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RML-star: RDF-star generation for RML

Home Page: https://w3id.org/rml/star/spec

License: Creative Commons Attribution 4.0 International

HTML 98.37% JavaScript 0.24% CSS 0.10% Python 1.29%

rml rdf-star ontology rml-mapping shacl

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smartniz aahmadai marioscrock dachafra

rml-star's Issues

spec Vs ontology

the Overview of RML-star terms reads more like an overview of the ontology, do we actually want this given we have a well-defined ontology where we can point to?

Make more clear, visible and explicit the change of prefixes (rr to rml) for subjectMaps and objectMaps

From #10 :
I noticed that prefix for subjectMap and objectMap has been changed from rr to rml. My issue was that there is no indication (at least from my understanding) in the text about this change. When I saw subjectMaps and objectMaps with rml prefix in the examples, I did not know if that was a mistake.

Testcases: add tests

Testcases are here: https://github.com/kg-construct/rml-star-test-cases

Do they cover the current spec?
Do they include invalid cases, thus throwing errors?

Useful for validating the SHACL shapes and make sure we cover everything

CSV mapping

Hi! I'm attempting to translate a CSV file containing patient information into RDF-STAR format. I'm working with RDF-star to add metadata to my records, where it is necessary. I'm using the morph-kgc and pyoxigraph libraries, both of which support RDF-star.

My goal is to generate certain triples asserted and quoted, while others solely asserted.

The problem is that the materialization of triples only occurs successfully if I use "AssertedTriplesMap" for innerTriples and "TriplesMap" for outerTriples. This generate only quoted triples. If I use "AssertedTriplesMap" for both inner and outer triples, the total number of generated triples is zero.
Furthermore, when attempting to have T1, T2, T3 asserted and quoted, and T4, T5, T6 only asserted (by removing OUT4, OUT5, OUT6), only T1, T2, T3 are generated.

Could you help me understand if it is feasible or if there are errors in my code?

This is the .py file:

import morph_kgc
import pyoxigraph

graph = morph_kgc.materialize_oxigraph('D:/morph_kgc_code/config.ini')
output = open('D:/mimic-iii-1.4-nq/PATIENTS.nq', 'wb')
pyoxigraph.serialize(graph, output, "application/n-quads")

This is the .ini file:

[DataSouce1]
mappings : D:/morph_kgc_code/patients_mapping.ttl

This is the .ttl file (not working):

@prefix rr: <http://www.w3.org/ns/r2rml#>.
@prefix rml: <http://semweb.mmlab.be/ns/rml#>.
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>.
@prefix mimic: <http://mimic-translation-project.org/>.
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix foaf: <http://xmlns.com/foaf/0.1/#term_>. 

@base <http://mimic-translation-project.org/> .

<T1> a rml:AssertedTriplesMap;
    rml:logicalSource [
        rml:source "D:/mimic-iii-clinical-database-1.4/PATIENTS.csv/PATIENTS.csv";
        rml:referenceFormulation rml:CSV
    ];

    rml:subjectMap [
        rr:template "http://mimic-translation-project.org/Patient/{SUBJECT_ID}"
    ];

    rr:predicateObjectMap [
        rr:predicate mimic:gender;
        rml:objectMap [
            rml:reference "GENDER"
        ];
    ].

<T2> a rml:AssertedTriplesMap;
    rml:logicalSource [
        rml:source "D:/mimic-iii-clinical-database-1.4/PATIENTS.csv/PATIENTS.csv";
        rml:referenceFormulation rml:CSV
    ];

    rml:subjectMap [
        rr:template "http://mimic-translation-project.org/Patient/{SUBJECT_ID}"
    ];

    rr:predicateObjectMap [
        rr:predicate mimic:dob;
        rml:objectMap [
            rml:reference "DOB";
            rr:datatype xsd:dateTime
        ];
    ].

<T3> a rml:AssertedTriplesMap;
    rml:logicalSource [
        rml:source "D:/mimic-iii-clinical-database-1.4/PATIENTS.csv/PATIENTS.csv";
        rml:referenceFormulation rml:CSV
    ];

    rml:subjectMap [
        rr:template "http://mimic-translation-project.org/Patient/{SUBJECT_ID}"
    ];

    rr:predicateObjectMap [
        rr:predicate mimic:dod;
        rml:objectMap [
            rml:reference "DOD";
            rr:datatype xsd:dateTime
        ];
    ].

<T4> a rml:AssertedTriplesMap;
    rml:logicalSource [
        rml:source "D:/mimic-iii-clinical-database-1.4/PATIENTS.csv/PATIENTS.csv";
        rml:referenceFormulation rml:CSV
    ];

    rml:subjectMap [
        rr:template "http://mimic-translation-project.org/Patient/{SUBJECT_ID}"
    ];

    rr:predicateObjectMap [
        rr:predicate mimic:dodHosp;
        rml:objectMap [
            rml:reference "DOD_HOSP";
            rr:datatype xsd:dateTime
        ];
    ].

