semantic web: collaboration and community. alitora systems semantic search & collaboration...

Semantic Web:Collaboration and Community

Alitora Systems 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.comNYC, SF

Marc Hadfield

Computer Science Previous:

CTO Financial Services Tech Start-Up Search, Semantics Research in NLP & applications to

BioMedical / BioInformatics Developer of kHarmony™ Semantic

DB

Agenda

Introduction Enabling Technology Memomics Presentation Memomics Web Application Demo Memomics API Demo Discussion and Q&A

Memomics.com Memomics

Semantic Web Infrastructure service Community driven Semantic & Ontology Resource Accessible via API

Goals: Community Vocabulary for the Semantic Web Repository of Semantic Information Community Process Driven Concept DNS

Semantic Web “Network Solutions” google.com IP 72.14.207.99 “apple (the fruit)” ?

Enable Semantic Applications, Embed Semantics in Apps

Philosophy Data Standards:

Bits ASCII EDI XML {Semantic Web} More convenient but arbitrary data formats, encapsulate

more “value” Standards are useful because they are standards:

Betamax vs. VHS, TCP/IP, BluRay, … Provide Overall Economic Advantage, trumps “better”

Semantic Web is at the end of arbitary-ness for data standards

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 Current gaps and missing pieces:

Data Technologies Processes, Infrastructure, Services

Limitations on growth and wide acceptance

Proliferation (unchecked) of ontologies is bad 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

Not one-size-fits-all Must allow Ontology Interchange

Semantic Web sources… Not Only:

OWL / RDF But including:

Microformats Topic Maps Taxonomies (Species, MeSH, DMOZ) HTML, XML, … (Wikipedia) SQL Databases (CRM/SFA: customer data) Deep Web…

Semantic Web – Namespaces Namespace limitations in OWL / RDF / XML

Fragile dependency chain Importing files into namespace not useful

Concepts are (pre)determined No “relative” concepts Can easily break with changes Example: Food & Wine Ontology Need persistence over time

Files as “container” problem Need finer grain control Distribute subsets of Ontologies

Externalize version control Microformats, no namespaces

Semantic Web

A is A

Semantic Web

Must become Easy (well, easier…)

Memomics Manifesto (I)

There can be no single ontology. There can be no single formulism. There can be no single ontology

delivery mechanism.

Memomics Manifesto (II) Concepts should be uniquely identifiable

the “Memes” of Memomics Don’t URLs do this? (we still have root…)

Concepts should be shared, re-used (when possible)

Webservices must have Semantic Annotations Mark-Up APIs not just data (Deep Web)

Compatible concepts should be aligned Allow multiple Ontologies to be used

seamlessly together.

Memomics Manifesto (III) 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 Use Cases:

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

Semantic Webservices Layer

Data Layer

Application Logic Layer

Transport Layer – SOAP/XML/HTTP

Interface Layer - WSDL

Service Oriented Architecture

Persistent Composite Apps

Enterprise Mash-Ups

WorkflowSLA-Policy

Security

Ad-Hoc Composite Apps

Orchestration ChoreographyData Mapping

Repository

BPEL

Registry

Dynamic Binding Registry

Enterprise User

Semantic Webservices Layer Semantic Webservices Layer

Enterprise User

Enterprise User Enterprise User

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 URI – directly mapping to a URL Concept Identifier Distributed Namespaces Embedding UMIS

Microformats, OWL/RDF, Webservices Com.Memomics.AlitoraSystems.upper.876576 href=“http://memomics.com/umis/<umis>” href=“http://memomics.com/umis/rdf/<umis>”

Backed by “Concept DNS” google.com IP 72.14.207.99 “apple (the fruit)”

Com.Memomics.AlitoraSystems.upper.876576 Compare To:

DOI, ISBN Microformats, RDF

UMIS Use of UMIS

apple Com.Memomics.AlitoraSystems.upper.876876

Apple Computer Com.Memomics.AlitoraSystems.business.433495

<service>.<issuer>.<namespace>.<instance>

Concept scheme concept://

Com.Memomics.AlitoraSystems.business.433495

kHarmony™

kHarmony™ Semantic Database Graph Database Focus on

Connections Graph Topology

Algorithms Semantic Search Semantic Web

Infrastructure

Journal Articles

NLP Normalization Model

Semantic Database

kHarmony – Example Query

SubgraphRoot = <umis>Distance = *Expand_edge = is_aExpand_edge =

has_a

Yields TreeRoot:Vehicle

Car, Boat, Engine, Steering Wheel, …

Populating kHarmony

Supports General HyperGraphs

Fill with… Existing Ontologies Community Built Ontologies Semantic Instance Data

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.”

Annotate Collaborate

Search

ASAPI Application

Disease:Breast Cancer

Protein:HER2/neu

Molecular Function

Drug:HerceptinGenentech

Patent

YOU

Jane

Fred

Gene:HER2

Dick

ASAPI

Alitora Systems API Search Memory / Clipboard Users Teams Memes Relationships Annotations

ASAPI Access Control

Segments (public / proprietary) baseline memomics proprietary / domain specific

Scope Private Public Team

Namespace – logical domain groupings

Memomics

Web Application API (REST / WSDL) Client App Plug-In (such as

Protégé)

Memomics

Tour…

Memomics

Search & Navigate Memes

Memomics

Collaboration Tools Teams Annotations Voting

Memomics

Ontology Editor (micro editing) “Wiki” Style

Functions: Add Meme Add MemeRelation Add Relationship Edit with Versioning

Memomics

Ontology Repository Uploads Downloads UMIS Concept Definition

Memomics

Embed Semantics via API: UMIS

Memomics - Ontology Editing

Change Management – Macro Editing Versioning Splitting Concepts Forwarding to Canonical

Ontology Alignment Exact (===) Related…(type of…) General Domain Specific

Memomics

Community Processes Ontology Construction Standard(s)

Example: Guidelines for Concept vs. Instance

Example: Guidelines for Domain & Range Teams as Working Groups Submit Ontology to Community Acceptance as “Authoritative”

Memomics Community Roles

Modeler Ontology Expert

Domain Expert Adds domain expertise to Ontology

Domain Specialist Adds individuals / instances, edits, reviews

Technologist Adds application specific knowledge

Enthusiast Adds individuals / instances, edits, reviews

Consumer Read Only

Memomics Usage Scenario:

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

Demo Community Interaction Create Teams Add Members Add Memes, Relations Add Annotations Messages Access via API

Memomics

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, patentsAvailable online. Can filter by

disease, gene, keyword, result of semantic lookup

Public financial information

Clinical Trials…

Patent Applications…

Memomics API Use

REST client /khREST/asapi/10/xml/search?query= Embed in PHP, Java, etc. Format in XML, JSON, RDF, … Resources:

Memory / Clipboard, Search, Team, …

WSDL Client

Memomics

Discussion Points How to best engage community? Organizing Ontology Work Groups? Community Acceptance processes? Motivating contributors & editors?

Alitora Systems Contact:

marc@alitora.com

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