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The Hereditary Ontology for Gut-Brain Axis Data

This version:
https://w3id.org/hereditary/ontology/gutbrain/
Latest version:
https://w3id.org/hereditary/ontology/gutbrain/
Ontology Version IRI:
https://w3id.org/hereditary/ontology/gutbrain/1.0/
Revision:
1.0
Authors:
Samuel Piron
Marco Martinelli
Gianmaria Silvello
Download serialization:
RDF/XML TTL
License:
https://creativecommons.org/licenses/by-sa/4.0/
Cite as:
Samuel Piron, Marco Martinelli, Gianmaria Silvello. The Hereditary Ontology for Gut-Brain Axis Data. Revision: 1.0. Retrieved from: https://w3id.org/hereditary/ontology/gutbrain/schema/1.0/
Ontology Specification Draft

Introduction back to ToC

An ontology of a given domain of interest is a formal representation of knowledge that provides a vocabulary for describing the domain of interest, annotations that explain and clarify each term in the vocabulary, and a logical theory (consisting of axioms and definitions) for the vocabulary, enabling effective modelling and validation of ontologies [1].

Ontologies encompass a multidisciplinary field that draws upon knowledge from information organization, natural language processing, information extraction, artificial intelligence, knowledge representation, and acquisition. In recent years, they have gained popularity as an emerging helpful technology for improving information, organization, management, and understanding. They are shared between communities and application systems, having a significant impact on areas where there is a vast amount of heterogeneous computer-based information, such as the World Wide Web and industrial software applications, knowledge management, and electronic records.

In the Semantic Web, ontologies can be seen as metadata that explicitly represent in a machine-processable way. Ontology-based reasoning services can apply semantics and are helpful for various things like consistency checking, query answering, and subsumption reasoning [2]. Due to their popularity, they are represented online in various languages (e.g., OWL, RDF, XML, FOL); each one facilitates interoperability in distributed environments. The availability of multi-format releases facilitates the application of ontologies within microservices, triplestores, rule engines, and data-integration workflows, eliminating the need for additional conversion processes [3].

GBO: Gut-Brain Ontology

In this project, we introduce GBO (Gut-Brain Ontology), a structured knowledge base designed to capture the interactions along the gut-brain axis. By formalizing both anatomical and microbiota relationships, GBO enables systematic exploration of how gut microbiota, metabolites, and immune signals influence neurological health and disease. Our primary focus surrounds a large spectrum of disorders from Amyotrophic Lateral Sclerosis, Multiple Sclerosis, Parkinson's disease, Alzheimer's disease, Frontotemporal Dementia, to stroke, diabetes, obesity, and neuropsychiatric conditions such as depression and ADHD; each of them has a connection to the gut-brain interaction. By integrating clinical phenotypes, experimental findings, and molecular pathways into a unified and consistent ontology, GBO will help researchers to discover new risk factors, predict treatment responses, and raise public awareness of the critical role the gut-brain axis plays in human health.

Existing Ontologies

LOD exposes open, external sources that can be reused. To design our ontology, we searched for existing ontologies and vocabularies to maximize reuse, interoperability, and scientific consistency. Because the gut-brain axis encompasses microbiology, neuroscience, and clinical medicine, no single resource covers the entire conceptual space; instead, the web provides a set of specialized ontologies, vocabularies, and thesauri for specific domains.

We now identify the knowledge bases used to represent individuals in our knowledge graph, along with a brief description.

