Disease List Entry (schema class)
A disease entry in the disease list.
URI: matrix_schema:DiseaseListEntry
Attributes
| Name | Description | Cardinality and Range |
|---|---|---|
| category_class | The disase identifier. Slot name should probably be renamed? | 1 String |
| label | The name of the disease. | 1 String |
| definition | The definition of the disease. | 0..1 String |
| synonyms | Any exact synonyms of the disease. | 1..* String |
| subsets | The subsets of the disease in which it is part. | 1..* String |
| crossreferences | Cross-references to other databases and ontologies. | 1..* String |
| is_matrix_manually_excluded | Flag to denote this disease was manually excluded from the disease list by a Matrix medical expert. | 1 Boolean |
| is_matrix_manually_included | Flag to denote this disease was manually included from the disease list by a Matrix medical expert. | 1 Boolean |
| is_clingen | Flag to denote that this disease term is used directly by https://clinicalgenome.org/ (a major authority on genetic diseases), which is a strong indication that it corresponds to a real disease entity. | 1 Boolean |
| is_grouping_subset | Flag to denote this disease is manually curated to be a grouping term. | 1 Boolean |
| is_grouping_subset_ancestor | Flag to denote this disease is a parent of a disease that was manually curated to be a grouping term. | 1 Boolean |
| is_orphanet_subtype | Flag to denote this disease is manually curated to be a disease subtype according to Orphanet (https://www.orpha.net/), one of the most important rare disease authorities in the world. | 1 Boolean |
| is_orphanet_subtype_descendant | Flag to denote this disease is a child/descendant of a disease that is manually curated to be a disease subtype according to Orphanet (https://www.orpha.net/), one of the most important rare disease authorities in the world. If it is a descendant of a subtype, it most likely is a subtype itself. |
1 Boolean |
| is_omimps | Flag to denote this disease is manually curated to be a phenotypic series according to OMIM (https://www.omim.org/), one of the most important genetic disease authorities in the world. A Phenotypic Series is a grouping of genetic heterogeneity of similar phenotypes across the genome. |
1 Boolean |
| is_omimps_descendant | Flag to denote this disease is a child/descendant of a disease that is manually curated to be a phenotypic series according to OMIM (https://www.omim.org/), one of the most important genetic disease authorities in the world. If it is a descendant of a phenotypic series, it most likely is a proper genetic disease entity (or subtype). |
1 Boolean |
| is_leaf | Flag to denote this disease is a leaf node in the disease hierarchy. A leaf node is a node that has no children in the hierarchy. |
1 Boolean |
| is_leaf_direct_parent | Flag to denote this disease is a direct parent of a leaf node in the disease hierarchy. A direct parent of a leaf rarely corresponds to a grouping, and often is a proper disease entity. |
1 Boolean |
| is_orphanet_disorder | Flag to denote this disease is manually curated to be a disease according to Orphanet (https://www.orpha.net/), one of the most important rare disease authorities in the world. A disorder according to Orphanet usually corresponds to a proper disease entity, not a grouping or a subtype. |
1 Boolean |
| is_omim | Flag to denote this disease is manually curated to be a disease according to OMIM (https://www.omim.org/), one of the most important genetic disease authorities in the world. A disease according to OMIM usually corresponds to a proper disease entity or a subtype, not a disease grouping. |
1 Boolean |
| is_icd_category | Flag to denote this disease was corresponds to an ICD category. Category codes (or subcategory codes), for example A01.1 (Paratyphoid fever A), can be recognised by containing a period (.) character and usually represent specific diagnosable diseases. |
1 Boolean |
| is_icd_chapter_code | Flag to denote this disease was corresponds to an ICD chapter code. Chapter codes (or block codes), for example A00-B99 (Certain infectious and parasitic diseases). These codes can be recognised by containing a dash (-) character, and usually represent broad categories of diseases. |
1 Boolean |
| is_icd_chapter_header | Flag to denote this disease was corresponds to an ICD chapter header. Chapter headers (or chapter titles), for example A00 (Cholera) can be identified by codes without dashes or periods and are usually the top-level categories within each chapter. Most of the time, these are not proper diseases, but groupings of diseases. |
1 Boolean |
| is_icd_billable | Flag to denote this disease was corresponds to an ICD code that is billable. Billable codes are usually the most specific codes that can be used for billing purposes, and are most of the time diagnosable diseases. |
1 Boolean |
| is_mondo_subtype | Flag to denote this disease was identified to be a subtype through lexical matching. This method is maintained by the Every Cure medical team and the Disease List team. |
1 Boolean |
| is_pathway_defect | Flag to denote this disease corresponds to a pathway defect rather than a proper disease. |
1 Boolean |
| is_susceptibility | Flag to denote this disease corresponds to a susceptibility rather than a proper disease. |
1 Boolean |
| is_paraphilic | Flag to denote this disease corresponds to a paraphilic disorder rather than a proper disease. |
1 Boolean |
| is_acquired | Flag to denote this disease corresponds to an acquired form of a disease. |
1 Boolean |
| is_andor | Flag to denote this disease corresponds to a disease that is a combination of two or more diseases. |
1 Boolean |
| is_withorwithout | Flag to denote this disease corresponds to a disease that can be present with or without some other pathological condition. |
1 Boolean |
| is_obsoletion_candidate | Flag to denote that this disease is marked for obsoletion in the (near) future. This status does not guarantee that the disease will be obsoleted, but it is a strong indication. |
