Validation and inference over LinkML instance data using souffle

Related tags

Data Analysisvalidationrdfsemantic-webdataloglogic-programmingreasoningsouffle-datalog-languagelinkml
Overview

linkml-datalog

Validation and inference over LinkML instance data using souffle

Requirements

This project requires souffle

After installing souffle, install the python here is a normal way.

Until this is released to pypi:

poetry install

Running

Pass in a schema and a data file

poetry run python -m linkml_datalog.engines.datalog_engine -d tmp -s personinfo.yaml example_personinfo_data.yaml

The output will be a ValidationReport object, in yaml

e.g.

- type: sh:MaxValue
  subject: https://example.org/P/003
  instantiates: Person
  predicate: age_in_years
  object_str: '100001'
  info: Maximum is 999

Currently, to look at inferred edges, consult the directory you specified in -d

E.g.

tmp/Person_grandfather_of.csv

Will have a subject and object tuple P:005 to P:001

How it works

  1. Schema is compiled to Souffle DL problem (see generated schema.dl file)
  2. Any embedded logic program in the schema is also added
  3. Data is converted to generic triple-like tuples (see *.facts)
  4. Souffle executed
  5. Inferred validation results turned into objects

Assuming input like this:

classes:
  Person:
    attributes:
      age:
        range: integer
        maximum_value: 999

The generated souffle program will look like this:

999."> 
.decl Person_age_in_years_asserted(i: identifier, v: value)
.decl Person_age_in_years(i: identifier, v: value)
.output Person_age_in_years
.output Person_age_in_years_asserted
Person_age_in_years(i, v) :- 
    Person_age_in_years_asserted(i, v).
Person_age_in_years_asserted(i, v) :- 
    Person(i),
    triple(i, "https://w3id.org/linkml/examples/personinfo/age_in_years", v).

validation_result(
  "sh:MaxValueTODO",
  i,
  "Person",
  "age_in_years",
  v,
  "Maximum is 999") :-
    Person(i),
    Person_age_in_years(i, v),
    literal_number(v,num),
    num > 999.

Motivation / Future Extensions

The above example shows functionality that could easily be achieved by other means:

  • jsonschema
  • shape languages: shex/shacl

In fact the core linkml library already has wrappers for these. See working with data in linkml guide.

However, jsonschema in particular offers very limited expressivity. There are many more opportunities for expressivity with linkml.

In particular, LinkML 1.2 introduces autoclassification rules, conditional logic, and complex expressions -- THESE ARE NOT TRANSLATED YET, but they will be in future.

For now, you can also include your own rules in the header of your schema as an annotation, e.g the following translates a 'reified' association modeling of relationships to direct slot assignments, and includes transitive inferences etc

has_familial_relationship_to(i, p, j) :-
    Person_has_familial_relationships(i, r),
    FamilialRelationship_related_to(r, j),
    FamilialRelationship_type(r, p).

Person_parent_of(i, j) :-
    has_familial_relationship_to(i, "https://example.org/FamilialRelations#02", j).

Person_ancestor_of(i, j) :-
        Person_parent_of(i, z),
        Person_ancestor_of(z, j).

Person_ancestor_of(i, j) :-
        Person_parent_of(i, j).

See tests for more details.

In future these will be compilable from higher level predicates

Background

See #196

You might also like...
PrimaryBid - Transform application Lifecycle Data and Design and ETL pipeline architecture for ingesting data from multiple sources to redshift
PrimaryBid - Transform application Lifecycle Data and Design and ETL pipeline architecture for ingesting data from multiple sources to redshift

Transform application Lifecycle Data and Design and ETL pipeline architecture for ingesting data from multiple sources to redshift This project is composed of two parts: Part1 and Part2

Emmanuel Boateng Sifah 1 Jan 19, 2022
fds is a tool for Data Scientists made by DAGsHub to version control data and code at once.
fds is a tool for Data Scientists made by DAGsHub to version control data and code at once.