  • National Cancer Institute Thesaurus (NCIT): Is a public domain thesaurus developed by the National Cancer Institute. Its main objective is to provide practitioners and annotators with a source of codes associated with terminology concepts, enabling them to annotate documents and facilitate information retrieval. Info
  • National Center for Biotechnology Information Taxonomy (NCBI Taxon): Consists of a single, hierarchically arranged list of organismal names across all domains of life. It provides organism names and classifications for every sequence in the nucleotide and protein sequence databases of the International Nucleotide Sequence Database Collaboration (INSDC). Info
  • Medical Subject Headings 2025 (MeSH): Is a comprehensive, controlled vocabulary thesaurus created by the National Library of Medicine (NLM) for indexing and cataloging biomedical and health-related information in databases like MEDLINE and PubMed. Info
  • Unified Medical Language System (UMLS): Consists of a metathesaurus of biomedical vocabularies developed by the US National Library of Medicine. It integrates families of biomedical vocabularies including MeSH, SNOMED CT, NCIT, GO, and OMIM, providing shared identifiers, mappings, and lexical variants to support interoperability and text mining across these resources. Info
  • Chemical Entities of Biological Interest (ChEBI): Consists of an OBO ontology of small molecular entities (metabolites, ions, drugs) with well-curated structures, roles, and relationships; widely used to standardize chemicals in pathway, metabolomics, and microbiome studies. Info
  • FoodOn v[8]: Consists of a controlled vocabulary to name all parts of animals, plants, and fungi which can bear a food role for humans and domesticated animals, as well as derived food products and the processes used to make them.
  • OHMI (Ontology of Host-Microbiome Interactions): Corresponds to a domain ontology modeling host, microbiome, environments, and their interactions (e.g., dysbiosis, phenotypes, experimental contexts), supporting integration of host-microbiome datasets. Info
  • STATO (STATistics Ontology): Corresponds to terms for statistical designs, variables, measures, and analyses (e.g., regression, ANOVA, effect sizes), used to standardize methods/results annotation and improve reproducibility. Info
  • OMIT Ontology: Used to establish data exchange standards and common data elements in the microRNA (miR) domain. Biologists and bioinformaticians can make use of OMIT to leverage emerging semantic technologies in knowledge acquisition and discovery for more effective identification of essential roles performed by miRs in humans’ various diseases and biological processes. Info
  • KEGG Orthology (KO): Consists of a database of molecular functions represented in terms of functional orthologs. It links genes (K numbers) to pathways, modules, enzymes, reactions, and compounds that are central for pathway mapping and functional profiling (including metagenomics). Info

We also employed Mondo Disease Ontology (Mondo) that describes particular disorders or diseases coming from the DDF category. Info

Design Principles

To provide consistency to GBO, we employed the following principles for defining classes and properties. These guidelines involve external reference, annotation properties, metadata, and naming conventions.

  • External Reference: Whenever we model clinical and laboratory information, it is preferable to use external ontologies to provide correspondence between widely used medical terminology. In this way, we promote data consistency across databases while ensuring the authority of the semantic meaning of the resources. We linked our individuals to external ones with the ontologies specified in the Existing Ontologies section. The table shows the number of matches for each external ontology made by each class.
  • Namespaces: GBO URIs are divided into two main namespaces: the schema namespace https://w3id.org/hereditary/ontology/schema/ and the resource namespace https://w3id.org/hereditary/ontology/resource/. All URIs that correspond to classes, object properties, and data properties belong to the first namespace, while instances belong to the second one. In addition to these, GBO also contains other instances with different namespaces, such as the SKOS Concept.
  • Metadata: All classes, data properties, and object properties have additional information. For each new instance created, we added specific information such as the label and definition, which provides a brief description of the example along with its source. We defined an external annotation property, skos:hasExactmatch, coming from the SKOS namespace, that is used only for classes. Since they have been defined using the GBO namespace, we added this property to ensure consistency, referring to the same external class in an external knowledge base.
  • Naming Conventions: Each property has a label and a definition that explains its use. Data properties include the name of the Domain Class so that its meaning is intuitive.

Simple Knowledge Organization System (SKOS)

During the ontology modelling, it is common to use external taxonomies to ensure terminology consistency, especially in the biomedical field. Despite the large number of comprehensive medical ontologies, reusing them entails significant costs that may outweigh the costs of a new implementation. In GBO, external sources have been employed to model humans, species, diseases, disorders, and lab techniques. The common aspect between these elements is that we are interested in the main idea behind the medical term. To avoid classism, a typical pattern in ontologies is to model an external hierarchy as a hierarchy of ontological classes. This occurs when we model a named individual that belongs to two classes: SKOS Concept and the one in GBO.