1 Boolean |
| is_unclassified_hereditary | Flag to denote that this disease has no descendants (is a leaf) and is classified broadly as an hereditary disease, but lacks any further classification. |
1 Boolean |
| official_matrix_filter | Flag to denote this disease corresponds to a disease that can be treated with small molecules or biologics. This flag is maintained as a combination of default filters by the Matrix team. Changes to this filter should be discussed on the Matrix disease list issue tracker (https://github.com/everycure-org/matrix-disease-list/issues). Warning. This flag is in early alpha state, and its use in production systems is not recommended. |
1 Boolean |
| harrisons_view | Tag to denote this disease to be part of a grouping according to the Harrison's textbook. Top-level classes in Mondo are manually curated by the Mondo team to "belong" to a Harrison's textbook chapter. Disagreements should be reported on the Mondo issue tracker (https://github.com/monarch-initiative/mondo/issues). |
1..* String |
| mondo_txgnn | Tag to denote this disease to be part of a grouping as defined by the txgnn paper. Disease classes in Mondo are manually curated by the Mondo team to "belong" to a txgnn category. Disagreements should be reported on the Mondo issue tracker (https://github.com/monarch-initiative/mondo/issues). |
1..* String |
| mondo_top_grouping | Tag to denote this disease to be a . Disease classes in Mondo are manually curated by the Mondo team to "belong" to a txgnn category. Disagreements should be reported on the Mondo issue tracker (https://github.com/monarch-initiative/mondo/issues). |
1..* String |
| medical_specialization | Tag this disease with a medical specialisation. Disease classes are automatically tagged by an LLM. Problems/issues should be reported on the Matrix disease list issue tracker (https://github.com/everycure-org/matrix-disease-list/issues). |
1..* String |
| txgnn | Tag this disease to be part of a grouping as defined by the txgnn paper. Disease classes in Mondo are automatically assigned to a txgnn category using an LLM. Problems/issues should be reported on the Matrix disease list issue tracker (https://github.com/everycure-org/matrix-disease-list/issues). |
1..* String |
| anatomical | Tag to denote this disease to be part of a grouping according to the anatomical location. Disease terms are automatically tagged using an LLM. Problems/issues should be reported on the Matrix disease list issue tracker (https://github.com/everycure-org/matrix-disease-list/issues). |
1..* String |
| is_pathogen_caused | Flag to denote if this disease is caused by a pathogen. Disease classes are automatically flagged using an LLM. Problems/issues should be reported on the Matrix disease list issue tracker (https://github.com/everycure-org/matrix-disease-list/issues). |
1 Boolean |
| is_cancer | Flag to denote if this disease corresponds to a cancer type. Disease classes are automatically flagged using an LLM. Problems/issues should be reported on the Matrix disease list issue tracker (https://github.com/everycure-org/matrix-disease-list/issues). |
1 Boolean |
| is_glucose_dysfunction | Flag to denote if this disease corresponds to a glucose dysfunction. Disease classes are automatically flagged using an LLM. tracker (https://github.com/everycure-org/matrix-disease-list/issues). |
1 Boolean |
| tag_existing_treatment | Flag to denote if this disease has some existing treatment. Disease classes are automatically flagged using an LLM. Problems/issues should be reported on the Matrix disease list issue tracker (https://github.com/everycure-org/matrix-disease-list/issues). |
1 Boolean |
| tag_qaly_lost | Tag denoting the degree to which Quality-Adjusted Life Year (QALY) lost. Disease terms are automatically tagged using an LLM. Problems/issues should be reported on the Matrix disease list issue tracker (https://github.com/everycure-org/matrix-disease-list/issues). |
1 String |
| subset_group_id | The identifier of a disease representing the subtype series this disease belongs to. | 0..1 String |
| subset_group_label | The name (label) of a disease representing the subtype series this disease belongs to. | 0..1 String |
| other_subsets_count | The number of other subtypes in the subset this disease belongs to. | 0..1 Integer |
Usages
| used by | used in | type | used |
|---|---|---|---|
| MatrixDiseaseList | disease_list_entries | range | DiseaseListEntry |
Identifier and Mapping Information
Schema Source
- from schema: https://w3id.org/everycure-org/matrix-schema
Mappings
| Mapping Type | Mapped Value |
|---|---|
| self | matrix_schema:DiseaseListEntry |
| native | matrix_schema:DiseaseListEntry |
LinkML Source
Direct
name: DiseaseListEntry
description: A disease entry in the disease list.
title: Disease List Entry
from_schema: https://w3id.org/everycure-org/matrix-schema
slots:
- category_class
- label
- definition
- synonyms
- subsets
- crossreferences
- is_matrix_manually_excluded
- is_matrix_manually_included
- is_clingen
- is_grouping_subset
- is_grouping_subset_ancestor
- is_orphanet_subtype
- is_orphanet_subtype_descendant
- is_omimps
- is_omimps_descendant
- is_leaf
- is_leaf_direct_parent
- is_orphanet_disorder
- is_omim
- is_icd_category
- is_icd_chapter_code
- is_icd_chapter_header
- is_icd_billable
- is_mondo_subtype
- is_pathway_defect
- is_susceptibility
- is_paraphilic
- is_acquired
- is_andor
- is_withorwithout
- is_obsoletion_candidate
- is_unclassified_hereditary
- official_matrix_filter
- harrisons_view
- mondo_txgnn
- mondo_top_grouping
- medical_specialization
- txgnn
- anatomical
- is_pathogen_caused
- is_cancer
- is_glucose_dysfunction
- tag_existing_treatment
- tag_qaly_lost
- subset_group_id
- subset_group_label
- other_subsets_count
slot_usage:
category_class:
name: category_class
required: true
label:
name: label
required: true
definition:
name: definition
required: false
synonyms:
name: synonyms
required: true
subsets:
name: subsets
required: true
crossreferences:
name: crossreferences
