwiseSimilarity\n domain_of:\n - Association\n - CompactAssociation\n - AssociationTypeMapping\n - Mapping\n - TermPairwiseSimilarity\n range: string\n subject_source:\n name: subject_source\n description: the source for the first entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n slot_uri: sssom:subject_source\n alias: subject_source\n owner: TermPairwiseSimilarity\n domain_of:\n - TermPairwiseSimilarity\n range: string\n object_id:\n name: object_id\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: object_id\n owner: TermPairwiseSimilarity\n domain_of:\n - Mapping\n - TermPairwiseSimilarity\n range: string\n required: true\n object_label:\n name: object_label\n description: The name of the object entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: name\n alias: object_label\n owner: TermPairwiseSimilarity\n domain_of:\n - Association\n - CompactAssociation\n - AssociationTypeMapping\n - Mapping\n - TermPairwiseSimilarity\n range: string\n object_source:\n name: object_source\n description: the source for the second entity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n slot_uri: sssom:object_source\n alias: object_source\n owner: TermPairwiseSimilarity\n domain_of:\n - TermPairwiseSimilarity\n range: string\n ancestor_id:\n name: ancestor_id\n description: the most recent common ancestor of the two compared entities. If\n there are multiple MRCAs then the most informative one is selected\n todos:\n - decide on what to do when there are multiple possible ancestos\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: ancestor_id\n owner: TermPairwiseSimilarity\n domain_of:\n - TermPairwiseSimilarity\n range: uriorcurie\n ancestor_label:\n name: ancestor_label\n description: the name or label of the ancestor concept\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: ancestor_label\n owner: TermPairwiseSimilarity\n domain_of:\n - TermPairwiseSimilarity\n range: string\n ancestor_source:\n name: ancestor_source\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: ancestor_source\n owner: TermPairwiseSimilarity\n domain_of:\n - TermPairwiseSimilarity\n range: string\n object_information_content:\n name: object_information_content\n description: The IC of the object\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: information_content\n alias: object_information_content\n owner: TermPairwiseSimilarity\n domain_of:\n - TermPairwiseSimilarity\n range: NegativeLogValue\n subject_information_content:\n name: subject_information_content\n description: The IC of the subject\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: information_content\n alias: subject_information_content\n owner: TermPairwiseSimilarity\n domain_of:\n - TermPairwiseSimilarity\n range: NegativeLogValue\n ancestor_information_content:\n name: ancestor_information_content\n description: The IC of the object\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: information_content\n alias: ancestor_information_content\n owner: TermPairwiseSimilarity\n domain_of:\n - TermPairwiseSimilarity\n range: NegativeLogValue\n jaccard_similarity:\n name: jaccard_similarity\n description: The number of concepts in the intersection divided by the number\n in the union\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: score\n alias: jaccard_similarity\n owner: TermPairwiseSimilarity\n domain_of:\n - TermPairwiseSimilarity\n range: ZeroToOne\n cosine_similarity:\n name: cosine_similarity\n description: the dot product of two node embeddings divided by the product of\n their lengths\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: score\n alias: cosine_similarity\n owner: TermPairwiseSimilarity\n domain_of:\n - TermPairwiseSimilarity\n range: float\n dice_similarity:\n name: dice_similarity\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: score\n alias: dice_similarity\n owner: TermPairwiseSimilarity\n domain_of:\n - TermPairwiseSimilarity\n range: ZeroToOne\n phenodigm_score:\n name: phenodigm_score\n description: the geometric mean of the jaccard similarity and the information\n content\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n is_a: score\n alias: phenodigm_score\n owner: TermPairwiseSimilarity\n domain_of:\n - TermPairwiseSimilarity\n range: NonNegativeFloat\n equals_expression: sqrt({jaccard_similarity} * {information_content})\nA simple pairwise similarity between two sets of concepts/terms
URI: https://w3id.org/monarch/monarch-py/:TermSetPairwiseSimilarity
classDiagram\n class TermSetPairwiseSimilarity\n click TermSetPairwiseSimilarity href \"../TermSetPairwiseSimilarity\"\n PairwiseSimilarity <|-- TermSetPairwiseSimilarity\n click PairwiseSimilarity href \"../PairwiseSimilarity\"\n\n TermSetPairwiseSimilarity : average_score\n\n TermSetPairwiseSimilarity : best_score\n\n TermSetPairwiseSimilarity : metric\n\n TermSetPairwiseSimilarity : object_best_matches\n\n\n\n\n TermSetPairwiseSimilarity --> \"*\" BestMatch : object_best_matches\n click BestMatch href \"../BestMatch\"\n\n\n TermSetPairwiseSimilarity : object_termset\n\n\n\n\n TermSetPairwiseSimilarity --> \"*\" TermInfo : object_termset\n click TermInfo href \"../TermInfo\"\n\n\n TermSetPairwiseSimilarity : subject_best_matches\n\n\n\n\n TermSetPairwiseSimilarity --> \"*\" BestMatch : subject_best_matches\n click BestMatch href \"../BestMatch\"\n\n\n TermSetPairwiseSimilarity : subject_termset\n\n\n\n\n TermSetPairwiseSimilarity --> \"*\" TermInfo : subject_termset\n click TermInfo href \"../TermInfo\"\nname: TermSetPairwiseSimilarity\ndescription: A simple pairwise similarity between two sets of concepts/terms\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: PairwiseSimilarity\nslots:\n- subject_termset\n- object_termset\n- subject_best_matches\n- object_best_matches\n- average_score\n- best_score\n- metric\nname: TermSetPairwiseSimilarity\ndescription: A simple pairwise similarity between two sets of concepts/terms\nfrom_schema: https://w3id.org/monarch/monarch-py\nis_a: PairwiseSimilarity\nattributes:\n subject_termset:\n name: subject_termset\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: subject_termset\n owner: TermSetPairwiseSimilarity\n domain_of:\n - TermSetPairwiseSimilarity\n range: TermInfo\n multivalued: true\n inlined: true\n object_termset:\n name: object_termset\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: object_termset\n owner: TermSetPairwiseSimilarity\n domain_of:\n - TermSetPairwiseSimilarity\n range: TermInfo\n multivalued: true\n inlined: true\n subject_best_matches:\n name: subject_best_matches\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: subject_best_matches\n owner: TermSetPairwiseSimilarity\n domain_of:\n - TermSetPairwiseSimilarity\n range: BestMatch\n multivalued: true\n inlined: true\n object_best_matches:\n name: object_best_matches\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: object_best_matches\n owner: TermSetPairwiseSimilarity\n domain_of:\n - TermSetPairwiseSimilarity\n range: BestMatch\n multivalued: true\n inlined: true\n average_score:\n name: average_score\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: average_score\n owner: TermSetPairwiseSimilarity\n domain_of:\n - TermSetPairwiseSimilarity\n range: float\n required: false\n best_score:\n name: best_score\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: best_score\n owner: TermSetPairwiseSimilarity\n domain_of:\n - TermSetPairwiseSimilarity\n range: float\n required: false\n metric:\n name: metric\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: metric\n owner: TermSetPairwiseSimilarity\n domain_of:\n - TermSetPairwiseSimilarity\n range: uriorcurie\nURI: https://w3id.org/monarch/monarch-py/:TextAnnotationResult
classDiagram\n class TextAnnotationResult\n click TextAnnotationResult href \"../TextAnnotationResult\"\n TextAnnotationResult : end\n\n TextAnnotationResult : start\n\n TextAnnotationResult : text\n\n TextAnnotationResult : tokens\n\n\n\n\n TextAnnotationResult --> \"*\" Entity : tokens\n click Entity href \"../Entity\"\nname: TextAnnotationResult\nfrom_schema: https://w3id.org/monarch/monarch-py\nslots:\n- text\n- tokens\n- start\n- end\nname: TextAnnotationResult\nfrom_schema: https://w3id.org/monarch/monarch-py\nattributes:\n text:\n name: text\n description: text without tokens\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: text\n owner: TextAnnotationResult\n domain_of:\n - TextAnnotationResult\n range: string\n inlined: true\n tokens:\n name: tokens\n description: A collection of entities or concepts\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: tokens\n owner: TextAnnotationResult\n domain_of:\n - TextAnnotationResult\n range: Entity\n multivalued: true\n inlined: true\n inlined_as_list: true\n start:\n name: start\n description: start position of the annotation\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: start\n owner: TextAnnotationResult\n domain_of:\n - TextAnnotationResult\n range: integer\n end:\n name: end\n description: end position of the annotation\n from_schema: https://w3id.org/monarch/monarch-py\n rank: 1000\n alias: end\n owner: TextAnnotationResult\n domain_of:\n - TextAnnotationResult\n range: integer\nA time object represents a (local) time of day, independent of any particular day
URI: xsd:time
base: XSDTime
uri: xsd:time
repr: str
a complete URI
URI: xsd:anyURI
base: URI
uri: xsd:anyURI
repr: str
a URI or a CURIE
URI: xsd:anyURI
base: URIorCURIE
uri: xsd:anyURI
repr: str
URI: xsd:float
base: float
uri: xsd:float
typeof: float
Describes the high-level category of agent who originally generated a statement of knowledge or other type of information.
URI: biolink:agent_type
"},{"location":"Data-Model/agent_type/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/agent_type/#properties","title":"Properties","text":"Range: String
Required: True
name: agent_type\ndescription: Describes the high-level category of agent who originally generated a statement\n of knowledge or other type of information.\nnotes:\n- The range in this schema is represented as a string, but is constrained to values\n from biolink:AgentTypeEnum at ingest time\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nslot_uri: biolink:agent_type\nalias: agent_type\ndomain_of:\n- Association\nrange: string\nrequired: true\nmultivalued: false\nURI: https://w3id.org/monarch/monarch-py/:aggregator_knowledge_source
"},{"location":"Data-Model/aggregator_knowledge_source/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/aggregator_knowledge_source/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: aggregator_knowledge_source\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: aggregator_knowledge_source\ndomain_of:\n- Association\nrange: string\nmultivalued: true\nthe most recent common ancestor of the two compared entities. If there are multiple MRCAs then the most informative one is selected
URI: https://w3id.org/monarch/monarch-py/:ancestor_id
"},{"location":"Data-Model/ancestor_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms no"},{"location":"Data-Model/ancestor_id/#properties","title":"Properties","text":"name: ancestor_id\ndescription: the most recent common ancestor of the two compared entities. If there\n are multiple MRCAs then the most informative one is selected\ntodos:\n- decide on what to do when there are multiple possible ancestos\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: ancestor_id\ndomain_of:\n- TermPairwiseSimilarity\nrange: uriorcurie\nThe IC of the object
URI: https://w3id.org/monarch/monarch-py/:ancestor_information_content
"},{"location":"Data-Model/ancestor_information_content/#inheritance","title":"Inheritance","text":"name: ancestor_information_content\ndescription: The IC of the object\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: information_content\nalias: ancestor_information_content\ndomain_of:\n- TermPairwiseSimilarity\nrange: NegativeLogValue\nthe name or label of the ancestor concept
URI: https://w3id.org/monarch/monarch-py/:ancestor_label
"},{"location":"Data-Model/ancestor_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms no"},{"location":"Data-Model/ancestor_label/#properties","title":"Properties","text":"name: ancestor_label\ndescription: the name or label of the ancestor concept\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: ancestor_label\ndomain_of:\n- TermPairwiseSimilarity\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:ancestor_source
"},{"location":"Data-Model/ancestor_source/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms no"},{"location":"Data-Model/ancestor_source/#properties","title":"Properties","text":"name: ancestor_source\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: ancestor_source\ndomain_of:\n- TermPairwiseSimilarity\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:associated_categories
"},{"location":"Data-Model/associated_categories/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MultiEntityAssociationResults no"},{"location":"Data-Model/associated_categories/#properties","title":"Properties","text":"Range: CategoryGroupedAssociationResults
Multivalued: True
Required: True
name: associated_categories\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: associated_categories\ndomain_of:\n- MultiEntityAssociationResults\nrange: CategoryGroupedAssociationResults\nrequired: true\nmultivalued: true\ninlined: true\ninlined_as_list: true\nURI: https://w3id.org/monarch/monarch-py/:association_counts
"},{"location":"Data-Model/association_counts/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Node UI container class extending Entity with additional information no"},{"location":"Data-Model/association_counts/#properties","title":"Properties","text":"Range: AssociationCount
Multivalued: True
Required: True
name: association_counts\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: association_counts\ndomain_of:\n- Node\nrange: AssociationCount\nrequired: true\nmultivalued: true\ninlined: true\ninlined_as_list: true\nURI: https://w3id.org/monarch/monarch-py/:average_score
"},{"location":"Data-Model/average_score/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermSetPairwiseSimilarity A simple pairwise similarity between two sets of concepts/terms no"},{"location":"Data-Model/average_score/#properties","title":"Properties","text":"name: average_score\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: average_score\ndomain_of:\n- TermSetPairwiseSimilarity\nrange: float\nrequired: false\nURI: https://w3id.org/monarch/monarch-py/:best_score
"},{"location":"Data-Model/best_score/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermSetPairwiseSimilarity A simple pairwise similarity between two sets of concepts/terms no"},{"location":"Data-Model/best_score/#properties","title":"Properties","text":"name: best_score\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: best_score\ndomain_of:\n- TermSetPairwiseSimilarity\nrange: float\nrequired: false\nURI: https://w3id.org/monarch/monarch-py/:category
"},{"location":"Data-Model/category/#inheritance","title":"Inheritance","text":"name: category\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: category\ndomain_of:\n- Association\n- AssociationCount\n- CompactAssociation\n- AssociationTypeMapping\n- Entity\nrange: string\nmultivalued: false\nA list of genes that are known to be causally associated with a disease
URI: https://w3id.org/monarch/monarch-py/:causal_gene
"},{"location":"Data-Model/causal_gene/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Node UI container class extending Entity with additional information no"},{"location":"Data-Model/causal_gene/#properties","title":"Properties","text":"Range: Entity
Multivalued: True
name: causal_gene\ndescription: A list of genes that are known to be causally associated with a disease\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: causal_gene\ndomain_of:\n- Node\nrange: Entity\nmultivalued: true\ninlined: true\ninlined_as_list: true\nA list of diseases that are known to be causally associated with a gene
URI: https://w3id.org/monarch/monarch-py/:causes_disease
"},{"location":"Data-Model/causes_disease/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Node UI container class extending Entity with additional information no"},{"location":"Data-Model/causes_disease/#properties","title":"Properties","text":"Range: Entity
Multivalued: True
name: causes_disease\ndescription: A list of diseases that are known to be causally associated with a gene\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: causes_disease\ndomain_of:\n- Node\nrange: Entity\nmultivalued: true\ninlined: true\ninlined_as_list: true\nthe dot product of two node embeddings divided by the product of their lengths
URI: https://w3id.org/monarch/monarch-py/:cosine_similarity
"},{"location":"Data-Model/cosine_similarity/#inheritance","title":"Inheritance","text":"name: cosine_similarity\ndescription: the dot product of two node embeddings divided by the product of their\n lengths\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: score\nalias: cosine_similarity\ndomain_of:\n- TermPairwiseSimilarity\nrange: float\ncount of documents
URI: https://w3id.org/monarch/monarch-py/:count
"},{"location":"Data-Model/count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AssociationCount no HistoBin no FacetValue no"},{"location":"Data-Model/count/#properties","title":"Properties","text":"name: count\ndescription: count of documents\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: count\ndomain_of:\n- FacetValue\nrange: integer\nThe category of the counterpart entity in a given association, eg. the category of the entity that is not the subject
URI: https://w3id.org/monarch/monarch-py/:counterpart_category
"},{"location":"Data-Model/counterpart_category/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CategoryGroupedAssociationResults no"},{"location":"Data-Model/counterpart_category/#properties","title":"Properties","text":"name: counterpart_category\ndescription: The category of the counterpart entity in a given association, eg. the\n category of the entity that is not the subject\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: counterpart_category\ndomain_of:\n- CategoryGroupedAssociationResults\nrange: string\nA boolean flag indicating that an entity is no longer considered current or valid.
