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LET'S MAKE A KNOWLEDGE GRAPH! A HANDS-ON, INTERACTIVE, LINKED DATA - - PowerPoint PPT Presentation

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LET'S MAKE A KNOWLEDGE GRAPH! A HANDS-ON, INTERACTIVE, LINKED DATA WORKSHOP PHUSE CSS 2019 Silver Spring, MD 2019-06-09 1 INSTRUCTOR Tim Williams Principal Statistical Solutions Analyst UCB BioSciences tim.williams@PhUSE.eu Assisted by:

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LET'S MAKE A KNOWLEDGE GRAPH! A HANDS-ON, INTERACTIVE, LINKED DATA WORKSHOP

PHUSE CSS 2019

Silver Spring, MD 2019-06-09

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INSTRUCTOR

Tim Williams Principal Statistical Solutions Analyst UCB BioSciences Assisted by: Nolan Nichols (Genentech) Content from: Johannes Ulander (S-Cubed) tim.williams@PhUSE.eu

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PREPARATION Your laptop [Power up!] Copy of:

  • 1. Exercises
  • 2. Graph Editor

Introduction

  • 3. Info sheet
  • 4. SPARQL reference

Log in to Cloud Server

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Workshop Files, Presentation PDF: (for later) https://github.com/phuse-org/LinkedDataWorkshop/CSS2019

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OUTLINE

  • 0. What is a Knowledge Graph?
  • 1. Create Your Study Graph
  • 2. Query Your Graph
  • 3. Extend to Other Graphs (Federated

Query)

  • 4. Ontology and Inference
  • 5. Merge Studies
  • 6. Discussion

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WHAT IS A KNOWLEDGE GRAPH?

An interconnected network of information consisting of meaningful relationships that are understandable by both people and computers. Built on Linked Data

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WHAT IS LINKED DATA?

Data that has meaningful (semantic) relationships Resource Description Framework (RDF)

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RDF TRIPLE DESCRIBING PERSON 1

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PERSON 1 NAME AND AGE

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"THINGS" NEED UNIQUE IDENTIFIERS

IRI: INTERNATIONALIZED RESOURCE IDENTIFIER

Unique Identier Uses HTTP://xx.xx.xx/xxxx

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WORKSHOP PREFIXES

Prexes shorten IRIs for readability

@prefix eg: <http://example.org/LDWorkshop#> . @prefix ncit: <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#> . @prefix schema: <http://schema.org/> .

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LITERALS

string

number

integer (INT)

date No links from a literal

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OUTLINE

  • 0. What is a Knowledge Graph?
  • 1. Create Your Study Graph
  • 2. Query Your Graph
  • 3. Extend to Other Graphs (Federated

Query)

  • 4. Ontology and Inference
  • 5. Merge Studies
  • 6. Discussion

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INTRODUCTION TO THE GRAPH EDITOR

See your handout Reference: .../doc/Graph Editor Introduction.pdf

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EXERCISE

  • 1. Create Your Study Graph
  • 2. Query Your Graph

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OUTLINE

  • 0. What is a Knowledge Graph?
  • 1. Create Your Study Graph
  • 2. Query Your Graph
  • 3. Extend to Other Graphs (Federated

Query)

  • 4. Ontology and Inference
  • 5. Merge Studies
  • 6. Discussion

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EXERCISE

  • 1. Link to ClinicalTrials.gov
  • 2. Link to DBPedia

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OUTLINE

  • 0. What is a Knowledge Graph?
  • 1. Create Your Study Graph
  • 2. Query Your Graph
  • 3. Extend to Other Graphs (Federated

Query)

  • 4. Ontology and Inference
  • 5. Merge Studies
  • 6. Discussion

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Ontology and Inference

Ontology

A vocabulary of things and how they relate to each other ...just more nodes and links Tools: Protege, TopBraid

Reasoner

An engine that applies the ontology to the graph and infers values and relationships not in your original data.

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THINK ABOUT THAT AGAIN:

Ontologies and Reasoning create values and relations not in your original data! StudyOntology.TTL

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A SUBSET OF THE STUDY ONTOLOGY FILE

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EXERCISE

  • 3. Ontology and Inference

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OUTLINE

  • 0. What is a Knowledge Graph?
  • 1. Create Your Study Graph
  • 2. Query Your Graph
  • 3. Extend to Other Graphs (Federated

Query)

  • 4. Ontology and Inference
  • 5. Merge Studies
  • 6. Discussion

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When IRIs are the same, merging is automagic!

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WITH RDF, MERGING BE LIKE:

What? How?

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EXERCISE

  • 4. Merge Studies

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ALLSTUDIES DATA POOL

BONUS! Visualize your Data Pool.

AllStudiesPoolVis.R

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OUTLINE

  • 0. What is a Knowledge Graph?
  • 1. Create Your Study Graph
  • 2. Query Your Graph
  • 3. Extend to Other Graphs (Federated

Query)

  • 4. Ontology and Inference
  • 5. Merge Studies
  • 6. Discussion...after nal words

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ACKNOWLEDGEMENTS

YOU! PhUSE Lauren - Prep Webinars and coordination PhUSE Admin Team Nolan Nichols (Genentech) Johannes Ulander (S-Cubed) Stardog Union Servers, graph database John Bresnahan - server cloning

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RESOURCES

Stardog Union

fetch.stardog.com/phuse/ www.stardog.com

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RESOURCES

Workshop materials, including the Graph Editor, SPARQL scripts, PDF of this presentation: And watch this space: https://github.com/phuse-org/LinkedDataWorkshop/CSS2019 https://github.com/phuse-

  • rg/LinkedDataEducation

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RESOURCES

Linked Data Introduction SPARQL in 11 Minutes https://www.youtube.com/watch?v=4x_xzT5eF5Q https://www.youtube.com/watch?v=FvGndkpa4K0

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PHUSE PROJECT BREAKOUT SESSION

"Going Translational With Linked Data" When: Monday 13:00 - 17:00pm Where: Fenton Room

Topics

Terminology mapping MedDRA as RDF Project Endpoint ...Other?

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DISCUSSION

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