The use of SKOS has two main advantages: first, it allows for saving space by reducing the number of required URIs (e.g., when defining more classes), and it reduces the complexity of the queries. The main drawback is that it prevents attaching class-specific characteristics directly to those classes. We adopted this pattern for all the class instances, except for Paper, PaperCollection, PaperTitle, PaperAbstract, Mention, and Sentence.

As the primary reference, we consulted other well-known resources. We defined new individuals that were not present in external ontologies with our namespace, GBO.

Document Class Hierarchy

In the GBO, we introduce dedicated classes for structuring the primary literature: Paper, Mention, and Sentence. They are central components for organizing research articles and their content.

Paper Modeling

The Paper class is designed to represent a general biomedical article within the ontology. Each paper has several key components:

  • PaperCollection: Represents a collection of related papers, linked by the contains property.
  • PaperTitle: Connected to each paper by the hasTitle property. It contains the title of the paper as a rdf:PlainLiteral.
  • PaperAbstract: Connected to each paper by the hasAbstract property. It contains the abstract of the paper as a rdf:PlainLiteral.
  • PaperAuthor: Specifies the authors of the paper. Its value is a rdf:PlainLiteral.
  • PaperId: Specifies the PubMed ID that identifies online the paper. Its value is a xsd:integer.
  • PaperJournal: Specifies the journal where the paper has been published. Its value is a rdf:PlainLiteral.
  • PaperYear: Specifies the publication year of the paper. Its value is a xsd:integer.
  • PaperAnnotator: Specifies which expert annotated the NER entities. Its value is a rdf:PlainLiteral.

Each Paper is linked to one or more Sentence instances via the partOf property. Sentences are extracted from the paper's title and abstract.

Mention

The Mention class captures every entity mention of an ontology individual within a paper's title or abstract. This establishes a connection between the paper and the individual found in it. They are composed of two main components:

  • Text Span: The exact portion of text from the sentence in which the individual appears, defined by the property hasMentionText. It captures the text's exact position inside a specific sentence.
  • Category: Each mention has the property taggedAs that identifies the label of the category associated with that text span (e.g., human, anatomical location, DDF).

During the data ingestion process, after the match process, the entity mentions are created using the raw text, and the individual is connected with them via the containedIn predicate. This relationship ensures that each term is traceable back to its exact textual source.

Sentence

We assign sent_id 0 to the sentence title, then sequentially index the others that are part of the abstract. Finally, we link each sentence to its corresponding entity mentions using the locatedIn property. Each sentence has two main properties:

  • hasSentenceText: shows the raw sentence text.
  • partOf: connects the sentence to its title or abstract.

Figure 1 illustrates how Paper, Sentence, and Mention interconnect to capture both document structure and the text occurrences of biomedical concepts.

Documents Modeling for Gut-Brain Data
Figure 1. Document classes and their metadata properties.

Categories Modeling

To support high-quality semantic connections of gut-brain interactions, GBO defines a set of fourteen distinct entity types, which are crucial for annotating biomedical entities across the dataset. These categories serve as a semantic foundation for analyzing relationships within the gut-brain axis. Each entity type is associated with a unique URI that links it to a standardized concept in an external knowledge base and is accompanied by an explanation that defines its scope and semantic meaning. All category instances are linked to external identifiers whenever possible or to our namespace.

A relevant aspect of our category modeling is the fine-grained representation of bacterial taxa. We treat Bacteria as a general skos:Concept corresponding to the Family level. At the same time, each expert-annotated bacterial entity mention is instantiated at the Species level, our ontology's most specific rank. During the data ingestion process, any species that cannot be matched to an external ontology is automatically linked back to the Bacteria skos:Concept, ensuring all entity mentions are mapped.

To make the GBO even more complete and consistent, we included additional categories specific to the gut-brain axis, such as Assay, Intervention or Procedure, Metabolite, or Specimen, even if we didn't employ them actively in this work.