required: true
is_matrix_manually_excluded:
name: is_matrix_manually_excluded
required: true
is_matrix_manually_included:
name: is_matrix_manually_included
required: true
is_clingen:
name: is_clingen
required: true
is_grouping_subset:
name: is_grouping_subset
required: true
is_grouping_subset_ancestor:
name: is_grouping_subset_ancestor
required: true
is_orphanet_subtype:
name: is_orphanet_subtype
required: true
is_orphanet_subtype_descendant:
name: is_orphanet_subtype_descendant
required: true
is_omimps:
name: is_omimps
required: true
is_omimps_descendant:
name: is_omimps_descendant
required: true
is_leaf:
name: is_leaf
required: true
is_leaf_direct_parent:
name: is_leaf_direct_parent
required: true
is_orphanet_disorder:
name: is_orphanet_disorder
required: true
is_omim:
name: is_omim
required: true
is_icd_category:
name: is_icd_category
required: true
is_icd_chapter_code:
name: is_icd_chapter_code
required: true
is_icd_chapter_header:
name: is_icd_chapter_header
required: true
is_icd_billable:
name: is_icd_billable
required: true
is_mondo_subtype:
name: is_mondo_subtype
required: true
is_pathway_defect:
name: is_pathway_defect
required: true
is_susceptibility:
name: is_susceptibility
required: true
is_paraphilic:
name: is_paraphilic
required: true
is_acquired:
name: is_acquired
required: true
is_andor:
name: is_andor
required: true
is_withorwithout:
name: is_withorwithout
required: true
is_obsoletion_candidate:
name: is_obsoletion_candidate
required: true
is_unclassified_hereditary:
name: is_unclassified_hereditary
required: true
official_matrix_filter:
name: official_matrix_filter
required: true
harrisons_view:
name: harrisons_view
required: true
mondo_txgnn:
name: mondo_txgnn
required: true
mondo_top_grouping:
name: mondo_top_grouping
required: true
medical_specialization:
name: medical_specialization
required: true
txgnn:
name: txgnn
required: true
anatomical:
name: anatomical
required: true
is_pathogen_caused:
name: is_pathogen_caused
required: true
is_cancer:
name: is_cancer
required: true
is_glucose_dysfunction:
name: is_glucose_dysfunction
required: true
tag_existing_treatment:
name: tag_existing_treatment
required: true
tag_qaly_lost:
name: tag_qaly_lost
required: true
subset_group_id:
name: subset_group_id
required: false
subset_group_label:
name: subset_group_label
required: false
other_subsets_count:
name: other_subsets_count
required: false
Induced
name: DiseaseListEntry
description: A disease entry in the disease list.
title: Disease List Entry
from_schema: https://w3id.org/everycure-org/matrix-schema
slot_usage:
category_class:
name: category_class
required: true
label:
name: label
required: true
definition:
name: definition
required: false
synonyms:
name: synonyms
required: true
subsets:
name: subsets
required: true
crossreferences:
name: crossreferences
required: true
is_matrix_manually_excluded:
name: is_matrix_manually_excluded
required: true
is_matrix_manually_included:
name: is_matrix_manually_included
required: true
is_clingen:
name: is_clingen
required: true
is_grouping_subset:
name: is_grouping_subset
required: true
is_grouping_subset_ancestor:
name: is_grouping_subset_ancestor
required: true
is_orphanet_subtype:
name: is_orphanet_subtype
required: true
is_orphanet_subtype_descendant:
name: is_orphanet_subtype_descendant
required: true
is_omimps:
name: is_omimps
required: true
is_omimps_descendant:
name: is_omimps_descendant
required: true
is_leaf:
name: is_leaf
required: true
is_leaf_direct_parent:
name: is_leaf_direct_parent
required: true
is_orphanet_disorder:
name: is_orphanet_disorder
required: true
is_omim:
name: is_omim
required: true
is_icd_category:
name: is_icd_category
required: true
is_icd_chapter_code:
name: is_icd_chapter_code
required: true
is_icd_chapter_header:
name: is_icd_chapter_header
required: true
is_icd_billable:
name: is_icd_billable
required: true
is_mondo_subtype:
name: is_mondo_subtype
required: true
is_pathway_defect:
name: is_pathway_defect
required: true
is_susceptibility:
name: is_susceptibility
required: true
is_paraphilic:
name: is_paraphilic
required: true
is_acquired:
name: is_acquired
required: true
is_andor:
name: is_andor
required: true
is_withorwithout:
name: is_withorwithout
required: true
is_obsoletion_candidate:
name: is_obsoletion_candidate
required: true
is_unclassified_hereditary:
name: is_unclassified_hereditary
required: true
official_matrix_filter:
name: official_matrix_filter
required: true
harrisons_view:
name: harrisons_view
required: true
mondo_txgnn:
name: mondo_txgnn
required: true
mondo_top_grouping:
name: mondo_top_grouping
required: true
medical_specialization:
name: medical_specialization
required: true
txgnn:
name: txgnn
required: true
anatomical:
name: anatomical
required: true
is_pathogen_caused:
name: is_pathogen_caused
required: true
is_cancer:
name: is_cancer
required: true
is_glucose_dysfunction:
name: is_glucose_dysfunction
required: true
tag_existing_treatment:
name: tag_existing_treatment
required: true
tag_qaly_lost:
name: tag_qaly_lost
required: true
subset_group_id:
name: subset_group_id
required: false
subset_group_label:
name: subset_group_label
required: false
other_subsets_count:
name: other_subsets_count
required: false
attributes:
category_class:
name: category_class
description: The disase identifier. Slot name should probably be renamed?
from_schema: https://w3id.org/everycure-org/matrix-schema
rank: 1000
alias: category_class
owner: DiseaseListEntry
domain_of:
- DiseaseListEntry
range: string
required: true
label:
name: label
description: The name of the disease.
from_schema: https://w3id.org/everycure-org/matrix-schema
rank: 1000
alias: label
owner: DiseaseListEntry
domain_of:
- DiseaseListEntry
range: string
required: true
definition:
name: definition
description: The definition of the disease.
from_schema: https://w3id.org/everycure-org/matrix-schema
rank: 1000
alias: definition
owner: DiseaseListEntry
domain_of:
- DiseaseListEntry
range: string
required: false
synonyms:
name: synonyms
description: Any exact synonyms of the disease.