Fast Data Science, AKA fds, is a CLI for Data Scientists to version control data and code at once, by conveniently wrapping git and dvc

DAGsHub 359 Dec 22, 2022
Python data processing, analysis, visualization, and data operations

Python This is a Python data processing, analysis, visualization and data operations of the source code warehouse, book ISBN: 9787115527592 Descriptio

FangWei 1 Jan 16, 2022
Demonstrate the breadth and depth of your data science skills by earning all of the Databricks Data Scientist credentials
Demonstrate the breadth and depth of your data science skills by earning all of the Databricks Data Scientist credentials

Data Scientist Learning Plan Demonstrate the breadth and depth of your data science skills by earning all of the Databricks Data Scientist credentials

Trung-Duy Nguyen 27 Nov 1, 2022
A real-time financial data streaming pipeline and visualization platform using Apache Kafka, Cassandra, and Bokeh.
A real-time financial data streaming pipeline and visualization platform using Apache Kafka, Cassandra, and Bokeh.

Realtime Financial Market Data Visualization and Analysis Introduction This repo shows my project about real-time stock data pipeline. All the code is

null 6 Sep 7, 2022
Tuplex is a parallel big data processing framework that runs data science pipelines written in Python at the speed of compiled code

Tuplex is a parallel big data processing framework that runs data science pipelines written in Python at the speed of compiled code. Tuplex has similar Python APIs to Apache Spark or Dask, but rather than invoking the Python interpreter, Tuplex generates optimized LLVM bytecode for the given pipeline and input data set.

Tuplex 791 Jan 4, 2023
A data parser for the internal syncing data format used by Fog of World.
A data parser for the internal syncing data format used by Fog of World.

A data parser for the internal syncing data format used by Fog of World. The parser is not designed to be a well-coded library with good performance, it is more like a demo for showing the data structure.

Zed(Zijun) Chen 40 Dec 12, 2022
Functional Data Analysis, or FDA, is the field of Statistics that analyses data that depend on a continuous parameter.
Functional Data Analysis, or FDA, is the field of Statistics that analyses data that depend on a continuous parameter.

Functional Data Analysis Python package

Grupo de Aprendizaje Automático - Universidad Autónoma de Madrid 184 Dec 27, 2022
Fancy data functions that will make your life as a data scientist easier.
Fancy data functions that will make your life as a data scientist easier.

WhiteBox Utilities Toolkit: Tools to make your life easier Fancy data functions that will make your life as a data scientist easier. Installing To ins

WhiteBox 3 Oct 3, 2022
Releases(v0.2.0)
Owner
Linked data Modeling Language
LinkML is a general purpose modeling language that can be used with linked data, JSON, and other formalisms
Linked data Modeling Language
GitHub Repository
PLStream: A Framework for Fast Polarity Labelling of Massive Data Streams

PLStream: A Framework for Fast Polarity Labelling of Massive Data Streams Motivation When dataset freshness is critical, the annotating of high speed

4 Aug 02, 2022
A Numba-based two-point correlation function calculator using a grid decomposition

A Numba-based two-point correlation function (2PCF) calculator using a grid decomposition. Like Corrfunc, but written in Numba, with simplicity and hackability in mind.

Lehman Garrison 3 Aug 24, 2022
A model checker for verifying properties in epistemic models

Epistemic Model Checker This is a model checker for verifying properties in epistemic models. The goal of the model checker is to check for Pluralisti

Thomas Träff 2 Dec 22, 2021
A computer algebra system written in pure Python

SymPy See the AUTHORS file for the list of authors. And many more people helped on the SymPy mailing list, reported bugs, helped organize SymPy's part

SymPy 9.9k Dec 31, 2022
A columnar data container that can be compressed.