Category Relations

GBO utilizes seventeen predicates, many of which are overloaded, meaning that the same predicate can link multiple combinations of head and tail entity types, resulting in over 50 possible (head, predicate, tail) triples. Figure 2 shows the Category ontology schema.

Documents Modeling for Gut-Brain Data
Figure 2. Categories and their relationships.

Moreover, Figure 3 presents the complete GBO, merging the document classes (Paper, Sentence, Mention) with the full set of entity categories and relations.

HEREDIATRY Ontology for Gut-Brain Data
Figure 3. The Gut-Brain Axis scheme. The diagram is divided in two different regions: on the left there are the documents and the taxonomy structure (Paper, Mention, Sentence, Species, Genus, Family etc.) and on the right there are the biological classes and experimental concepts (Disease, Disorder or Finding, Microbiome, Biomedical Technique etc.)

Namespace declarations

Table 1: Namespaces used in the document
[Ontology NS Prefix]<https://w3id.org/hereditary/ontology/gutbrain/schema/>
[Ontology Individual Prefix]<https://w3id.org/hereditary/ontology/gutbrain/resource/>
dc<http://purl.org/dc/elements/1.1/>
obo<http://purl.obolibrary.org/obo/>
orcid<https://orcid.org/0000-0002-0676-682>
owl<http://www.w3.org/2002/07/owl#>
rdf<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
rdfs<http://www.w3.org/2000/01/rdf-schema#>
schema<https://w3id.org/brainteaser/ontology/schema/>
skos<http://www.w3.org/2004/02/skos/core#>
terms<http://purl.org/dc/terms/>
xml<http://www.w3.org/XML/1998/namespace>
xsd<http://www.w3.org/2001/XMLSchema#>

Overview back to ToC

This ontology has the following classes and properties.

Classes

Data Properties

Cross-reference for classes, object properties and data properties back to ToC

This section provides details for each class and property defined by The Hereditary Ontology for Gut-Brain Axis Data.

Classes

Anatomic Site c back to ToC or Class ToC

IRI: https://w3id.org/brainteaser/ontology/schema/AnatomicalSite

Named locations of or within the body. [Definition Source: NCIT]
is in range of
strike op

Animal c back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/Animal

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]
has super-classes
Organism c

Assay c back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/genomics/schema/Assay

is defined by
https://raw.githubusercontent.com/Vezzero/ThesisPiron/main/gutbrainv1.rdf
The assay used to produce measurement. [Definition Source: Phenopacket v2]
has sub-classes
Biomedical Technique c , Statistical Technique c

Biomedical Technique c back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/BiomedicalTechnique

Research concerned with the application of biological and physiological principles to clinical medicine. [Definition Source: NCIT]
has super-classes
Assay c
is in range of
usedBy op

Chemical c back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/Chemical

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]
has super-classes
Intervention or Procedure c

Class c back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/Class

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]
has super-classes
Phylum c
has sub-classes
Order c

Dietary Supplement c back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/DietarySupplement

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]
has super-classes
Food c

Disease, Disorder or Finding c back to ToC or Class ToC

IRI: https://w3id.org/brainteaser/ontology/schema/DiseaseDisorderOrFinding

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]
is in domain of
strike op , target op , treatedBy op
is in range of
changeEffect op , influence op , isLinkedTo op

Domain c back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/Domain

A taxonomic category above that of Kingdom.
has sub-classes
Super Kingdom c

Drug c back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/Drug

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]
has super-classes
Intervention or Procedure c
is in domain of
changeEffect op , impact op

Experimental Result c back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/ExperimentalResult

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

Family c back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/Family

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]
has super-classes
Order c
has sub-classes
Genus c

Food c back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/Food

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]
has super-classes
Intervention or Procedure c
has sub-classes
Dietary Supplement c

Gene c back to ToC or Class ToC

IRI: https://w3id.org/brainteaser/ontology/schema/Gene

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]
is in range of
changeExpression op

Genome c back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/Genome

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 c back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/Genus

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]
has super-classes
Family c
has sub-classes
Species c

