Semantic MOBY

1
Semantic MOBY

• Gary Schiltz
• Semantic MOBY User Group Meeting
• June 8-9, 2006

2
Semantic MOBY Architecture (simplified)
Resource
Resource Provider
3
Semantic MOBY Architecture (simplified)
Resource
Resource Provider
4
Semantic MOBY Architecture (simplified)
Resource
Give me the sequence for medicago, TIGR TC
Number TC93917
Resource Provider
5
Semantic MOBY Architecture (simplified)
Resource
Give me the sequence for medicago, TIGR TC
Number TC93917
BLAST this sequence that I just looked up
Resource Provider
6
Semantic MOBY Architecture (simplified)
Invocation
Resource
Give me the sequence for medicago, TIGR TC
Number TC93917
BLAST this sequence that I just looked up
Resource Provider
7
Semantic MOBY Architecture (simplified)

• HTTP messaging
• GET retrieves description
• POST invokes resource
• Payload of messages is OWL DL graphs serialized
  as RDF

Invocation
Resource
Give me the sequence for medicago, TIGR TC
Number TC93917
BLAST this sequence that I just looked up
Resource Provider
8
Semantic MOBY Architecture (simplified)
Resource
Give me the sequence for medicago, TIGR TC
Number TC93917
BLAST this sequence that I just looked up
Resource Provider
Invocation
9
Semantic MOBY Architecture (simplified)
I found some Moby resources! Ill remember them.
Resource
Give me the sequence for medicago, TIGR TC
Number TC93917
BLAST this sequence that I just looked up
Resource Provider
Invocation
10
Semantic MOBY Architecture (simplified)
Registration
I found some Moby resources! Ill remember them.
Resource
Give me the sequence for medicago, TIGR TC
Number TC93917
BLAST this sequence that I just looked up
Resource Provider
Invocation
11
Semantic MOBY Architecture (simplified)
Registration
I found some Moby resources! Ill remember them.
I found some Moby resources! Ill remember them.
Do you know of any Moby resources that return a
sequence given a TIGR TC Number?
Resource
Give me the sequence for medicago, TIGR TC
Number TC93917
BLAST this sequence that I just looked up
Resource Provider
Invocation
12
Semantic MOBY Architecture (simplified)
Discovery
Registration
I found some Moby resources! Ill remember them.
I found some Moby resources! Ill remember them.
Do you know of any Moby resources that return a
sequence given a TIGR TC Number?
Resource
Give me the sequence for medicago, TIGR TC
Number TC93917
BLAST this sequence that I just looked up
Resource Provider
Day 1
Invocation
13
Semantic MOBY Architecture (simplified)
Day 2
Discovery
Registration
I found some Moby resources! Ill remember them.
I found some Moby resources! Ill remember them.
Do you know of any Moby resources that return a
sequence given a TIGR TC Number?
Resource
Give me the sequence for medicago, TIGR TC
Number TC93917
BLAST this sequence that I just looked up
Resource Provider
Invocation
14
RDF Introduction

• RDF consists of Statements, each with
• Subject an object being described
• Property aka predicate a characteristic of
  the subject
• Object the value of the property
• Subjects and properties take the form of a URI
  Object can be URI or literal value
• A collection of statements is called a Graph
• Graphs are serialized in RDF/XML syntax

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RDF/XML Example

• lt?xml version"1.0" encoding"UTF-8"?gt
• lt!DOCTYPE rdfRDF
• lt!ENTITY rdf "http//www.w3.org/1999/02/22
  -rdf-syntax-ns"gt
• lt!ENTITY rdfs "http//www.w3.org/2000/01/rd
  f-schema"gt
• lt!ENTITY owl "http//www.w3.org/2002/07/ow
  l"gt
• lt!ENTITY xsd "http//www.w3.org/2001/XMLSc
  hema"gt
• lt!ENTITY fasta "http//www.tigr.org/smoby/on
  tologies/fasta/"gt
• gt
• ltrdfRDF xmlnsrdf "rdf"
• xmlnsrdfs "rdfs"
• xmlnsowl "owl"
• xmlnsxsd "xsd"
• xmlnsfasta "fasta"gt
• ltowlOntology rdfabout"fastaowlOntology"/gt
  
• ltowlDatatypeProperty rdfabout"fastaspecie
  sName"gt