Unmaintained Package Notice Unfortunately, and due to lack of resources, the Blosc Development Team is unable to maintain this package anymore. During

944 Dec 09, 2022
MoRecon - A tool for reconstructing missing frames in motion capture data.

MoRecon - A tool for reconstructing missing frames in motion capture data.

Yuki Nishidate 38 Dec 03, 2022
Hydrogen (or other pure gas phase species) depressurization calculations

HydDown Hydrogen (or other pure gas phase species) depressurization calculations This code is published under an MIT license. Install as simple as: pi

Anders Andreasen 13 Nov 26, 2022
Repositori untuk menyimpan material Long Course STMKGxHMGI tentang Geophysical Python for Seismic Data Analysis

Long Course "Geophysical Python for Seismic Data Analysis" Instruktur: Dr.rer.nat. Wiwit Suryanto, M.Si Dipersiapkan oleh: Anang Sahroni Waktu: Sesi 1

Anang Sahroni 0 Dec 04, 2021
Semi-Automated Data Processing

Perform semi automated exploratory data analysis, feature engineering and feature selection on provided dataset by visualizing every possibilities on each step and assisting the user to make a meanin

Arun Singh Babal 1 Jan 17, 2022
Geospatial data-science analysis on reasons behind delay in Grab ride-share services

Grab x Pulis Detailed analysis done to investigate possible reasons for delay in Grab services for NUS Data Analytics Competition 2022, to be found in

Keng Hwee 6 Jun 07, 2022
A probabilistic programming library for Bayesian deep learning, generative models, based on Tensorflow

ZhuSuan is a Python probabilistic programming library for Bayesian deep learning, which conjoins the complimentary advantages of Bayesian methods and

Tsinghua Machine Learning Group 2.2k Dec 28, 2022
Numerical Analysis toolkit centred around PDEs, for demonstration and understanding purposes not production

Numerics Numerical Analysis toolkit centred around PDEs, for demonstration and understanding purposes not production Use procedure: Initialise a new i

George Whittle 1 Nov 13, 2021
Amundsen is a metadata driven application for improving the productivity of data analysts, data scientists and engineers when interacting with data.

Amundsen is a metadata driven application for improving the productivity of data analysts, data scientists and engineers when interacting with data.

Amundsen 3.7k Jan 03, 2023
VHub - An API that permits uploading of vulnerability datasets and return of the serialized data

VHub - An API that permits uploading of vulnerability datasets and return of the serialized data

André Rodrigues 2 Feb 14, 2022
Hangar is version control for tensor data. Commit, branch, merge, revert, and collaborate in the data-defined software era.

Overview docs tests package Hangar is version control for tensor data. Commit, branch, merge, revert, and collaborate in the data-defined software era

Tensorwerk 193 Nov 29, 2022
The Master's in Data Science Program run by the Faculty of Mathematics and Information Science

The Master's in Data Science Program run by the Faculty of Mathematics and Information Science is among the first European programs in Data Science and is fully focused on data engineering and data a

Amir Ali 2 Jun 17, 2022
This is an analysis and prediction project for house prices in King County, USA based on certain features of the house

This is a project for analysis and estimation of House Prices in King County USA The .csv file contains the data of the house and the .ipynb file con

Amit Prakash 1 Jan 21, 2022
🌍 Create 3d-printable STLs from satellite elevation data 🌏

mapa 🌍 Create 3d-printable STLs from satellite elevation data Installation pip install mapa Usage mapa uses numpy and numba under the hood to crunch

Fabian Gebhart 13 Dec 15, 2022
Modular analysis tools for neurophysiology data

Neuroanalysis Modular and interactive tools for analysis of neurophysiology data, with emphasis on patch-clamp electrophysiology. Functions for runnin

Allen Institute 5 Dec 22, 2021
Data analysis and visualisation projects from a range of individual projects and applications

Python-Data-Analysis-and-Visualisation-Projects Data analysis and visualisation projects from a range of individual projects and applications. Python

Tom Ritman-Meer 1 Jan 25, 2022