URI: https://w3id.org/monarch/monarch-py/:deprecated
"},{"location":"Data-Model/deprecated/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SearchResult no Node UI container class extending Entity with additional information no Entity Represents an Entity in the Monarch KG data model no"},{"location":"Data-Model/deprecated/#properties","title":"Properties","text":"name: deprecated\ndescription: A boolean flag indicating that an entity is no longer considered current\n or valid.\nfrom_schema: https://w3id.org/monarch/monarch-py\nexact_mappings:\n- oboInOwl:ObsoleteClass\nrank: 1000\nalias: deprecated\ndomain_of:\n- Entity\nrange: boolean\nURI: https://w3id.org/monarch/monarch-py/:description
"},{"location":"Data-Model/description/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SearchResult no Node UI container class extending Entity with additional information no Entity Represents an Entity in the Monarch KG data model no"},{"location":"Data-Model/description/#properties","title":"Properties","text":"name: description\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: description\ndomain_of:\n- Entity\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:dice_similarity
"},{"location":"Data-Model/dice_similarity/#inheritance","title":"Inheritance","text":"name: dice_similarity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: score\nalias: dice_similarity\ndomain_of:\n- TermPairwiseSimilarity\nrange: ZeroToOne\nThe directionality of the association relative to a given entity for an association_count. If the entity is the subject or in the subject closure, the direction is forwards, if it is the object or in the object closure, the direction is backwards.
URI: https://w3id.org/monarch/monarch-py/:direction
"},{"location":"Data-Model/direction/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/direction/#properties","title":"Properties","text":"Range: AssociationDirectionEnum
Required: True
name: direction\ndescription: The directionality of the association relative to a given entity for\n an association_count. If the entity is the subject or in the subject closure, the\n direction is forwards, if it is the object or in the object closure, the direction\n is backwards.\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: direction\ndomain_of:\n- DirectionalAssociation\nrange: AssociationDirectionEnum\nrequired: true\nA context qualifier representing a disease or condition in which a relationship expressed in an association took place.
URI: https://w3id.org/monarch/monarch-py/:disease_context_qualifier
"},{"location":"Data-Model/disease_context_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/disease_context_qualifier/#properties","title":"Properties","text":"name: disease_context_qualifier\ndescription: A context qualifier representing a disease or condition in which a relationship\n expressed in an association took place.\nexamples:\n- value: MONDO:0004979\n- value: MONDO:0005148\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: disease_context_qualifier\ndomain_of:\n- Association\nrange: string\nThe category of the disease_context_qualifier entity
URI: https://w3id.org/monarch/monarch-py/:disease_context_qualifier_category
"},{"location":"Data-Model/disease_context_qualifier_category/#inheritance","title":"Inheritance","text":"name: disease_context_qualifier_category\ndescription: The category of the disease_context_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: category\nalias: disease_context_qualifier_category\ndomain_of:\n- Association\nrange: string\nField containing disease_context_qualifier id and the ids of all of it's ancestors
URI: https://w3id.org/monarch/monarch-py/:disease_context_qualifier_closure
"},{"location":"Data-Model/disease_context_qualifier_closure/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/disease_context_qualifier_closure/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: disease_context_qualifier_closure\ndescription: Field containing disease_context_qualifier id and the ids of all of it's\n ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: disease_context_qualifier_closure\ndomain_of:\n- Association\nrange: string\nmultivalued: true\nField containing disease_context_qualifier name and the names of all of it's ancestors
URI: https://w3id.org/monarch/monarch-py/:disease_context_qualifier_closure_label
"},{"location":"Data-Model/disease_context_qualifier_closure_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/disease_context_qualifier_closure_label/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: disease_context_qualifier_closure_label\ndescription: Field containing disease_context_qualifier name and the names of all\n of it's ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: disease_context_qualifier_closure_label\ndomain_of:\n- Association\nrange: string\nmultivalued: true\nThe name of the disease_context_qualifier entity
URI: https://w3id.org/monarch/monarch-py/:disease_context_qualifier_label
"},{"location":"Data-Model/disease_context_qualifier_label/#inheritance","title":"Inheritance","text":"name: disease_context_qualifier_label\ndescription: The name of the disease_context_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: name\nalias: disease_context_qualifier_label\ndomain_of:\n- Association\nrange: string\nThe namespace/prefix of the disease_context_qualifier entity
URI: https://w3id.org/monarch/monarch-py/:disease_context_qualifier_namespace
"},{"location":"Data-Model/disease_context_qualifier_namespace/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/disease_context_qualifier_namespace/#properties","title":"Properties","text":"name: disease_context_qualifier_namespace\ndescription: The namespace/prefix of the disease_context_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: disease_context_qualifier_namespace\ndomain_of:\n- Association\nrange: string\nend position of the annotation
URI: https://w3id.org/monarch/monarch-py/:end
"},{"location":"Data-Model/end/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextAnnotationResult no"},{"location":"Data-Model/end/#properties","title":"Properties","text":"name: end\ndescription: end position of the annotation\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: end\ndomain_of:\n- TextAnnotationResult\nrange: integer\ncount of supporting documents, evidence codes, and sources supplying evidence
URI: https://w3id.org/monarch/monarch-py/:evidence_count
"},{"location":"Data-Model/evidence_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/evidence_count/#properties","title":"Properties","text":"name: evidence_count\ndescription: count of supporting documents, evidence codes, and sources supplying\n evidence\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: evidence_count\ndomain_of:\n- Association\nrange: integer\nExpandedCurie with id and url for xrefs
URI: https://w3id.org/monarch/monarch-py/:external_links
"},{"location":"Data-Model/external_links/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Node UI container class extending Entity with additional information no"},{"location":"Data-Model/external_links/#properties","title":"Properties","text":"Range: ExpandedCurie
Multivalued: True
name: external_links\ndescription: ExpandedCurie with id and url for xrefs\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: external_links\ndomain_of:\n- Node\nrange: ExpandedCurie\nmultivalued: true\ninlined: true\ninlined_as_list: true\nCollection of facet field responses with the field values and counts
URI: https://w3id.org/monarch/monarch-py/:facet_fields
"},{"location":"Data-Model/facet_fields/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CompactAssociationResults no SearchResults no AssociationResults no AssociationTableResults no"},{"location":"Data-Model/facet_fields/#properties","title":"Properties","text":"Range: FacetField
Multivalued: True
name: facet_fields\ndescription: Collection of facet field responses with the field values and counts\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: facet_fields\ndomain_of:\n- AssociationResults\n- CompactAssociationResults\n- AssociationTableResults\n- SearchResults\nrange: FacetField\nmultivalued: true\ninlined: true\ninlined_as_list: true\nCollection of facet query responses with the query string values and counts
URI: https://w3id.org/monarch/monarch-py/:facet_queries
"},{"location":"Data-Model/facet_queries/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CompactAssociationResults no SearchResults no AssociationResults no AssociationTableResults no"},{"location":"Data-Model/facet_queries/#properties","title":"Properties","text":"Range: FacetValue
Multivalued: True
name: facet_queries\ndescription: Collection of facet query responses with the query string values and\n counts\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: facet_queries\ndomain_of:\n- AssociationResults\n- CompactAssociationResults\n- AssociationTableResults\n- SearchResults\nrange: FacetValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\nCollection of FacetValue label/value instances belonging to a FacetField
URI: https://w3id.org/monarch/monarch-py/:facet_values
"},{"location":"Data-Model/facet_values/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot FacetField no"},{"location":"Data-Model/facet_values/#properties","title":"Properties","text":"Range: FacetValue
Multivalued: True
name: facet_values\ndescription: Collection of FacetValue label/value instances belonging to a FacetField\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: facet_values\ndomain_of:\n- FacetField\nrange: FacetValue\nmultivalued: true\ninlined: true\ninlined_as_list: true\nURI: https://w3id.org/monarch/monarch-py/:frequency_qualifier
"},{"location":"Data-Model/frequency_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/frequency_qualifier/#properties","title":"Properties","text":"name: frequency_qualifier\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: frequency_qualifier\ndomain_of:\n- Association\nrange: string\nThe category of the frequency_qualifier entity
URI: https://w3id.org/monarch/monarch-py/:frequency_qualifier_category
"},{"location":"Data-Model/frequency_qualifier_category/#inheritance","title":"Inheritance","text":"name: frequency_qualifier_category\ndescription: The category of the frequency_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: category\nalias: frequency_qualifier_category\ndomain_of:\n- Association\nrange: string\nThe name of the frequency_qualifier entity
URI: https://w3id.org/monarch/monarch-py/:frequency_qualifier_label
"},{"location":"Data-Model/frequency_qualifier_label/#inheritance","title":"Inheritance","text":"name: frequency_qualifier_label\ndescription: The name of the frequency_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: name\nalias: frequency_qualifier_label\ndomain_of:\n- Association\nrange: string\nThe namespace/prefix of the frequency_qualifier entity
URI: https://w3id.org/monarch/monarch-py/:frequency_qualifier_namespace
"},{"location":"Data-Model/frequency_qualifier_namespace/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/frequency_qualifier_namespace/#properties","title":"Properties","text":"name: frequency_qualifier_namespace\ndescription: The namespace/prefix of the frequency_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: frequency_qualifier_namespace\ndomain_of:\n- Association\nrange: string\nThe long form name of an entity
URI: https://w3id.org/monarch/monarch-py/:full_name
"},{"location":"Data-Model/full_name/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SearchResult no Node UI container class extending Entity with additional information no Entity Represents an Entity in the Monarch KG data model no"},{"location":"Data-Model/full_name/#properties","title":"Properties","text":"name: full_name\ndescription: The long form name of an entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: full_name\ndomain_of:\n- Entity\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:graph_stats
"},{"location":"Data-Model/graph_stats/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Release A class to hold information about a release of the Monarch KG no"},{"location":"Data-Model/graph_stats/#properties","title":"Properties","text":"Instances of this class should have identifiers with one of the following prefixes:
name: graph_stats\nid_prefixes:\n- string\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: graph_stats\ndomain_of:\n- Release\nrange: string\nA concatenation of fields used to group associations with the same essential/defining properties
URI: https://w3id.org/monarch/monarch-py/:grouping_key
"},{"location":"Data-Model/grouping_key/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/grouping_key/#properties","title":"Properties","text":"name: grouping_key\ndescription: A concatenation of fields used to group associations with the same essential/defining\n properties\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: grouping_key\ndomain_of:\n- Association\nrange: string\ncount of out of has_total representing a frequency
URI: https://w3id.org/monarch/monarch-py/:has_count
"},{"location":"Data-Model/has_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/has_count/#properties","title":"Properties","text":"name: has_count\ndescription: count of out of has_total representing a frequency\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: has_count\ndomain_of:\n- Association\nrange: integer\nURI: https://w3id.org/monarch/monarch-py/:has_evidence
"},{"location":"Data-Model/has_evidence/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/has_evidence/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: has_evidence\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: has_evidence\ndomain_of:\n- Association\nrange: string\nmultivalued: true\nList of ExpandedCuries with id and url for evidence
URI: https://w3id.org/monarch/monarch-py/:has_evidence_links
"},{"location":"Data-Model/has_evidence_links/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/has_evidence_links/#properties","title":"Properties","text":"Range: ExpandedCurie
Multivalued: True
name: has_evidence_links\ndescription: List of ExpandedCuries with id and url for evidence\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: has_evidence_links\ndomain_of:\n- Association\nrange: ExpandedCurie\nmultivalued: true\ninlined: true\ninlined_as_list: true\npercentage, which may be calculated from has_count and has_total, as 100 * quotient or provided directly, rounded to the integer level
URI: https://w3id.org/monarch/monarch-py/:has_percentage
"},{"location":"Data-Model/has_percentage/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/has_percentage/#properties","title":"Properties","text":"name: has_percentage\ndescription: percentage, which may be calculated from has_count and has_total, as\n 100 * quotient or provided directly, rounded to the integer level\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: has_percentage\ndomain_of:\n- Association\nrange: float\nA list of phenotype identifiers that are known to be associated with this entity
URI: https://w3id.org/monarch/monarch-py/:has_phenotype
"},{"location":"Data-Model/has_phenotype/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SearchResult no Node UI container class extending Entity with additional information no Entity Represents an Entity in the Monarch KG data model no"},{"location":"Data-Model/has_phenotype/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: has_phenotype\ndescription: A list of phenotype identifiers that are known to be associated with\n this entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: has_phenotype\ndomain_of:\n- Entity\nrange: string\nmultivalued: true\ninlined: true\ninlined_as_list: true\nA list of phenotype identifiers that are known to be associated with this entity expanded to include all ancestors
URI: https://w3id.org/monarch/monarch-py/:has_phenotype_closure
"},{"location":"Data-Model/has_phenotype_closure/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SearchResult no Node UI container class extending Entity with additional information no Entity Represents an Entity in the Monarch KG data model no"},{"location":"Data-Model/has_phenotype_closure/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: has_phenotype_closure\ndescription: A list of phenotype identifiers that are known to be associated with\n this entity expanded to include all ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: has_phenotype_closure\ndomain_of:\n- Entity\nrange: string\nmultivalued: true\ninlined: true\ninlined_as_list: true\nA list of phenotype labels that are known to be associated with this entity expanded to include all ancestors
URI: https://w3id.org/monarch/monarch-py/:has_phenotype_closure_label
"},{"location":"Data-Model/has_phenotype_closure_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SearchResult no Node UI container class extending Entity with additional information no Entity Represents an Entity in the Monarch KG data model no"},{"location":"Data-Model/has_phenotype_closure_label/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: has_phenotype_closure_label\ndescription: A list of phenotype labels that are known to be associated with this\n entity expanded to include all ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: has_phenotype_closure_label\ndomain_of:\n- Entity\nrange: string\nmultivalued: true\ninlined: true\ninlined_as_list: true\nA count of the number of phenotypes that are known to be associated with this entity
URI: https://w3id.org/monarch/monarch-py/:has_phenotype_count
"},{"location":"Data-Model/has_phenotype_count/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SearchResult no Node UI container class extending Entity with additional information no Entity Represents an Entity in the Monarch KG data model no"},{"location":"Data-Model/has_phenotype_count/#properties","title":"Properties","text":"name: has_phenotype_count\ndescription: A count of the number of phenotypes that are known to be associated with\n this entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: has_phenotype_count\ndomain_of:\n- Entity\nrange: integer\nA list of phenotype labels that are known to be associated with this entity
URI: https://w3id.org/monarch/monarch-py/:has_phenotype_label
"},{"location":"Data-Model/has_phenotype_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SearchResult no Node UI container class extending Entity with additional information no Entity Represents an Entity in the Monarch KG data model no"},{"location":"Data-Model/has_phenotype_label/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: has_phenotype_label\ndescription: A list of phenotype labels that are known to be associated with this\n entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: has_phenotype_label\ndomain_of:\n- Entity\nrange: string\nmultivalued: true\ninlined: true\ninlined_as_list: true\nquotient, which should be 1/100 of has_percentage
URI: https://w3id.org/monarch/monarch-py/:has_quotient
"},{"location":"Data-Model/has_quotient/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/has_quotient/#properties","title":"Properties","text":"name: has_quotient\ndescription: quotient, which should be 1/100 of has_percentage\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: has_quotient\ndomain_of:\n- Association\nrange: float\ntotal, devided by has_count, representing a frequency
URI: https://w3id.org/monarch/monarch-py/:has_total
"},{"location":"Data-Model/has_total/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/has_total/#properties","title":"Properties","text":"name: has_total\ndescription: total, devided by has_count, representing a frequency\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: has_total\ndomain_of:\n- Association\nrange: integer\nmatching text snippet containing html tags
URI: https://w3id.org/monarch/monarch-py/:highlight
"},{"location":"Data-Model/highlight/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SearchResult no"},{"location":"Data-Model/highlight/#properties","title":"Properties","text":"name: highlight\ndescription: matching text snippet containing html tags\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: highlight\ndomain_of:\n- SearchResult\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:id
"},{"location":"Data-Model/id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SearchResult no Entity Represents an Entity in the Monarch KG data model no DirectionalAssociation An association that gives it's direction relative to a specified entity no MultiEntityAssociationResults no Association no ExpandedCurie A curie bundled along with its expanded url no TermInfo no HistoPheno no Mapping A minimal class to hold a SSSOM mapping no Node UI container class extending Entity with additional information no HistoBin no"},{"location":"Data-Model/id/#properties","title":"Properties","text":"Range: String
Required: True
name: id\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nidentifier: true\nalias: id\ndomain_of:\n- Association\n- ExpandedCurie\n- Entity\n- HistoPheno\n- HistoBin\n- Mapping\n- MultiEntityAssociationResults\n- TermInfo\nrange: string\nrequired: true\nThe biolink taxon that the entity is in the closure of.