from_schema: https://w3id.org/everycure-org/matrix-schema
rank: 1000
alias: synonyms
owner: DiseaseListEntry
domain_of:
- DiseaseListEntry
range: string
required: true
multivalued: true
inlined: true
inlined_as_list: true
subsets:
name: subsets
description: The subsets of the disease in which it is part.
from_schema: https://w3id.org/everycure-org/matrix-schema
rank: 1000
alias: subsets
owner: DiseaseListEntry
domain_of:
- DiseaseListEntry
range: string
required: true
multivalued: true
inlined: true
inlined_as_list: true
crossreferences:
name: crossreferences
description: Cross-references to other databases and ontologies.
from_schema: https://w3id.org/everycure-org/matrix-schema
rank: 1000
alias: crossreferences
owner: DiseaseListEntry
domain_of:
- DiseaseListEntry
range: string
required: true
multivalued: true
inlined: true
inlined_as_list: true
is_matrix_manually_excluded:
name: is_matrix_manually_excluded
annotations:
attribute_type:
tag: attribute_type
value: filter
curation_type:
tag: curation_type
value: manual_everycure
description: Flag to denote this disease was manually excluded from the disease
list by a Matrix medical expert.
from_schema: https://w3id.org/everycure-org/matrix-schema
see_also:
- https://github.com/everycure-org/matrix-disease-list/blob/main/src/excluded-diseases.robot.tsv
rank: 1000
alias: is_matrix_manually_excluded
owner: DiseaseListEntry
domain_of:
- DiseaseListEntry
range: boolean
required: true
is_matrix_manually_included:
name: is_matrix_manually_included
annotations:
attribute_type:
tag: attribute_type
value: filter
curation_type:
tag: curation_type
value: manual_everycure
description: Flag to denote this disease was manually included from the disease
list by a Matrix medical expert.
from_schema: https://w3id.org/everycure-org/matrix-schema
see_also:
- https://github.com/everycure-org/matrix-disease-list/blob/main/src/included-diseases.robot.tsv
rank: 1000
alias: is_matrix_manually_included
owner: DiseaseListEntry
domain_of:
- DiseaseListEntry
range: boolean
required: true
is_clingen:
name: is_clingen
annotations:
attribute_type:
tag: attribute_type
value: filter
curation_type:
tag: curation_type
value: external_source
description: Flag to denote that this disease term is used directly by https://clinicalgenome.org/
(a major authority on genetic diseases), which is a strong indication that it
corresponds to a real disease entity.
from_schema: https://w3id.org/everycure-org/matrix-schema
see_also:
- https://github.com/everycure-org/matrix-disease-list/blob/main/sparql/matrix-disease-list-filters.sparql
- https://clinicalgenome.org/
rank: 1000
alias: is_clingen
owner: DiseaseListEntry
domain_of:
- DiseaseListEntry
range: boolean
required: true
is_grouping_subset:
name: is_grouping_subset
annotations:
attribute_type:
tag: attribute_type
value: filter
curation_type:
tag: curation_type
value: manual_mondo
description: Flag to denote this disease is manually curated to be a grouping
term.
from_schema: https://w3id.org/everycure-org/matrix-schema
see_also:
- https://github.com/everycure-org/matrix-disease-list/blob/main/sparql/matrix-disease-list-filters.sparql
rank: 1000
alias: is_grouping_subset
owner: DiseaseListEntry
domain_of:
- DiseaseListEntry
range: boolean
required: true
is_grouping_subset_ancestor:
name: is_grouping_subset_ancestor
annotations:
attribute_type:
tag: attribute_type
value: filter
curation_type:
tag: curation_type
value: ontology_hierarchy
description: Flag to denote this disease is a parent of a disease that was manually
curated to be a grouping term.
from_schema: https://w3id.org/everycure-org/matrix-schema
see_also:
- https://github.com/everycure-org/matrix-disease-list/blob/main/sparql/matrix-disease-list-filters.sparql
rank: 1000
alias: is_grouping_subset_ancestor
owner: DiseaseListEntry
domain_of:
- DiseaseListEntry
range: boolean
required: true
is_orphanet_subtype:
name: is_orphanet_subtype
annotations:
attribute_type:
tag: attribute_type
value: filter
curation_type:
tag: curation_type
value: manual_mondo
description: Flag to denote this disease is manually curated to be a disease subtype
according to Orphanet (https://www.orpha.net/), one of the most important rare
disease authorities in the world.
from_schema: https://w3id.org/everycure-org/matrix-schema
see_also:
- https://github.com/everycure-org/matrix-disease-list/blob/main/sparql/matrix-disease-list-filters.sparql
- https://www.orpha.net/
- https://www.orpha.net/pdfs/orphacom/cahiers/docs/GB/eproc_disease_inventory_R1_Nom_Dis_EP_04.pdf
rank: 1000
alias: is_orphanet_subtype
owner: DiseaseListEntry
domain_of:
- DiseaseListEntry
range: boolean
required: true
is_orphanet_subtype_descendant:
name: is_orphanet_subtype_descendant
annotations:
attribute_type:
tag: attribute_type
value: filter
curation_type:
tag: curation_type
value: ontology_hierarchy
description: 'Flag to denote this disease is a child/descendant of a disease that
is manually curated to be a disease subtype according to Orphanet (https://www.orpha.net/),
one of the most important rare disease authorities in the world. If it is a
descendant of a subtype, it most likely is a subtype itself.
