License: CC-BY 4.0 Int.
Author: Egon Willighagen
With thanks to Andra Waagmeester and Marvin Martens for contributions.
ShEx or Shape Expressions is a formal language to describe ("express") how a piece of RDF can take form ("shape"). The people that have worked with eXtensible Markup Language (XML) in the past know the approach as schema, as in Document Type Definitions (DTD), XML Schema, or Schematron. The people that know SPARQL, a shape expression is quite similar, but instead of asking for data, the structure describes what data is expected. The people that do not know either, a shape expression basically explains what information we expect for a certain resource.
This document gives a number of example shapes for frameworks bioinformaticians may work with. It does not intend to replace these documents:
We start with a basic shape expression for a WikiPathways RDF DataNode for a gene:
<http://identifiers.org/ncbigene/5604>
a wp:GeneProduct , wp:DataNode ;
rdfs:label "MAP2K1"^^xsd:string ;
dc:identifier <http://identifiers.org/ncbigene/5604> ;
dc:source "Entrez Gene"^^xsd:string ;
dcterms:identifier "5604"^^xsd:string ;
dcterms:isPartOf <http://identifiers.org/wikipathways/WP4806_r110852> ;
wp:bdbEnsembl <http://identifiers.org/ensembl/ENSG00000169032> ;
wp:bdbEntrezGene <http://identifiers.org/ncbigene/5604> ;
wp:bdbHgncSymbol <http://identifiers.org/hgnc.symbol/MAP2K1> ;
wp:bdbUniprot <http://identifiers.org/uniprot/Q02750> , <http://identifiers.org/uniprot/A4QPA9> , <http://identifiers.org/uniprot/H3BRW9> ;
wp:isAbout <http://rdf.wikipathways.org/Pathway/WP4806_r110852/DataNode/b64f4> .We can define a shape expression that requires that all gene products have an identifier and a Ensembl identifier mapped with BridgeDb:
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX wp: <http://vocabularies.wikipathways.org/wp#>
<gene> {
dc:identifier IRI ;
dc:source xsd:string ;
wp:bdbEnsembl IRI
}
See also this readme.
For interactions in the pathways we can also define shape expressions. For example, a general interaction would look like this:
@prefix wp: <http://vocabularies.wikipathways.org/wp#> .
@prefix dcterms: <http://purl.org/dc/terms/> .
<http://rdf.wikipathways.org/Pathway/WP4806_r110852/WP/Interaction/ae20c>
a wp:DirectedInteraction , wp:Interaction ;
dcterms:isPartOf <http://identifiers.org/wikipathways/WP4806_r110852> ;
wp:isAbout <http://rdf.wikipathways.org/Pathway/WP4806_r110852/Interaction/ae20c> ;
wp:participants <http://identifiers.org/ncbigene/2549> , <http://identifiers.org/ensembl/ENSG00000146648> ;
wp:source <http://identifiers.org/ensembl/ENSG00000146648> ;
wp:target <http://identifiers.org/ncbigene/2549> .We can then define a simple shape for an interaction:
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX wp: <http://vocabularies.wikipathways.org/wp#>
<interaction> {
wp:participants IRI {1,}
}
This shape can be extended to expect a wp:source and wp:target for directed interactions:
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX wp: <http://vocabularies.wikipathways.org/wp#>
<interaction> {
wp:participants IRI {2,} ;
wp:source IRI ;
wp:target IRI
}
See also this readme.
Another interesting aspect of ShEx is that shapes can reference other shapes. For example, take the following adverse outcome pathway RDF (thx to Marvin for the example):
@prefix aop.relationships: <http://identifiers.org/aop.relationships/> .
@prefix aop: <http://identifiers.org/aop/> .
@prefix aop.events: <http://identifiers.org/aop.events/> .
@prefix aopo: <http://aopkb.org/aop_ontology#> .
@prefix dc: <http://purl.org/dc/elements/1.1/> .
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
aop.relationships:597
a aopo:KeyEventRelationship ;
dc:identifier aop.relationships:597 ;
rdfs:label "KER 597" ;
foaf:page <http://identifiers.org/aop.relationships/597> ;
dcterms:created "2016-11-29T18:41:34" ;
dcterms:modified "2016-12-03T16:37:58" ;
aopo:has_upstream_key_event aop.events:593 ;
aopo:has_downstream_key_event aop.events:585 ;
dcterms:isPartOf aop:95 .
aop.events:593
a aopo:KeyEvent ;
dc:identifier aop.events:593 ;
rdfs:label "KE 593" ;
foaf:page <http://identifiers.org/aop.events/593> ;
dc:title "Inhibition, Ether-a-go-go (ERG) voltage-gated potassium channel " ;
dcterms:alternative "Inhibition, Ether-a-go-go (ERG) voltage-gated potassium channel " ;
dc:source "AOPWiki" ;
dcterms:isPartOf aop:95 .Here, each key event relationship requires two key events. We can then define two shapes and
say that the object of, in this case, the aopo:has_upstream_key_event predicate should be
something that adheres to the other shape:
prefix aopo: <http://aopkb.org/aop_ontology#>
<ker> {
aopo:has_upstream_key_event @<ke> ;
aopo:has_downstream_key_event @<ke>
}
<ke> {
a [ aopo:KeyEvent ]
}
See also this readme.
The eNanoMapper project developed a RDF format for nanosafety data, which is currently being completed in the NanoCommons project. The Adding nanomaterial data tutorial shows example RDF fragments for key properties. This document describe basic shape expressions for the bits of information in the format.
The example given is:
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix owner: <https://nanocommons.github.io/tutorials/demo/owner/> .
@prefix void: <http://rdfs.org/ns/void#> .
owner:NT18-DS
a void:Dataset ;
dcterms:license <https://creativecommons.org/publicdomain/zero/1.0/> ;
dcterms:publisher "Egon Willighagen"@en ;
dcterms:description "Nanomaterials I am excited about."@en ;
dcterms:title "Exciting nanomaterials"@en .We can define a shape expression that requires all these predicate to be present:
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX owner: <https://nanocommons.github.io/tutorials/demo/owner/>
PREFIX void: <http://rdfs.org/ns/void#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
<dataset> {
a [ void:Dataset ] ;
dcterms:license IRI ;
dcterms:publisher rdf:langString ;
dcterms:description rdf:langString ;
dcterms:title rdf:langString
}