URI: https://w3id.org/monarch/monarch-py/:in_taxon
"},{"location":"Data-Model/in_taxon/#inheritance","title":"Inheritance","text":"name: in_taxon\ndescription: The biolink taxon that the entity is in the closure of.\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: in_taxon\ndomain_of:\n- Entity\n- Node\nrange: string\nThe label of the biolink taxon that the entity is in the closure of.
URI: https://w3id.org/monarch/monarch-py/:in_taxon_label
"},{"location":"Data-Model/in_taxon_label/#inheritance","title":"Inheritance","text":"name: in_taxon_label\ndescription: The label of the biolink taxon that the entity is in the closure of.\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: in_taxon_label\ndomain_of:\n- Entity\n- Node\nrange: string\nThe IC is the negative log of the probability of the concept
URI: https://w3id.org/monarch/monarch-py/:information_content
"},{"location":"Data-Model/information_content/#inheritance","title":"Inheritance","text":"name: information_content\ndescription: The IC is the negative log of the probability of the concept\nfrom_schema: https://w3id.org/monarch/monarch-py\naliases:\n- IC\nrank: 1000\nis_a: score\nabstract: true\nalias: information_content\nrange: NegativeLogValue\nURI: https://w3id.org/monarch/monarch-py/:inheritance
"},{"location":"Data-Model/inheritance/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Node UI container class extending Entity with additional information no"},{"location":"Data-Model/inheritance/#properties","title":"Properties","text":"name: inheritance\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: inheritance\ndomain_of:\n- Node\nrange: Entity\ninlined: true\nURI: https://w3id.org/monarch/monarch-py/:intersection_count
"},{"location":"Data-Model/intersection_count/#inheritance","title":"Inheritance","text":"name: intersection_count\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: score\nalias: intersection_count\nrange: ItemCount\nURI: https://w3id.org/monarch/monarch-py/:iri
"},{"location":"Data-Model/iri/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SearchResult no Node UI container class extending Entity with additional information no Entity Represents an Entity in the Monarch KG data model no"},{"location":"Data-Model/iri/#properties","title":"Properties","text":"name: iri\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: iri\ndomain_of:\n- Entity\nrange: string\nA collection of items, with the type to be overriden by slot_usage
URI: https://w3id.org/monarch/monarch-py/:items
"},{"location":"Data-Model/items/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MappingResults SSSOM Mappings returned as a results collection yes AssociationTableResults yes SearchResults yes EntityResults yes AssociationCountList Container class for a list of association counts yes CategoryGroupedAssociationResults yes HistoPheno yes CompactAssociationResults yes AssociationResults yes"},{"location":"Data-Model/items/#properties","title":"Properties","text":"Range: String
Multivalued: True
Required: True
name: items\ndescription: A collection of items, with the type to be overriden by slot_usage\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: items\ndomain_of:\n- AssociationCountList\n- AssociationResults\n- CompactAssociationResults\n- AssociationTableResults\n- CategoryGroupedAssociationResults\n- EntityResults\n- HistoPheno\n- MappingResults\n- SearchResults\nrange: string\nrequired: true\nmultivalued: true\ninlined: true\ninlined_as_list: true\nThe number of concepts in the intersection divided by the number in the union
URI: https://w3id.org/monarch/monarch-py/:jaccard_similarity
"},{"location":"Data-Model/jaccard_similarity/#inheritance","title":"Inheritance","text":"name: jaccard_similarity\ndescription: The number of concepts in the intersection divided by the number in the\n union\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: score\nalias: jaccard_similarity\ndomain_of:\n- TermPairwiseSimilarity\nrange: ZeroToOne\nURI: https://w3id.org/monarch/monarch-py/:kg
"},{"location":"Data-Model/kg/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Release A class to hold information about a release of the Monarch KG no"},{"location":"Data-Model/kg/#properties","title":"Properties","text":"Instances of this class should have identifiers with one of the following prefixes:
name: kg\nid_prefixes:\n- string\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: kg\ndomain_of:\n- Release\nrange: string\nDescribes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true.
URI: biolink:knowledge_level
"},{"location":"Data-Model/knowledge_level/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/knowledge_level/#properties","title":"Properties","text":"Range: String
Required: True
name: knowledge_level\ndescription: Describes the level of knowledge expressed in a statement, based on the\n reasoning or analysis methods used to generate the statement, or the scope or specificity\n of what the statement expresses to be true.\nnotes:\n- The range in this schema is represented as a string, but is constrained to values\n from biolink:KnowledgeLevelEnum at ingest time\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nslot_uri: biolink:knowledge_level\nalias: knowledge_level\ndomain_of:\n- Association\nrange: string\nrequired: true\nmultivalued: false\nURI: https://w3id.org/monarch/monarch-py/:knowledge_source
"},{"location":"Data-Model/knowledge_source/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: knowledge_source\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: knowledge_source\nrange: string\nmultivalued: true\nURI: https://w3id.org/monarch/monarch-py/:label
"},{"location":"Data-Model/label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AssociationCount no FacetValue no TermInfo no FacetField no HistoBin no"},{"location":"Data-Model/label/#properties","title":"Properties","text":"Range: String
Required: True
name: label\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: label\ndomain_of:\n- FacetValue\n- FacetField\n- TermInfo\nrange: string\nrequired: true\nnumber of items to return in a response
URI: https://w3id.org/monarch/monarch-py/:limit
"},{"location":"Data-Model/limit/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MappingResults SSSOM Mappings returned as a results collection no AssociationTableResults no SearchResults no EntityResults no MultiEntityAssociationResults no CategoryGroupedAssociationResults no Results no CompactAssociationResults no AssociationResults no"},{"location":"Data-Model/limit/#properties","title":"Properties","text":"Range: Integer
Required: True
name: limit\ndescription: number of items to return in a response\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: limit\ndomain_of:\n- Results\nrange: integer\nrequired: true\nURI: https://w3id.org/monarch/monarch-py/:mapping_justification
"},{"location":"Data-Model/mapping_justification/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Mapping A minimal class to hold a SSSOM mapping no"},{"location":"Data-Model/mapping_justification/#properties","title":"Properties","text":"name: mapping_justification\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: mapping_justification\ndomain_of:\n- Mapping\nrange: string\nList of ExpandedCuries with id and url for mapped entities
URI: https://w3id.org/monarch/monarch-py/:mappings
"},{"location":"Data-Model/mappings/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Node UI container class extending Entity with additional information no"},{"location":"Data-Model/mappings/#properties","title":"Properties","text":"Range: ExpandedCurie
Multivalued: True
name: mappings\ndescription: List of ExpandedCuries with id and url for mapped entities\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: mappings\ndomain_of:\n- Node\nrange: ExpandedCurie\nmultivalued: true\ninlined: true\ninlined_as_list: true\nURI: https://w3id.org/monarch/monarch-py/:match_source
"},{"location":"Data-Model/match_source/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BestMatch no"},{"location":"Data-Model/match_source/#properties","title":"Properties","text":"Range: String
Required: True
name: match_source\ncomments:\n- note that the match_source is either the subject or the object\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nidentifier: true\nalias: match_source\nowner: BestMatch\ndomain_of:\n- BestMatch\nrange: string\nrequired: true\nURI: https://w3id.org/monarch/monarch-py/:match_source_label
"},{"location":"Data-Model/match_source_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BestMatch no"},{"location":"Data-Model/match_source_label/#properties","title":"Properties","text":"name: match_source_label\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: match_source_label\nowner: BestMatch\ndomain_of:\n- BestMatch\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:match_subsumer
"},{"location":"Data-Model/match_subsumer/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BestMatch no"},{"location":"Data-Model/match_subsumer/#properties","title":"Properties","text":"name: match_subsumer\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: match_subsumer\nowner: BestMatch\ndomain_of:\n- BestMatch\nrange: uriorcurie\nURI: https://w3id.org/monarch/monarch-py/:match_subsumer_label
"},{"location":"Data-Model/match_subsumer_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BestMatch no"},{"location":"Data-Model/match_subsumer_label/#properties","title":"Properties","text":"name: match_subsumer_label\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: match_subsumer_label\nowner: BestMatch\ndomain_of:\n- BestMatch\nrange: string\nthe entity matches
URI: https://w3id.org/monarch/monarch-py/:match_target
"},{"location":"Data-Model/match_target/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BestMatch no"},{"location":"Data-Model/match_target/#properties","title":"Properties","text":"name: match_target\ndescription: the entity matches\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: match_target\nowner: BestMatch\ndomain_of:\n- BestMatch\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:match_target_label
"},{"location":"Data-Model/match_target_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BestMatch no"},{"location":"Data-Model/match_target_label/#properties","title":"Properties","text":"name: match_target_label\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: match_target_label\nowner: BestMatch\ndomain_of:\n- BestMatch\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:metadata
"},{"location":"Data-Model/metadata/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Release A class to hold information about a release of the Monarch KG no"},{"location":"Data-Model/metadata/#properties","title":"Properties","text":"Instances of this class should have identifiers with one of the following prefixes:
name: metadata\nid_prefixes:\n- string\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: metadata\ndomain_of:\n- Release\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:metric
"},{"location":"Data-Model/metric/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermSetPairwiseSimilarity A simple pairwise similarity between two sets of concepts/terms no"},{"location":"Data-Model/metric/#properties","title":"Properties","text":"name: metric\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: metric\ndomain_of:\n- TermSetPairwiseSimilarity\nrange: uriorcurie\nData models for the Monarch Initiative data access library
URI: https://w3id.org/monarch/monarch-py
"},{"location":"Data-Model/name/","title":"Slot: name","text":"URI: https://w3id.org/monarch/monarch-py/:name
"},{"location":"Data-Model/name/#inheritance","title":"Inheritance","text":"name: name\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: name\ndomain_of:\n- Entity\n- MultiEntityAssociationResults\nrange: string\nThe namespace/prefix portion of this entity's identifier
URI: https://w3id.org/monarch/monarch-py/:namespace
"},{"location":"Data-Model/namespace/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SearchResult no Node UI container class extending Entity with additional information no Entity Represents an Entity in the Monarch KG data model no"},{"location":"Data-Model/namespace/#properties","title":"Properties","text":"name: namespace\ndescription: The namespace/prefix portion of this entity's identifier\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: namespace\ndomain_of:\n- Entity\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:negated
"},{"location":"Data-Model/negated/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CompactAssociation no Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/negated/#properties","title":"Properties","text":"name: negated\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: negated\ndomain_of:\n- Association\n- CompactAssociation\nrange: boolean\nURI: https://w3id.org/monarch/monarch-py/:neo4j
"},{"location":"Data-Model/neo4j/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Release A class to hold information about a release of the Monarch KG no"},{"location":"Data-Model/neo4j/#properties","title":"Properties","text":"Instances of this class should have identifiers with one of the following prefixes:
name: neo4j\nid_prefixes:\n- string\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: neo4j\ndomain_of:\n- Release\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:node_hierarchy
"},{"location":"Data-Model/node_hierarchy/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Node UI container class extending Entity with additional information no"},{"location":"Data-Model/node_hierarchy/#properties","title":"Properties","text":"name: node_hierarchy\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: node_hierarchy\ndomain_of:\n- Node\nrange: NodeHierarchy\ninlined: true\nURI: https://w3id.org/monarch/monarch-py/:object
"},{"location":"Data-Model/object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CompactAssociation no Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/object/#properties","title":"Properties","text":"Range: String
Required: True
name: object\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: object\ndomain_of:\n- Association\n- CompactAssociation\nrange: string\nrequired: true\nURI: https://w3id.org/monarch/monarch-py/:object_best_matches
"},{"location":"Data-Model/object_best_matches/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermSetPairwiseSimilarity A simple pairwise similarity between two sets of concepts/terms no"},{"location":"Data-Model/object_best_matches/#properties","title":"Properties","text":"Range: BestMatch
Multivalued: True
name: object_best_matches\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: object_best_matches\ndomain_of:\n- TermSetPairwiseSimilarity\nrange: BestMatch\nmultivalued: true\ninlined: true\nThe category of the object entity
URI: https://w3id.org/monarch/monarch-py/:object_category
"},{"location":"Data-Model/object_category/#inheritance","title":"Inheritance","text":"name: object_category\ndescription: The category of the object entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: category\nalias: object_category\ndomain_of:\n- Association\nrange: string\nField containing object id and the ids of all of it's ancestors
URI: https://w3id.org/monarch/monarch-py/:object_closure
"},{"location":"Data-Model/object_closure/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/object_closure/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: object_closure\ndescription: Field containing object id and the ids of all of it's ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: object_closure\ndomain_of:\n- Association\nrange: string\nmultivalued: true\nField containing object name and the names of all of it's ancestors
URI: https://w3id.org/monarch/monarch-py/:object_closure_label
"},{"location":"Data-Model/object_closure_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/object_closure_label/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: object_closure_label\ndescription: Field containing object name and the names of all of it's ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: object_closure_label\ndomain_of:\n- Association\nrange: string\nmultivalued: true\nURI: https://w3id.org/monarch/monarch-py/:object_id
"},{"location":"Data-Model/object_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms no Mapping A minimal class to hold a SSSOM mapping no"},{"location":"Data-Model/object_id/#properties","title":"Properties","text":"Range: String
Required: True
name: object_id\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: object_id\ndomain_of:\n- Mapping\n- TermPairwiseSimilarity\nrange: string\nrequired: true\nThe IC of the object
URI: https://w3id.org/monarch/monarch-py/:object_information_content
"},{"location":"Data-Model/object_information_content/#inheritance","title":"Inheritance","text":"name: object_information_content\ndescription: The IC of the object\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: information_content\nalias: object_information_content\ndomain_of:\n- TermPairwiseSimilarity\nrange: NegativeLogValue\nThe name of the object entity
URI: https://w3id.org/monarch/monarch-py/:object_label
"},{"location":"Data-Model/object_label/#inheritance","title":"Inheritance","text":"name: object_label\ndescription: The name of the object entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: name\nalias: object_label\ndomain_of:\n- Association\n- CompactAssociation\n- AssociationTypeMapping\n- Mapping\n- TermPairwiseSimilarity\nrange: string\nThe namespace/prefix of the object entity
