MATRIX Data Model Documentation
The collected MATRIX schemas
Schema PURL: https://w3id.org/everycure-org/matrix-schema
Introduction
Here, you can find the collected documentation of all public data products created by the Matrix project. This includes the schemas for our KG products and the disease list.
Index (all classes, enums and elements)
Classes
| Class | Description |
|---|---|
| DiseaseListEntry | A disease entry in the disease list. |
| MatrixDiseaseList | A list of diseases. |
| MatrixEdge | An edge representing a relationship between two nodes in the Biolink knowledge graph. |
| MatrixEdgeList | A container for MatrixEdge objects. |
| MatrixNode | A node in the Biolink knowledge graph. |
| MatrixNodeList | A container for MatrixNode objects. |
Columns/Slots/Fields
| Slot | Description |
|---|---|
| agent_type | Type of agent involved in the relationship |
| aggregator_knowledge_source | Aggregators of the knowledge |
| all_categories | All categories associated with the entity |
| anatomical | Tag to denote this disease to be part of a grouping according to the anatomic... |
| attribute_type | The type of attribute |
| category | Biolink category of the entity |
| category_class | The disase identifier |
| crossreferences | Cross-references to other databases and ontologies |
| curation_type | The type of curation (manual / automatic) |
| definition | The definition of the disease |
| description | Detailed description of the entity |
| disease_list_entries | A list of disease list entries |
| edges | A list of edges |
| equivalent_identifiers | List of equivalent identifiers for the entity |
| harrisons_view | Tag to denote this disease to be part of a grouping according to the Harrison... |
| id | A unique identifier for a thing |
| international_resource_identifier | IRI of the entity |
| is_acquired | Flag to denote this disease corresponds to an acquired form of a disease |
| is_andor | Flag to denote this disease corresponds to a disease that is a combination of... |
| is_cancer | Flag to denote if this disease corresponds to a cancer type |
| is_clingen | Flag to denote that this disease term is used directly by https://clinicalgen... |
| is_glucose_dysfunction | Flag to denote if this disease corresponds to a glucose dysfunction |
| is_grouping_subset | Flag to denote this disease is manually curated to be a grouping term |
| is_grouping_subset_ancestor | Flag to denote this disease is a parent of a disease that was manually curate... |
| is_icd_billable | Flag to denote this disease was corresponds to an ICD code that is billable |
| is_icd_category | Flag to denote this disease was corresponds to an ICD category |
| is_icd_chapter_code | Flag to denote this disease was corresponds to an ICD chapter code |
| is_icd_chapter_header | Flag to denote this disease was corresponds to an ICD chapter header |
| is_leaf | Flag to denote this disease is a leaf node in the disease hierarchy |
| is_leaf_direct_parent | Flag to denote this disease is a direct parent of a leaf node in the disease ... |
| is_matrix_manually_excluded | Flag to denote this disease was manually excluded from the disease list by a ... |
| is_matrix_manually_included | Flag to denote this disease was manually included from the disease list by a ... |
| is_mondo_subtype | Flag to denote this disease was identified to be a subtype through lexical ma... |
| is_obsoletion_candidate | Flag to denote that this disease is marked for obsoletion in the (near) futur... |
| is_omim | Flag to denote this disease is manually curated to be a disease according to ... |
| is_omimps | Flag to denote this disease is manually curated to be a phenotypic series acc... |
| is_omimps_descendant | Flag to denote this disease is a child/descendant of a disease that is manual... |
| is_orphanet_disorder | Flag to denote this disease is manually curated to be a disease according to ... |
| is_orphanet_subtype | Flag to denote this disease is manually curated to be a disease subtype accor... |
| is_orphanet_subtype_descendant | Flag to denote this disease is a child/descendant of a disease that is manual... |
| is_paraphilic | Flag to denote this disease corresponds to a paraphilic disorder rather than ... |
| is_pathogen_caused | Flag to denote if this disease is caused by a pathogen |
| is_pathway_defect | Flag to denote this disease corresponds to a pathway defect rather than a pro... |
| is_susceptibility | Flag to denote this disease corresponds to a susceptibility rather than a pro... |
| is_unclassified_hereditary | Flag to denote that this disease has no descendants (is a leaf) and is class... |
| is_withorwithout | Flag to denote this disease corresponds to a disease that can be present with... |
| knowledge_level | Knowledge level of the relationship |
| label | The name of the disease |
| labels | Alternative labels for the entity |
| medical_specialization | Tag this disease with a medical specialisation |
| mondo_top_grouping | Tag to denote this disease to be a |
| mondo_txgnn | Tag to denote this disease to be part of a grouping as defined by the txgnn p... |
| name | Human-readable name of the entity |
| nodes | A list of edges |
| num_references | Number of references supporting this edge |
| num_sentences | Number of sentences supporting this edge |
| object | The object entity in the edge |
| object_aspect_qualifier | Aspect qualifier for the object |
| object_direction_qualifier | Direction qualifier for the object |
| official_matrix_filter | Flag to denote this disease corresponds to a disease that can be treated with... |
| other_subsets_count | The number of other subtypes in the subset this disease belongs to |
| predicate | The predicate defining the relationship |
| primary_knowledge_source | Primary source of the knowledge in the edge |
| publications | Publications associated with the entity |
| subject | The subject entity in the edge |
| subject_aspect_qualifier | Aspect qualifier for the subject |
| subject_direction_qualifier | Direction qualifier for the subject |
| subset_group_id | The identifier of a disease representing the subtype series this disease belo... |
| subset_group_label | The name (label) of a disease representing the subtype series this disease be... |
| subsets | The subsets of the disease in which it is part |
| synonyms | Any exact synonyms of the disease |
| tag_existing_treatment | Flag to denote if this disease has some existing treatment |
| tag_qaly_lost | Tag denoting the degree to which Quality-Adjusted Life Year (QALY) lost |
| txgnn | Tag this disease to be part of a grouping as defined by the txgnn paper |
| upstream_data_source | Sources from which this entity's data originates |
Enumerations
| Enumeration | Description |
|---|---|
| AgentTypeEnum | |
| AttributeTypeEnum | Code used to describe the nature of a slot, for documentative purposes |
| CurationTypeEnum | Code used to describe how a slot / attribute was curated |
| KnowledgeLevelEnum | |
| NodeCategoryEnum | |
| PredicateEnum |