Download Memomics.com

Semantic Web:
Collaboration and Community
Alitora Systems
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Semantic Search & Collaboration
Start-Up Software Company, Software-as-a-Service
Premium Semantic Data, Services, Apps
Sector: Biomedical/Pharma – Early Adopters
Memomics: Semantic Application Platform
Founders:
 Marc Hadfield “Tech Guy”
 Peter Berger “Business Guy”
http://www.alitora.com
NYC, SF
Marc Hadfield
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Computer Science
Previous:
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CTO Financial Services Tech Start-Up
Search, Semantics
Research in NLP & applications to
BioMedical / BioInformatics
Developer of kHarmony™ Semantic DB
Agenda
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Introduction
Enabling Technology
Memomics Presentation
Memomics Web Application Demo
Memomics API Demo
Discussion and Q&A
Memomics.com
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Memomics
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Semantic Web Infrastructure service
Community driven Semantic & Ontology Resource
Accessible via API
Goals:
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Community Vocabulary for the Semantic Web
Repository of Semantic Information
Community Process Driven
Concept DNS
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Semantic Web “Network Solutions”
google.com  IP 72.14.207.99
“apple (the fruit)”  ?
Enable Semantic Applications, Embed Semantics in Apps
Philosophy
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Data Standards:
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More convenient but arbitrary data formats, encapsulate more
“value”
Standards are useful because they are standards:
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Bits  ASCII  EDI  XML  {Semantic Web}
Betamax vs. VHS, TCP/IP, BluRay, …
Provide Overall Economic Advantage, trumps “better”
Semantic Web is at the end of arbitary-ness for data standards
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Humans often don’t agree on meaning, are wrong, or inaccurate
No “standard meaning” is possible
(i.e. “1984” and unthinkable thoughts)
Meaning must remain fully expressive
A protocol to encode meaning & determine “meaning agreement”
is possible, enabling knowledge aggregation
Semantic Web
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Current gaps and missing pieces:
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Data
Technologies
Processes, Infrastructure, Services
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Limitations on growth and wide acceptance
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Proliferation (unchecked) of ontologies is bad
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No better than no ontologies
Reinventing Babel, might as well stick with XML
Point of Ontologies is a shared world-view
Narrow, domain specific Ontologies are typically more useful than general
Ontologies
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Not one-size-fits-all
Must allow Ontology Interchange
Semantic Web sources…
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Not Only:
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OWL / RDF
But including:
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Microformats
Topic Maps
Taxonomies (Species, MeSH, DMOZ)
HTML, XML, … (Wikipedia)
SQL Databases (CRM/SFA: customer data)
Deep Web…
Semantic Web – Namespaces
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Namespace limitations in OWL / RDF / XML
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Importing files into namespace not useful
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Fragile dependency chain
Concepts are (pre)determined
No “relative” concepts
Can easily break with changes
Example: Food & Wine Ontology
Need persistence over time
Files as “container” problem
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Need finer grain control
Distribute subsets of Ontologies
Externalize version control
Microformats, no namespaces
Semantic Web
A is A
Semantic Web
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Must become Easy (well, easier…)
Memomics Manifesto (I)
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There can be no single ontology.
There can be no single formulism.
There can be no single ontology
delivery mechanism.
Memomics Manifesto (II)
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Concepts should be uniquely identifiable
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Concepts should be shared, re-used (when
possible)
Webservices must have Semantic Annotations
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the “Memes” of Memomics
Don’t URLs do this? (we still have root…)
Mark-Up APIs not just data (Deep Web)
Compatible concepts should be aligned
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Allow multiple Ontologies to be used seamlessly
together.
Memomics Manifesto (III)
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The community will use Ontologies in a variety of
ways for a variety of purposes, both “formal” and
“informal”.
Ontologies should not necessarily be “fragile” (logic),
but formally formed Ontologies suitable for inference
algorithms should be available wherever possible.
The true developers of Ontologies will be a mixture of
Ontology Experts, Domain Experts, Technologists,
and End Users.
No one should own an Ontology that is used by the
entire Community.
Memomics.com
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Use Cases:
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Competitive Intelligence Platform that’s aware of
Companies, Products, Competitors, Suppliers, …
News or Blog that’s aware of your favorite topics,
the relationships between topics, and can
reorganize information accordingly…
Wine store that’s aware of…
Social Network that’s aware of...