URI: https://w3id.org/monarch/monarch-py/:object_namespace
"},{"location":"Data-Model/object_namespace/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/object_namespace/#properties","title":"Properties","text":"name: object_namespace\ndescription: The namespace/prefix of the object entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: object_namespace\ndomain_of:\n- Association\nrange: string\nthe source for the second entity
URI: sssom:object_source
"},{"location":"Data-Model/object_source/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms no"},{"location":"Data-Model/object_source/#properties","title":"Properties","text":"name: object_source\ndescription: the source for the second entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nslot_uri: sssom:object_source\nalias: object_source\ndomain_of:\n- TermPairwiseSimilarity\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:object_taxon
"},{"location":"Data-Model/object_taxon/#inheritance","title":"Inheritance","text":"name: object_taxon\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: in_taxon\nalias: object_taxon\ndomain_of:\n- Association\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:object_taxon_label
"},{"location":"Data-Model/object_taxon_label/#inheritance","title":"Inheritance","text":"name: object_taxon_label\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: in_taxon_label\nalias: object_taxon_label\ndomain_of:\n- Association\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:object_termset
"},{"location":"Data-Model/object_termset/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermSetPairwiseSimilarity A simple pairwise similarity between two sets of concepts/terms no"},{"location":"Data-Model/object_termset/#properties","title":"Properties","text":"Range: TermInfo
Multivalued: True
name: object_termset\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: object_termset\ndomain_of:\n- TermSetPairwiseSimilarity\nrange: TermInfo\nmultivalued: true\ninlined: true\noffset into the total number of items
URI: https://w3id.org/monarch/monarch-py/:offset
"},{"location":"Data-Model/offset/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MappingResults SSSOM Mappings returned as a results collection no AssociationTableResults no SearchResults no EntityResults no MultiEntityAssociationResults no CategoryGroupedAssociationResults no Results no CompactAssociationResults no AssociationResults no"},{"location":"Data-Model/offset/#properties","title":"Properties","text":"Range: Integer
Required: True
name: offset\ndescription: offset into the total number of items\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: offset\ndomain_of:\n- Results\nrange: integer\nrequired: true\nURI: https://w3id.org/monarch/monarch-py/:onset_qualifier
"},{"location":"Data-Model/onset_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/onset_qualifier/#properties","title":"Properties","text":"name: onset_qualifier\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: onset_qualifier\ndomain_of:\n- Association\nrange: string\nThe category of the onset_qualifier entity
URI: https://w3id.org/monarch/monarch-py/:onset_qualifier_category
"},{"location":"Data-Model/onset_qualifier_category/#inheritance","title":"Inheritance","text":"name: onset_qualifier_category\ndescription: The category of the onset_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: category\nalias: onset_qualifier_category\ndomain_of:\n- Association\nrange: string\nThe name of the onset_qualifier entity
URI: https://w3id.org/monarch/monarch-py/:onset_qualifier_label
"},{"location":"Data-Model/onset_qualifier_label/#inheritance","title":"Inheritance","text":"name: onset_qualifier_label\ndescription: The name of the onset_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: name\nalias: onset_qualifier_label\ndomain_of:\n- Association\nrange: string\nThe namespace/prefix of the onset_qualifier entity
URI: https://w3id.org/monarch/monarch-py/:onset_qualifier_namespace
"},{"location":"Data-Model/onset_qualifier_namespace/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/onset_qualifier_namespace/#properties","title":"Properties","text":"name: onset_qualifier_namespace\ndescription: The namespace/prefix of the onset_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: onset_qualifier_namespace\ndomain_of:\n- Association\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:original_object
"},{"location":"Data-Model/original_object/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/original_object/#properties","title":"Properties","text":"name: original_object\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: original_object\ndomain_of:\n- Association\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:original_subject
"},{"location":"Data-Model/original_subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/original_subject/#properties","title":"Properties","text":"name: original_subject\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: original_subject\ndomain_of:\n- Association\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:overlap_coefficient
"},{"location":"Data-Model/overlap_coefficient/#inheritance","title":"Inheritance","text":"name: overlap_coefficient\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: score\nalias: overlap_coefficient\nrange: ZeroToOne\nURI: https://w3id.org/monarch/monarch-py/:pathway
"},{"location":"Data-Model/pathway/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/pathway/#properties","title":"Properties","text":"name: pathway\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: pathway\ndomain_of:\n- Association\nrange: string\nthe geometric mean of the jaccard similarity and the information content
URI: https://w3id.org/monarch/monarch-py/:phenodigm_score
"},{"location":"Data-Model/phenodigm_score/#inheritance","title":"Inheritance","text":"name: phenodigm_score\ndescription: the geometric mean of the jaccard similarity and the information content\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: score\nalias: phenodigm_score\ndomain_of:\n- TermPairwiseSimilarity\nrange: NonNegativeFloat\nequals_expression: sqrt({jaccard_similarity} * {information_content})\nURI: https://w3id.org/monarch/monarch-py/:predicate
"},{"location":"Data-Model/predicate/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CompactAssociation no Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/predicate/#properties","title":"Properties","text":"Range: String
Required: True
name: predicate\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: predicate\ndomain_of:\n- Association\n- CompactAssociation\nrange: string\nrequired: true\nmultivalued: false\nURI: https://w3id.org/monarch/monarch-py/:predicate_id
"},{"location":"Data-Model/predicate_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Mapping A minimal class to hold a SSSOM mapping no"},{"location":"Data-Model/predicate_id/#properties","title":"Properties","text":"Range: String
Required: True
name: predicate_id\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: predicate_id\ndomain_of:\n- Mapping\nrange: string\nrequired: true\nURI: https://w3id.org/monarch/monarch-py/:primary_knowledge_source
"},{"location":"Data-Model/primary_knowledge_source/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/primary_knowledge_source/#properties","title":"Properties","text":"name: primary_knowledge_source\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: primary_knowledge_source\ndomain_of:\n- Association\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:provided_by
"},{"location":"Data-Model/provided_by/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SearchResult no DirectionalAssociation An association that gives it's direction relative to a specified entity no Entity Represents an Entity in the Monarch KG data model no Association no Node UI container class extending Entity with additional information no"},{"location":"Data-Model/provided_by/#properties","title":"Properties","text":"name: provided_by\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: provided_by\ndomain_of:\n- Association\n- Entity\nrange: string\nA link to the docs for the knowledge source that provided the node/edge.
URI: https://w3id.org/monarch/monarch-py/:provided_by_link
"},{"location":"Data-Model/provided_by_link/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot DirectionalAssociation An association that gives it's direction relative to a specified entity no Association no Node UI container class extending Entity with additional information no"},{"location":"Data-Model/provided_by_link/#properties","title":"Properties","text":"name: provided_by_link\ndescription: A link to the docs for the knowledge source that provided the node/edge.\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: provided_by_link\ndomain_of:\n- Association\n- Node\nrange: ExpandedCurie\ninlined: true\nURI: https://w3id.org/monarch/monarch-py/:publications
"},{"location":"Data-Model/publications/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/publications/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: publications\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: publications\ndomain_of:\n- Association\nrange: string\nmultivalued: true\nList of ExpandedCuries with id and url for publications
URI: https://w3id.org/monarch/monarch-py/:publications_links
"},{"location":"Data-Model/publications_links/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/publications_links/#properties","title":"Properties","text":"Range: ExpandedCurie
Multivalued: True
name: publications_links\ndescription: List of ExpandedCuries with id and url for publications\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: publications_links\ndomain_of:\n- Association\nrange: ExpandedCurie\nmultivalued: true\ninlined: true\ninlined_as_list: true\nURI: https://w3id.org/monarch/monarch-py/:qc_report
"},{"location":"Data-Model/qc_report/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Release A class to hold information about a release of the Monarch KG no"},{"location":"Data-Model/qc_report/#properties","title":"Properties","text":"Instances of this class should have identifiers with one of the following prefixes:
name: qc_report\nid_prefixes:\n- string\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: qc_report\ndomain_of:\n- Release\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:qualifier
"},{"location":"Data-Model/qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/qualifier/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: qualifier\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: qualifier\ndomain_of:\n- Association\nrange: string\nmultivalued: true\nThe category of the frequency_qualifier entity
URI: https://w3id.org/monarch/monarch-py/:qualifier_category
"},{"location":"Data-Model/qualifier_category/#inheritance","title":"Inheritance","text":"name: qualifier_category\ndescription: The category of the frequency_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: category\nalias: qualifier_category\ndomain_of:\n- Association\nrange: string\nThe name of the frequency_qualifier entity
URI: https://w3id.org/monarch/monarch-py/:qualifier_label
"},{"location":"Data-Model/qualifier_label/#inheritance","title":"Inheritance","text":"name: qualifier_label\ndescription: The name of the frequency_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: name\nalias: qualifier_label\ndomain_of:\n- Association\nrange: string\nThe namespace/prefix of the frequency_qualifier entity
URI: https://w3id.org/monarch/monarch-py/:qualifier_namespace
"},{"location":"Data-Model/qualifier_namespace/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/qualifier_namespace/#properties","title":"Properties","text":"name: qualifier_namespace\ndescription: The namespace/prefix of the frequency_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: qualifier_namespace\ndomain_of:\n- Association\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:qualifiers
"},{"location":"Data-Model/qualifiers/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/qualifiers/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: qualifiers\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: qualifiers\ndomain_of:\n- Association\nrange: string\nmultivalued: true\nThe category of the frequency_qualifier entity
URI: https://w3id.org/monarch/monarch-py/:qualifiers_category
"},{"location":"Data-Model/qualifiers_category/#inheritance","title":"Inheritance","text":"name: qualifiers_category\ndescription: The category of the frequency_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: category\nalias: qualifiers_category\ndomain_of:\n- Association\nrange: string\nField containing frequency_qualifier id and the ids of all of it's ancestors
URI: https://w3id.org/monarch/monarch-py/:qualifiers_closure
"},{"location":"Data-Model/qualifiers_closure/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: qualifiers_closure\ndescription: Field containing frequency_qualifier id and the ids of all of it's ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: qualifiers_closure\nrange: string\nmultivalued: true\nField containing frequency_qualifier name and the names of all of it's ancestors
URI: https://w3id.org/monarch/monarch-py/:qualifiers_closure_label
"},{"location":"Data-Model/qualifiers_closure_label/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: qualifiers_closure_label\ndescription: Field containing frequency_qualifier name and the names of all of it's\n ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: qualifiers_closure_label\nrange: string\nmultivalued: true\nThe name of the frequency_qualifier entity
URI: https://w3id.org/monarch/monarch-py/:qualifiers_label
"},{"location":"Data-Model/qualifiers_label/#inheritance","title":"Inheritance","text":"name: qualifiers_label\ndescription: The name of the frequency_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: name\nalias: qualifiers_label\ndomain_of:\n- Association\nrange: string\nThe namespace/prefix of the frequency_qualifier entity
URI: https://w3id.org/monarch/monarch-py/:qualifiers_namespace
"},{"location":"Data-Model/qualifiers_namespace/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/qualifiers_namespace/#properties","title":"Properties","text":"name: qualifiers_namespace\ndescription: The namespace/prefix of the frequency_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: qualifiers_namespace\ndomain_of:\n- Association\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:score
"},{"location":"Data-Model/score/#inheritance","title":"Inheritance","text":"name: score\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: score\ndomain_of:\n- SearchResult\n- BestMatch\n- SemsimSearchResult\nrange: float\nURI: https://w3id.org/monarch/monarch-py/:sex_qualifier
"},{"location":"Data-Model/sex_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/sex_qualifier/#properties","title":"Properties","text":"name: sex_qualifier\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: sex_qualifier\ndomain_of:\n- Association\nrange: string\nThe category of the sex_qualifier entity
URI: https://w3id.org/monarch/monarch-py/:sex_qualifier_category
"},{"location":"Data-Model/sex_qualifier_category/#inheritance","title":"Inheritance","text":"name: sex_qualifier_category\ndescription: The category of the sex_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: category\nalias: sex_qualifier_category\ndomain_of:\n- Association\nrange: string\nThe name of the sex_qualifier entity
URI: https://w3id.org/monarch/monarch-py/:sex_qualifier_label
"},{"location":"Data-Model/sex_qualifier_label/#inheritance","title":"Inheritance","text":"name: sex_qualifier_label\ndescription: The name of the sex_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: name\nalias: sex_qualifier_label\ndomain_of:\n- Association\nrange: string\nThe namespace/prefix of the sex_qualifier entity
URI: https://w3id.org/monarch/monarch-py/:sex_qualifier_namespace
"},{"location":"Data-Model/sex_qualifier_namespace/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/sex_qualifier_namespace/#properties","title":"Properties","text":"name: sex_qualifier_namespace\ndescription: The namespace/prefix of the sex_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: sex_qualifier_namespace\ndomain_of:\n- Association\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:similarity
"},{"location":"Data-Model/similarity/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot BestMatch no SemsimSearchResult no"},{"location":"Data-Model/similarity/#properties","title":"Properties","text":"name: similarity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: similarity\ndomain_of:\n- BestMatch\n- SemsimSearchResult\nrange: TermSetPairwiseSimilarity\nURI: https://w3id.org/monarch/monarch-py/:solr
"},{"location":"Data-Model/solr/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Release A class to hold information about a release of the Monarch KG no"},{"location":"Data-Model/solr/#properties","title":"Properties","text":"Instances of this class should have identifiers with one of the following prefixes:
name: solr\nid_prefixes:\n- string\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: solr\ndomain_of:\n- Release\nrange: string\nA context qualifier representing a species in which a relationship expressed in an association took place.
