Validation CLI

The Bioregistry packages a set of CLI tools in the subcommand bioregistry validate that can be used to check the prefix map in a JSON-LD, Turtle, and eventually other document formats for their conformance to the Bioregistry and offer actionable suggestions for improvement.

Validating JSON-LD

The bioregistry validate jsonld that can be used to check the prefix map in a JSON-LD document (either a local file or remote) conform to the Bioregistry.

For example, running the following returns a system exit of 1 because Bioregistry collections indeed are Bioregistry-compliant by construction:

$ bioregistry validate jsonld "https://bioregistry.io/api/collection/0000002?format=context"

However, the Prefix Commons vendored Gene Ontology (GO) context is not valid against the Bioregistry. It can be checked with:

$ bioregistry validate jsonld "https://raw.githubusercontent.com/prefixcommons/prefixcommons-py/master/prefixcommons/registry/go_context.jsonld" --tablefmt rst

prefix

uri_prefix

issue

solution

BIOMD

http://www.ebi.ac.uk/compneur-srv/biomodels-main/publ-model.do?mid=

non-standard CURIE prefix

Switch to standard prefix: biomodels.db

COG_Function

http://www.ncbi.nlm.nih.gov/COG/grace/shokog.cgi?fun=

unknown CURIE prefix

WB

http://identifiers.org/wormbase/

non-standard CURIE prefix

Switch to standard prefix: wormbase

FBbt

http://purl.obolibrary.org/obo/FBbt_

non-standard CURIE prefix

Switch to standard prefix: fbbt

KEGG_LIGAND

http://www.genome.jp/dbget-bin/www_bget?cpd:

non-standard CURIE prefix

Switch to standard prefix: kegg.ligand

PSO_GIT

https://github.com/Planteome/plant-stress-ontology/issues/

unknown CURIE prefix

MaizeGDB_stock

http://maizegdb.org/data_center/stock?id=

unknown CURIE prefix

…

There are two things that might be the problem. First, the resource might use stylized (i.e. mixed case) prefixes. Therefore, we could try passing --use-preferred to respect prefix stylization

$ bioregistry validate jsonld --use-preferred "https://raw.githubusercontent.com/prefixcommons/prefixcommons-py/master/prefixcommons/registry/go_context.jsonld"

prefix

uri_prefix

issue

solution

BIOMD

http://www.ebi.ac.uk/compneur-srv/biomodels-main/publ-model.do?mid=

non-standard CURIE prefix

Switch to preferred prefix: biomodels.db

COG_Function

http://www.ncbi.nlm.nih.gov/COG/grace/shokog.cgi?fun=

unknown CURIE prefix

WB

http://identifiers.org/wormbase/

non-standard CURIE prefix

Switch to preferred prefix: WormBase

KEGG_LIGAND

http://www.genome.jp/dbget-bin/www_bget?cpd:

non-standard CURIE prefix

Switch to preferred prefix: kegg.ligand

PSO_GIT

https://github.com/Planteome/plant-stress-ontology/issues/

unknown CURIE prefix

MaizeGDB_stock

http://maizegdb.org/data_center/stock?id=

unknown CURIE prefix

NCBI_GP

http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=

unknown CURIE prefix

…

Second, we could use a pre-defined community context that might have deviations from the vanilla Bioregistry context using the --context option in combination with one of the contexts’ keys (see all contexts):

$ bioregistry validate jsonld --context obo "https://raw.githubusercontent.com/prefixcommons/prefixcommons-py/master/prefixcommons/registry/go_context.jsonld"

prefix

uri_prefix

issue

solution

BIOMD

http://www.ebi.ac.uk/compneur-srv/biomodels-main/publ-model.do?mid=

non-standard CURIE prefix

Switch to standard prefix: biomodels.db

COG_Function

http://www.ncbi.nlm.nih.gov/COG/grace/shokog.cgi?fun=

unknown CURIE prefix

WB

http://identifiers.org/wormbase/

non-standard CURIE prefix

Switch to standard prefix: WormBase

KEGG_LIGAND

http://www.genome.jp/dbget-bin/www_bget?cpd:

unknown CURIE prefix

PSO_GIT

https://github.com/Planteome/plant-stress-ontology/issues/

unknown CURIE prefix

MaizeGDB_stock

http://maizegdb.org/data_center/stock?id=

unknown CURIE prefix

NCBI_GP

http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=

unknown CURIE prefix

…

It turns out that the GO JSON-LD file doesn’t even validate against the OBO context!

Validating RDF in Turtle

RDF data stored in Turtle files typically begins with a stanza defining a prefix map. For example, one of the turtle files in the Chemotion Knowledge Graph (Chemotion-KG) begins with the following six prefixes:

@prefix nfdicore: <https://nfdi.fiz-karlsruhe.de/ontology/> .
@prefix ns1: <http://purls.helmholtz-metadaten.de/mwo/> .
@prefix ns2: <http://purl.obolibrary.org/obo/chebi/> .
@prefix obo: <http://purl.obolibrary.org/obo/> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

The bioregistry validate jsonld command can be used to check the prefix map in this file and give feedback on non-standard CURIE prefix usage, unknown CURIE prefixes, etc. while giving suggestions for fixes, when possible.

