EMbuilder

Etemenanki Builder

Template builder for multiple Linked Data representations:

YARRRML
OBDA (Ontology Based Database Acccess)
ShEx (Shape Expression)
SPARQL 1.1

Instalation:

pip install EMbuilder

Use case:

It consumes JSON object with all prefixes, triplets (including object's datatype) and configuration parameter as data input. You can use this example (below) or you can use test.py as an use case for creating your templates based on one of EJP-RD Common Data Elements:

from embuilder.builder import EMB

data = {
  "prefixes" : {
    "rdf" : "http://www.w3.org/1999/02/22-rdf-syntax-ns#" ,
    "rdfs" : "http://www.w3.org/2000/01/rdf-schema#" ,
    "obo" : "http://purl.obolibrary.org/obo/" ,
    "sio" : "http://semanticscience.org/resource/" ,
    "xsd" : "http://www.w3.org/2001/XMLSchema#",
    "this" : "http://my_example.com/"},

  "triplets" : [
    ["this:$(pid)_$(uniqid)_ID","sio:denotes","this:$(pid)_$(uniqid)_Role","iri"],
    ["this:$(pid)_$(uniqid)_Entity","sio:has-role","this:$(pid)_$(uniqid)_Role","iri"],
    ["this:$(pid)_$(uniqid)_Role","sio:is-realized-in","this:$(pid)_$(uniqid)_Process","iri"],
    ["this:$(pid)_$(uniqid)_Process","sio:has-output","this:$(pid)_$(uniqid)_Output","iri"],
    ["this:$(pid)_$(uniqid)_Output","sio:refers-to","this:$(pid)_$(uniqid)_Attribute","iri"],
    ["this:$(pid)_$(uniqid)_Entity","sio:has-attribute","this:$(pid)_$(uniqid)_Attribute","iri"],

    ["this:$(pid)_$(uniqid)_ID","rdf:type","sio:identifier","iri"],
    ["this:$(pid)_$(uniqid)_Entity","rdf:type","sio:person","iri"],
    ["this:$(pid)_$(uniqid)_Role","rdf:type","sio:role","iri"],
    ["this:$(pid)_$(uniqid)_Process","rdf:type","sio:process","iri"],
    ["this:$(pid)_$(uniqid)_Output","rdf:type","sio:information-content-entity","iri"],
    ["this:$(pid)_$(uniqid)_Attribute","rdf:type","sio:attribute","iri"],
    ["this:$(pid)_$(uniqid)_Output","sio:has-value","$(datetime)","xsd:date"]],

  "config" : {
    "source_name" : "source_cde_test",
    "configuration" : "ejp",    
    "csv_name" : "source_1",
    "basicURI" : "this"
    }
}

yarrrml = EMB(data["config"], data["prefixes"],data["triplets"])

test_yarrrml = yarrrml.transform_ShEx()
print(test_yarrrml)
test_shex = yarrrml.transform_YARRRML()
print(test_shex)
test_obda = yarrrml.transform_OBDA()
print(test_obda)
test_sparql = yarrrml.transform_SPARQL()
print(test_sparql)

Documentation:

Configuration parameter:

source_name: (mandatory for YARRRML and OBDA representations) used to create each inidividual template object.
configuration: (mandatory for YARRRML and ShEx representations) used to define a certain workflow to operate. ejp in case of custom transformation required to fit with EJP-RD CDE-in-a-box workflow requirements, if not, define as default.
csv_name: (mandatory in case of configuration: default for YARRRML representation) used to define input CSV name.
basicURI: (mandatory for ShEx and SPARQL representations) used to identify basic URI prefix to create proper representations.

API usage:

This module was implemented as a Web service using FastAPI and Docker to make it run. You can obtain the Docker Image from Dockerhub.

Pull the image pabloalarconm/embuilder and run it!

docker run -p 8000:8000 pabloalarconm/embuilder

Its configured to run at your localhost, port 8000. Please check http://localhost:8000/docs to interact with Swagger UI documentation of each funcion. To know more about Docker configuration, you can find here current Dockerfile for this implementation.