URI: https://w3id.org/monarch/monarch-py/:species_context_qualifier
"},{"location":"Data-Model/species_context_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/species_context_qualifier/#properties","title":"Properties","text":"name: species_context_qualifier\ndescription: A context qualifier representing a species in which a relationship expressed\n in an association took place.\nexamples:\n- value: NCBITaxon:9606\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: species_context_qualifier\ndomain_of:\n- Association\nrange: string\nThe category of the species_context_qualifier entity
URI: https://w3id.org/monarch/monarch-py/:species_context_qualifier_category
"},{"location":"Data-Model/species_context_qualifier_category/#inheritance","title":"Inheritance","text":"name: species_context_qualifier_category\ndescription: The category of the species_context_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: category\nalias: species_context_qualifier_category\ndomain_of:\n- Association\nrange: string\nThe name of the species_context_qualifier entity
URI: https://w3id.org/monarch/monarch-py/:species_context_qualifier_label
"},{"location":"Data-Model/species_context_qualifier_label/#inheritance","title":"Inheritance","text":"name: species_context_qualifier_label\ndescription: The name of the species_context_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: name\nalias: species_context_qualifier_label\ndomain_of:\n- Association\nrange: string\nThe namespace/prefix of the species_context_qualifier entity
URI: https://w3id.org/monarch/monarch-py/:species_context_qualifier_namespace
"},{"location":"Data-Model/species_context_qualifier_namespace/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/species_context_qualifier_namespace/#properties","title":"Properties","text":"name: species_context_qualifier_namespace\ndescription: The namespace/prefix of the species_context_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: species_context_qualifier_namespace\ndomain_of:\n- Association\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:sqlite
"},{"location":"Data-Model/sqlite/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Release A class to hold information about a release of the Monarch KG no"},{"location":"Data-Model/sqlite/#properties","title":"Properties","text":"Instances of this class should have identifiers with one of the following prefixes:
name: sqlite\nid_prefixes:\n- string\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: sqlite\ndomain_of:\n- Release\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:stage_qualifier
"},{"location":"Data-Model/stage_qualifier/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/stage_qualifier/#properties","title":"Properties","text":"name: stage_qualifier\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: stage_qualifier\ndomain_of:\n- Association\nrange: string\nThe category of the stage_qualifier entity
URI: https://w3id.org/monarch/monarch-py/:stage_qualifier_category
"},{"location":"Data-Model/stage_qualifier_category/#inheritance","title":"Inheritance","text":"name: stage_qualifier_category\ndescription: The category of the stage_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: category\nalias: stage_qualifier_category\ndomain_of:\n- Association\nrange: string\nThe name of the stage_qualifier entity
URI: https://w3id.org/monarch/monarch-py/:stage_qualifier_label
"},{"location":"Data-Model/stage_qualifier_label/#inheritance","title":"Inheritance","text":"name: stage_qualifier_label\ndescription: The name of the stage_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: name\nalias: stage_qualifier_label\ndomain_of:\n- Association\nrange: string\nThe namespace/prefix of the stage_qualifier entity
URI: https://w3id.org/monarch/monarch-py/:stage_qualifier_namespace
"},{"location":"Data-Model/stage_qualifier_namespace/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/stage_qualifier_namespace/#properties","title":"Properties","text":"name: stage_qualifier_namespace\ndescription: The namespace/prefix of the stage_qualifier entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: stage_qualifier_namespace\ndomain_of:\n- Association\nrange: string\nstart position of the annotation
URI: https://w3id.org/monarch/monarch-py/:start
"},{"location":"Data-Model/start/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextAnnotationResult no"},{"location":"Data-Model/start/#properties","title":"Properties","text":"name: start\ndescription: start position of the annotation\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: start\ndomain_of:\n- TextAnnotationResult\nrange: integer\nURI: https://w3id.org/monarch/monarch-py/:sub_classes
"},{"location":"Data-Model/sub_classes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot NodeHierarchy no"},{"location":"Data-Model/sub_classes/#properties","title":"Properties","text":"Range: Entity
Multivalued: True
Required: True
name: sub_classes\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: sub_classes\ndomain_of:\n- NodeHierarchy\nrange: Entity\nrequired: true\nmultivalued: true\ninlined: true\ninlined_as_list: true\nURI: https://w3id.org/monarch/monarch-py/:subject
"},{"location":"Data-Model/subject/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot CompactAssociation no Association no SemsimSearchResult yes DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/subject/#properties","title":"Properties","text":"Range: String
Required: True
name: subject\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: subject\ndomain_of:\n- Association\n- CompactAssociation\n- SemsimSearchResult\nrange: string\nrequired: true\nURI: https://w3id.org/monarch/monarch-py/:subject_best_matches
"},{"location":"Data-Model/subject_best_matches/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermSetPairwiseSimilarity A simple pairwise similarity between two sets of concepts/terms no"},{"location":"Data-Model/subject_best_matches/#properties","title":"Properties","text":"Range: BestMatch
Multivalued: True
name: subject_best_matches\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: subject_best_matches\ndomain_of:\n- TermSetPairwiseSimilarity\nrange: BestMatch\nmultivalued: true\ninlined: true\nThe category of the subject entity
URI: https://w3id.org/monarch/monarch-py/:subject_category
"},{"location":"Data-Model/subject_category/#inheritance","title":"Inheritance","text":"name: subject_category\ndescription: The category of the subject entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: category\nalias: subject_category\ndomain_of:\n- Association\nrange: string\nField containing subject id and the ids of all of it's ancestors
URI: https://w3id.org/monarch/monarch-py/:subject_closure
"},{"location":"Data-Model/subject_closure/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/subject_closure/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: subject_closure\ndescription: Field containing subject id and the ids of all of it's ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: subject_closure\ndomain_of:\n- Association\nrange: string\nmultivalued: true\nField containing subject name and the names of all of it's ancestors
URI: https://w3id.org/monarch/monarch-py/:subject_closure_label
"},{"location":"Data-Model/subject_closure_label/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/subject_closure_label/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: subject_closure_label\ndescription: Field containing subject name and the names of all of it's ancestors\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: subject_closure_label\ndomain_of:\n- Association\nrange: string\nmultivalued: true\nURI: https://w3id.org/monarch/monarch-py/:subject_id
"},{"location":"Data-Model/subject_id/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms no Mapping A minimal class to hold a SSSOM mapping no"},{"location":"Data-Model/subject_id/#properties","title":"Properties","text":"Range: String
Required: True
name: subject_id\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: subject_id\ndomain_of:\n- Mapping\n- TermPairwiseSimilarity\nrange: string\nrequired: true\nThe IC of the subject
URI: https://w3id.org/monarch/monarch-py/:subject_information_content
"},{"location":"Data-Model/subject_information_content/#inheritance","title":"Inheritance","text":"name: subject_information_content\ndescription: The IC of the subject\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: information_content\nalias: subject_information_content\ndomain_of:\n- TermPairwiseSimilarity\nrange: NegativeLogValue\nThe name of the subject entity
URI: https://w3id.org/monarch/monarch-py/:subject_label
"},{"location":"Data-Model/subject_label/#inheritance","title":"Inheritance","text":"name: subject_label\ndescription: The name of the subject entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: name\nalias: subject_label\ndomain_of:\n- Association\n- CompactAssociation\n- AssociationTypeMapping\n- Mapping\n- TermPairwiseSimilarity\nrange: string\nThe namespace/prefix of the subject entity
URI: https://w3id.org/monarch/monarch-py/:subject_namespace
"},{"location":"Data-Model/subject_namespace/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Association no DirectionalAssociation An association that gives it's direction relative to a specified entity no"},{"location":"Data-Model/subject_namespace/#properties","title":"Properties","text":"name: subject_namespace\ndescription: The namespace/prefix of the subject entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: subject_namespace\ndomain_of:\n- Association\nrange: string\nthe source for the first entity
URI: sssom:subject_source
"},{"location":"Data-Model/subject_source/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermPairwiseSimilarity A simple pairwise similarity between two atomic concepts/terms no"},{"location":"Data-Model/subject_source/#properties","title":"Properties","text":"name: subject_source\ndescription: the source for the first entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nslot_uri: sssom:subject_source\nalias: subject_source\ndomain_of:\n- TermPairwiseSimilarity\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:subject_taxon
"},{"location":"Data-Model/subject_taxon/#inheritance","title":"Inheritance","text":"name: subject_taxon\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: in_taxon\nalias: subject_taxon\ndomain_of:\n- Association\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:subject_taxon_label
"},{"location":"Data-Model/subject_taxon_label/#inheritance","title":"Inheritance","text":"name: subject_taxon_label\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: in_taxon_label\nalias: subject_taxon_label\ndomain_of:\n- Association\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:subject_termset
"},{"location":"Data-Model/subject_termset/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TermSetPairwiseSimilarity A simple pairwise similarity between two sets of concepts/terms no"},{"location":"Data-Model/subject_termset/#properties","title":"Properties","text":"Range: TermInfo
Multivalued: True
name: subject_termset\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: subject_termset\ndomain_of:\n- TermSetPairwiseSimilarity\nrange: TermInfo\nmultivalued: true\ninlined: true\nURI: https://w3id.org/monarch/monarch-py/:subsumed_by_score
"},{"location":"Data-Model/subsumed_by_score/#inheritance","title":"Inheritance","text":"name: subsumed_by_score\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: score\nalias: subsumed_by_score\nrange: ZeroToOne\nURI: https://w3id.org/monarch/monarch-py/:subsumes_score
"},{"location":"Data-Model/subsumes_score/#inheritance","title":"Inheritance","text":"name: subsumes_score\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: score\nalias: subsumes_score\nrange: ZeroToOne\nURI: https://w3id.org/monarch/monarch-py/:super_classes
"},{"location":"Data-Model/super_classes/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot NodeHierarchy no"},{"location":"Data-Model/super_classes/#properties","title":"Properties","text":"Range: Entity
Multivalued: True
Required: True
name: super_classes\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: super_classes\ndomain_of:\n- NodeHierarchy\nrange: Entity\nrequired: true\nmultivalued: true\ninlined: true\ninlined_as_list: true\nURI: https://w3id.org/monarch/monarch-py/:symbol
"},{"location":"Data-Model/symbol/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SearchResult no Node UI container class extending Entity with additional information no Entity Represents an Entity in the Monarch KG data model no"},{"location":"Data-Model/symbol/#properties","title":"Properties","text":"name: symbol\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: symbol\ndomain_of:\n- Entity\nrange: string\nWhether the association type is symmetric, i.e. the subject and object labels are interchangeable.
URI: https://w3id.org/monarch/monarch-py/:symmetric
"},{"location":"Data-Model/symmetric/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot AssociationTypeMapping A data class to hold the necessary information to produce association type co... yes"},{"location":"Data-Model/symmetric/#properties","title":"Properties","text":"name: symmetric\ndescription: Whether the association type is symmetric, i.e. the subject and object\n labels are interchangeable.\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: symmetric\ndomain_of:\n- AssociationTypeMapping\nrange: boolean\nURI: https://w3id.org/monarch/monarch-py/:synonym
"},{"location":"Data-Model/synonym/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SearchResult no Node UI container class extending Entity with additional information no Entity Represents an Entity in the Monarch KG data model no"},{"location":"Data-Model/synonym/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: synonym\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: synonym\ndomain_of:\n- Entity\nrange: string\nmultivalued: true\ntext without tokens
URI: https://w3id.org/monarch/monarch-py/:text
"},{"location":"Data-Model/text/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextAnnotationResult no"},{"location":"Data-Model/text/#properties","title":"Properties","text":"name: text\ndescription: text without tokens\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: text\ndomain_of:\n- TextAnnotationResult\nrange: string\ninlined: true\nA collection of entities or concepts
URI: https://w3id.org/monarch/monarch-py/:tokens
"},{"location":"Data-Model/tokens/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot TextAnnotationResult no"},{"location":"Data-Model/tokens/#properties","title":"Properties","text":"Range: Entity
Multivalued: True
name: tokens\ndescription: A collection of entities or concepts\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: tokens\ndomain_of:\n- TextAnnotationResult\nrange: Entity\nmultivalued: true\ninlined: true\ninlined_as_list: true\ntotal number of items matching a query
URI: https://w3id.org/monarch/monarch-py/:total
"},{"location":"Data-Model/total/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot MappingResults SSSOM Mappings returned as a results collection no AssociationTableResults no SearchResults no EntityResults no MultiEntityAssociationResults no CategoryGroupedAssociationResults no Results no CompactAssociationResults no AssociationResults no"},{"location":"Data-Model/total/#properties","title":"Properties","text":"Range: Integer
Required: True
name: total\ndescription: total number of items matching a query\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: total\ndomain_of:\n- Results\nrange: integer\nrequired: true\nURI: https://w3id.org/monarch/monarch-py/:union_count
"},{"location":"Data-Model/union_count/#inheritance","title":"Inheritance","text":"name: union_count\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nis_a: score\nalias: union_count\nrange: ItemCount\nThe URI of the entity
URI: https://w3id.org/monarch/monarch-py/:uri
"},{"location":"Data-Model/uri/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SearchResult no Node UI container class extending Entity with additional information no Entity Represents an Entity in the Monarch KG data model no"},{"location":"Data-Model/uri/#properties","title":"Properties","text":"name: uri\ndescription: The URI of the entity\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: uri\ndomain_of:\n- Entity\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:url
"},{"location":"Data-Model/url/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Release A class to hold information about a release of the Monarch KG no ExpandedCurie A curie bundled along with its expanded url no"},{"location":"Data-Model/url/#properties","title":"Properties","text":"name: url\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: url\ndomain_of:\n- ExpandedCurie\n- Release\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:version
"},{"location":"Data-Model/version/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot Release A class to hold information about a release of the Monarch KG no"},{"location":"Data-Model/version/#properties","title":"Properties","text":"Instances of this class should have identifiers with one of the following prefixes:
name: version\nid_prefixes:\n- string\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: version\ndomain_of:\n- Release\nrange: string\nURI: https://w3id.org/monarch/monarch-py/:xref
"},{"location":"Data-Model/xref/#applicable-classes","title":"Applicable Classes","text":"Name Description Modifies Slot SearchResult no Node UI container class extending Entity with additional information no Entity Represents an Entity in the Monarch KG data model no"},{"location":"Data-Model/xref/#properties","title":"Properties","text":"Range: String
Multivalued: True
name: xref\nfrom_schema: https://w3id.org/monarch/monarch-py\nrank: 1000\nalias: xref\ndomain_of:\n- Entity\nrange: string\nmultivalued: true\nA FastAPI is also available for browsing the knowledge graph produced by the Monarch Initiative, which wraps the monarch-py library.
