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RDF config (senbero)

TODO

  • design
    • provides spec for validation of data type & cardinality to generate ShEx
  • implement
    • support multiple models to be loaded in combination at once
  • test

GOAL

  • DONE: capture the RDF data strucuture in ease
  • DONE: generate SPARQL queries
  • generate SPARQLet for SPARQList
  • generate Grasp config file
  • DONE: generate schema chart
  • DONE: generate TogoStanza
  • generate ShEx and validate RDF data

SPECIFICATION

USAGE

Installation

  • Pre-requirements:
    • To generate Ruby version of TogoStanza, install TogoStanza gem by running gem install togostanza
    • To generate JavaScript version of TogoStanza, install ts command by downloading the latest release for your environment (e.g., ts_0.0.19_darwin_amd64.zip for macOS)
% git clone https://github.com/dbcls/rdf-config.git

% cd rdf-config

% export PATH="./bin:$PATH"
% export RUBYLIB="./lib"
  • TODO:
    • Installer will be provided soon!

Generate schema ascii art

% rdf-config --config config/refex --senbero
RefExEntry (refexo:RefExEntry)
    |-- refexo:exValue
    |       `-- ex_value ("Ex value")
    |-- dct:identifier
    |       `-- refex_id ("RFX0016539731")
    |-- rdfs:seeAlso
    |       `-- see_also ("<http://identifiers.org/affy.probeset/224348_s_at>")
    `-- refexo:refexSample
            `-- RefExSample ("<http://refex.dbcls.jp/sample/RES00000884>")
RefExSample (refexo:RefExSample)
    |-- dct:identifier
    |       `-- sample_id ("RES00000100")
    |-- refexo:organism
    |       `-- taxonomy ("<http://identifiers.org/taxonomy/9606>")
    |-- refexo:refexTissueClass10
    |       `-- class10 ("refexo:v04_10")
    |-- refexo:refexTissueClass40
    |       `-- class40 ("refexo:v20_4")
    |-- refexo:sex
    |       `-- sex ("obo:PATO_0000383")
    |-- refexo:refexAlphabeticalUniqOrder
    |       `-- unique_order (210)
    |-- refexo:refexRefinedDescription
    |       `-- ref_description ("uterus, adult")
    |-- refexo:refexSampleCategory
    |       `-- sample_category ("developmental")
    |-- refexo:sampleReference / refexo:belongsToCellType
    |       `-- cell_type ("obo:CL_0000003")
    |-- refexo:sampleReference / refexo:belongsToDisease
    |       `-- disease ("obo:DOID_0050686")
    |-- refexo:sampleReference / refexo:belongsToDevelopmentSite
    |       `-- dev_site ("obo:CL_0000134")
    `-- refexo:sampleReference / refexo:sample
            `-- refexo_sample ("<http://fantom.gsc.riken.jp/5/sstar/FF:10828-111C9>")

Generate schema diagram

% rdf-config --config config/refex --schema > refex.svg

RefEx schema

Generate SPARQL query

% rdf-config --config config/nbrc --sparql
# https://integbio.jp/rdf/sparql

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
PREFIX dct: <http://purl.org/dc/terms/>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX pubmed: <http://rdf.ncbi.nlm.nih.gov/pubmed/>
PREFIX taxonomy: <http://identifiers.org/taxonomy/>
PREFIX sio: <http://semanticscience.org/resource/>
PREFIX obo: <http://purl.obolibrary.org/obo/>
PREFIX mccv: <http://purl.jp/bio/10/mccv#>
PREFIX meo: <http://purl.jp/bio/11/meo/>
PREFIX mpo: <http://purl.jp/bio/10/mpo/>
PREFIX nbrc: <http://purl.jp/bio/103/nite/cultures/>

SELECT ?s ?nbrc_id ?clade ?name ?alias ?taxid ?attribute ?habitat
WHERE {
  ?s a mccv:MCCV_000001 .
  ?s dct:identifier ?nbrc_id .
  ?s mccv:MCCV_000038 ?clade .
  ?s skos:prefLabel ?name .
  ?s skos:altLabel ?alias .
  ?s mccv:MCCV_000065 ?taxid .
  ?s mccv:MCCV_000028 / mccv:MCCV_000072 / sio:SIO_000008 ?attribute .
  ?s mccv:MCCV_000028 / mccv:MCCV_000072 / mccv:MCCV_000030 ?habitat .
}
LIMIT 100

Generate TogoStanza

JavaScript version

% rdf-config --config config/hint --stanza hint_pair
Stanza template has been generated successfully.
To view the stanza, run (cd stanza/javascript; ts server) and open http://localhost:8080/

Ruby version (it may take a while for the first time to install dependencies)

% rdf-config --config config/hint --stanza_rb hint_pair
Stanza template has been generated successfully.
To view the stanza, run (cd stanza/ruby; bundle exec rackup) and open http://localhost:9292/

Run via Docker Container

% docker run --rm -it -v <path to config file dir>:/config dbcls/rdf-config:<docker image tag> rdf-config --config /config/<config dir name> [options]

See available docker image tags at Docker Hub

Authors

  • Toshiaki Katayama (DBCLS)
  • Tatsuya Nishizawa (IMSBIO)

License

  • MIT License