Tutorial

3roundstones.com

@3roundstones
The Bipolar Enterprise

<HTML>

Enterprise Data

Documents
Today’s Data on the Web
Linked Data on the Web
Person

Michael
a

Galway Airport

first name

Hausenblas

last name

collector
collected at
collect...
Chris Welty

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

Callimachus
Enterprise

Point to,
include

<HTML>

Enterprise Data

Documents
Callimachus
Enterprise
A data integration platform

Callimachus Enterprise supports distributed, in-browser
workflow creati...
Callimachus
Enterprise

Callimachus
Open Source

Licensed

Community supported

Commercial support

in-browser development...
Structured data on the Web
David Wood
Marsha Zaidman
Luke Ruth
WITH Michael Hausenblas

oo
rP

riz

es

FOREWORD BY Tim Be...
Callimachus
Enterprise

Files and Formats

Actions:!
• SPARQL 1.1 queries
• SPARQL 1.1 Update
• XProc pipelines
• XQuery
•...
Callimachus
Enterprise

Social features:!
• OpenAnnotation tags and
categories for all resources.
• Timeline of user activ...
Callimachus

Callimachus
Enterprise

or

REST API
named query

endpoint(s)

OWL Class

Callimachus Template
XHTML+RDFa

or...
Data

XProc pipeline

named query

OWL Class

Callimachus Template
XHTML+RDFa

Web pages
Rendering Instances of
OWL Classes
Advantages:!
•

Most simple approach; lots of
examples and documentation

Consideration...
SPARQL Named Queries
Advantages:!
•

Like a stored procedure called via a
URL

•

Accepts parameters!

•

named query

Can...
XProc Pipelines
Advantages:!
•

Accepts parameters!

•

Can combine data from various sources in
complex ways, including r...
Getting Started
Get Callimachus 1.3
callimachusproject.org
3roundstones.com
User Invitation
•

Your	
  custom	
  J2EE	
  authentication	
  here!
Create your Profile
You can upload a number of different file types into
Callimachus, but start easy by choosing a PDF
document or an image.
You Can Upload:
•

PDF files (presentations or documents)

•

Text documents

•

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

•

HT...
Try uploading a PDF
file
You can get back to your profile from anywhere by selecting
the “My Documents” option from the main menu.
Tutorial

3roundstones.com

@3roundstones
Bonobos!
Bonobos!
@prefix dbpedia: <http://dbpedia.org/resource/> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@pre...
Bonobos!
dbpedia:
Bonobo

a

Mary

rdfs:label
rdfs:comment

Mary
Mary is a pleasant bonobo.
Tutorial

3roundstones.com

@3roundstones
Biomarkerpedia
Biomarkerpedia
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix bmterms: <http://biomarkerpedia.org/rdf/2013/...
Biomarkerpedia
bmterms:
Protein
bmterms:
Biomarker
ERBB2

a
a

bmterms:
related
her2

bmterms:
therapeuticArea

rdfs:label...
Tutorial

3roundstones.com

@3roundstones
Contributing to
•

Callimachus

Open Source Developers
•

Server
•
•

Some JavaScript, Bash/BAT

•
•

Mostly Java

RDF, SP...
Contributing to
•

Callimachus
Enterprise

Corporate Developers
•

Feature requests
•
•

•

Considered on a case-by-case b...
Getting Support
•

Callimachus Open Source users can join community
discussions via http://callimachusproject.org

•

Call...
Tutorial

3roundstones.com

@3roundstones
Callimachus Enterprise 1.3 Tutorial
Callimachus Enterprise 1.3 Tutorial
Callimachus Enterprise 1.3 Tutorial
Callimachus Enterprise 1.3 Tutorial
Callimachus Enterprise 1.3 Tutorial
Callimachus Enterprise 1.3 Tutorial
Callimachus Enterprise 1.3 Tutorial
Callimachus Enterprise 1.3 Tutorial
Callimachus Enterprise 1.3 Tutorial
Callimachus Enterprise 1.3 Tutorial
Callimachus Enterprise 1.3 Tutorial
Callimachus Enterprise 1.3 Tutorial
Callimachus Enterprise 1.3 Tutorial
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Callimachus Enterprise 1.3 Tutorial

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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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Callimachus Enterprise 1.3 Tutorial