'
from_schema: https://w3id.org/everycure-org/matrix-schema
see_also:
- http://dev.everycure.org/schema/is_orphanet_subtype
- https://github.com/everycure-org/matrix-disease-list/blob/main/sparql/matrix-disease-list-filters.sparql
rank: 1000
alias: is_orphanet_subtype_descendant
owner: DiseaseListEntry
domain_of:
- DiseaseListEntry
range: boolean
required: true
is_omimps:
name: is_omimps
annotations:
attribute_type:
tag: attribute_type
value: filter
curation_type:
tag: curation_type
value: manual_mondo
description: 'Flag to denote this disease is manually curated to be a phenotypic
series according to OMIM (https://www.omim.org/), one of the most important
genetic disease authorities in the world. A Phenotypic Series is a grouping
of genetic heterogeneity of similar phenotypes across the genome.
'
from_schema: https://w3id.org/everycure-org/matrix-schema
see_also:
- https://github.com/everycure-org/matrix-disease-list/blob/main/sparql/matrix-disease-list-filters.sparql
- https://www.omim.org/
- https://www.omim.org/help/faq#1_14
rank: 1000
alias: is_omimps
owner: DiseaseListEntry
domain_of:
- DiseaseListEntry
range: boolean
required: true
is_omimps_descendant:
name: is_omimps_descendant
annotations:
attribute_type:
tag: attribute_type
value: filter
curation_type:
tag: curation_type
value: ontology_hierarchy
description: 'Flag to denote this disease is a child/descendant of a disease that
is manually curated to be a phenotypic series according to OMIM (https://www.omim.org/),
one of the most important genetic disease authorities in the world. If it is
a descendant of a phenotypic series, it most likely is a proper genetic disease
entity (or subtype).
'
from_schema: https://w3id.org/everycure-org/matrix-schema
see_also:
- https://github.com/everycure-org/matrix-disease-list/blob/main/sparql/matrix-disease-list-filters.sparql
- https://www.omim.org/
- https://www.omim.org/help/faq#1_14
- http://dev.everycure.org/schema/is_omimps
rank: 1000
alias: is_omimps_descendant
owner: DiseaseListEntry
domain_of:
- DiseaseListEntry
range: boolean
required: true
is_leaf:
name: is_leaf
annotations:
attribute_type:
tag: attribute_type
value: filter
curation_type:
tag: curation_type
value: ontology_hierarchy
description: 'Flag to denote this disease is a leaf node in the disease hierarchy. A
leaf node is a node that has no children in the hierarchy.
'
from_schema: https://w3id.org/everycure-org/matrix-schema
see_also:
- https://github.com/everycure-org/matrix-disease-list/blob/main/sparql/matrix-disease-list-filters.sparql
rank: 1000
alias: is_leaf
owner: DiseaseListEntry
domain_of:
- DiseaseListEntry
range: boolean
required: true
is_leaf_direct_parent:
name: is_leaf_direct_parent
annotations:
attribute_type:
tag: attribute_type
value: filter
curation_type:
tag: curation_type
value: ontology_hierarchy
description: 'Flag to denote this disease is a direct parent of a leaf node in
the disease hierarchy. A direct parent of a leaf rarely corresponds to a grouping,
and often is a proper disease entity.
'
from_schema: https://w3id.org/everycure-org/matrix-schema
see_also:
- https://github.com/everycure-org/matrix-disease-list/blob/main/sparql/matrix-disease-list-filters.sparql
rank: 1000
alias: is_leaf_direct_parent
owner: DiseaseListEntry
domain_of:
- DiseaseListEntry
range: boolean
required: true
is_orphanet_disorder:
name: is_orphanet_disorder
annotations:
attribute_type:
tag: attribute_type
value: filter
curation_type:
tag: curation_type
value: manual_mondo
description: 'Flag to denote this disease is manually curated to be a disease
according to Orphanet (https://www.orpha.net/), one of the most important rare
disease authorities in the world. A disorder according to Orphanet usually
corresponds to a proper disease entity, not a grouping or a subtype.
'
from_schema: https://w3id.org/everycure-org/matrix-schema
see_also:
- https://www.orpha.net/
- https://www.orpha.net/pdfs/orphacom/cahiers/docs/GB/eproc_disease_inventory_R1_Nom_Dis_EP_04.pdf
- https://github.com/everycure-org/matrix-disease-list/blob/main/sparql/matrix-disease-list-filters.sparql
rank: 1000
alias: is_orphanet_disorder
owner: DiseaseListEntry
domain_of:
- DiseaseListEntry
range: boolean
required: true
is_omim:
name: is_omim
annotations:
attribute_type:
tag: attribute_type
value: filter
curation_type:
tag: curation_type
value: manual_mondo
description: 'Flag to denote this disease is manually curated to be a disease
according to OMIM (https://www.omim.org/), one of the most important genetic
disease authorities in the world. A disease according to OMIM usually corresponds
to a proper disease entity or a subtype, not a disease grouping.
'
from_schema: https://w3id.org/everycure-org/matrix-schema
see_also:
- https://github.com/everycure-org/matrix-disease-list/blob/main/sparql/matrix-disease-list-filters.sparql
- https://www.omim.org/
rank: 1000
alias: is_omim
owner: DiseaseListEntry
domain_of:
- DiseaseListEntry
range: boolean
required: true
is_icd_category:
name: is_icd_category
annotations:
attribute_type:
tag: attribute_type
value: filter
curation_type:
tag: curation_type
value: manual_mondo
description: 'Flag to denote this disease was corresponds to an ICD category.
Category codes (or subcategory codes), for example A01.1 (Paratyphoid fever
A), can be recognised by containing a period (.) character and usually represent
specific diagnosable diseases.
'
from_schema: https://w3id.org/everycure-org/matrix-schema
see_also:
- https://github.com/everycure-org/matrix-disease-list/blob/main/sparql/matrix-disease-list-filters.sparql
- https://en.wikipedia.org/wiki/ICD-10
rank: 1000
alias: is_icd_category
owner: DiseaseListEntry
domain_of:
- DiseaseListEntry
range: boolean
required: true
is_icd_chapter_code:
name: is_icd_chapter_code
annotations:
attribute_type:
tag: attribute_type
value: filter
curation_type:
tag: curation_type
value: manual_mondo
description: 'Flag to denote this disease was corresponds to an ICD chapter code.