Running the command on the file that contains the example prefixes from above gives the following output:

$ bioregistry validate ttl --tablefmt rst https://github.com/ISE-FIZKarlsruhe/chemotion-kg/raw/4cb5c24af/processing/output_bfo_compliant.ttl

prefix

uri_prefix

issue

solution

nfdicore

https://nfdi.fiz-karlsruhe.de/ontology/

non-standard CURIE prefix

Switch to standard prefix: nfdi.core

ns1

http://purls.helmholtz-metadaten.de/mwo/

unknown CURIE prefix

Consider switching to the more specific CURIE/URI prefix pair mwo: http://purls.helmholtz-metadaten.de/mwo/mwo_

ns2

http://purl.obolibrary.org/obo/chebi/

unknown CURIE prefix

Validating Prefix Maps in LinkML

LinkML enables defining a data model with YAML. Each definition also includes a prefix map, which can be validate against the Bioregistry. Here’s an abridged excerpt of one such configuration:

id: https://w3id.org/nfdi4cat/catcore
name: catcore-metadata
title: CatCore Metadata Reference Model

prefixes:
  catcore: https://w3id.org/nfdi4cat/catcore/
  voc4cat: https://w3id.org/nfdi4cat/voc4cat_
  CHMO: http://purl.obolibrary.org/obo/CHMO_
  OBI: http://purl.obolibrary.org/obo/OBI_
  AFR: http://purl.allotrope.org/ontologies/result#AFR_
  AFP: http://purl.allotrope.org/ontologies/process#AFP_
  AFQ: http://purl.allotrope.org/ontologies/quality#AFQ_
  NCIT: http://purl.obolibrary.org/obo/NCIT_
  nmrCV: 'http://nmrML.org/nmrCV#NMR:'
  linkml: https://w3id.org/linkml/
  AFRL: http://purl.allotrope.org/ontologies/role#AFRL_
  APOLLO_SV: http://purl.obolibrary.org/obo/APOLLO_SV_
  SIO: http://semanticscience.org/resource/SIO_

default_prefix: catcore

The bioregistry validate linkml command can be used to check the prefix map in this file and give feedback on non-standard CURIE prefix usage, unknown CURIE prefixes, etc. while giving suggestions for fixes, when possible.

Running the command on the file that contains the example prefixes from above gives the following output:

$ bioregistry validate linkml --tablefmt rst --use-preferred https://github.com/HendrikBorgelt/CatCore/raw/refs/heads/main/src/catcore/schema/catcore.yaml

prefix

uri_prefix

issue

solution

catcore

https://w3id.org/nfdi4cat/catcore/

unknown CURIE prefix

AFR

http://purl.allotrope.org/ontologies/result#AFR_

unknown CURIE prefix

AFP

http://purl.allotrope.org/ontologies/process#AFP_

unknown CURIE prefix

AFQ

http://purl.allotrope.org/ontologies/quality#AFQ_

unknown CURIE prefix

nmrCV

http://nmrML.org/nmrCV#NMR:

non-standard CURIE prefix

Switch to preferred prefix: NMR

AFRL

http://purl.allotrope.org/ontologies/role#AFRL_

unknown CURIE prefix

SIO

http://semanticscience.org/resource/SIO_

non-standard CURIE prefix

Switch to preferred prefix: sio

Note that LinkML is developed by members of the OBO Community, and therefore, its prefixes often skew towards OBO community preferences. Therefore, you might want to use the --use-preferred flag.

Reference

Functions

format_messages(messages)

Format messages as a human-readable string.

tabulate_messages(messages[, tablefmt])

Format messages into a table using tabulate.

validate_jsonld(obj, **kwargs)

Validate a JSON-LD object.

validate_linkml(path_or_url, **kwargs)

Validate a LinkML YAML configuration's prefix map.

validate_prefix_map(prefix_map, **kwargs)

Validate a prefix map.

validate_ttl(url, **kwargs)

Validate a remote Turtle file.

validate_virtuoso(url, **kwargs)

Validate a Virtuoso SPARQL endpoint's prefix map.

Classes

Message(*, prefix, uri_prefix, error[, ...])

A message.

Class Inheritance Diagram

digraph inheritance4d2a126726 { bgcolor=transparent; rankdir=LR; size="8.0, 12.0"; "BaseModel" [fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",tooltip="!!! abstract \"Usage Documentation\""]; "Message" [URL="api/bioregistry.validate.Message.html#bioregistry.validate.Message",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="A message."]; "BaseModel" -> "Message" [arrowsize=0.5,style="setlinewidth(0.5)"]; }