In this lab session you will setup and make some basic tests of the main tools that will be used during this course, and navigate through the example given in Lecture 1.

Tooling setup

1. Visual Paradigm: CASE Tool supporting UML and other languages, it provides report generation and code engineering capabilities, e.g., code generation.

Download Community edition, and follow this tutorial:

(a) Section 1: Introduction to Visual Paradigm
(a1) What is Visual Paradigm? - 10min

(b) Section 2: Diagramming
(b1) User Interface Walk-through - 19min
(b2) Drawing Diagram - 20min
(b3) Resource-Centric Interface -12min
(b4) Using Connectors - 5min
(b5) Making Better Look Diagrams - 13min

(c) Section 3: Notations & Standards
(c1) Introduction to BPMN - 17min
(c2) Introduction to UML (Part 1) - 13min
(c3) Introduction to UML (Part 2) - 19min

(d) Section 4: Understanding Model & View Concept
(d1) Model Repository - 6min
(d2) Understanding the Concept of View - 7min

(e) Section 6: Generating Documentation
(e1) Generating Specification - 21min

2. Protégé: free, open source ontology editor and a knowledge management system.

Download it and follow these steps:

(a) 'A Simple Protege Tutorial 1: Intro' (~2min)
https://www.youtube.com/watch?v=R9ERlUgvgwM

(b) 'A Simple Protege Tutorial 2: Creating the Ontology Classes (~4min)
https://www.youtube.com/watch?v=g5IGHpCSIow&t=23s

3. Apache Jena Fuseki: is a SPARQL server. It can run as a operating system service, as a Java web application (WAR file), and as a standalone server.

(a) Download binary distribution of Fuseki and test it: Downloading and Running Jena Fuseki Server (~2min)
https://www.youtube.com/watch?v=JZp70uFsZS0&t=32s

4. OpenRefine: is an open-source desktop application for data cleanup and transformation to other formats, an activity commonly known as data wrangling.

(a) Download, and follow tutorial

5. RDF Libraries for programming

5.1. Java - Apache Jena: A free and open source Java framework for building Semantic Web and Linked Data applications.

(a) Read Getting Started, and The core RDF API

(b) Setup with Eclipse & test by following this tutorial (import Jena maven project) or this tutorial (import Jena binaries/jar)

5.2. Python - RDFLib: a Python library for working with RDF, it contains parsers/serializers for almost all RDF serializations, e.g., RDF/XML, Turtle, N-Triples, and JSON-LD.

(a) Read GitHub page, and Introduction to lib

(b) Setup & test: follow getting started

Observation: if you choose Python, we recommend to use Jupyter notebook, or Visual Studio Code.

Exercise (optional)

1. Navigate through the URIs of the example given in Lecture 1:

Mosquito: http://purl.obolibrary.org/obo/MIRO_40000015

Transmits: http://purl.obolibrary.org/obo/IDOMAL_0000187

Malaria: http://purl.obolibrary.org/obo/IDOMAL_0001052

Search and navigate these concepts and ontologies also on BioPortal (https://bioportal.bioontology.org)

2. Open an ontology used in this example in Protégé (Open from URI), and navigate through the classes, and (object and data) properties:

Search the ontology on BioPortal (https://bioportal.bioontology.org), find the download URL and open it on Protégé.