Author: Samuel Piron
type: Ontology
version IRI: https://w3id.org/hereditary/ontology/gutbrain/1.0/
imports: core
creator: https://orcid.org/0000-0003-4970-4554
creator: https://orcid.org/0009-0001-1596-8642
creator: https://orcid.org/0009-0006-5558-4295
description: The Hereditary ontology models phenoclinical, genomics and scientific aspects of the gut-brain axis to provide a unifying layer to query different database sources through an Ontology-Based Data Access (OBDA) framework. This part of the ontology focuses on gut-brain data.
license: Copyright 2024-2027 University of Padua, Italy Licensed under the Creative Commons Attribution 4.0 International License https://creativecommons.org/licenses/by/4.0/ You may obtain a copy of the License at https://creativecommons.org/licenses/by/4.0/legalcode This work has been supported by the HEREDITARY project https://hereditary-project.eu/ funded by the European Union’s Horizon Europe research and innovation programme under the grant agreement No GA101137074
title: The Hereditary Ontology for GutBrain Data
version info: 1.0

Contributor
type: AnnotationProperty
description: The guidelines for using names of persons or organizations as creators also apply to contributors. Typically, the name of a Contributor should be used to indicate the entity.
issued: 1999-07-02
comment: An entity responsible for making contributions to the resource.
note: A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/contributor) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/). See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation.

Coverage
type: AnnotationProperty
description: Spatial topic and spatial applicability may be a named place or a location specified by its geographic coordinates. Temporal topic may be a named period, date, or date range. A jurisdiction may be a named administrative entity or a geographic place to which the resource applies. Recommended practice is to use a controlled vocabulary such as the Getty Thesaurus of Geographic Names [[TGN](https://www.getty.edu/research/tools/vocabulary/tgn/index.html)]. Where appropriate, named places or time periods may be used in preference to numeric identifiers such as sets of coordinates or date ranges.
issued: 1999-07-02
comment: The spatial or temporal topic of the resource, spatial applicability of the resource, or jurisdiction under which the resource is relevant.
note: A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/coverage) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/). See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation.

Creator
type: AnnotationProperty
description: Examples of a Creator include a person, an organization, or a service. Typically, the name of a Creator should be used to indicate the entity.
issued: 1999-07-02
comment: An entity primarily responsible for making the resource.
note: A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/creator) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/). See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation.

Date
type: AnnotationProperty
description: Date may be used to express temporal information at any level of granularity. Recommended practice is to express the date, date/time, or period of time according to ISO 8601-1 [[ISO 8601-1](https://www.iso.org/iso-8601-date-and-time-format.html)] or a published profile of the ISO standard, such as the W3C Note on Date and Time Formats [[W3CDTF](https://www.w3.org/TR/NOTE-datetime)] or the Extended Date/Time Format Specification [[EDTF](http://www.loc.gov/standards/datetime/)]. If the full date is unknown, month and year (YYYY-MM) or just year (YYYY) may be used. Date ranges may be specified using ISO 8601 period of time specification in which start and end dates are separated by a '/' (slash) character. Either the start or end date may be missing.
issued: 1999-07-02
comment: A point or period of time associated with an event in the lifecycle of the resource.
note: A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/date) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/). See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation.

Description
type: AnnotationProperty
description: Description may include but is not limited to: an abstract, a table of contents, a graphical representation, or a free-text account of the resource.
issued: 1999-07-02
comment: An account of the resource.
note: A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/description) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/). See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation.

Format
type: AnnotationProperty
description: Recommended practice is to use a controlled vocabulary where available. For example, for file formats one could use the list of Internet Media Types [[MIME](https://www.iana.org/assignments/media-types/media-types.xhtml)].
issued: 1999-07-02
comment: The file format, physical medium, or dimensions of the resource.
note: A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/format) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/). See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation.

Identifier
type: AnnotationProperty
description: Recommended practice is to identify the resource by means of a string conforming to an identification system.
issued: 1999-07-02
comment: An unambiguous reference to the resource within a given context.
note: A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/identifier) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/). See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation.

