kglab 0.1.3

Python wrapper for knowledge graph abstraction layer

kglab

The kglab library provides a simple abstraction layer in Python for building and using knowledge graphs.

SPECIAL REQUEST: Which features would you like to see the most in an open source Python library for building and using knowledge graphs? Please add suggestions to this online survey: https://forms.gle/FMHgtmxHYWocprMn6 This will help us prioritize our roadmap for kglab.

Background

For several KG projects, we kept reusing a similar working set of libraries:

• rdflib
• networkx
• pyvis
• pytextrank
• richcontext.scholapi
• skosify

Each of these libraries provides a useful piece of the puzzle when you need to leverage knowledge representation, graph algorithms, entity linking, interactive visualization, metadata queries, axioms, etc. However, some of them are relatively low-level (e.g., rdflib) or perhaps not maintained as much (e.g., skosify) and there are challenges integrating them. Challenges we kept having to reinvent work-arounds to resolve.

There are general operations that one must perform on knowledge graphs:

• building triples
• quality assurance (e.g., axioms)
• managing a mix of namespaces
• serialization to/from multiple formats
• parallel processing across a cluster
• interactive visualization
• queries
• graph algorithms
• transitivity and other forms of enriching a graph
• embedding (deep learning integration)
• inference (e.g., PSL, Bayesian Networks, Causal, MLN, etc.)
• other ML integrations

The kglab library provides a reasonably "Pythonic" abstraction layer for these operations on KGs. The class definitions can be subclassed and extended to handle specific needs.

Meanwhile, we're also extending some of the key components with distributed versions, based on ray for better use of horizontal scale-out and parallelization.

NB: this repo is UNDER CONSTRUCTION and will undergo much iteration prior to the "KG 101" tutorial at https://www.knowledgeconnexions.world/talks/kg-101/

See wiki for further details.

Installation

Dependencies:

• Python 3.6+
• rdflib
• rdflib-json
• pandas
• numpy
• pyarrow
• NetworkX
• dateutil
• pyvis
• matplotlib
• pslpython
• gensim
• pylev

To install from PyPi:

pip install kglab

If you work directly from this Git repo, be sure to install the dependencies as well:

pip install -r requirements.txt

If you would like to run a local Notebook install Jupyter Lab:

If you use conda, you can install it with:

conda install -c conda-forge jupyterlab

If you use pip, you can install it with:

pip install jupyterlab

If installing via pip install --user you must add the user-level bin directory to your PATH environment variable in order to launch JupyterLab.

If you are using a Unix derivative (FreeBSD, GNU / Linux, OS X), you can achieve this by using the export PATH="$HOME/.local/bin:$PATH" command.

Once installed, launch JupyterLab with:

jupyter-lab

Tutorial Outline

1. Building a graph in RDF using rdflib

• ex01_0.ipynb
  • examine the dataset
• ex01_1.ipynb
  • construct a graph from RDF triples
  • using multiple namespaces
  • proper handling of literals
  • serialization to strings and files using Turtle and JSON-LD

2. Leveraging the kglab abstraction layer

• ex01_2.ipynb
  • construct and serialize the same graph using kglab

3. Interactive graph visualization with pyvis

• ex01_3.ipynb
  • render triples as an interactive graph

4. Build a medium size KG from a CSV dataset

• ex01_4.ipynb
  • iterate through a dataset, representing a recipe for each row
  • compare relative file sizes for different serialization formats

5. Running SPARQL queries

• ex01_5.ipynb
  • load the medium size KG from the earlier example
  • run a SPARQL query to identify recipes with special ingredients and cooking times
  • use SPARQL queries and post-processing to create annotations

6. Graph algorithms with networkx

• ex01_6.ipynb
  • load the medium size KG from the earlier example
  • run graph algorithms in networkx to analyze properties of the KG

7. Statistical relational learning with pslpython

• ex01_7.ipynb
  • use RDF to represent the "simple acquaintance" PSL example graph
  • load the graph into a KG
  • visualize the KG
  • run PSL to infer uncertainty in the knows relation for grounded nodes

8. Vector embedding with gensim

• ex01_8.ipynb
  • curating annotations
  • analyze ingredient labels from 250K recipes
  • use vector embedding to rank relatedness for labels
  • add string similarity for an approximate pareto archive

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Production Use Cases

• Derwen and its client projects

Kudos

Many thanks to our contributors: @jake-aft, @dmoore247, plus general support from Derwen, Inc. and The Knowledge Graph Conference.