Human c back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/Human

Members of the species Homo sapiens. [Definition Source: NCBITaxon]
has super-classes
Organism c

Intervention or Procedure c back to ToC or Class ToC

IRI: https://w3id.org/brainteaser/ontology/schema/InterventionOrProcedure

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]
has sub-classes
Chemical c , Drug c , Food c
is in range of
treatedBy op

Mention c back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/Mention

Word or Phrase that is inside a sentence.
is in domain of
hasMentionText dp , taggedAs dp

Metabolite c back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/Metabolite

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

Microbiome c back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/Microbiome

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]
is in domain of
isLinkedTo op
is in range of
impact op , producedBy op , relatedTo op

Microbiota c back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/Microbiota

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]
is in domain of
partOf op

Neurotransmitter c back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/Neurotransmitter

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]
is in domain of
relatedTo op

Order c back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/Order

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]
has super-classes
Class c
has sub-classes
Family c

Organism c back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/Organism

A living entity. [Definition Source: NCIT]
has sub-classes
Animal c , Human c
is in range of
administered op , target op

Paper c back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/Paper

An article reporting original research, published in a peer-reviewed journal. [Definition Source: ONTOAVIDA]
is in domain of
hasAbstract op , hasTitle op , paperAnnotator dp , paperAuthor dp , paperId dp , paperJournal dp , paperYear dp
is in range of
contains op

Paper Abstract c back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/PaperAbstract

A written summary of the important points of a scientific article. [Definition Source: NCIT]
is in domain of
hasAbstractText dp
is in range of
hasAbstract op

Paper Collection c back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/PaperCollection

The type of the collection where the papers are stored.

Paper Title c back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/PaperTitle

An official descriptive name of a document, e.g. the long name of a study protocol provided by the study sponsor. [Definition Source: NCIT]
is in domain of
hasTitleText dp
is in range of
hasTitle op

Phylum c back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/Phylum

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]
has super-classes
Super Kingdom c
has sub-classes
Class c

Sentence c back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/Sentence

is defined by
https://raw.githubusercontent.com/Vezzero/ThesisPiron/main/gutbrainv1.rdf
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]
is in domain of
hasSentenceText dp
is in range of
composedOf op

Species c back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/Species

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]
has super-classes
Genus c

Specimen c back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/Specimen

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 c back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/SpecimenCollectionProcess

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 c back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/StatisticalTechnique

A method of calculating, analyzing, or representing statistical data. [Definition Source: NCIT]
has super-classes
Assay c

Super Kingdom c back to ToC or Class ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/SuperKingdom

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]
has super-classes
Domain c
has sub-classes
Phylum c

Object Properties

administered op back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/administered

It defines the relationship between the intervention or procedure and the organism.
has domain
Dietary Supplement c or Intervention or Procedure c
has range
Organism c

affect op back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/affect

It defines a relatioship between a disease and another disease.
has domain
Disease, Disorder or Finding c
has range
Disease, Disorder or Finding c

changeAbundance op back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/changeAbundance

It defines the relationship between the bacteria or microbiome and te disease, disorder or finding.
has domain
Disease, Disorder or Finding c or Intervention or Procedure c
has range
Microbiome c or Species c

changeEffect op back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/changeEffect

It indicates that a drug or substance alters or modifies the course or symptoms of a disease or disorder.
has domain
Drug c
has range
Disease, Disorder or Finding c

changeExpression op back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/changeExpression

It explains how a bacteria or the microbiome can change the expression of a gene.
has domain
Dietary Supplement c or Microbiome c or Intervention or Procedure c or Species c
has range
Gene c

comparedTo op back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/comparedTo

It defines the relationship between an instance of microbiome and another microbiome.
has domain
Microbiome c
has range
Microbiome c

composedOf op back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/composedOf

This relationship describes the connection between the abstracts and titles and the sentences that compose them.
has domain
Paper Abstract c or Paper Title c
has range
Sentence c

containedIn op back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/containedIn

