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.
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
The Hereditary Ontology for GutBrain Data
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.
An entity responsible for making contributions to the resource.
Contributor
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.
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.
The spatial or temporal topic of the resource, spatial applicability of the resource, or jurisdiction under which the resource is relevant.
Coverage
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.
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.
An entity primarily responsible for making the resource.
Creator
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 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.
A point or period of time associated with an event in the lifecycle of the resource.
Date
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 may include but is not limited to: an abstract, a table of contents, a graphical representation, or a free-text account of the resource.
An account of the resource.
Description
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.
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)].
The file format, physical medium, or dimensions of the resource.
Format
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.
Recommended practice is to identify the resource by means of a string conforming to an identification system.
An unambiguous reference to the resource within a given context.
Identifier
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.
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.
A language of the resource.
Language
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.
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.
An entity responsible for making the resource available.
Publisher
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.
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.
A related resource.
Relation
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.
Typically, rights information includes a statement about various property rights associated with the resource, including intellectual property rights.
Information about rights held in and over the resource.
Rights
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.
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.
A related resource from which the described resource is derived.
Source
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.
Typically, the subject will be represented using keywords, key phrases, or classification codes. Recommended best practice is to use a controlled vocabulary.
The topic of the resource.
Subject
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.
A name given to the resource.
Title
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.
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.
The nature or genre of the resource.
Type
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.
The guidelines for using names of persons or organizations as creators apply to contributors.
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.
An entity responsible for making the resource.
It defines the relationship between the intervention or procedure and the organism.
administered
It defines a relatioship between a disease and another disease.
It defines the relationship between the bacteria or microbiome and te disease, disorder or finding.
changeAbundance
It indicates that a drug or substance alters or modifies the course or symptoms of a disease or disorder.
changeEffect
It explains how a bacteria or the microbiome can change the expression of a gene.
changeExpression
It defines the relationship between an instance of microbiome and another microbiome.
comparedTo
This relationship describes the connection between the abstracts and titles and the sentences that compose them.
composedOf
It describes the relationship between the mention and the sentence and the entities and the mention.
containedIn
It explains that each collection is composed of papers.
contains
It underlines that a paper contains an abstract.
hasAbstract
It underlines that a paper contains a title.
hasTitle
It describes the effect or change when is strongly associated with alterations in biological or microbiological aspects, like microbiota or gut health.
impact
Represents the effect or impact of a dietary supplements or other substances and often diseases, disorders, or health conditions.
influence
It explains what can influence disease, disorder or finding.
interact
isA
It defines a relatioship between microbiota and a disease or health condition.
isLinkedTo
It defines the relationship between an organism and its location in the Microbiome.
locatedIn
It defines the relationship between bacterias that are part of microbiota and microbiome.
partOf
It defines the relationship between the drug or metabolite and the microbiome.
producedBy
It defines the relationship between the neurotransmitter and the microbiome.
relatedTo
It defines the relationship between the disease, disorder and finding and the anatomical location.
strike
It is used to specify that a particular disease or health disorder primarily affects or concerns a specific population or biological entity.
target
It explains that the disease, disorder or finding is treated by the intervention or procedure.
treatedBy
This relationship suggests the employment or use of specific biomedical techniques or methods on particular biological entities, usually in experimental setups.
usedBy
The full abstract of the paper as a single text string.
hasAbstractText
The exact text span that was annotated (e.g., the words in the title/abstract that constitute an individual or relation mention).
hasMentionText
The complete sentence from the source document.
hasSentenceText
The paper’s title as a single text string.
hasTitleText
The identifier of the expert who annotated the paper (e.g., expert_7).
paperAnnotator
The author list for the paper.
paperAuthor
The unique paper identifier in your corpus (e.g., PubMed ID).
paperId
The journal where the paper was published.
paperJournal
The publication year of the paper.
paperYear
One or more human-readable tags assigned to a mention or paper (e.g., drug, bacteria, DDF), mirroring the category.
taggedAs
Named locations of or within the body. [Definition Source: NCIT]
Anatomic Site
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]
Disease, Disorder or Finding
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]
Gene
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]
Intervention or Procedure
The assay used to produce measurement. [Definition Source: Phenopacket v2]
Assay
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]
Species
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]
Animal
Research concerned with the application of biological and physiological principles to clinical medicine. [Definition Source: NCIT]
Biomedical Technique
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]
Chemical
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]
Class
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]
Dietary Supplement
A taxonomic category above that of Kingdom.
Domain
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]
Drug
The outcome of an experiment or set of experiments, including observations and primary, processed, and analyzed data. [Definition Source: NCIT]
Experimental Result
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]
Family
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]
Food
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]
Genome
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]
Genus
Members of the species Homo sapiens. [Definition Source: NCBI]
Human
Word or Phrase that is inside a sentence.
Mention
Any substance involved in metabolism, either as a product of metabolism or as necessary for metabolism. [Definition Source: NCIT]
Metabolite
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]
Microbiome
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]
Microbiota
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]
Neurotransmitter
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]
Order
A living entity. [Definition Source: NCIT]
Organism
An article reporting original research, published in a peer-reviewed journal. [Definition Source: ONTOAVIDA]
Paper
A written summary of the important points of a scientific article. [Definition Source: NCIT]
Paper Abstract
The type of the collection where the papers are stored.
Paper Collection
An official descriptive name of a document, e.g. the long name of a study protocol provided by the study sponsor. [Definition Source: NCIT]
Paper Title
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]
Phylum
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]
Sentence
A material entity that is collected for potential use as an input upon which measurements or observations are performed. [Definition Source: OBI]
Specimen
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]
Specimen Collection Process
A method of calculating, analyzing, or representing statistical data. [Definition Source: NCIT]
Statistical Technique
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]
Super Kingdom
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]