Language
type: AnnotationProperty
description: Recommended practice is to use either a non-literal value representing a language from a controlled vocabulary such as ISO 639-2 or ISO 639-3, or a literal value consisting of an IETF Best Current Practice 47 [[IETF-BCP47](https://tools.ietf.org/html/bcp47)] language tag.
issued: 1999-07-02
comment: A language of the resource.
note: A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/language) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/). See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation.

Publisher
type: AnnotationProperty
description: Examples of a Publisher include a person, an organization, or a service. Typically, the name of a Publisher should be used to indicate the entity.
issued: 1999-07-02
comment: An entity responsible for making the resource available.
note: A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/publisher) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/). See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation.

Relation
type: AnnotationProperty
description: Recommended practice is to identify the related resource by means of a URI. If this is not possible or feasible, a string conforming to a formal identification system may be provided.
issued: 1999-07-02
comment: A related resource.
note: A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/relation) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/). See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation.

Rights
type: AnnotationProperty
description: Typically, rights information includes a statement about various property rights associated with the resource, including intellectual property rights.
issued: 1999-07-02
comment: Information about rights held in and over the resource.
note: A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/rights) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/). See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation.

Source
type: AnnotationProperty
description: The described resource may be derived from the related resource in whole or in part. Recommended best practice is to identify the related resource by means of a string conforming to a formal identification system.
issued: 1999-07-02
comment: A related resource from which the described resource is derived.
note: A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/source) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/). See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation.

Subject
type: AnnotationProperty
description: Typically, the subject will be represented using keywords, key phrases, or classification codes. Recommended best practice is to use a controlled vocabulary.
issued: 1999-07-02
comment: The topic of the resource.
note: A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/subject) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/). See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation.

Title
type: AnnotationProperty
issued: 1999-07-02
comment: A name given to the resource.
note: A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/title) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/). See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation.

Type
type: AnnotationProperty
description: Recommended practice is to use a controlled vocabulary such as the DCMI Type Vocabulary [[DCMI-TYPE](http://dublincore.org/documents/dcmi-type-vocabulary/)]. To describe the file format, physical medium, or dimensions of the resource, use the Format element.
issued: 1999-07-02
comment: The nature or genre of the resource.
note: A [second property](/specifications/dublin-core/dcmi-terms/#http://purl.org/dc/terms/type) with the same name as this property has been declared in the [dcterms: namespace](http://purl.org/dc/terms/). See the Introduction to the document [DCMI Metadata Terms](/specifications/dublin-core/dcmi-terms/) for an explanation.

Contributor
description: The guidelines for using names of persons or organizations as creators apply to contributors.
issued: 2008-01-14
comment: An entity responsible for making contributions to the resource.
sub property of: Contributor

Creator
description: Recommended practice is to identify the creator with a URI. If this is not possible or feasible, a literal value that identifies the creator may be provided.
issued: 2008-01-14
comment: An entity responsible for making the resource.
sub property of: Creator
sub property of: Contributor

Description
description: Description may include but is not limited to: an abstract, a table of contents, a graphical representation, or a free-text account of the resource.
issued: 2008-01-14
comment: An account of the resource.
sub property of: Description

administered
type: ObjectProperty
domain: Class
  union of: Intervention or Procedure
  union of: Dietary Supplement
range: Organism
comment: It defines the relationship between the intervention or procedure and the organism.

affect
type: ObjectProperty
domain: Disease, Disorder or Finding
range: Disease, Disorder or Finding
comment: It defines a relatioship between a disease and another disease.

changeAbundance
type: ObjectProperty
domain: Class
  union of: Disease, Disorder or Finding
  union of: Intervention or Procedure
range: Class
  union of: Species
  union of: Microbiome
comment: It defines the relationship between the bacteria or microbiome and te disease, disorder or finding.

changeEffect
type: ObjectProperty
domain: Drug
range: Disease, Disorder or Finding
comment: It indicates that a drug or substance alters or modifies the course or symptoms of a disease or disorder.

changeExpression
type: ObjectProperty
domain: Class
  union of: Intervention or Procedure
  union of: Species
  union of: Dietary Supplement
  union of: Microbiome
range: Gene
comment: It explains how a bacteria or the microbiome can change the expression of a gene.