It describes the relationship between the mention and the sentence and the entities and the mention.
has domain
Animal c or Biomedical Technique c or Dietary Supplement c or Drug c or Food c or Human c or Microbiome c or Organism c or Statistical Technique c or Assay c or Anatomic Site c or Disease, Disorder or Finding c or Gene c or Intervention or Procedure c or Species c
has range
Mention c

contains op back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/contains

It explains that each collection is composed of papers.
has domain
Paper Collection c
has range
Paper c

hasAbstract op back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/hasAbstract

It underlines that a paper contains an abstract.
has domain
Paper c
has range
Paper Abstract c

hasTitle op back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/hasTitle

It underlines that a paper contains a title.
has domain
Paper c
has range
Paper Title c

impact op back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/impact

It describes the effect or change when is strongly associated with alterations in biological or microbiological aspects, like microbiota or gut health.
has domain
Drug c
has range
Microbiome c

influence op back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/influence

Represents the effect or impact of a dietary supplements or other substances and often diseases, disorders, or health conditions.
has domain
Intervention or Procedure c or Species c
has range
Disease, Disorder or Finding c

interact op back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/interact

It explains what can influence disease, disorder or finding.
has domain
Chemical c or Drug c or Disease, Disorder or Finding c or Species c
has range
Chemical c or Drug c or Intervention or Procedure c or Species c

isA op back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/isA

It defines a relatioship between a disease and another disease.
has domain
Disease, Disorder or Finding c
has range
Disease, Disorder or Finding c

isLinkedTo op back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/isLinkedTo

It defines a relatioship between microbiota and a disease or health condition.
has domain
Microbiome c
has range
Disease, Disorder or Finding c

locatedIn op back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/locatedIn

It defines the relationship between an organism and its location in the Microbiome.
has domain
Chemical c or Mention c or Microbiome c or Anatomic Site c
has range
Organism c or Sentence c or Anatomic Site c

partOf op back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/partOf

It defines the relationship between bacterias that are part of microbiota and microbiome.
has domain
Genome c or Metabolite c or Microbiome c or Sentence c or Gene c or Species c
has range
Chemical c or Genome c or Microbiome c or Microbiota c or Paper Abstract c or Paper Title c

producedBy op back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/producedBy

It defines the relationship between the drug or metabolite and the microbiome.
has domain
Drug c or Metabolite c
has range
Microbiome c

relatedTo op back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/relatedTo

It defines the relationship between the neurotransmitter and the microbiome.
has domain
Neurotransmitter c
has range
Microbiome c

strike op back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/strike

It defines the relationship between the disease, disorder and finding and the anatomical location.
has domain
Disease, Disorder or Finding c
has range
Anatomic Site c

target op back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/target

It is used to specify that a particular disease or health disorder primarily affects or concerns a specific population or biological entity.
has domain
Disease, Disorder or Finding c
has range
Organism c

treatedBy op back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/treatedBy

It explains that the disease, disorder or finding is treated by the intervention or procedure.
has domain
Disease, Disorder or Finding c
has range
Intervention or Procedure c

usedBy op back to ToC or Object Property ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/usedBy

This relationship suggests the employment or use of specific biomedical techniques or methods on particular biological entities, usually in experimental setups.
has domain
Animal c or Human c or Microbiome c
has range
Biomedical Technique c

Data Properties

hasAbstractText dp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/hasAbstractText

The full abstract of the paper as a single text string.
has domain
Paper Abstract c
has range
plain literal

hasMentionText dp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/hasMentionText

The exact text span that was annotated (e.g., the words in the title/abstract that constitute an individual or relation mention).
has domain
Mention c
has range
plain literal

hasSentenceText dp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/hasSentenceText

The complete sentence from the source document.
has domain
Sentence c
has range
plain literal

hasTitleText dp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/hasTitleText

The paper’s title as a single text string.
has domain
Paper Title c
has range
plain literal

paperAnnotator dp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/paperAnnotator

The identifier of the expert who annotated the paper (e.g., expert_7).
has domain
Paper c
has range
plain literal

paperAuthor dp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/paperAuthor

The author list for the paper.
has domain
Paper c
has range
plain literal

paperId dp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/paperId

The unique paper identifier in your corpus (e.g., PubMed ID).
has domain
Paper c
has range
integer

paperJournal dp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/paperJournal