Chapter codes (or block codes), for example A00-B99 (Certain infectious and
parasitic diseases). These codes can be recognised by containing a dash (-)
character, and usually represent broad categories of diseases.
'
from_schema: https://w3id.org/everycure-org/matrix-schema
see_also:
- https://github.com/everycure-org/matrix-disease-list/blob/main/sparql/matrix-disease-list-filters.sparql
- https://en.wikipedia.org/wiki/ICD-10
rank: 1000
alias: is_icd_chapter_code
owner: DiseaseListEntry
domain_of:
- DiseaseListEntry
range: boolean
required: true
is_icd_chapter_header:
name: is_icd_chapter_header
annotations:
attribute_type:
tag: attribute_type
value: filter
curation_type:
tag: curation_type
value: manual_mondo
description: 'Flag to denote this disease was corresponds to an ICD chapter header.
Chapter headers (or chapter titles), for example A00 (Cholera) can be identified
by codes without dashes or periods and are usually the top-level categories
within each chapter. Most of the time, these are not proper diseases, but groupings
of diseases.
'
from_schema: https://w3id.org/everycure-org/matrix-schema
see_also:
- https://github.com/everycure-org/matrix-disease-list/blob/main/sparql/matrix-disease-list-filters.sparql
- https://en.wikipedia.org/wiki/ICD-10
rank: 1000
alias: is_icd_chapter_header
owner: DiseaseListEntry
domain_of:
- DiseaseListEntry
range: boolean
required: true
is_icd_billable:
name: is_icd_billable
annotations:
attribute_type:
tag: attribute_type
value: filter
curation_type:
tag: curation_type
value: external_source
description: 'Flag to denote this disease was corresponds to an ICD code that
is billable. Billable codes are usually the most specific codes that can be
used for billing purposes, and are most of the time diagnosable diseases.
'
from_schema: https://w3id.org/everycure-org/matrix-schema
see_also:
- https://github.com/everycure-org/matrix-disease-list/blob/main/sparql/matrix-disease-list-filters.sparql
- https://www.cms.gov/files/document/valid-icd-10-list.xlsx
rank: 1000
alias: is_icd_billable
owner: DiseaseListEntry
domain_of:
- DiseaseListEntry
range: boolean
required: true
is_mondo_subtype:
name: is_mondo_subtype
annotations:
attribute_type:
tag: attribute_type
value: filter
curation_type:
tag: curation_type
value: manual_everycure
description: 'Flag to denote this disease was identified to be a subtype through
lexical matching. This method is maintained by the Every Cure medical team and
the Disease List team.
'
from_schema: https://w3id.org/everycure-org/matrix-schema
see_also:
- https://github.com/everycure-org/matrix-disease-list/issues/46
- https://github.com/everycure-org/matrix-disease-list/blob/febc3358a446cc36321ff44ae74064c49011fd5c/scripts/matrix-disease-list.py#L478C5-L478C51
rank: 1000
alias: is_mondo_subtype
owner: DiseaseListEntry
domain_of:
- DiseaseListEntry
range: boolean
required: true
is_pathway_defect:
name: is_pathway_defect
annotations:
attribute_type:
tag: attribute_type
value: filter
curation_type:
tag: curation_type
value: manual_everycure
description: 'Flag to denote this disease corresponds to a pathway defect rather
than a proper disease.
'
from_schema: https://w3id.org/everycure-org/matrix-schema
see_also:
- https://github.com/everycure-org/matrix-disease-list/issues/51
- https://github.com/everycure-org/matrix-disease-list/blob/main/src/excluded-diseases.robot.tsv
rank: 1000
alias: is_pathway_defect
owner: DiseaseListEntry
domain_of:
- DiseaseListEntry
range: boolean
required: true
is_susceptibility:
name: is_susceptibility
annotations:
attribute_type:
tag: attribute_type
value: filter
curation_type:
tag: curation_type
value: lexical_matching
description: 'Flag to denote this disease corresponds to a susceptibility rather
than a proper disease.
'
from_schema: https://w3id.org/everycure-org/matrix-schema
see_also:
- https://github.com/everycure-org/matrix-disease-list/issues/36
- https://github.com/everycure-org/matrix-disease-list/blob/main/sparql/inject-susceptibility-subset.ru
rank: 1000
alias: is_susceptibility
owner: DiseaseListEntry
domain_of:
- DiseaseListEntry
range: boolean
required: true
is_paraphilic:
name: is_paraphilic
annotations:
attribute_type:
tag: attribute_type
value: filter
curation_type:
tag: curation_type
value: manual_everycure
description: 'Flag to denote this disease corresponds to a paraphilic disorder
rather than a proper disease.
'
from_schema: https://w3id.org/everycure-org/matrix-schema
see_also:
- https://github.com/everycure-org/matrix-disease-list/issues/42
- https://github.com/everycure-org/matrix-disease-list/blob/main/src/excluded-diseases.robot.tsv
rank: 1000
alias: is_paraphilic
owner: DiseaseListEntry
domain_of:
- DiseaseListEntry
range: boolean
required: true
is_acquired:
name: is_acquired
annotations:
attribute_type:
tag: attribute_type
value: filter
curation_type:
tag: curation_type
value: lexical_matching
description: 'Flag to denote this disease corresponds to an acquired form of a
disease.
'
from_schema: https://w3id.org/everycure-org/matrix-schema
see_also:
- https://github.com/everycure-org/matrix-disease-list/blob/main/sparql/matrix-disease-list-filters.sparql
- https://github.com/everycure-org/matrix-disease-list/issues/53
rank: 1000
alias: is_acquired
owner: DiseaseListEntry
domain_of:
- DiseaseListEntry
range: boolean
required: true
is_andor:
name: is_andor
annotations:
attribute_type:
tag: attribute_type
value: filter
curation_type:
tag: curation_type
value: lexical_matching
description: 'Flag to denote this disease corresponds to a disease that is a combination
of two or more diseases.