comparedTo
type: ObjectProperty
domain: Microbiome
range: Microbiome
comment: It defines the relationship between an instance of microbiome and another microbiome.

composedOf
type: ObjectProperty
domain: Class
  union of: Paper Abstract
  union of: Paper Title
range: Sentence
comment: This relationship describes the connection between the abstracts and titles and the sentences that compose them.

containedIn
type: ObjectProperty
domain: Class
  union of: Anatomic Site
  union of: Disease, Disorder or Finding
  union of: Gene
  union of: Intervention or Procedure
  union of: Assay
  union of: Species
  union of: Animal
  union of: Biomedical Technique
  union of: Dietary Supplement
  union of: Drug
  union of: Food
  union of: Human
  union of: Microbiome
  union of: Organism
  union of: Statistical Technique
comment: It describes the relationship between the mention and the sentence and the entities and the mention.

contains
type: ObjectProperty
domain: Collection
range: Paper
comment: It explains that each collection is composed of papers.

hasAbstract
type: ObjectProperty
domain: Paper
range: Paper Abstract
comment: It underlines that a paper contains an abstract.

hasTitle
type: ObjectProperty
domain: Paper
range: Paper Title
comment: It underlines that a paper contains a title.

impact
type: ObjectProperty
domain: Drug
range: Microbiome
comment: It describes the effect or change when is strongly associated with alterations in biological or microbiological aspects, like microbiota or gut health.

influence
type: ObjectProperty
domain: Class
  union of: Intervention or Procedure
  union of: Species
range: Disease, Disorder or Finding
comment: Represents the effect or impact of a dietary supplements or other substances and often diseases, disorders, or health conditions.

interact
type: ObjectProperty
domain: Class
  union of: Disease, Disorder or Finding
  union of: Species
  union of: Chemical
  union of: Drug
range: Class
  union of: Intervention or Procedure
  union of: Species
  union of: Chemical
  union of: Drug
comment: It explains what can influence disease, disorder or finding.

isA
type: ObjectProperty
domain: Disease, Disorder or Finding
range: Disease, Disorder or Finding
comment: It defines a relatioship between a disease and another disease.

isLinkedTo
type: ObjectProperty
domain: Microbiome
range: Disease, Disorder or Finding
comment: It defines a relatioship between microbiota and a disease or health condition.

locatedIn
type: ObjectProperty
domain: Class
  union of: Anatomic Site
  union of: Chemical
  union of: Mention
  union of: Microbiome
range: Class
  union of: Anatomic Site
  union of: Organism
  union of: Sentence
comment: It defines the relationship between an organism and its location in the Microbiome.

partOf
type: ObjectProperty
domain: Class
  union of: Gene
  union of: Species
  union of: Genome
  union of: Metabolite
  union of: Microbiome
  union of: Sentence
range: Class
  union of: Chemical
  union of: Genome
  union of: Microbiome
  union of: Microbiota
  union of: Paper Abstract
  union of: Paper Title
comment: It defines the relationship between bacterias that are part of microbiota and microbiome.

producedBy
type: ObjectProperty
domain: Class
  union of: Drug
  union of: Metabolite
range: Microbiome
comment: It defines the relationship between the drug or metabolite and the microbiome.

relatedTo
type: ObjectProperty
domain: Neurotransmitter
range: Microbiome
comment: It defines the relationship between the neurotransmitter and the microbiome.

strike
type: ObjectProperty
domain: Disease, Disorder or Finding
range: Anatomic Site
comment: It defines the relationship between the disease, disorder and finding and the anatomical location.

target
type: ObjectProperty
domain: Disease, Disorder or Finding
range: Organism
comment: It is used to specify that a particular disease or health disorder primarily affects or concerns a specific population or biological entity.

treatedBy
type: ObjectProperty
domain: Disease, Disorder or Finding
range: Intervention or Procedure
comment: It explains that the disease, disorder or finding is treated by the intervention or procedure.

usedBy
type: ObjectProperty
domain: Class
  union of: Animal
  union of: Human
  union of: Microbiome
range: Biomedical Technique
comment: This relationship suggests the employment or use of specific biomedical techniques or methods on particular biological entities, usually in experimental setups.

