BioChemStructure DRAFT Type

Version: 0.1-DRAFT-2019_06_20 (2019-06-20)

If you spot any errors or omissions with this type, please file an issue in our GitHub.

Canonical URL

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).

Latest types

Latest release: none

Latest draft: 0.1-DRAFT-2019_06_20

Previous types

Previous version: none

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)

Egon Willighagen

Steffen Neumann

Other team members

Anna Gaulton

Ricardo Arcila

David Mendez

Group	Task & Issues

Key to specification table

Green properties/types are proposed by Bioschemas, or indicate proposed changes by Bioschemas to Schema.org
Red properties/types exist in the core of Schema.org
Blue properties/types exist in the pending area of Schema.org
Black properties/types are reused from external vocabularies/ontologies

Property	Expected Type	Description
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.