'
from_schema: https://w3id.org/everycure-org/matrix-schema
see_also:
- https://github.com/everycure-org/matrix-disease-list/blob/main/sparql/matrix-disease-list-filters.sparql
- https://github.com/everycure-org/matrix-disease-list/issues/39
rank: 1000
alias: is_andor
owner: DiseaseListEntry
domain_of:
- DiseaseListEntry
range: boolean
required: true
is_withorwithout:
name: is_withorwithout
annotations:
attribute_type:
tag: attribute_type
value: filter
curation_type:
tag: curation_type
value: lexical_matching
description: 'Flag to denote this disease corresponds to a disease that can be
present with or without some other pathological condition.
'
from_schema: https://w3id.org/everycure-org/matrix-schema
see_also:
- https://github.com/everycure-org/matrix-disease-list/blob/main/sparql/matrix-disease-list-filters.sparql
- https://github.com/everycure-org/matrix-disease-list/issues/40
rank: 1000
alias: is_withorwithout
owner: DiseaseListEntry
domain_of:
- DiseaseListEntry
range: boolean
required: true
is_obsoletion_candidate:
name: is_obsoletion_candidate
annotations:
attribute_type:
tag: attribute_type
value: filter
curation_type:
tag: curation_type
value: manual_mondo
description: 'Flag to denote that this disease is marked for obsoletion in the
(near) future. This status does not guarantee that the disease will be obsoleted,
but it is a strong indication.
'
from_schema: https://w3id.org/everycure-org/matrix-schema
rank: 1000
alias: is_obsoletion_candidate
owner: DiseaseListEntry
domain_of:
- DiseaseListEntry
range: boolean
required: true
is_unclassified_hereditary:
name: is_unclassified_hereditary
annotations:
attribute_type:
tag: attribute_type
value: filter
curation_type:
tag: curation_type
value: ontology_hierarchy
description: 'Flag to denote that this disease has no descendants (is a leaf)
and is classified broadly as an hereditary disease, but lacks any further classification.
'
from_schema: https://w3id.org/everycure-org/matrix-schema
see_also:
- https://github.com/everycure-org/matrix-disease-list/blob/main/sparql/matrix-disease-list-filters.sparql
rank: 1000
alias: is_unclassified_hereditary
owner: DiseaseListEntry
domain_of:
- DiseaseListEntry
range: boolean
required: true
official_matrix_filter:
name: official_matrix_filter
annotations:
annotations:
tag: annotations
attribute_type:
tag: attribute_type
value: filter
curation_type:
tag: curation_type
value: manual_everycure
description: 'Flag to denote this disease corresponds to a disease that can be
treated with small molecules or biologics. This flag is maintained as a combination
of default filters by the Matrix team. Changes to this filter should be discussed
on the Matrix disease list issue tracker (https://github.com/everycure-org/matrix-disease-list/issues).
**Warning**. This flag is in early alpha state, and its use in production systems
is not recommended.
'
from_schema: https://w3id.org/everycure-org/matrix-schema
rank: 1000
alias: official_matrix_filter
owner: DiseaseListEntry
domain_of:
- DiseaseListEntry
range: boolean
required: true
harrisons_view:
name: harrisons_view
annotations:
attribute_type:
tag: attribute_type
value: grouping
curation_type:
tag: curation_type
value: manual_mondo
description: 'Tag to denote this disease to be part of a grouping according to
the Harrison''s textbook. Top-level classes in Mondo are manually curated by
the Mondo team to "belong" to a Harrison''s textbook chapter. Disagreements
should be reported on the Mondo issue tracker (https://github.com/monarch-initiative/mondo/issues).
'
from_schema: https://w3id.org/everycure-org/matrix-schema
see_also:
- https://accessmedicine.mhmedical.com/book.aspx?bookID=3095
rank: 1000
alias: harrisons_view
owner: DiseaseListEntry
domain_of:
- DiseaseListEntry
range: string
required: true
multivalued: true
mondo_txgnn:
name: mondo_txgnn
annotations:
attribute_type:
tag: attribute_type
value: grouping
curation_type:
tag: curation_type
value: manual_mondo
description: 'Tag to denote this disease to be part of a grouping as defined by
the txgnn paper. Disease classes in Mondo are manually curated by the Mondo
team to "belong" to a txgnn category. Disagreements should be reported on the
Mondo issue tracker (https://github.com/monarch-initiative/mondo/issues).
'
from_schema: https://w3id.org/everycure-org/matrix-schema
see_also:
- https://pmc.ncbi.nlm.nih.gov/articles/PMC11645266/
rank: 1000
alias: mondo_txgnn
owner: DiseaseListEntry
domain_of:
- DiseaseListEntry
range: string
required: true
multivalued: true
mondo_top_grouping:
name: mondo_top_grouping
annotations:
attribute_type:
tag: attribute_type
value: grouping
curation_type:
tag: curation_type
value: manual_mondo
description: 'Tag to denote this disease to be a . Disease classes in Mondo are
manually curated by the Mondo team to "belong" to a txgnn category. Disagreements
should be reported on the Mondo issue tracker (https://github.com/monarch-initiative/mondo/issues).
'
from_schema: https://w3id.org/everycure-org/matrix-schema
rank: 1000
alias: mondo_top_grouping
owner: DiseaseListEntry
domain_of:
- DiseaseListEntry
range: string
required: true
multivalued: true
inlined: true
inlined_as_list: true
medical_specialization:
name: medical_specialization
annotations:
attribute_type:
tag: attribute_type
value: grouping
curation_type:
tag: curation_type
value: llm
description: 'Tag this disease with a medical specialisation. Disease classes
are automatically tagged by an LLM. Problems/issues should be reported on the
Matrix disease list issue tracker (https://github.com/everycure-org/matrix-disease-list/issues).
