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coco: The data model for Coconut Knowledge Graph

Latest version:
http://coconutKG.aksw.org/ontology#
Revision:
SNAPSHOT
Authors:
Louis Westerheide
Download serialization:
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License:
http://insertlicenseURIhere.example.org
Visualization:
Visualize with WebVowl
Cite as:
Louis Westerheide. COCONUT[KG]. Revision: SNAPSHOT.
Ontology Specification Draft

Abstract

The Coconut Ontology contains the data model of Coconut Knowledge Graph. It facilitates the knowledge graph data manipulation and consumption through concepts such as natural products, molecules, and their respective properties.

Introduction back to ToC

This is a place holder text for the introduction. The introduction should briefly describe the ontology, its motivation, state of the art and goals.

Namespace declarations

Table 1: Namespaces used in the document
coco<http://coconutKG.aksw.org/ontology#>
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#>
terms<http://purl.org/dc/terms/>
vann<http://purl.org/vocab/vann/>
xml<http://www.w3.org/XML/1998/namespace>
xsd<http://www.w3.org/2001/XMLSchema#>

coco: CoconutKG: Overview back to ToC

This ontology has the following classes and properties.

Classes

Object Properties

Data Properties

coco: CoconutKG: Description back to ToC

COCONUT[KG] is a knowledge graph based on the Coconut Dataset, which is a comprehensive platform that facilitates natural product research by providing data, tools, and other resources and provides services for the deposition, curation, and reuse of data.

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

This section provides details for each class and property defined by coco: CoconutKG.

Classes

Citationc back to ToC or Class ToC

IRI: http://coconutKG.aksw.org/ontology#Citation

An article, book or document with a DOI in which a molecule or a collection was mentioned.
is in domain of
Active Citation dp, Authors dp, Citation DOI dp, Citation Title dp
is in range of
citedIn op

Classificationc back to ToC or Class ToC

IRI: http://coconutKG.aksw.org/ontology#Classification

Attributes related to the classification molecules.
is in domain of
Parent Molecule dp, has Stereo dp, has Variants dp, is Parent dp, is Tautomer dp
is in range of
classifiedBy op

Collectionc back to ToC or Class ToC

IRI: http://coconutKG.aksw.org/ontology#Collection

Groups of molecules are organized within collections, each linked to metadata such as titles, descriptions, and related jobs.
is in domain of
Collection DOI dp, Collection Slug dp, Collection Title dp, Comments dp, Description dp, Identifier dp, Image dp, Is Public dp, Job Info dp, Job Status dp, Molecule Count dp, Photo dp, URL dp, includes op, isRepresentedIn op

Constitutional Descriptorc back to ToC or Class ToC

IRI: http://coconutKG.aksw.org/ontology#ConstitutionalDescriptor

Constitutional descriptors of a chemical compound.
has super-classes
Descriptor c
is in domain of
Chemical Class dp, Chemical Sub Class dp, Chemical Super Class dp, Direct Parent Classification dp, Fraction CSP3 dp, Molecular Formula dp, Molecular Weight dp, NPLikeness dp

Countsc back to ToC or Class ToC

IRI: http://coconutKG.aksw.org/ontology#Counts

Attributes counting variants, collections, and other related data of a molecule.
is in domain of
Citation Count dp, Collection Count dp, Geo Count dp, Organism Count dp, Synonym Count dp, Variants Count dp
is in range of
hasAmounts op

Descriptive Informationc back to ToC or Class ToC

IRI: http://coconutKG.aksw.org/ontology#DescriptiveInformation

Descriptive information related to synonyms, comments, or other textual metadata of a molecule.
is in domain of
Annotation Level dp, Comment dp, Name Trust Level dp, Structural Comments dp, Synonyms dp
is in range of
isExplainedThrough op

Descriptorc back to ToC or Class ToC

IRI: http://coconutKG.aksw.org/ontology#Descriptor

Descriptors of a molecule.
has sub-classes
Constitutional Descriptor c, Electronic Descriptor c, Geometrical Descriptor c, Topological Descriptor c
is in domain of
defines op