hasAbstractText
type: DatatypeProperty
domain: Paper Abstract
range: PlainLiteral
comment: The full abstract of the paper as a single text string.

hasMentionText
type: DatatypeProperty
domain: Mention
range: PlainLiteral
comment: The exact text span that was annotated (e.g., the words in the title/abstract that constitute an individual or relation mention).

hasSentenceText
type: DatatypeProperty
domain: Sentence
range: PlainLiteral
comment: The complete sentence from the source document.

hasTitleText
type: DatatypeProperty
domain: Paper Title
range: PlainLiteral
comment: The paper’s title as a single text string.

paperAnnotator
type: DatatypeProperty
domain: Paper
range: PlainLiteral
comment: The identifier of the expert who annotated the paper (e.g., expert_7).

paperAuthor
type: DatatypeProperty
domain: Paper
range: PlainLiteral
comment: The author list for the paper.

paperId
type: DatatypeProperty
domain: Paper
range: integer
comment: The unique paper identifier in your corpus (e.g., PubMed ID).

paperJournal
type: DatatypeProperty
domain: Paper
range: PlainLiteral
comment: The journal where the paper was published.

paperYear
type: DatatypeProperty
domain: Paper
range: gYear
comment: The publication year of the paper.

taggedAs
type: DatatypeProperty
domain: Mention
range: PlainLiteral
comment: One or more human-readable tags assigned to a mention or paper (e.g., drug, bacteria, DDF), mirroring the category.

Anatomic Site
type: Class
comment: Named locations of or within the body. [Definition Source: NCIT]

Disease, Disorder or Finding
type: Class
comment: A condition that is relevant to human neoplasms and non-neoplastic disorders. This includes observations, test results, history and other concepts relevant to the characterization of human pathologic conditions. [Definition Source: NCIT]

Gene
type: Class
comment: A functional unit of heredity which occupies a specific position on a particular chromosome and serves as the template for a product that contributes to a phenotype or a biological function. [Definition Source: NCIT]

Intervention or Procedure
type: Class
comment: An activity that produces an effect, or that is intended to alter the course of a disease in a patient or population. This is a general term that encompasses the medical, social, behavioral, and environmental acts that can have preventive, therapeutic, or palliative effects. [Definition Source: NCIT]

Assay
type: Class
comment: The assay used to produce measurement. [Definition Source: Phenopacket v2]

Species
type: Class
subclass of: Genus
comment: A group of organisms that differ from all other groups of organisms and that are capable of breeding and producing fertile offspring. [Definition Source: NCIT]

Animal
type: Class
subclass of: Organism
comment: A non-human living organism that has membranous cell walls, requires oxygen and organic foods, and is capable of voluntary movement, as distinguished from a plant or mineral. [Definition Source: NCIT]

Biomedical Technique
type: Class
subclass of: Assay
comment: Research concerned with the application of biological and physiological principles to clinical medicine. [Definition Source: NCIT]

Chemical
type: Class
subclass of: Intervention or Procedure
comment: A chemical substance is a portion of matter of constant composition, composed of molecular entities of the same type or of different types. [Definition Source: CHEBI]

Class
subclass of: Phylum
comment: A collection of taxonomic subdivisions directly under Phylum. It is a major group of organisms, e.g. Mammalia, Reptilia, Gastropoda, Insecta, etc that contains a large number of different sublineages, but have shared characteristics in common (e.g. warm-blooded, fur, six legs etc). [Definition Source: NCIT]

Dietary Supplement
type: Class
subclass of: Food
comment: Oral preparations containing dietary ingredient(s) intended to supplement the diet. Dietary ingredients include vitamins, minerals, herbs, amino acids, extracts and metabolites. [Definition Source: NCIT]

Domain
type: Class
comment: A taxonomic category above that of Kingdom.