The journal where the paper was published.
has domain
Paper c
has range
plain literal

paperYear dp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/paperYear

The publication year of the paper.
has domain
Paper c
has range
g year

taggedAs dp back to ToC or Data Property ToC

IRI: https://w3id.org/hereditary/ontology/gutbrain/schema/taggedAs

One or more human-readable tags assigned to a mention or paper (e.g., drug, bacteria, DDF), mirroring the category.
has domain
Mention c
has range
plain literal

Annotation Properties

Creator ap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/elements/1.1/creator

is defined by
http://purl.org/dc/elements/1.1/
An entity primarily responsible for making the resource.

exact match ap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/2004/02/skos/core#exactMatch

license ap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/license

Legend back to ToC

c: Classes
op: Object Properties
dp: Data Properties
ni: Named Individuals
ap: Annotation Properties

4. References back to ToC

[1] Fabian Neuhaus. "What is an Ontology?" 2018. arXiv: 1810.09171 [cs.AI].

[2] Ying Ding and Schubert Foo. "Ontology research and development. Part I - A review of ontology generation". In: Journal of Information Science 28 (Apr. 2002), pp. 123–136. DOI: 10.1177/016555150202802004.

[3] Hossam Ishkewy, Hany Harb, and Hassan Farahat. "A Comprehensive Semantic Web Survey". In: Al-Azhar University Engineering Journal (JAUES), 9 (Dec. 2014), p. 2014.

[4] Jennifer Golbeck et al. "The National Cancer Institute’s Thesaurus and Ontology". In: SSRN Electronic Journal (Jan. 2003). DOI: 10.2139/ssrn.3199007.

[5] Kirill Degtyarenko et al. "ChEBI: a database and ontology for chemical entities of biological interest". In: Nucleic Acids Research 36. Database issue (Jan. 2008), pp. D344–D350. DOI: 10.1093/nar/gkm791.

[6] Damion Dooley et al. "FoodOn: a harmonized food ontology to increase global food traceability, quality control and data integration". In: npj Science of Food 2 (Dec. 2018). DOI: 10.1038/s41538-018-0032-6.

[7] Yongcun He et al. "OHMI: The ontology of host-microbiome interactions". In: Journal of Biomedical Semantics 10 (Dec. 2019). DOI: 10.1186/s133326-019-0217-1.

[8] Christopher Townsend et al. "OMIT: Domain Ontology and Knowledge Acquisition in MicroRNA Target Prediction". In: On the Move to Meaningful Internet Systems, OTM 2010. Ed. by Robert Meersman, Tharam Dillon, and Pilar Herrero. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010, pp. 1160–1167. ISBN: 978-3-642-16949-6.

[9] Xizeng Mao et al. "Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary". In: Bioinformatics 21.19 (Apr. 2005), pp. 3787–3793. ISSN: 1367-4803. DOI: 10.1093/bioinformatics/bti430.

[10] Guglielmo Faggioli et al. "The BrainTeaser Ontology for ALS and MS Clinical Data. Version 3.0. Zenodo, July 2024. DOI: 10.5281/zenodo.12789731.

[11] Elena Simperl. "Reusing ontologies on the Semantic Web: A feasibility study". In: Data & Knowledge Engineering 68.10 (2009), pp. 905-925. ISSN: 0169-023X. DOI: 10.1016/j.datak.2009.02.002.

[12] C. E. Lipscomb. “Medical Subject Headings (MeSH)”. In: Bull Med Libr Assoc 88.3 (July 2000), pp. 265–266. url: https://pmc.ncbi.nlm.nih.gov/articles/PMC35238/

5. Acknowledgments back to ToC

The authors would like to thank Silvio Peroni for developing LODE, a Live OWL Documentation Environment, which is used for representing the Cross Referencing Section of this document and Daniel Garijo for developing Widoco, the program used to create the template used in this documentation.