Electronic Descriptorc back to ToC or Class ToC

IRI: http://coconutKG.aksw.org/ontology#ElectronicDescriptor

Electronic descriptors of a chemical compound.
has super-classes
Descriptor c
is in domain of
AlogP dp, Formal Charge dp, Hydrogen Bond Acceptors dp, Hydrogen Bond Acceptors Lipinski dp, Hydrogen Bond Donors dp, Hydrogen Bond Donors Lipinski dp, Lipinski Rule Of Five Violations dp, Qed Drug Likeliness dp

Entryc back to ToC or Class ToC

IRI: http://coconutKG.aksw.org/ontology#Entry

is in domain of
Entry Canonical Smiles dp, Entry Error Code dp, Entry Errors dp, Entry Link dp, Entry Molecular Formula dp, Entry Name dp, Entry Organism Part dp, Entry Parent Canonical Smiles dp, Entry Precise Location dp, Entry Standardized Canonical Smiles dp, Entry Status dp, Entry Structural Comments dp, Entry has stereocenters dp, Entry is invalid dp, Reference ID dp, citedIn op, contains op
is in range of
isRepresentedIn op

GeoLocationc back to ToC or Class ToC

IRI: http://coconutKG.aksw.org/ontology#GeoLocation

A geographical location where an organism is reported to be found.
is in domain of
Location Name dp
is in range of
foundIn op

Geometrical Descriptorc back to ToC or Class ToC

IRI: http://coconutKG.aksw.org/ontology#GeometricalDescriptor

Geometrical descriptors of a chemical compound.
has super-classes
Descriptor c
is in domain of
Exact Molecular Weight dp, Heavy Atom Count dp, Total Atom Count dp, Van Der Walls Volume dp

Identifierc back to ToC or Class ToC

IRI: http://coconutKG.aksw.org/ontology#Identifier

Unique Identifiers for a given molecule.
is in domain of
Canonical Smiles dp, IUPAC Name dp, Molecule Identifier dp, Molecule Name dp, Standard Inchi dp, Standard Inchi Key dp, Sugar Free Smiles dp
is in range of
labeledBy op

Moleculec back to ToC or Class ToC

IRI: http://coconutKG.aksw.org/ontology#Molecule

A group of atoms bonded together, representing the smallest fundamental unit of a chemical compound that can take part in a chemical reaction.
is in domain of
classifiedBy op, describedBy op, foundIn op, hasAmounts op, hasStatus op, isExplainedThrough op, labeledBy op, originatesFrom op
is in range of
contains op, includes op, specifiesExtractionLocationOf op

Organismc back to ToC or Class ToC

IRI: http://coconutKG.aksw.org/ontology#Organism

A living thing that has an organized structure. The biological origin of a given molecule.
is in domain of
IRI dp, Organism Name dp, Organism Parts dp, Rank dp
is in range of
originatesFrom op, specifiesLocationOf op

Propertiesc back to ToC or Class ToC

IRI: http://coconutKG.aksw.org/ontology#Properties

The chemical and biological properties of a molecule.
is in range of
defines op, describedBy op

SampleLocationc back to ToC or Class ToC

IRI: http://coconutKG.aksw.org/ontology#SampleLocation

Sample location within the organism from where the sample of the compound is taken.
is in domain of
Sample Location Collections dp, Sample Location IRI dp, Sample Location Molecule Count dp, Sample Location Name dp, Sample Location Slug dp, specifiesExtractionLocationOf op, specifiesLocationOf op

Statusc back to ToC or Class ToC

IRI: http://coconutKG.aksw.org/ontology#Status

Current state and activity of a molecule.
is in domain of
Active dp, Status dp, is Placeholder dp
is in range of
hasStatus op

Topological Descriptorc back to ToC or Class ToC

IRI: http://coconutKG.aksw.org/ontology#TopologicalDescriptor

has super-classes
Descriptor c
is in domain of
Aromatic Ring Count dp, Contains Linear Sugars dp, Contains Ring Sugars dp, Contains Sugar dp, Murko Framework dp, Number Of Minimal Rings dp, Rotatable Bond Count dp, Topological Polar Surface Area dp