Drug
type: Class
subclass of: Intervention or Procedure
comment: Any substance which when absorbed into a living organism may modify one or more of its functions. The term is generally accepted for a substance taken for a therapeutic purpose, but is also commonly used for abused substances. [Definition Source: CHEBI]

Experimental Result
type: Class
comment: The outcome of an experiment or set of experiments, including observations and primary, processed, and analyzed data. [Definition Source: NCIT]

Family
type: Class
subclass of: Order
comment: A taxonomic category between Order and Genus. It consists of a group of organisms among which the differences are quite minor, e.g. Equiidae - horses and their relatives. [Definition Source: NCIT]

Food
type: Class
subclass of: Intervention or Procedure
comment: A functional unit of heredity which occupies a specific position on a particular chromosome and serves as the template for a product that contributes to a phenotype or a biological function. [Definition Source: SNOMEDCT]

Genome
type: Class
comment: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA. [Definition Source: MeSH]

Genus
type: Class
subclass of: Family
comment: A taxonomic category ranking below a family (or Subfamily) and above a species and generally consisting of a group of species exhibiting similar characteristics. [Definition Source: NCIT]

Human
type: Class
subclass of: Organism
comment: Members of the species Homo sapiens. [Definition Source: NCBI]

Mention
type: Class
comment: Word or Phrase that is inside a sentence.

Metabolite
type: Class
comment: Any substance involved in metabolism, either as a product of metabolism or as necessary for metabolism. [Definition Source: NCIT]

Microbiome
type: Class
comment: This term refers to the entire habitat, including the microorganisms (bacteria, archaea, lower and higher eukaryotes, and viruses), their genomes (i.e., genes), and the surrounding environmental conditions. [Definition Source: OHMI]

Microbiota
type: Class
comment: Microbiota are the range of microorganisms that may be commensal, mutualistic, or pathogenic found in and on all multicellular organisms, including plants. [Definition Source: Wikipedia]

Neurotransmitter
type: Class
comment: Endogenous signaling molecules that alter the behavior of neurons or effector cells. Neurotransmitter is used here in its most general sense, including not only messengers that act directly to regulate ion channels, but also those that act through second messenger systems, and those that act at a distance from their site of release. Included are neuromodulators, neuroregulators, neuromediators, and neurohumors, whether or not acting at synapses. [Definition Source: NCIT]

Order
type: Class
subclass of: Class
comment: A taxonomic category between Class and Family. It is group of organisms that although differing quite a bit among themselves still have a large degree of characteristics in common. [Definition Source: NCIT]

Organism
type: Class
comment: A living entity. [Definition Source: NCIT]

Paper
type: Class
comment: An article reporting original research, published in a peer-reviewed journal. [Definition Source: ONTOAVIDA]

Paper Abstract
type: Class
comment: A written summary of the important points of a scientific article. [Definition Source: NCIT]

Paper Collection
type: Class
comment: The type of the collection where the papers are stored.

Paper Title
type: Class
comment: An official descriptive name of a document, e.g. the long name of a study protocol provided by the study sponsor. [Definition Source: NCIT]

Phylum
type: Class
subclass of: Super Kingdom
comment: A major division of a biological kingdom, consisting of closely-related classes; represents a basic fundamental pattern of organization and, presumably, a common descent. [Definition Source: NCIT]

Sentence
type: Class
comment: A set of words that is complete in itself, conveying a statement, question, exclamation, or command and typically containing an explicit or implied subject and a predicate containing a finite verb. [Definition Source: NCIT]

Species
type: Class
comment: A group of organisms that differ from all other groups of organisms and that are capable of breeding and producing fertile offspring. [Definition Source: NCIT]

Specimen
type: Class
comment: A material entity that is collected for potential use as an input upon which measurements or observations are performed. [Definition Source: OBI]

Specimen Collection Process
type: Class
comment: A planned process with the objective to obtain a material entity for potential use as an input upon which measurements or observations are performed. [Definition Source: OBI]

Statistical Technique
type: Class
subclass of: Assay
comment: A method of calculating, analyzing, or representing statistical data. [Definition Source: NCIT]

Super Kingdom
type: Class
subclass of: Domain
comment: The highest taxonomic rank, immediately above phylum or division. There are five biological kingdoms (Monera, Protista, Plantae, Fungi, Animalia) into which organisms are grouped, based on common characteristics. [Definition Source: NCIT]

OMIT_0003283
comment: Brain_diseases refers to a collective term for various medical conditions that affect the structure or function of the brain, including neurological disorders, neurodegenerative diseases, and psychiatric conditions. [Definition Source: llama3-8b-8192]
comment: OMIT Match