Software Agent that can…
Web Services Stack
Enterprise User
Enterprise User
Enterprise User
Enterprise User
Sem antic Webservic es Layer
Ad-Hoc Com posite Apps
Persistent Com posite Apps
Enterprise Mash-Ups
Servic e Oriented Arc hitec ture
Sem antic Webservic es Layer
Sem antic Webservic es Layer
Data
Mapping
Dynam ic
Binding
Workflow
Orc hestration
BPEL
Choreography
SLA-Polic y
Sec urity
Registry
Registry
Interfac e Layer - WSDL
Transport Layer – SOAP/XML/HTTP
Applic ation Logic Layer
Data Layer
Repository
Supporting Tech:
Alitora Systems:
 UMIS – Concept Identifier; Concept DNS
 kHarmony – Semantic Database
 ASAPI – Semantic Search and Collaboration API
Internet Community:
 OWL / RDF
 JENA, Parsers, Inference Engines
 Microformats / HTML / XML / CSS
 REST Webservices, WSDL / SOAP Webservices
 Protégé
UMIS
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URI – directly mapping to a URL
Concept Identifier
Distributed Namespaces
Embedding UMIS
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Backed by “Concept DNS”
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Microformats, OWL/RDF, Webservices
Com.Memomics.AlitoraSystems.upper.876576
href=“http://memomics.com/umis/<umis>”
href=“http://memomics.com/umis/rdf/<umis>”
google.com  IP 72.14.207.99
“apple (the fruit)”  Com.Memomics.AlitoraSystems.upper.876576
Compare To:
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DOI, ISBN
Microformats, RDF
UMIS
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Use of UMIS
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apple 
Com.Memomics.AlitoraSystems.upper.876876
Apple Computer 
Com.Memomics.AlitoraSystems.business.433495
<service>.<issuer>.<namespace>.<instance>
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Concept scheme
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concept://Com.Memomics.AlitoraSystems.business.433495
kHarmony™
kHarmony™ Semantic Database
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Graph Database
Focus on Connections
Graph Topology
Algorithms
Semantic Search
Semantic Web
Infrastructure
NLP
Normalization
Model
Semantic Database
Journal Articles
kHarmony – Example Query
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Subgraph
Root = <umis>
Distance = *
Expand_edge = is_a
Expand_edge = has_a
Yields Tree
Root:Vehicle 
Car, Boat, Engine,
Steering Wheel, …
Populating kHarmony
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Supports General HyperGraphs
Fill with…
 Existing Ontologies
 Community Built Ontologies
 Semantic Instance Data
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People, Companies, Places, Websites, …
Semantic Parser
Aside: Example Semantic Parse
“Suppression of endogenous Bim greatly inhibits Gadd45a induction
of apoptosis.”
[action, inhibit,
[action, suppress,
[unknown],
[gp, endogenous Bim]
],
[action, induce,
[gp, Gadd45a],
[process, apoptosis]
],
]
Aside: Normalization – Entity Extraction
Heuristics
Bayesian
String Similarity
Abbreviation
Expansion
Species Context
Aside: Populating kHarmony
“Suppression of endogenous Bim greatly
inhibits Gadd45a induction of
apoptosis.”
ASAPI Application
Search
Annotate
Collaborate
YOU
Molecular Function
Jane
Disease:Breast Cancer
Dick
Protein:HER2/neu
Gene:HER2
Drug:Herceptin
Genentech
Patent
Fred
ASAPI
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Alitora Systems API
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Search
Memory / Clipboard
Users
Teams
Memes
Relationships
Annotations
ASAPI
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Access Control
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Segments (public / proprietary)
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Scope
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baseline
memomics
proprietary / domain specific
Private
Public
Team
Namespace – logical domain groupings
Memomics
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Web Application
API (REST / WSDL)
Client App Plug-In (such as Protégé)
Memomics
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Tour…
Memomics
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Search & Navigate Memes
Memomics
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Collaboration Tools
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Teams
Annotations
Voting
Memomics
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Ontology Editor (micro editing)
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“Wiki” Style
Functions:
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Add Meme
Add MemeRelation
Add Relationship
Edit with Versioning
Memomics
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Ontology Repository
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Uploads
Downloads
UMIS  Concept Definition
Memomics
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Embed Semantics via API: UMIS
Memomics - Ontology Editing
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Change Management – Macro Editing
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Versioning
Splitting Concepts
Forwarding to Canonical
Ontology Alignment
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Exact (===)
Related…(type of…)
General   Domain Specific
Memomics
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Community Processes
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Ontology Construction Standard(s)
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Example: Guidelines for Concept vs. Instance
Example: Guidelines for Domain & Range
Teams as Working Groups
Submit Ontology to Community
Acceptance as “Authoritative”
Memomics
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Community Roles
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Modeler
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Domain Expert
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Adds application specific knowledge
Enthusiast
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Adds individuals / instances, edits, reviews
Technologist
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Adds domain expertise to Ontology
Domain Specialist
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Ontology Expert
Adds individuals / instances, edits, reviews
Consumer
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Read Only
Memomics
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Usage Scenario:
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Domain Selected
Working Group formed from Memomics Community
Upload Existing Owl files, if any
Edit via Plug-in or WebApp
Tweak via Community, Add Instances
Public Review
Available via API for Embedding in Apps
Community voting
Accepted for “Authoritative” Status
Embed in Public-Authoritative Apps
Memomics
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Demo Community Interaction
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Create Teams
Add Members
Add Memes, Relations
Add Annotations
Messages
Access via API
Memomics
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Demo Application
Mash-Up of Semantic Search Pharma,
Drug, Chemical, Patent, Gene, and Disease
information
Drill down into chemical
or drug detail.
Select a manufacturer
for details about their
activity
Contextual
drug/substance
information from PubMed
Clinical trials, patents
Available online. Can filter by
disease, gene, keyword, result of
semantic lookup
Public financial information
Clinical Trials…
Patent Applications…
Memomics API Use
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REST client
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/khREST/asapi/10/xml/search?query=
Embed in PHP, Java, etc.
Format in XML, JSON, RDF, …
Resources:
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Memory / Clipboard, Search, Team, …
WSDL Client
Memomics
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Discussion Points
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How to best engage community?
Organizing Ontology Work Groups?
Community Acceptance processes?
Motivating contributors & editors?
Alitora Systems
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Contact:
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[email protected]
Sign Up for API use
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[email protected]
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Mailing Lists
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Community Wiki