Object Properties

citedInop back to ToC or Object Property ToC

IRI: http://coconutKG.aksw.org/ontology#citedIn

The entry and its corresponding citation.
has domain
Entry c
has range
Citation c

classifiedByop back to ToC or Object Property ToC

IRI: http://coconutKG.aksw.org/ontology#classifiedBy

A molecule is classified by its classification.
has domain
Molecule c
has range
Classification c

containsop back to ToC or Object Property ToC

IRI: http://coconutKG.aksw.org/ontology#contains

An entry contains a given molecule.
has domain
Entry c
has range
Molecule c

definesop back to ToC or Object Property ToC

IRI: http://coconutKG.aksw.org/ontology#defines

has domain
Descriptor c
has range
Properties c

describedByop back to ToC or Object Property ToC

IRI: http://coconutKG.aksw.org/ontology#describedBy

A molecule is descriped by its properties.
has domain
Molecule c
has range
Properties c

foundInop back to ToC or Object Property ToC

IRI: http://coconutKG.aksw.org/ontology#foundIn

A molecule is found in a geo location.
has domain
Molecule c
has range
GeoLocation c

hasAmountsop back to ToC or Object Property ToC

IRI: http://coconutKG.aksw.org/ontology#hasAmounts

A molecule has certain amounts of different countable properties.
has domain
Molecule c
has range
Counts c

hasStatusop back to ToC or Object Property ToC

IRI: http://coconutKG.aksw.org/ontology#hasStatus

A molecule has various statuses.
has domain
Molecule c
has range
Status c

includesop back to ToC or Object Property ToC

IRI: http://coconutKG.aksw.org/ontology#includes

The collection includes a molecule.
has domain
Collection c
has range
Molecule c

isExplainedThroughop back to ToC or Object Property ToC

IRI: http://coconutKG.aksw.org/ontology#isExplainedThrough

A molecule is explained through its descriptive information.
has domain
Molecule c
has range
Descriptive Information c

isRepresentedInop back to ToC or Object Property ToC

IRI: http://coconutKG.aksw.org/ontology#isRepresentedIn

A collection is represented in an entry.
has domain
Collection c
has range
Entry c

labeledByop back to ToC or Object Property ToC

IRI: http://coconutKG.aksw.org/ontology#labeledBy

A molceule is labeled by an Identifier.
has domain
Molecule c
has range
Identifier c

originatesFromop back to ToC or Object Property ToC

IRI: http://coconutKG.aksw.org/ontology#originatesFrom

The molecule origintes from a certain organism.
has domain
Molecule c
has range
Organism c

specifiesExtractionLocationOfop back to ToC or Object Property ToC

IRI: http://coconutKG.aksw.org/ontology#specifiesExtractionLocationOf

The sample location specifies from where the molecule was extracted from.
has domain
SampleLocation c
has range
Molecule c

specifiesLocationOfop back to ToC or Object Property ToC

IRI: http://coconutKG.aksw.org/ontology#specifiesLocationOf

The sample location specifies the location of the organism it originated from.
has domain
SampleLocation c
has range
Organism c

Data Properties

Activedp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#active

Indicates whether the molecule is currently active or inactive.
has domain
Status c
has range
boolean

Active Citationdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#activeCitation

Determines wheater a citation is still active or not.
has domain
Citation c
has range
boolean

AlogPdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#AlogP

The logarithm of the partition between n-octanol and water (logP). AlogP is used to estimate the lipophilicity of a molecule, which is an important factor in drug absorption and distribution.
has domain
Electronic Descriptor c
has range
decimal

Annotation Leveldp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#annotationLevel

A numerical value indicating the thoroughness or depth of the annotation provided for the molecule, reflecting its level of detail.
has domain
Descriptive Information c
has range
int

Aromatic Ring Countdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#aromaticRingCount

The number of aromatic rings in a molecule.
has domain
Topological Descriptor c
has range
int

Authorsdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#authors

The names of the authors of the citation.
has domain
Citation c
has range
string

Canonical Smilesdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#canonicalSmiles

The canonical Simplified Molecular Input Line Entry System (SMILES) notation for the molecule, representing its structure in a line of text.
has domain
Identifier c
has range
string