It is included automatically as part of monarch-py when installed via pip or pipx.
A local development server can be started with the command:
monarch-api\nor using uvicorn:
# Using uvicorn directly:\npoetry run uvicorn src.monarch_py.api.main:app --reload\n\n# Using the Makefile shortcut:\ncd <path-to>/monarch-app\nmake dev-api\nThe API is then available at http://127.0.0.1:8000/v3/api.
Swagger documentation is available at http://127.0.0.1:8000/v3/docs, and a ReDoc interface at http://127.0.0.1:8000/v3/redoc.
API Reference
Data Response Model
"},{"location":"FastAPI/Endpoints/","title":"Monarch API Endpoints","text":"This section contains API reference for the various endpoints provided by monarch-api.
autocomplete","text":"Autocomplete for semantic similarity lookups, prioritizes entities which have direct phenotype associations. Note: This API endpoint is experimental and may evolve or disappear over time.
Parameters:
Name Type Description Defaultq str Query string to autocomplete against
Query(default='*:*', title='Query string to autocomplete against', examples=['fanc', 'ehler']) Returns:
Type DescriptionSearchResults SearchResults
"},{"location":"Usage/","title":"Usage","text":"monarch-py can be used via command line, or as a Python module.
"},{"location":"Usage/#cli","title":"CLI","text":""},{"location":"Usage/#overview","title":"Overview","text":"monarch-py can be used to query various implementations of the Monarch knowledge graph. The default, and more feature-rich, implementation is Solr, and is the default.
Subcommands are available to specify the backend.
For example:
# The following two commands are equivalent,\n# as both query the Solr KG\n$ monarch entity MONDO:0012933 \n$ monarch solr entity MONDO:0012933\n\n# Whereas the following specifies the SQL implementation\n$ monarch sql entity MONDO:0012933\nYou can also use an environment variable to specify a Solr URL to query a different Solr instance. monarch-py checks for the MONARCH_SOLR_URL environment variable, and uses it if it exists. If not, it uses the default Solr URL of http://localhost:8983/solr.
CLI commands are listed here, or can be found by running monarch --help.
TBD
"},{"location":"Usage/CLI/","title":"monarch","text":"Usage:
$ monarch [OPTIONS] COMMAND [ARGS]...\nOptions:
-v, --version: Show the currently installed version-q, --quiet: Set log level to warning-d, --debug: Set log level to debug--install-completion: Install completion for the current shell.--show-completion: Show completion for the current shell, to copy it or customize the installation.--help: Show this message and exit.Commands:
association-counts: Retrieve the association counts for a...association-tableassociations: Paginate through associationsautocomplete: Return entity autcomplete matches for a...compare: Compare two sets of phenotypes using...entity: Retrieve an entity by IDhistopheno: Retrieve the histopheno associations for a...mappingsmulti-entity-associations: Paginate through associations for multiple...release: Retrieve metadata for a specific releasereleases: List all available releases of the Monarch...schema: Print the linkml schema for the data modelsearch: Search for entitiessolrsqltest: Test the CLImonarch association-counts","text":"Retrieve the association counts for a given entity
Usage:
$ monarch association-counts [OPTIONS] ENTITY_ID\nArguments:
ENTITY_ID: The entity to get association counts for [required]Options:
-f, --format [json|yaml|tsv|table]: The format of the output (json, yaml, tsv, table) [default: json]-O, --output TEXT: Path to file to write command output (stdout if not specified)--help: Show this message and exit.monarch association-table","text":"Usage:
$ monarch association-table [OPTIONS] ENTITY_ID CATEGORY:{biolink:PairwiseGeneToGeneInteraction|biolink:GeneToExpressionSiteAssociation|biolink:VariantToGeneAssociation|biolink:MacromolecularMachineToBiologicalProcessAssociation|biolink:GeneToPhenotypicFeatureAssociation|biolink:MacromolecularMachineToMolecularActivityAssociation|biolink:MacromolecularMachineToCellularComponentAssociation|biolink:Association|biolink:GeneToGeneHomologyAssociation|biolink:GenotypeToPhenotypicFeatureAssociation|biolink:DiseaseToPhenotypicFeatureAssociation|biolink:GeneToPathwayAssociation|biolink:DiseaseOrPhenotypicFeatureToLocationAssociation|biolink:ChemicalToPathwayAssociation|biolink:GenotypeToDiseaseAssociation|biolink:CorrelatedGeneToDiseaseAssociation|biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation|biolink:VariantToDiseaseAssociation|biolink:CausalGeneToDiseaseAssociation|biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation}\nArguments:
ENTITY_ID: The entity to get associations for [required]CATEGORY:{biolink:PairwiseGeneToGeneInteraction|biolink:GeneToExpressionSiteAssociation|biolink:VariantToGeneAssociation|biolink:MacromolecularMachineToBiologicalProcessAssociation|biolink:GeneToPhenotypicFeatureAssociation|biolink:MacromolecularMachineToMolecularActivityAssociation|biolink:MacromolecularMachineToCellularComponentAssociation|biolink:Association|biolink:GeneToGeneHomologyAssociation|biolink:GenotypeToPhenotypicFeatureAssociation|biolink:DiseaseToPhenotypicFeatureAssociation|biolink:GeneToPathwayAssociation|biolink:DiseaseOrPhenotypicFeatureToLocationAssociation|biolink:ChemicalToPathwayAssociation|biolink:GenotypeToDiseaseAssociation|biolink:CorrelatedGeneToDiseaseAssociation|biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation|biolink:VariantToDiseaseAssociation|biolink:CausalGeneToDiseaseAssociation|biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation}: The association category to get associations for, ex. biolink:GeneToPhenotypicFeatureAssociation [required]Options:
-q, --query TEXT-t, --traverse-orthologs: Whether to traverse orthologs when getting associations-s, --sort TEXT-l, --limit INTEGER: The number of results to return [default: 20]--offset INTEGER: The offset of the first result to be retrieved [default: 0]-f, --format [json|yaml|tsv|table]: The format of the output (json, yaml, tsv, table) [default: json]-O, --output TEXT: Path to file to write command output (stdout if not specified)--help: Show this message and exit.monarch associations","text":"Paginate through associations
Usage:
$ monarch associations [OPTIONS]\nOptions:
-c, --category [biolink:PairwiseGeneToGeneInteraction|biolink:GeneToExpressionSiteAssociation|biolink:VariantToGeneAssociation|biolink:MacromolecularMachineToBiologicalProcessAssociation|biolink:GeneToPhenotypicFeatureAssociation|biolink:MacromolecularMachineToMolecularActivityAssociation|biolink:MacromolecularMachineToCellularComponentAssociation|biolink:Association|biolink:GeneToGeneHomologyAssociation|biolink:GenotypeToPhenotypicFeatureAssociation|biolink:DiseaseToPhenotypicFeatureAssociation|biolink:GeneToPathwayAssociation|biolink:DiseaseOrPhenotypicFeatureToLocationAssociation|biolink:ChemicalToPathwayAssociation|biolink:GenotypeToDiseaseAssociation|biolink:CorrelatedGeneToDiseaseAssociation|biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation|biolink:VariantToDiseaseAssociation|biolink:CausalGeneToDiseaseAssociation|biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation]: Category to get associations for-s, --subject TEXT: Subject ID to get associations for-p, --predicate [biolink:interacts_with|biolink:expressed_in|biolink:has_phenotype|biolink:is_sequence_variant_of|biolink:enables|biolink:actively_involved_in|biolink:orthologous_to|biolink:located_in|biolink:subclass_of|biolink:related_to|biolink:participates_in|biolink:acts_upstream_of_or_within|biolink:active_in|biolink:part_of|biolink:model_of|biolink:causes|biolink:acts_upstream_of|biolink:has_mode_of_inheritance|biolink:contributes_to|biolink:gene_associated_with_condition|biolink:treats_or_applied_or_studied_to_treat|biolink:colocalizes_with|biolink:acts_upstream_of_positive_effect|biolink:acts_upstream_of_or_within_positive_effect|biolink:acts_upstream_of_negative_effect|biolink:acts_upstream_of_or_within_negative_effect]: Predicate ID to get associations for-o, --object TEXT: Object ID to get associations for-e, --entity TEXT: Entity (subject or object) ID to get associations for-d, --direct: Whether to exclude associations with subject/object as ancestors-C, --compact: Whether to return a compact representation of the associations-l, --limit INTEGER: The number of results to return [default: 20]--offset INTEGER: The offset of the first result to be retrieved [default: 0]-f, --format [json|yaml|tsv|table]: The format of the output (json, yaml, tsv, table) [default: json]-O, --output TEXT: Path to file to write command output (stdout if not specified)--help: Show this message and exit.monarch autocomplete","text":"Return entity autcomplete matches for a query string
Usage:
$ monarch autocomplete [OPTIONS] Q\nArguments:
Q: Query string to autocomplete against [required]Options:
-f, --format [json|yaml|tsv|table]: The format of the output (json, yaml, tsv, table) [default: json]-O, --output TEXT: Path to file to write command output (stdout if not specified)--help: Show this message and exit.monarch compare","text":"Compare two sets of phenotypes using semantic similarity via SemSimian
Usage:
$ monarch compare [OPTIONS] SUBJECTS OBJECTS\nArguments:
SUBJECTS: Comma separated list of subjects to compare [required]OBJECTS: Comma separated list of objects to compare [required]Options:
-m, --metric [ancestor_information_content|jaccard_similarity|phenodigm_score]: The metric to use for comparison [default: ancestor_information_content]-f, --format [json|yaml|tsv|table]: The format of the output (json, yaml, tsv, table) [default: json]-O, --output TEXT: Path to file to write command output (stdout if not specified)--help: Show this message and exit.monarch entity","text":"Retrieve an entity by ID
Usage:
$ monarch entity [OPTIONS] ENTITY_ID\nArguments:
ENTITY_ID: The identifier of the entity to be retrieved [required]Options:
-e, --extra: Include extra fields in the output (association_counts and node_hierarchy)-f, --format [json|yaml|tsv|table]: The format of the output (json, yaml, tsv, table) [default: json]-O, --output TEXT: Path to file to write command output (stdout if not specified)--help: Show this message and exit.monarch histopheno","text":"Retrieve the histopheno associations for a given subject
Usage:
$ monarch histopheno [OPTIONS] SUBJECT\nArguments:
SUBJECT: The subject of the association [required]Options:
-f, --format [json|yaml|tsv|table]: The format of the output (json, yaml, tsv, table) [default: json]-O, --output TEXT: Path to file to write command output (stdout if not specified)--help: Show this message and exit.monarch mappings","text":"Usage:
$ monarch mappings [OPTIONS]\nOptions:
-e, --entity-id TEXT: entity ID to get mappings for-s, --subject-id TEXT: subject ID to get mappings for-p, --predicate-id [skos:exactMatch|skos:broadMatch]: predicate ID to get mappings for-o, --object-id TEXT: object ID to get mappings for-m, --mapping-justification TEXT: mapping justification to get mappings for-l, --limit INTEGER: The number of results to return [default: 20]--offset INTEGER: The offset of the first result to be retrieved [default: 0]-f, --format [json|yaml|tsv|table]: The format of the output (json, yaml, tsv, table) [default: json]-O, --output TEXT: Path to file to write command output (stdout if not specified)--help: Show this message and exit.monarch multi-entity-associations","text":"Paginate through associations for multiple entities
Usage:
$ monarch multi-entity-associations [OPTIONS]\nOptions:
-e, --entity TEXT: Comma-separated list of entities-c, --counterpart-category TEXT: A comma-separated list of counterpart categories-l, --limit INTEGER: The number of results to return [default: 20]--offset INTEGER: The offset of the first result to be retrieved [default: 0]-f, --format [json|yaml|tsv|table]: The format of the output (json, yaml, tsv, table) [default: json]-O, --output TEXT: Path to file to write command output (stdout if not specified)--help: Show this message and exit.monarch release","text":"Retrieve metadata for a specific release
Usage:
$ monarch release [OPTIONS] RELEASE_VER\nArguments:
RELEASE_VER: The release version to get metadata for [required]Options:
-f, --format [json|yaml|tsv|table]: The format of the output (json, yaml, tsv, table) [default: json]-O, --output TEXT: Path to file to write command output (stdout if not specified)--help: Show this message and exit.monarch releases","text":"List all available releases of the Monarch Knowledge Graph
Usage:
$ monarch releases [OPTIONS]\nOptions:
--dev: Get dev releases of the KG (default is False)-l, --limit INTEGER: The number of results to return [default: 0]--help: Show this message and exit.monarch schema","text":"Print the linkml schema for the data model
Usage:
$ monarch schema [OPTIONS]\nOptions:
--help: Show this message and exit.monarch search","text":"Search for entities
Usage:
$ monarch search [OPTIONS]\nOptions:
-q, --query TEXT: [default: :*]-c, --category [biolink:SequenceVariant|biolink:Gene|biolink:Genotype|biolink:PhenotypicFeature|biolink:BiologicalProcessOrActivity|biolink:Disease|biolink:GrossAnatomicalStructure|biolink:Cell|biolink:Pathway|biolink:NamedThing|biolink:AnatomicalEntity|biolink:CellularComponent|biolink:MolecularEntity|biolink:BiologicalProcess|biolink:MacromolecularComplex|biolink:MolecularActivity|biolink:Protein|biolink:CellularOrganism|biolink:Vertebrate|biolink:Virus|biolink:BehavioralFeature|biolink:ChemicalEntity|biolink:LifeStage|biolink:PathologicalProcess|biolink:Drug|biolink:SmallMolecule|biolink:OrganismTaxon|biolink:InformationContentEntity|biolink:NucleicAcidEntity|biolink:EvidenceType|biolink:RNAProduct|biolink:Transcript|biolink:Fungus|biolink:Plant|biolink:ProcessedMaterial|biolink:Activity|biolink:Agent|biolink:ConfidenceLevel|biolink:Dataset|biolink:EnvironmentalFeature|biolink:GeneticInheritance|biolink:Haplotype|biolink:Invertebrate|biolink:Mammal|biolink:PopulationOfIndividualOrganisms|biolink:ProteinFamily|biolink:Publication|biolink:AccessibleDnaRegion|biolink:Bacterium|biolink:BiologicalSex|biolink:CellLine|biolink:ChemicalExposure|biolink:ChemicalMixture|biolink:DatasetDistribution|biolink:DiagnosticAid|biolink:DrugExposure|biolink:EnvironmentalProcess|biolink:Event|biolink:Exon|biolink:Genome|biolink:GenotypicSex|biolink:Human|biolink:IndividualOrganism|biolink:MaterialSample|biolink:MicroRNA|biolink:OrganismalEntity|biolink:Patent|biolink:PhenotypicSex|biolink:Polypeptide|biolink:ProteinDomain|biolink:ReagentTargetedGene|biolink:RegulatoryRegion|biolink:SiRNA|biolink:Snv|biolink:Study|biolink:StudyVariable|biolink:TranscriptionFactorBindingSite|biolink:Treatment|biolink:WebPage|biolink:Zygosity]-t, --in-taxon-label TEXT-ff, --facet-fields TEXT-fq, --facet-queries TEXT-l, --limit INTEGER: The number of results to return [default: 20]--offset INTEGER: The offset of the first result to be retrieved [default: 0]-f, --format [json|yaml|tsv|table]: The format of the output (json, yaml, tsv, table) [default: json]-O, --output TEXT: Path to file to write command output (stdout if not specified)--help: Show this message and exit.monarch solr","text":"Usage:
$ monarch solr [OPTIONS] COMMAND [ARGS]...\nOptions:
-q, --quiet: Set log level to warning-d, --debug: Set log level to debug--help: Show this message and exit.Commands:
association-counts: Retrieve the association counts for a...association-tableassociations: Paginate through associationsautocomplete: Return entity autcomplete matches for a...download: Download the Monarch Solr KG.entity: Retrieve an entity by IDhistopheno: Retrieve the histopheno associations for a...mappingsmulti-entity-associations: Paginate through associations for multiple...search: Search for entitiesstart: Starts a local Solr container.status: Checks the status of the local Solr...stop: Stops the local Solr container.monarch solr association-counts","text":"Retrieve the association counts for a given entity
Usage:
$ monarch solr association-counts [OPTIONS] ENTITY_ID\nArguments:
ENTITY_ID: The entity to get association counts for [required]Options:
-f, --format [json|yaml|tsv|table]: The format of the output (json, yaml, tsv, table) [default: json]-O, --output TEXT: Path to file to write command output (stdout if not specified)--help: Show this message and exit.monarch solr association-table","text":"Usage:
$ monarch solr association-table [OPTIONS] ENTITY_ID CATEGORY:{biolink:PairwiseGeneToGeneInteraction|biolink:GeneToExpressionSiteAssociation|biolink:VariantToGeneAssociation|biolink:MacromolecularMachineToBiologicalProcessAssociation|biolink:GeneToPhenotypicFeatureAssociation|biolink:MacromolecularMachineToMolecularActivityAssociation|biolink:MacromolecularMachineToCellularComponentAssociation|biolink:Association|biolink:GeneToGeneHomologyAssociation|biolink:GenotypeToPhenotypicFeatureAssociation|biolink:DiseaseToPhenotypicFeatureAssociation|biolink:GeneToPathwayAssociation|biolink:DiseaseOrPhenotypicFeatureToLocationAssociation|biolink:ChemicalToPathwayAssociation|biolink:GenotypeToDiseaseAssociation|biolink:CorrelatedGeneToDiseaseAssociation|biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation|biolink:VariantToDiseaseAssociation|biolink:CausalGeneToDiseaseAssociation|biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation}\nArguments:
ENTITY_ID: The entity to get associations for [required]CATEGORY:{biolink:PairwiseGeneToGeneInteraction|biolink:GeneToExpressionSiteAssociation|biolink:VariantToGeneAssociation|biolink:MacromolecularMachineToBiologicalProcessAssociation|biolink:GeneToPhenotypicFeatureAssociation|biolink:MacromolecularMachineToMolecularActivityAssociation|biolink:MacromolecularMachineToCellularComponentAssociation|biolink:Association|biolink:GeneToGeneHomologyAssociation|biolink:GenotypeToPhenotypicFeatureAssociation|biolink:DiseaseToPhenotypicFeatureAssociation|biolink:GeneToPathwayAssociation|biolink:DiseaseOrPhenotypicFeatureToLocationAssociation|biolink:ChemicalToPathwayAssociation|biolink:GenotypeToDiseaseAssociation|biolink:CorrelatedGeneToDiseaseAssociation|biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation|biolink:VariantToDiseaseAssociation|biolink:CausalGeneToDiseaseAssociation|biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation}: The association category to get associations for, ex. biolink:GeneToPhenotypicFeatureAssociation [required]Options:
-q, --query TEXT-t, --traverse-orthologs: Whether to traverse orthologs when getting associations-s, --sort TEXT-l, --limit INTEGER: The number of results to return [default: 20]--offset INTEGER: The offset of the first result to be retrieved [default: 0]-f, --format [json|yaml|tsv|table]: The format of the output (json, yaml, tsv, table) [default: json]-O, --output TEXT: Path to file to write command output (stdout if not specified)--help: Show this message and exit.monarch solr associations","text":"Paginate through associations
Usage:
$ monarch solr associations [OPTIONS]\nOptions:
-c, --category [biolink:PairwiseGeneToGeneInteraction|biolink:GeneToExpressionSiteAssociation|biolink:VariantToGeneAssociation|biolink:MacromolecularMachineToBiologicalProcessAssociation|biolink:GeneToPhenotypicFeatureAssociation|biolink:MacromolecularMachineToMolecularActivityAssociation|biolink:MacromolecularMachineToCellularComponentAssociation|biolink:Association|biolink:GeneToGeneHomologyAssociation|biolink:GenotypeToPhenotypicFeatureAssociation|biolink:DiseaseToPhenotypicFeatureAssociation|biolink:GeneToPathwayAssociation|biolink:DiseaseOrPhenotypicFeatureToLocationAssociation|biolink:ChemicalToPathwayAssociation|biolink:GenotypeToDiseaseAssociation|biolink:CorrelatedGeneToDiseaseAssociation|biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation|biolink:VariantToDiseaseAssociation|biolink:CausalGeneToDiseaseAssociation|biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation]: Category to get associations for-s, --subject TEXT: Subject ID to get associations for-p, --predicate [biolink:interacts_with|biolink:expressed_in|biolink:has_phenotype|biolink:is_sequence_variant_of|biolink:enables|biolink:actively_involved_in|biolink:orthologous_to|biolink:located_in|biolink:subclass_of|biolink:related_to|biolink:participates_in|biolink:acts_upstream_of_or_within|biolink:active_in|biolink:part_of|biolink:model_of|biolink:causes|biolink:acts_upstream_of|biolink:has_mode_of_inheritance|biolink:contributes_to|biolink:gene_associated_with_condition|biolink:treats_or_applied_or_studied_to_treat|biolink:colocalizes_with|biolink:acts_upstream_of_positive_effect|biolink:acts_upstream_of_or_within_positive_effect|biolink:acts_upstream_of_negative_effect|biolink:acts_upstream_of_or_within_negative_effect]: Predicate ID to get associations for-o, --object TEXT: Object ID to get associations for-e, --entity TEXT: Entity (subject or object) ID to get associations for-d, --direct: Whether to exclude associations with subject/object as ancestors-C, --compact: Whether to return a compact representation of the associations-l, --limit INTEGER: The number of results to return [default: 20]--offset INTEGER: The offset of the first result to be retrieved [default: 0]-f, --format [json|yaml|tsv|table]: The format of the output (json, yaml, tsv, table) [default: json]-O, --output TEXT: Path to file to write command output (stdout if not specified)--help: Show this message and exit.monarch solr autocomplete","text":"Return entity autcomplete matches for a query string
Usage:
$ monarch solr autocomplete [OPTIONS] Q\nArguments:
Q: Query string to autocomplete against [required]Options:
-f, --format [json|yaml|tsv|table]: The format of the output (json, yaml, tsv, table) [default: json]-O, --output TEXT: Path to file to write command output (stdout if not specified)--help: Show this message and exit.monarch solr download","text":"Download the Monarch Solr KG.
Usage:
$ monarch solr download [OPTIONS] [VERSION]\nArguments:
[VERSION]: The version of the Solr KG to download (latest, dev, or a specific version) [default: latest]Options:
--overwrite: Overwrite the existing Solr KG if it exists--help: Show this message and exit.monarch solr entity","text":"Retrieve an entity by ID
Usage:
$ monarch solr entity [OPTIONS] ENTITY_ID\nArguments:
ENTITY_ID: The identifier of the entity to be retrieved [required]Options:
-e, --extra: Include extra fields in the output (association_counts and node_hierarchy)-f, --format [json|yaml|tsv|table]: The format of the output (json, yaml, tsv, table) [default: json]-O, --output TEXT: Path to file to write command output (stdout if not specified)--help: Show this message and exit.monarch solr histopheno","text":"Retrieve the histopheno associations for a given subject
Usage:
$ monarch solr histopheno [OPTIONS] SUBJECT\nArguments:
SUBJECT: The subject of the association [required]Options:
-f, --format [json|yaml|tsv|table]: The format of the output (json, yaml, tsv, table) [default: json]-O, --output TEXT: Path to file to write command output (stdout if not specified)--help: Show this message and exit.monarch solr mappings","text":"Usage:
$ monarch solr mappings [OPTIONS]\nOptions:
-e, --entity-id TEXT: entity ID to get mappings for-s, --subject-id TEXT: subject ID to get mappings for-p, --predicate-id [skos:exactMatch|skos:broadMatch]: predicate ID to get mappings for-o, --object-id TEXT: object ID to get mappings for-m, --mapping-justification TEXT: mapping justification to get mappings for-l, --limit INTEGER: The number of results to return [default: 20]--offset INTEGER: The offset of the first result to be retrieved [default: 0]-f, --format [json|yaml|tsv|table]: The format of the output (json, yaml, tsv, table) [default: json]-O, --output TEXT: Path to file to write command output (stdout if not specified)--help: Show this message and exit.monarch solr multi-entity-associations","text":"Paginate through associations for multiple entities
Usage:
$ monarch solr multi-entity-associations [OPTIONS]\nOptions:
-e, --entity TEXT: Comma-separated list of entities-c, --counterpart-category TEXT: A comma-separated list of counterpart categories-l, --limit INTEGER: The number of results to return [default: 20]--offset INTEGER: The offset of the first result to be retrieved [default: 0]-f, --format [json|yaml|tsv|table]: The format of the output (json, yaml, tsv, table) [default: json]-O, --output TEXT: Path to file to write command output (stdout if not specified)--help: Show this message and exit.monarch solr search","text":"Search for entities
Usage:
$ monarch solr search [OPTIONS]\nOptions:
-q, --query TEXT: [default: :*]-c, --category [biolink:SequenceVariant|biolink:Gene|biolink:Genotype|biolink:PhenotypicFeature|biolink:BiologicalProcessOrActivity|biolink:Disease|biolink:GrossAnatomicalStructure|biolink:Cell|biolink:Pathway|biolink:NamedThing|biolink:AnatomicalEntity|biolink:CellularComponent|biolink:MolecularEntity|biolink:BiologicalProcess|biolink:MacromolecularComplex|biolink:MolecularActivity|biolink:Protein|biolink:CellularOrganism|biolink:Vertebrate|biolink:Virus|biolink:BehavioralFeature|biolink:ChemicalEntity|biolink:LifeStage|biolink:PathologicalProcess|biolink:Drug|biolink:SmallMolecule|biolink:OrganismTaxon|biolink:InformationContentEntity|biolink:NucleicAcidEntity|biolink:EvidenceType|biolink:RNAProduct|biolink:Transcript|biolink:Fungus|biolink:Plant|biolink:ProcessedMaterial|biolink:Activity|biolink:Agent|biolink:ConfidenceLevel|biolink:Dataset|biolink:EnvironmentalFeature|biolink:GeneticInheritance|biolink:Haplotype|biolink:Invertebrate|biolink:Mammal|biolink:PopulationOfIndividualOrganisms|biolink:ProteinFamily|biolink:Publication|biolink:AccessibleDnaRegion|biolink:Bacterium|biolink:BiologicalSex|biolink:CellLine|biolink:ChemicalExposure|biolink:ChemicalMixture|biolink:DatasetDistribution|biolink:DiagnosticAid|biolink:DrugExposure|biolink:EnvironmentalProcess|biolink:Event|biolink:Exon|biolink:Genome|biolink:GenotypicSex|biolink:Human|biolink:IndividualOrganism|biolink:MaterialSample|biolink:MicroRNA|biolink:OrganismalEntity|biolink:Patent|biolink:PhenotypicSex|biolink:Polypeptide|biolink:ProteinDomain|biolink:ReagentTargetedGene|biolink:RegulatoryRegion|biolink:SiRNA|biolink:Snv|biolink:Study|biolink:StudyVariable|biolink:TranscriptionFactorBindingSite|biolink:Treatment|biolink:WebPage|biolink:Zygosity]-t, --in-taxon-label TEXT-ff, --facet-fields TEXT-fq, --facet-queries TEXT-l, --limit INTEGER: The number of results to return [default: 20]--offset INTEGER: The offset of the first result to be retrieved [default: 0]-f, --format [json|yaml|tsv|table]: The format of the output (json, yaml, tsv, table) [default: json]-O, --output TEXT: Path to file to write command output (stdout if not specified)--help: Show this message and exit.monarch solr start","text":"Starts a local Solr container.
Usage:
$ monarch solr start [OPTIONS]\nOptions:
--update / --no-update: [default: no-update]--help: Show this message and exit.monarch solr status","text":"Checks the status of the local Solr container.
Usage:
$ monarch solr status [OPTIONS]\nOptions:
--help: Show this message and exit.monarch solr stop","text":"Stops the local Solr container.
Usage:
$ monarch solr stop [OPTIONS]\nOptions:
--help: Show this message and exit.monarch sql","text":"Usage:
$ monarch sql [OPTIONS] COMMAND [ARGS]...\nOptions:
-q, --quiet: Set log level to warning-d, --debug: Set log level to debug--help: Show this message and exit.Commands:
associations: Paginate through associationsentity: Retrieve an entity by IDmonarch sql associations","text":"Paginate through associations
Usage:
$ monarch sql associations [OPTIONS]\nOptions:
-c, --category [biolink:PairwiseGeneToGeneInteraction|biolink:GeneToExpressionSiteAssociation|biolink:VariantToGeneAssociation|biolink:MacromolecularMachineToBiologicalProcessAssociation|biolink:GeneToPhenotypicFeatureAssociation|biolink:MacromolecularMachineToMolecularActivityAssociation|biolink:MacromolecularMachineToCellularComponentAssociation|biolink:Association|biolink:GeneToGeneHomologyAssociation|biolink:GenotypeToPhenotypicFeatureAssociation|biolink:DiseaseToPhenotypicFeatureAssociation|biolink:GeneToPathwayAssociation|biolink:DiseaseOrPhenotypicFeatureToLocationAssociation|biolink:ChemicalToPathwayAssociation|biolink:GenotypeToDiseaseAssociation|biolink:CorrelatedGeneToDiseaseAssociation|biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation|biolink:VariantToDiseaseAssociation|biolink:CausalGeneToDiseaseAssociation|biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation]: Category to get associations for-s, --subject TEXT: Subject ID to get associations for-p, --predicate [biolink:interacts_with|biolink:expressed_in|biolink:has_phenotype|biolink:is_sequence_variant_of|biolink:enables|biolink:actively_involved_in|biolink:orthologous_to|biolink:located_in|biolink:subclass_of|biolink:related_to|biolink:participates_in|biolink:acts_upstream_of_or_within|biolink:active_in|biolink:part_of|biolink:model_of|biolink:causes|biolink:acts_upstream_of|biolink:has_mode_of_inheritance|biolink:contributes_to|biolink:gene_associated_with_condition|biolink:treats_or_applied_or_studied_to_treat|biolink:colocalizes_with|biolink:acts_upstream_of_positive_effect|biolink:acts_upstream_of_or_within_positive_effect|biolink:acts_upstream_of_negative_effect|biolink:acts_upstream_of_or_within_negative_effect]: Predicate ID to get associations for-o, --object TEXT: Object ID to get associations for-e, --entity TEXT: Entity (subject or object) ID to get associations for-d, --direct: Whether to exclude associations with subject/object as ancestors-C, --compact: Whether to return a compact representation of the associations-l, --limit INTEGER: The number of results to return [default: 20]--offset INTEGER: The offset of the first result to be retrieved [default: 0]-f, --format [json|yaml|tsv|table]: The format of the output (json, yaml, tsv, table) [default: json]-O, --output TEXT: Path to file to write command output (stdout if not specified)--help: Show this message and exit.monarch sql entity","text":"Retrieve an entity by ID
Usage:
$ monarch sql entity [OPTIONS] ENTITY_ID\nArguments:
ENTITY_ID: The identifier of the entity to be retrieved [required]Options:
-e, --extra: Include extra fields in the output (association_counts and node_hierarchy) [required]-u, --update: Whether to re-download the Monarch KG [required]-f, --format [json|yaml|tsv|table]: The format of the output (json, yaml, tsv, table) [default: json]-O, --output TEXT: Path to file to write command output (stdout if not specified)--help: Show this message and exit.monarch test","text":"Test the CLI
Usage:
$ monarch test [OPTIONS]\nOptions:
--help: Show this message and exit.monarch-py provides implementations of the abstract Interfaces for different Monarch KG endpoints/backends.