<T5> a rml:AssertedTriplesMap;
    rml:logicalSource [
        rml:source "D:/mimic-iii-clinical-database-1.4/PATIENTS.csv/PATIENTS.csv";
        rml:referenceFormulation rml:CSV
    ];

    rml:subjectMap [
        rr:template "http://mimic-translation-project.org/Patient/{SUBJECT_ID}"
    ];

    rr:predicateObjectMap [
        rr:predicate mimic:dodSSN;
        rml:objectMap [
            rml:reference "DOD_SSN";
            rr:datatype xsd:dateTime
        ];
    ].

<T6> a rml:AssertedTriplesMap;
    rml:logicalSource [
        rml:source "D:/mimic-iii-clinical-database-1.4/PATIENTS.csv/PATIENTS.csv";
        rml:referenceFormulation rml:CSV
    ];

    rml:subjectMap [
        rr:template "http://mimic-translation-project.org/Patient/{SUBJECT_ID}"
    ];

    rr:predicateObjectMap [
        rr:predicate mimic:expireFlag;
        rml:objectMap [
            rml:reference "EXPIRE_FLAG";
            rr:datatype xsd:boolean
        ];
    ].
    
    
<OUT1> a rml:AssertedTriplesMap;
    rml:logicalSource [
        rml:source "D:/mimic-iii-clinical-database-1.4/PATIENTS.csv/PATIENTS.csv";
        rml:referenceFormulation rml:CSV
    ];
    rml:subjectMap [
        rml:quotedTriplesMap <T1>
    ];
    rr:predicateObjectMap [
        rr:predicate mimic:confidence ;
        rml:objectMap [
            rr:constant <http://purl.bioontology.org/ontology/SNOMEDCT/263495000>
        ]
    ].

<OUT2> a rml:AssertedTriplesMap;
    rml:logicalSource [
        rml:source "D:/mimic-iii-clinical-database-1.4/PATIENTS.csv/PATIENTS.csv";
        rml:referenceFormulation rml:CSV
    ];
    rml:subjectMap [
        rml:quotedTriplesMap <T2>
    ];
    rr:predicateObjectMap [
        rr:predicate mimic:snomedPredicate ;
        rml:objectMap [
            rr:constant <http://purl.bioontology.org/ontology/SNOMEDCT/184099003>
        ]
    ].

        
<OUT3> a rml:AssertedTriplesMap;
    rml:logicalSource [
        rml:source "D:/mimic-iii-clinical-database-1.4/PATIENTS.csv/PATIENTS.csv";
        rml:referenceFormulation rml:CSV
    ];
    rml:subjectMap [
        rml:quotedTriplesMap <T3>
    ];
    rr:predicateObjectMap [
        rr:predicate mimic:snomedPredicate ;
        rml:objectMap [
            rr:constant <http://purl.bioontology.org/ontology/SNOMEDCT/399753006>
        ]
    ].

create docs folder for the github pages

including the updated version of the spec

Use the W3C - CG template

https://www.w3.org/community/reports/reqs/

exhaustive description of all possible cases

@thomas-delva the spec is definitely good for a first iteration but we might need to show the details for each possible case as we did it for the logical target. in principle bring all the knowledge from the Excel to the spec.

This is not so pressing right now

Documentation minor issues

Here are minor issues to update in the dev.html, that I saw while updating the rml-cc spec:

issueBase: https://github.com/kg-construct/rml-star-spec/issues : remove the "-spec"
"https://rml.io/" to change with w3id-based url
copyrightStart: "2021": update year
namespace definition: rml: http://semweb.mmlab.be/ns/rml#

definitions improvement

the definitions which are currently in the overleaf are very good and detailed, but we might need to replace them with a more coherent story. My suggestion would be to use them instead of the definition we currently have here because they are really good!

Update diagram

New diagram to be consistent with the rest of the RML specs

Fix (unused) datatypes in examples

From #10 :
Two examples use the rr:datatype xsd:float clause but the results don't reflect it; in other words, ^^xsd:float does not appear as part of the resulting triples.

Examples of the Syntax of RML-Star

Hello,

I have noticed some things in the examples that I would like to bring to your attention. First, two examples use the rr:datatype xsd:float clause but the results don't reflect it; in other words, ^^xsd:float does not appear as part of the resulting triples. This can confuse those who only use the examples as a guide. Second, there is no example where rml:quotedTriplesMap is used as an objectMap. Finally, I noticed that prefix for subjectMap and objectMap has been changed from rr to rml. My issue was that there is no indication (at least from my understanding) in the text about this change. When I saw subjectMaps and objectMaps with rml prefix in the examples, I did not know if that was a mistake.

Sincerely,
Enrique Iglesias

Link from spec to github

with the original RML spec I could not find the link from the spec to the github. It took a lot of questions for people pointing me from one to the other before I found out where to ask questions. This spec is better as it points to github.io which allows one to guess what the link is. But guesses are not as good as links. Also if someone came to this repo they would have to guess where the spec was located, making it more difficult to send feeback.
See kg-construct/rml-questions#23 (comment)

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