Chemical Classdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#chemicalClass

Chemical Class generated using ClassyFire.
has domain
Constitutional Descriptor c
has range
string

Chemical Sub Classdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#chemicalSubClass

Chemical Sub Class generated using ClassyFire.
has domain
Constitutional Descriptor c
has range
string

Chemical Super Classdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#chemicalSuperClass

Chemical Super Class generated using ClassyFire.
has domain
Constitutional Descriptor c
has range
string

Citation Countdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#citationCount

The number of times the molecule has been cited in literature or other references.
has domain
Counts c
has range
int

Citation DOIdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#citationDoi

The DOI (Digital Object Identifier) of the citation.
has domain
Citation c
has range
string

Citation Titledp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#citationTitle

The title of the citation.
has domain
Citation c
has range
string

Collection Countdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#collectionCount

The total number of collections in which the molecule is included.
has domain
Counts c
has range
int

Collection DOIdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#collectionDoi

The Digital Object Identifier (DOI) assigned to the collection.
has domain
Collection c
has range
string

Collection Slugdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#collectionSlug

A user- and search engine-friendly text consisting of one or a few words as part of a URL
has domain
Collection c
has range
string

Collection Titledp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#collectionTitle

The title of the collection.
has domain
Collection c
has range
string

Commentdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#comment

General remarks or additional notes regarding the molecule.
has domain
Descriptive Information c
has range
string

Commentsdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#comments

Additional remarks or notes about the collection that might provide further context or insight.
has domain
Collection c
has range
string

Contains Linear Sugarsdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#containsLinearSugars

Utilizing the Sugar Removal Utility to check for the presence of linear sugars.
has domain
Topological Descriptor c
has range
boolean

Contains Ring Sugarsdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#containsRingSugars

Utilizing the Sugar Removal Utility to check for the presence of circular sugars.
has domain
Topological Descriptor c
has range
boolean

Contains Sugardp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#containsSugar

Utilizing the Sugar Removal Utility to check for the presence of circular or linear sugars.
has domain
Topological Descriptor c
has range
boolean

Descriptiondp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#description

The description of a given Collection.
has domain
Collection c
has range
string

Direct Parent Classificationdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#directParentClassification

Direct Parent Classification generated using ClassyFire.
has domain
Constitutional Descriptor c
has range
string

Entry Canonical Smilesdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#entryCanonicalSmiles

has domain
Entry c
has range
string

Entry Error Codedp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#entryErrorCode

has domain
Entry c
has range
int

Entry Errorsdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#entryErrors

has domain
Entry c
has range
string

Entry has stereocentersdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#entryHasStereocenters

has domain
Entry c
has range
boolean

Entry is invaliddp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#entryIsInvalid

has domain
Entry c
has range
boolean

Entry Molecular Formuladp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#entryMolecularFormula

has domain
Entry c
has range
string

Entry Namedp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#entryName

has domain
Entry c
has range
string

Entry Organism Partdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#entryOrganismPart

has domain
Entry c
has range
string

Entry Parent Canonical Smilesdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#entryParentCanonicalSmiles

has domain
Entry c
has range
string

Entry Precise Locationdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#entryPreciseLocation

has domain
Entry c
has range
string

Entry Standardized Canonical Smilesdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#entryStandardizedCanonicalSmiles

has domain
Entry c
has range
string

Entry Statusdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#entryStatus

has domain
Entry c
has range
string

Entry Structural Commentsdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#entryStructuralComments

has domain
Entry c
has range
string

Exact Molecular Weightdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#exactMolecularWeight

The exact molecular weight of the molecule which is based on the isotope masses of the atoms in the molecule.
has domain
Geometrical Descriptor c
has range
decimal

Formal Chargedp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#formalCharge

The formal charge of the molecule.
has domain
Electronic Descriptor c
has range
string

Fraction CSP3dp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#fractioncsp3

The fraction of C atoms that are SP3 hybridized.
has domain
Constitutional Descriptor c
has range
decimal

