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BioChemStructure DRAFT Type

Version: 0.1-DRAFT (2019-06-20)


Contributors

The following people have been involved in the creation of this specification document. They are all members of the Chemicals group.

Group Leader(s)
Other team members

Canonical URL

http://bioschemas.org/BioChemStructure

Schema.org hierarchy

This is a new Type that fits into the schema.org hierarchy as follows:
Thing > BioChemEntity > BioChemStructure

Description

WwPDB and related data including modelled and hypothetical data. As well as 3D data for chemicals, e.g. stereo chemistry images in an analyzable format (not pure images).




Key to specification table

Schema.org properties where the Expected Types have been changed, or new (i.e., Bioschemas created) properties/types are green.

Schema.org properties/types are red.

Pending Schema.org properties/types are blue.

External (i.e., from 3rd party ontology) properties/types are black.


CD = Cardinality


PropertyExpected TypeDescription
Properties from BioChemStructure
boundMolecule BioChemEntity  or
ChemicalSubstance  or
DefinedTerm  or
MolecularEntity  or
URL 
Molecule, e.g., ligand, bound to this BioChem structure
creationMethod PropertyValue  or
Text  or
URL 
Method used to create or obtain this annotation or BioChemEntity; please use PropertyValue if you want to include any evidence.
hasAssociatedBioChemEntity Protein  or
RNA 
Used to define the actual protein or RNA.
massResolution Quantity Mass spectometry resolution in the form '<Number> <Unit of measure>', for example '2.85 Å'
sequenceLocation SequenceRange A range/position location where this annotation or BioChemEntity is located reagrding another BioChemEntity, for instance a BioChemStructure in a Protein.
Properties from BioChemEntity
associatedDisease MedicalCondition  or
PropertyValue  or
URL 
Disease associated to this BioChemEntity. Such disease can be a MedicalCondition or a URL. If you want to add an evidence supporting the association, please use PropertyValue.
bioChemInteraction BioChemEntity A BioChemEntity that is known to interact with this item.
bioChemSimilarity BioChemEntity A similar molecular entity, e.g., obtained by fingerprint similarity algorithms.
biologicalRole DefinedTerm A role played by the molecular entity within a biological context.
hasBioChemEntityPart BioChemEntity Indicates a BioChemEntity that (in some sense) has this BioChemEntity as a part.
Inverse property: isPartOfBioChemEntity.
hasMolecularFunction DefinedTerm  or
PropertyValue  or
URL 
Molecular function performed by this BioChemEntity; please use PropertyValue if you want to include any evidence.
hasRepresentation PropertyValue  or
Text  or
URL 
A common representation such as a protein sequence or chemical structure for this entity. For images use schema.org/image.
hasSequenceAnnotation PropertyValue  or
SequenceAnnotation 
Pointer to a sequence annotation; please use PropertyValue if you want to include any evidence.
isEncodedByBioChemEntity DNA  or
Gene  or
RNA 
Another BioChemEntity encoding by this one.
Inverse property: encodesBioChemEntity.
isInvolvedInBiologicalProcess DefinedTerm  or
PropertyValue  or
URL 
Biological process this BioChemEntity is involved in; please use PropertyValue if you want to include any evidence.
isLocatedInSubcellularLocation DefinedTerm  or
PropertyValue  or
URL 
Subcellular location where this BioChemEntity is located; please use PropertyValue if you want to include any evidence.
isMatchedBy SequenceMatchingModel A model matching this BioChemEntity.
isPartOfBioChemEntity BioChemEntity Indicates a BioChemEntity that is (in some sense) a part of this BioChemEntity.
Inverse property: hasBioChemEntityPart.
taxonomicRange DefinedTerm  or
Taxon  or
Text  or
URL 
The taxonomic grouping of the organism that expresses, encodes, or in someway related to the BioChemEntity.
Properties from Thing
additionalType URL An additional type for the item, typically used for adding more specific types from external vocabularies in microdata syntax. This is a relationship between something and a class that the thing is in. In RDFa syntax, it is better to use the native RDFa syntax - the 'typeof' attribute - for multiple types. Schema.org tools may have only weaker understanding of extra types, in particular those defined externally.
alternateName Text An alias for the item.
description Text A description of the item.
disambiguatingDescription Text A sub property of description. A short description of the item used to disambiguate from other, similar items. Information from other properties (in particular, name) may be necessary for the description to be useful for disambiguation.
identifier PropertyValue  or
Text  or
URL 
The identifier property represents any kind of identifier for any kind of Thing, such as ISBNs, GTIN codes, UUIDs etc. Schema.org provides dedicated properties for representing many of these, either as textual strings or as URL (URI) links. See background notes for more details.
image ImageObject  or
URL 
An image of the item. This can be a URL or a fully described ImageObject.
mainEntityOfPage CreativeWork  or
URL 
Indicates a page (or other CreativeWork) for which this thing is the main entity being described. See background notes for details.
Inverse property: mainEntity.
name Text The name of the item.
potentialAction Action Indicates a potential Action, which describes an idealized action in which this thing would play an 'object' role.
sameAs URL URL of a reference Web page that unambiguously indicates the item's identity. E.g. the URL of the item's Wikipedia page, Wikidata entry, or official website.
subjectOf CreativeWork  or
Event 
A CreativeWork or Event about this Thing..
Inverse property: about.
url URL URL of the item.

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