  1. 1. Tutorial 3roundstones.com @3roundstones
  2. 2. The Bipolar Enterprise <HTML> Enterprise Data Documents
  3. 3. Today’s Data on the Web
  4. 4. Linked Data on the Web Person Michael a Galway Airport first name Hausenblas last name collector collected at collected by my data measurement ... a measurement date 2011-01-01 or value units of measure 0 degrees Centigrade
  5. 5. 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.”
  6. 6. Read Callimachus Enterprise Point to, include <HTML> Enterprise Data Documents
  7. 7. Callimachus Enterprise A data integration platform Callimachus Enterprise supports distributed, in-browser workflow creation, editing and publication using the Linked Data model.
  8. 8. Callimachus Enterprise Callimachus 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
  9. 9. Structured data on the Web David Wood Marsha Zaidman Luke Ruth WITH Michael Hausenblas oo rP riz es FOREWORD BY Tim Berners-Lee 2 D MANNING
  10. 10. Callimachus Enterprise Files and Formats Actions:! • SPARQL 1.1 queries • SPARQL 1.1 Update • XProc pipelines • XQuery • PURLs RDF Constructs:! • RDF Turtle • RDF/XML • Folders • SKOS Concepts • RDFS Classes Users & Groups:! • User profiles • Groups & domains 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 Data Sources:! • RDF Databases • SQL Databases • HTTP(S) servers returning text or XML • Other Callimachus servers
  11. 11. Callimachus Enterprise Social features:! • OpenAnnotation tags and categories for all resources. • Timeline of user activities. • Exposed as Linked Data 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.
  12. 12. Callimachus Callimachus Enterprise or REST API named query endpoint(s) OWL Class Callimachus Template XHTML+RDFa or Generated HTML Page Generated HTML Form AJ AX XProc pipeline
  13. 13. Data XProc pipeline named query OWL Class Callimachus Template XHTML+RDFa Web pages
  14. 14. 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) OWL Class Callimachus Template XHTML+RDFa or Generated HTML Page Generated HTML Form
  15. 15. SPARQL Named Queries Advantages:! • Like a stored procedure called via a URL • Accepts parameters! • named query Can query multiple SPARQL endpoints Considerations:! • Need to know SPARQL syntax Callimachus Template XHTML+RDFa or Generated HTML Page Generated HTML Form
  16. 16. XProc Pipelines Advantages:! • Accepts parameters! • Can combine data from various sources in complex ways, including remote HTTP calls • Callimachus Template XHTML+RDFa Can render results into any textual data type Considerations:! • XProc pipeline Need to learn XProc syntax: http://xproc.org/ or Generated HTML Page Generated HTML Form
  17. 17. Getting Started
  18. 18. Get Callimachus 1.3 callimachusproject.org 3roundstones.com
  19. 19. User Invitation
  20. 20. • Your  custom  J2EE  authentication  here!
  21. 21. Create your Profile
  22. 22. You can upload a number of different file types into Callimachus, but start easy by choosing a PDF document or an image.
  23. 23. 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!
  24. 24. Try uploading a PDF file
  25. 25. You can get back to your profile from anywhere by selecting the “My Documents” option from the main menu.
  26. 26. Tutorial 3roundstones.com @3roundstones
  27. 27. Bonobos!
  28. 28. 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.” .
  29. 29. Bonobos! dbpedia: Bonobo a Mary rdfs:label rdfs:comment Mary Mary is a pleasant bonobo.
  30. 30. Tutorial 3roundstones.com @3roundstones
  31. 31. Biomarkerpedia
  32. 32. Biomarkerpedia @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 .
  33. 33. Biomarkerpedia bmterms: Protein bmterms: Biomarker ERBB2 a a bmterms: related her2 bmterms: therapeuticArea rdfs:label bmterms: device HER2 bmterms: cro bmterms: therapeuticArea bmterms: oncology bmterms: breast_cancer rdfs:label INFORM HER2 Dual ISH DNA Probe cocktail assay rdfs:label Wuxi AppTec
  34. 34. Tutorial 3roundstones.com @3roundstones
  35. 35. Contributing to • Callimachus Open Source Developers • Server • • Some JavaScript, Bash/BAT • • Mostly Java RDF, SPARQL 1.1, PURLs, XProc, XSLT, XQuery Client: • (X)HTML, RDFa, JavaScript/JQuery, Bootstrap 3, Less, CSS3 • Documents in DocBook articles and books
  36. 36. Contributing to • Callimachus Enterprise 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
  37. 37. 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 support@3roundstones.com • 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.
  38. 38. Tutorial 3roundstones.com @3roundstones

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