Geo Countdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#geoCount

The count of geographical occurrences or representations related to the molecule.
has domain
Counts c
has range
int

has Stereodp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#hasStereo

Indicates whether the molecule has stereochemistry, which refers to the spatial arrangement of atoms in a molecule.
has domain
Classification c
has range
boolean

has Variantsdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#hasVariants

Indicates if there are alternative forms or variants of the entity.
has domain
Classification c
has range
boolean

Heavy Atom Countdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#heavyAtomCount

Total count of the heavy atoms.
has domain
Geometrical Descriptor c
has range
int

Hydrogen Bond Acceptorsdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#hydrogenBondAcceptors

The number of Hydrogen Bond Acceptors in a molecule.
has domain
Electronic Descriptor c
has range
int

Hydrogen Bond Acceptors Lipinskidp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#hydrogenBondAcceptorsLipinski

Number of Hydrogen Bond Acceptors in a molecule using the Lipinski module.
has domain
Electronic Descriptor c
has range
int

Hydrogen Bond Donorsdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#hydrogenBondDonors

The number of Hydrogen Bond Donors in a molecule.
has domain
Electronic Descriptor c
has range
int

Hydrogen Bond Donors Lipinskidp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#hydrogenBondDonorsLipinski

Number of Hydrogen Bond Donors in a molecule using the Lipinski module.
has domain
Electronic Descriptor c
has range
int

Identifierdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#collectionIdentifier

The identifier of the collection.
has domain
Collection c
has range
string

Imagedp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#image

An additional or alternative image related to the collection.
has domain
Collection c
has range
string

IRIdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#iri

The IRI (Internationalized Resource Identifier) is the internationalised version of the URI (Uniform Resource Identifier)
has domain
Organism c
has range
string

is Parentdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#isParent

Indicates whether the molecule serves as a parent classification in a hierarchical relationship, meaning it has child entities or variants.
has domain
Classification c
has range
boolean

is Placeholderdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#isPlaceholder

Indicates whether the molecule is a placeholder in the dataset, serving as a temporary or default entry without full attributes.
has domain
Status c
has range
boolean

Is Publicdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#isPublic

Indicates whether the collection is publicly accessible or private.
has domain
Collection c
has range
boolean

is Tautomerdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#isTautomer

Indicates whether the molecule is a tautomer, which is a specific type of chemical structure that can easily interconvert with another form.
has domain
Classification c
has range
boolean

IUPAC Namedp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#iupacName

The name assigned to the molecule according to the International Union of Pure and Applied Chemistry (IUPAC) nomenclature rules, providing a standardized name for communication.
has domain
Identifier c
has range
string

Job Infodp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#jobInfo

Information about any tasks or processes performed on the collection.
has domain
Collection c
has range
string

Job Statusdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#jobStatus

The current status of any processing or tasks associated with the collection.
has domain
Collection c
has range
string

Lipinski Rule Of Five Violationsdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#LipinskiRuleOfFiveViolations

A custom function to determine the number of Lipinski's rule violations for a given molecule.
has domain
Electronic Descriptor c
has range
int

Location Namedp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#locationName

The name of the location where the molecule was found.
has domain
GeoLocation c
has range
string

Molecular Formuladp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#molecularFormula

The molecular formula is a string that represents the types and number of atoms in the molecule.
has domain
Constitutional Descriptor c
has range
string

Molecular Weightdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#molecularWeight

The average molecular weight of the molecule.
has domain
Constitutional Descriptor c
has range
decimal

Molecule Countdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#moleculeCount

The number of molecules included within the collection.
has domain
Collection c
has range
int

Molecule Identifierdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#moleculeIdentifier

A unique identifier assigned to the molecule.
has domain
Identifier c
has range
string

Molecule Namedp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#moleculeName

The common or preferred name of the molecule, which may be used in various contexts and could differ from the IUPAC name.
has domain
Identifier c
has range
string

Murko Frameworkdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#murkoFramework

Custom function based on CDK to get the Murko Framework.
has domain
Topological Descriptor c
has range
string

Name Trust Leveldp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#nameTrustLevel

A numerical value representing the confidence or reliability of the name assigned to the molecule, indicating how well it is established in scientific literature.
has domain
Descriptive Information c
has range
int

NPLikenessdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#npLikeness

NPLikeness score generated using RDKit. The likelyness of a molecule to be a natural product.
has domain
Constitutional Descriptor c
has range
decimal

Number Of Minimal Ringsdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#numberOfMinimalRings

The number rings present in a molecule.
has domain
Topological Descriptor c
has range
int

Organism Countdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#organismCount

The total number of organisms associated with the molecule.
has domain
Counts c
has range
int

Organism Namedp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#organismName

The name of the organism.
has domain
Organism c
has range
string

Organism Partsdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#organismParts

The parts of the organism from which molecules can be extracted.
has domain
Organism c
has range
string

Parent Moleculedp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#parentMolecule

Molecule parent classification, allowing for traceability in hierarchical relationships.
has domain
Classification c
has range
int

Photodp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#photo

An image or visual representation associated with the collection.
has domain
Collection c
has range
string

Qed Drug Likelinessdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#qedDrugLikeliness

Quantative estimation of drug-likeness (q weighted sum).
has domain
Electronic Descriptor c
has range
decimal

Rankdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#rank

The hierarchical rank that helps categorize and describe the relationships from organisms to other organisms.
has domain
Organism c
has range
string

Reference IDdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#referenceID

has domain
Entry c
has range
string

Rotatable Bond Countdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#rotatableBondCount

The number of rotatable bonds in a molecule.
has domain
Topological Descriptor c
has range
int

Sample Location Collectionsdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#sampleLocationCollections

The corresponding collections of the given sample location.
has domain
SampleLocation c
has range
string

Sample Location IRIdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#sampleLocationIRI

The IRI of the sample location.
has domain
SampleLocation c
has range
string

Sample Location Molecule Countdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#sampleLocationMoleculeCount

Count of molecules found in a sample location.
has domain
SampleLocation c
has range
int

Sample Location Namedp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#sampleLocationName

The name of the sample location.
has domain
SampleLocation c
has range
string

Sample Location Slugdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#sampleLocationSlug

The slug of the sample location name.
has domain
SampleLocation c
has range
string

Standard Inchidp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#standardInchi

The Standard International Chemical Identifier (InChI) for the molecule, providing a unique textual representation of its structure.
has domain
Identifier c
has range
string

Standard Inchi Keydp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#standardInchiKey

A hashed version of the InChI, known as the InChI Key, designed for easy digital searching and identification of the molecule.
has domain
Identifier c
has range
string

Statusdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#status

A textual description of the current state or condition of the molecule.
has domain
Status c
has range
string

Structural Commentsdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#structuralComments

Observations or notes about the structural characteristics of the molecule.
has domain
Descriptive Information c
has range
string

Sugar Free Smilesdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#sugarFreeSmiles

A SMILES representation of the molecule that excludes sugars.
has domain
Identifier c
has range
string

Synonym Countdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#synonymCount

The total number of synonyms associated with the molecule.
has domain
Counts c
has range
int

Synonymsdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#synonyms

A list of alternative names or terms that refer to the same molecule.
has domain
Descriptive Information c
has range
string

Topological Polar Surface Areadp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#topologicalPolarSurfaceArea

Topological Polar Surface Area (TPSA) of a molecule. TPSA is an important descriptor in medicinal chemistry and drug design, as it provides an estimate of the polar surface area of a molecule.
has domain
Topological Descriptor c
has range
decimal

Total Atom Countdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#totalAtomCount

Total count of the atoms.
has domain
Geometrical Descriptor c
has range
int

URLdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#url

The web address where the collection can be accessed or viewed.
has domain
Collection c
has range
string

Van Der Walls Volumedp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#vanDerWallsVolume

The function calculates the volume of a molecule using RDKit's molecular modelling functionalities. It adds hydrogens to the molecule, embeds it into 3D space, and computes the molecular volume.
has domain
Geometrical Descriptor c
has range
decimal

Variants Countdp back to ToC or Data Property ToC

IRI: http://coconutKG.aksw.org/ontology#variantsCount

The total number of variants associated with the molecule.
has domain
Counts c
has range
int

Legend back to ToC

c: Classes
op: Object Properties
dp: Data Properties

References back to ToC

Add your references here. It is recommended to have them as a list.

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.