'
from_schema: https://w3id.org/everycure-org/matrix-schema
rank: 1000
alias: medical_specialization
owner: DiseaseListEntry
domain_of:
- DiseaseListEntry
range: string
required: true
multivalued: true
txgnn:
name: txgnn
annotations:
attribute_type:
tag: attribute_type
value: grouping
curation_type:
tag: curation_type
value: llm
description: 'Tag this disease to be part of a grouping as defined by the txgnn
paper. Disease classes in Mondo are automatically assigned to a txgnn category
using an LLM. Problems/issues should be reported on the Matrix disease list
issue tracker (https://github.com/everycure-org/matrix-disease-list/issues).
'
from_schema: https://w3id.org/everycure-org/matrix-schema
see_also:
- https://pmc.ncbi.nlm.nih.gov/articles/PMC11645266/
rank: 1000
alias: txgnn
owner: DiseaseListEntry
domain_of:
- DiseaseListEntry
range: string
required: true
multivalued: true
inlined: true
inlined_as_list: true
anatomical:
name: anatomical
annotations:
attribute_type:
tag: attribute_type
value: grouping
curation_type:
tag: curation_type
value: llm
description: 'Tag to denote this disease to be part of a grouping according to
the anatomical location. Disease terms are automatically tagged using an LLM.
Problems/issues should be reported on the Matrix disease list issue tracker
(https://github.com/everycure-org/matrix-disease-list/issues).
'
from_schema: https://w3id.org/everycure-org/matrix-schema
rank: 1000
alias: anatomical
owner: DiseaseListEntry
domain_of:
- DiseaseListEntry
range: string
required: true
multivalued: true
inlined: true
inlined_as_list: true
is_pathogen_caused:
name: is_pathogen_caused
annotations:
attribute_type:
tag: attribute_type
value: filter
curation_type:
tag: curation_type
value: llm
description: 'Flag to denote if this disease is caused by a pathogen. Disease
classes are automatically flagged using an LLM. Problems/issues should be reported
on the Matrix disease list issue tracker (https://github.com/everycure-org/matrix-disease-list/issues).
'
from_schema: https://w3id.org/everycure-org/matrix-schema
rank: 1000
alias: is_pathogen_caused
owner: DiseaseListEntry
domain_of:
- DiseaseListEntry
range: boolean
required: true
is_cancer:
name: is_cancer
annotations:
attribute_type:
tag: attribute_type
value: filter
curation_type:
tag: curation_type
value: llm
description: 'Flag to denote if this disease corresponds to a cancer type. Disease
classes are automatically flagged using an LLM. Problems/issues should be reported
on the Matrix disease list issue tracker (https://github.com/everycure-org/matrix-disease-list/issues).
'
from_schema: https://w3id.org/everycure-org/matrix-schema
rank: 1000
alias: is_cancer
owner: DiseaseListEntry
domain_of:
- DiseaseListEntry
range: boolean
required: true
is_glucose_dysfunction:
name: is_glucose_dysfunction
annotations:
attribute_type:
tag: attribute_type
value: filter
curation_type:
tag: curation_type
value: llm
description: 'Flag to denote if this disease corresponds to a glucose dysfunction.
Disease classes are automatically flagged using an LLM. tracker (https://github.com/everycure-org/matrix-disease-list/issues).
'
from_schema: https://w3id.org/everycure-org/matrix-schema
rank: 1000
alias: is_glucose_dysfunction
owner: DiseaseListEntry
domain_of:
- DiseaseListEntry
range: boolean
required: true
tag_existing_treatment:
name: tag_existing_treatment
annotations:
attribute_type:
tag: attribute_type
value: filter
curation_type:
tag: curation_type
value: llm
description: 'Flag to denote if this disease has some existing treatment. Disease
classes are automatically flagged using an LLM. Problems/issues should be reported
on the Matrix disease list issue tracker (https://github.com/everycure-org/matrix-disease-list/issues).
'
from_schema: https://w3id.org/everycure-org/matrix-schema
rank: 1000
alias: tag_existing_treatment
owner: DiseaseListEntry
domain_of:
- DiseaseListEntry
range: boolean
required: true
tag_qaly_lost:
name: tag_qaly_lost
annotations:
curation_type:
tag: curation_type
value: llm
description: 'Tag denoting the degree to which Quality-Adjusted Life Year (QALY)
lost. Disease terms are automatically tagged using an LLM. Problems/issues should
be reported on the Matrix disease list issue tracker (https://github.com/everycure-org/matrix-disease-list/issues).
'
from_schema: https://w3id.org/everycure-org/matrix-schema
rank: 1000
alias: tag_qaly_lost
owner: DiseaseListEntry
domain_of:
- DiseaseListEntry
range: string
required: true
pattern: ^(low|medium|high|very_high|none)$
subset_group_id:
name: subset_group_id
description: The identifier of a disease representing the subtype series this
disease belongs to.
from_schema: https://w3id.org/everycure-org/matrix-schema
rank: 1000
alias: subset_group_id
owner: DiseaseListEntry
domain_of:
- DiseaseListEntry
range: string
required: false
subset_group_label:
name: subset_group_label
description: The name (label) of a disease representing the subtype series this
disease belongs to.
from_schema: https://w3id.org/everycure-org/matrix-schema
rank: 1000
alias: subset_group_label
owner: DiseaseListEntry
domain_of:
- DiseaseListEntry
range: string
required: false
other_subsets_count:
name: other_subsets_count
description: The number of other subtypes in the subset this disease belongs to.
from_schema: https://w3id.org/everycure-org/matrix-schema
rank: 1000
alias: other_subsets_count
owner: DiseaseListEntry
domain_of:
- DiseaseListEntry
range: integer
required: false