SQLImplementation dataclass","text":" Bases: EntityInterface, AssociationInterface
Implementation of Monarch Interfaces for SQL endpoint
"},{"location":"Usage/Implementations/SQL/#src.monarch_py.implementations.sql.sql_implementation.SQLImplementation.get_associations","title":"get_associations","text":"Retrieve paginated association records, with filter options
Parameters:
Name Type Description Defaultcategory str Filter to only associations matching the specified category. Defaults to None.
None predicate str Filter to only associations matching the specified predicate. Defaults to None.
None subject str Filter to only associations matching the specified subject. Defaults to None.
None object str Filter to only associations matching the specified object. Defaults to None.
None subject_closure str Filter to only associations with the specified term ID as an ancestor of the subject. Defaults to None.
None object_closure str Filter to only associations the specified term ID as an ancestor of the object. Defaults to None.
None entity str Filter to only associations where the specified entity is the subject or the object. Defaults to None.
None association_type str Filter to only associations matching the specified association label. Defaults to None.
requiredcompact bool Whether to return compact or full association records. Defaults to False.
False offset int Result offset, for pagination. Defaults to 0.
0 limit int Limit results to specified number. Defaults to 20.
20 Returns:
Name Type DescriptionAssociationResults Union[AssociationResults, CompactAssociationResults] Dataclass representing results of an association search.
"},{"location":"Usage/Implementations/SQL/#src.monarch_py.implementations.sql.sql_implementation.SQLImplementation.get_entity","title":"get_entity","text":"Retrieve a specific entity by exact ID match, writh optional extras
Parameters:
Name Type Description Defaultid str id of the entity to search for.
requiredget_association_counts bool Whether to get association counts. Defaults to False.
requiredget_hierarchy bool Whether to get the entity hierarchy. Defaults to False.
requiredReturns:
Name Type DescriptionEntity Entity Dataclass representing results of an entity search.
"},{"location":"Usage/Implementations/Solr/","title":"Solr","text":""},{"location":"Usage/Implementations/Solr/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation","title":"SolrImplementation dataclass","text":" Bases: EntityInterface, AssociationInterface, SearchInterface, GroundingInterface
Implementation of Monarch Interfaces for Solr endpoint
"},{"location":"Usage/Implementations/Solr/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.get_association_counts","title":"get_association_counts","text":"Get list of association counts for a given entity
"},{"location":"Usage/Implementations/Solr/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.get_associations","title":"get_associations","text":"Retrieve paginated association records, with filter options
Parameters:
Name Type Description Defaultcategory List[AssociationCategory] Filter to only associations matching the specified categories. Defaults to None.
None predicate List[AssociationPredicate] Filter to only associations matching the specified predicates. Defaults to None.
None subject Optional[List[str]] Filter to only associations matching the specified subjects. Defaults to None.
None object Optional[List[str]] Filter to only associations matching the specified objects. Defaults to None.
None subject_closure Optional[str] Filter to only associations with the specified term ID as an ancestor of the subject. Defaults to None
None object_closure Optional[str] Filter to only associations with the specified term ID as an ancestor of the object. Defaults to None
None entity Optional[List[str]] Filter to only associations where the specified entities are the subject or the object. Defaults to None.
None q Optional[str] Query string to search within matches. Defaults to None.
None facet_fields Optional[List[str]] List of fields to include facet counts for. Defaults to None.
None facet_queries Optional[List[str]] List of queries to include facet counts for. Defaults to None.
None filter_queries Optional[List[str]] List of queries to filter results by. Defaults to None.
None compact bool Return compact results with fewer fields. Defaults to False.
False offset int Result offset, for pagination. Defaults to 0.
0 limit int Limit results to specified number. Defaults to 20.
20 Returns:
Name Type DescriptionAssociationResults Union[AssociationResults, CompactAssociation] Dataclass representing results of an association search.
"},{"location":"Usage/Implementations/Solr/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.get_counterpart_entities","title":"get_counterpart_entities","text":"Get a list of entities directly associated with this_entity fetched from associations in the Solr index
Parameters:
Name Type Description Defaultthis_entity Entity The entity to get associations for
requiredentity str an entity ID occurring in either the subject or object. Defaults to None.
None subject str an entity ID occurring in the subject. Defaults to None.
None predicate str a predicate value. Defaults to None.
None object str an entity ID occurring in the object. Defaults to None.
None"},{"location":"Usage/Implementations/Solr/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.get_entity","title":"get_entity","text":"Retrieve a specific entity by exact ID match, with optional extras
Parameters:
Name Type Description Defaultid str id of the entity to search for.
requiredextra bool Whether to include association counts and hierarchy in the response.
requiredReturns:
Name Type DescriptionEntity Optional[Union[Node, Entity]] Dataclass representing results of an entity search.
Node Optional[Union[Node, Entity]] Dataclass representing results of an entity search with extra=True.
"},{"location":"Usage/Implementations/Solr/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.get_histopheno","title":"get_histopheno","text":"Get histopheno counts for a given subject_closure
"},{"location":"Usage/Implementations/Solr/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.get_multi_entity_associations","title":"get_multi_entity_associations","text":"Get associations between multiple entities and counterparts of a given category
Parameters:
Name Type Description Defaultentity List[str] List of entity IDs to get associations for
requiredcounterpart_category List[str] List of categories of counterpart entity to get associations for. Defaults to None.
None offset int Result offset, for pagination. Defaults to 0.
0 limit int Limit results to specified number. Defaults to 20.
requiredlimit_per_group int Limit results to specified number per group. Defaults to 20.
20"},{"location":"Usage/Implementations/Solr/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.ground_entity","title":"ground_entity","text":"Grounds a single entity
Parameters:
Name Type Description Defaulttext str Text to ground
requiredReturns:
Name Type DescriptionEntity List[Entity] Dataclass representing a single entity
"},{"location":"Usage/Implementations/Solr/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.search","title":"search","text":"Search for entities by label, with optional filters
Parameters:
Name Type Description Defaultq str Query string. Defaults to \":\".
'*:*' offset int Result offset, for pagination. Defaults to 0.
0 limit int Limit results to specified number. Defaults to 20.
20 category List[str] Filter to only entities matching the specified categories. Defaults to None.
None in_taxon_label List[str] Filter to only entities matching the specified taxon label. Defaults to None.
None facet_fields List[str] List of fields to include facet counts for. Defaults to None.
None facet_queries List[str] List of queries to include facet counts for. Defaults to None.
None filter_queries List[str] List of queries to filter results by. Defaults to None.
None sort str Sort results by the specified field. Defaults to None.
None Returns:
Name Type DescriptionSearchResults SearchResults Dataclass representing results of a search.
"},{"location":"Usage/Implementations/Solr/#src.monarch_py.implementations.solr.solr_implementation.SolrImplementation.solr_is_available","title":"solr_is_available","text":"Check if the Solr instance is available
"},{"location":"Usage/Interfaces/","title":"Interfaces","text":"monarch-py provides a collection of interfaces that abstractify implementation details, and provide a coherent set of graph operations.
Developers can code according to the interface, mostly ignoring whether the implementation is a relational database, a local file, etc.
"},{"location":"Usage/Interfaces/#interface","title":"Interface","text":"AssociationInterface","text":" Bases: ABC
Abstract interface for associations in the Monarch KG
"},{"location":"Usage/Interfaces/Association/#src.monarch_py.interfaces.association_interface.AssociationInterface.get_associations","title":"get_associations abstractmethod","text":"Retrieve paginated association records, with filter options
Parameters:
Name Type Description Defaultcategory str Filter to only associations matching the specified category. Defaults to None.
None predicate str Filter to only associations matching the specified predicate. Defaults to None.
None subject str Filter to only associations matching the specified subject. Defaults to None.
None subject_closure str Filter to only associations with the specified term ID as an ancestor of the subject. Defaults to None
None object str Filter to only associations matching the specified object. Defaults to None.
None object_closure str Filter to only associations with the specified term ID as an ancestor of the object. Defaults to None
None entity str Filter to only associations where the specified entity is the subject or the object. Defaults to None.
None offset int Result offset, for pagination. Defaults to 0.
0 limit int Limit results to specified number. Defaults to 20.
20 Raises:
Type DescriptionNotImplementedError Use a specific implementation (see the documentation for a list of implementations)
Returns:
Type DescriptionAssociationResults AssociationResults: Dataclass representing results of an association search.
"},{"location":"Usage/Interfaces/Entity/","title":"Entity","text":""},{"location":"Usage/Interfaces/Entity/#src.monarch_py.interfaces.entity_interface.EntityInterface","title":"EntityInterface","text":" Bases: ABC
Abstract interface for entities in the Monarch KG
"},{"location":"Usage/Interfaces/Entity/#src.monarch_py.interfaces.entity_interface.EntityInterface.get_entity","title":"get_entity abstractmethod","text":"Retrieve a specific entity by exact ID match, with optional extras
Parameters:
Name Type Description Defaultid str id of the entity to search for.
requiredget_association_counts bool Whether to get a count of associations for the entity. Defaults to False.
False get_hierarchy bool Whether to get the entity's heirarchy in the data model. Defaults to False.
False Raises:
Type DescriptionNotImplementedError Use a specific implementation (see the documentation for a list of implementations)
Returns:
Name Type DescriptionEntity Entity Dataclass representing results of an entity search.
"},{"location":"Usage/Interfaces/Query/","title":"Query","text":""},{"location":"Usage/Interfaces/Query/#src.monarch_py.interfaces.query_interface.QueryInterface","title":"QueryInterface","text":" Bases: ABC
Abstract interface for querying the Monarch KG in a SQL way
"},{"location":"Usage/Interfaces/Query/#src.monarch_py.interfaces.query_interface.QueryInterface.query","title":"query abstractmethod","text":"Parameters:
Name Type Description Defaultq str Query string to match against
requiredcategory str Limit results to only this category
requiredtaxon str Limit results to only this taxon
requiredoffset int Offset of the first result to return, defaults to 0
requiredlimit int Limit the number of results to return, defaults to 20
requiredRaises:
Type DescriptionNotImplementedError Use a specific implementation (see the documentation for a list of implementations)
Returns:
Name Type DescriptionEntityResults EntityResults Dataclass representing results of a generic entity search.
"},{"location":"Usage/Interfaces/Search/","title":"Search","text":""},{"location":"Usage/Interfaces/Search/#src.monarch_py.interfaces.search_interface.SearchInterface","title":"SearchInterface","text":" Bases: ABC
Abstract interface for searching the Monarch KG in a Lucene way
"},{"location":"Usage/Interfaces/Search/#src.monarch_py.interfaces.search_interface.SearchInterface.autocomplete","title":"autocomplete","text":"Parameters:
Name Type Description Defaultq str Query string to match against
requiredRaises:
Type DescriptionNotImplementedError Use a specific implementation (see the documentation for a list of implementations)
Returns:
Name Type DescriptionSearchResults SearchResults Dataclass representing results of a generic entity search.
"},{"location":"Usage/Interfaces/Search/#src.monarch_py.interfaces.search_interface.SearchInterface.get_association_counts","title":"get_association_counts","text":"Get counts of associations for a given entity Args: entity (str): Entity to get association counts for Returns: List[FacetValue]: List of FacetValue objects representing the counts of associations for the given entity
"},{"location":"Usage/Interfaces/Search/#src.monarch_py.interfaces.search_interface.SearchInterface.get_association_facets","title":"get_association_facets","text":"Get facet counts and facet query counts for associations Args: facet_fields (List[str]): Facet fields to return counts for facet_queries (List[str]): Facet queries to return counts for category (str): Filter to only associations matching the specified category predicate (str): Filter to only associations matching the specified predicate subject (str): Filter to only associations matching the specified subject subject_closure (str): Filter to only associations with the specified term ID as an ancestor of the subject object (str): Filter to only associations matching the specified object object_closure (str): Filter to only associations with the specified term ID as an ancestor of the object entity (str): Filter to only associations where the specified entity is the subject or the object Returns: SearchResults: Dataclass representing results of a search, with zero rows returned but total count and faceting information populated
"},{"location":"Usage/Interfaces/Search/#src.monarch_py.interfaces.search_interface.SearchInterface.get_association_table","title":"get_association_table","text":"Get associations for an entity matching a specified type, with optional search and sort parameters
Parameters:
Name Type Description Defaultentity str Entity to get associations for
requiredcategory str Category of associations to return
requiredquery str Query string to match against
None sort str Sort order, defaults to None
None offset int Offset of the first result to return, defaults to 0
0 limit int Limit the number of results to return, defaults to 20
5 Returns:
Name Type DescriptionAssociationResults AssociationTableResults Dataclass representing results of an association search.
"},{"location":"Usage/Interfaces/Search/#src.monarch_py.interfaces.search_interface.SearchInterface.search","title":"search abstractmethod","text":"Parameters:
Name Type Description Defaultq str Query string to match against
requiredcategory str Limit results to only this category
None taxon str Limit results to only this taxon
requiredoffset int Offset of the first result to return, defaults to 0
0 limit int Limit the number of results to return, defaults to 20
20 Raises:
Type DescriptionNotImplementedError Use a specific implementation (see the documentation for a list of implementations)
Returns:
Name Type DescriptionEntityResults SearchResults Dataclass representing results of a generic entity search.
"}]} \ No newline at end of file diff --git a/docs/sitemap.xml b/docs/sitemap.xml index 7fe36f28..e5140fea 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -2,1217 +2,1217 @@