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Callimachus Enterprise 1.3 Tutorial

May 07, 2015

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Slides for a half-day tutorial on Callimachus Enterprise. Originally delivered at the Conference on Semantics in Healthcare and Life Sciences (CSHALS) 2014 in Boston, MA, USA.
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Page 1: Callimachus Enterprise 1.3 Tutorial

Tutorial

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Page 2: Callimachus Enterprise 1.3 Tutorial

The Bipolar Enterprise

<HTML>

Enterprise Data Documents

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Today’s Data on the Web

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Linked Data on the Web

my data

collector

collected by

measurement

Michael

first name

Hausenblaslast name

Person

a

a measurement

2011-01-01date

0

valueunits of measure

degrees Centigrade

...

Galway Airport

collected at

or

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Chris Welty

“Semantic Technology is not an end in itself, it is a means to an end, a set of tools and techniques for supporting

modern data analytics. It goes alongside other essential technologies

like machine learning, databases, information retrieval, etc.”

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<HTML>

Enterprise Data Documents

Read Point to, include

Callimachus Enterprise

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Callimachus Enterprise supports distributed, in-browser workflow creation, editing and publication using the

Linked Data model.

A data integration platform

Callimachus Enterprise

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Open Source Licensed

Community supported Commercial support

in-browser development, deployment, backups

Linked Data publication

User profiles, social sharing

Document, app management

OpenAnnotation support

External datasources

Shared deployments, realms

Enterprise management

CallimachusCallimachus Enterprise

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M A N N I N G

David WoodMarsha ZaidmanLuke RuthWITH Michael Hausenblas

FOREWORD BY Tim Berners-Lee

Structured data on the Web

2 Door P

rizes

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Files and FormatsActions:!• SPARQL 1.1 queries • SPARQL 1.1 Update • XProc pipelines • XQuery • PURLs

Documents:!• DocBook articles and books • HTML (optional theming) • CSS files • JavaScript files • XSLT files • Plain text files • Image files (PNG, JPG, GIF, SVG) • PDF files

RDF Constructs:!• RDF Turtle • RDF/XML • Folders • SKOS Concepts • RDFS Classes

Users & Groups:!• User profiles • Groups & domains

Data Sources:!• RDF Databases • SQL Databases • HTTP(S) servers returning text or XML • Other Callimachus servers

Callimachus Enterprise

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User Profile

Document management:!• Documents & folders

associated with user profiles. • Folders can contain data,

documents and Callimachus applications.

• In-browser editing tools are available for many document types.

Social features:!• OpenAnnotation tags and

categories for all resources. • Timeline of user activities. • Exposed as Linked Data

Callimachus Enterprise

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orCallimachusCallimachus Enterprise

GeneratedHTML Page

GeneratedHTML Form

or

Callimachus TemplateXHTML+RDFa

endpoint(s)named query

REST APIOWL Class

AJAX

XProc pipeline

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Callimachus TemplateXHTML+RDFa

named query OWL ClassXProc pipeline

Data

Web pages

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Rendering Instances of OWL Classes

Advantages:!

• Most simple approach; lots of examples and documentation

Considerations:!

• Need to associate OWL classes in your data with Callimachus classes via the class explorer.

• Limited to data in the default RDF database (Sesame)

GeneratedHTML Page

GeneratedHTML Form

or

Callimachus TemplateXHTML+RDFa

OWL Class

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SPARQL Named QueriesAdvantages:!

• Like a stored procedure called via a URL

• Accepts parameters!

• Can query multiple SPARQL endpoints

Considerations:!

• Need to know SPARQL syntax

GeneratedHTML Page

GeneratedHTML Form

or

Callimachus TemplateXHTML+RDFa

named query

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XProc PipelinesAdvantages:!

• Accepts parameters!

• Can combine data from various sources in complex ways, including remote HTTP calls

• Can render results into any textual data type

Considerations:!

• Need to learn XProc syntax: http://xproc.org/

GeneratedHTML Page

GeneratedHTML Form

or

Callimachus TemplateXHTML+RDFa

XProc pipeline

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Getting Started

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Get Callimachus 1.3callimachusproject.org

3roundstones.com

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User Invitation

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• Your  custom  J2EE  authentication  here!

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Create your Profile

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You can upload a number of different file types into Callimachus, but start easy by choosing a PDF

document or an image.

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You Can Upload:• PDF files (presentations or documents)

• Text documents

• Image files (.png, .jpg, .gif, .svg)

• HTML files, CSS stylesheets, JavaScript files

• RDF data! (Turtle, N3, RDF/XML)Developers can also create Linked Data applications!

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Try uploading a PDF file

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You can get back to your profile from anywhere by selecting the “My Documents” option from the main menu.

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Tutorial

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Bonobos!

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Bonobos!

@prefix dbpedia: <http://dbpedia.org/resource/> . @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . !<Mary> a dbpedia:Bonobo ; rdfs:label "Mary" ; rdfs:comment "Mary is a pleasant bonobo.” .

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Bonobos!

Mary

dbpedia:Bonobo

a

Mary

rdfs:label

Mary is a pleasant bonobo.

rdfs:comment

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Tutorial

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Biomarkerpedia

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@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . @prefix bmterms: <http://biomarkerpedia.org/rdf/2013/schema/1.0/schema.ttl#> . !<her2> a bmterms:Biomarker, bmterms:Protein ; rdfs:label "HER2" ; bmterms:related <erbb2> ; bmterms:therpeuticArea bmareas:oncology ; bmterms:therpeuticArea bmareas:breast_cancer ; bmterms:drug drug:Ado-Trastuzumab-Emtansine ; bmterms:device device:INFORM-HER2-Dual-ISH-DNA-Probe-cocktail-assay ; bmterms:cro bmo:wuxiapptec .

Biomarkerpedia

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Biomarkerpedia

her2

bmterms:Biomarker

a

HER2

rdfs:label

bmterms:Protein

aERBB2

bmterms:related

bmterms:oncology

bmterms:therapeuticArea

bmterms:breast_cancer

bmterms:therapeuticArea

bmterms:device

INFORM HER2 Dual ISH DNA Probe cocktail assay

rdfs:label

bmterms:cro

Wuxi AppTec

rdfs:label

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Tutorial

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Contributing to• Open Source Developers

• Server

• Mostly Java

• Some JavaScript, Bash/BAT

• RDF, SPARQL 1.1, PURLs, XProc, XSLT, XQuery

• Client:

• (X)HTML, RDFa, JavaScript/JQuery, Bootstrap 3, Less, CSS3

• Documents in DocBook articles and books

Callimachus

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Contributing to• Corporate Developers

• Feature requests

• Considered on a case-by-case basis

• Often associated with a services contract

• Code contributions

• Accepted with appropriate legal releases/licenses

Callimachus Enterprise

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Getting Support• Callimachus Open Source users can join community

discussions via http://callimachusproject.org

• Callimachus Enterprise customers can open a support ticket by sending email to [email protected]

• Urgent requests can be made by calling 3 Round Stones at +1.877.290.2127. Please note that we are located in the U.S. Eastern timezone.

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Tutorial

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