David W. Embley Brigham Young University Provo, Utah, USA WoK: A Web of Knowledge

A Web of Pages  A Web of Facts Birthdate of my great grandpa Orson Price and mileage of red Nissans, 1990 or newer Location and size of chromosome 17 US states with property crime rates above 1%

Fundamental questions – What is knowledge? – What are facts? – How does one know? Philosophy – Ontology – Epistemology – Logic and reasoning Toward a Web of Knowledge

Existence  asks “What exists?” Concepts, relationships, and constraints with formal foundation Ontology

The nature of knowledge  asks: “What is knowledge?” and “How is knowledge acquired?” Populated conceptual model Epistemology

Principles of valid inference  asks: “What is known?” and “What can be inferred?” For us, it answers: what can be inferred (in a formal sense) from conceptualized data. Logic and Reasoning Find price and mileage of red Nissans, 1990 or newer

Distill knowledge from the wealth of digital web data Annotate web pages Need a computational alembic to algorithmically turn raw symbols contained in web pages into knowledge Making this Work  How? Fact Annotation … …

Turning Raw Symbols into Knowledge Symbols: $ 11, K Nissan CD AC Data: price(11,500) mileage(117K) make(Nissan) Conceptualized data: – Car(C 123 ) has Price($11,500) – Car(C 123 ) has Mileage(117,000) – Car(C 123 ) has Make(Nissan) – Car(C 123 ) has Feature(AC) Knowledge – “Correct” facts – Provenance

Actualization (with Extraction Ontologies) Find me the price and mileage of all red Nissans – I want a 1990 or newer.

Data Extraction Demo

Semantic Annotation Demo

Free-Form Query Demo

Explanation: How it Works Extraction Ontologies Semantic Annotation Free-Form Query Interpretation

Extraction Ontologies Object sets Relationship sets Participation constraints Lexical Non-lexical Primary object set Aggregation Generalization/Specialization

Extraction Ontologies External Rep.: \s*[$]\s*(\d{1,3})*(\.\d{2})? Key Word Phrase Left Context: $ Data Frame: Internal Representation: float Values Key Words: ([Pp]rice)|([Cc]ost)| … Operators Operator: > Key Words: (more\s*than)|(more\s*costly)|…

Generality & Resiliency of Extraction Ontologies Generality: assumptions about web pages – Data rich – Narrow domain – Document types Single-record documents (hard, but doable) Multiple-record documents (harder) Records with scattered components (even harder) Resiliency: declarative – Still works when web pages change – Works for new, unseen pages in the same domain – Scalable, but takes work to declare the extraction ontology

Semantic Annotation

Free-Form Query Interpretation Parse Free-Form Query (with respect to data extraction ontology) Select Ontology Formulate Query Expression Run Query Over Semantically Annotated Data

Parse Free-Form Query “Find me the and of all s – I want a ”pricemileageredNissan1996or newer >= Operator

Select Ontology “Find me the price and mileage of all red Nissans – I want a 1996 or newer”

Conjunctive queries and aggregate queries Projection on mentioned object sets Selection via values and operator keywords – Color = “red” – Make = “Nissan” – Year >= 1996 >= Operator Formulate Query Expression

For Let Where Return Formulate Query Expression

Run Query Over Semantically Annotated Data

How do we create extraction ontologies? – Manual creation requires several dozen person hours – Semi-automatic creation TISP (Table Interpretation by Sibling Pages) TANGO (Table ANalysis for Generating Ontologies) Nested Schemas with Regular Expressions Synergistic Bootstrapping Form-based Information Harvesting How do we scale up? – Practicalities of technology transfer and usage – Millions of queries over zillions of facts for thousands of ontologies Great! But Problems Still Need Resolution

Manual Creation

-Library of instance recognizers -Library of lexicons

Automatic Annotation with TISP (Table Interpretation with Sibling Pages) Recognize tables (discard non-tables) Locate table labels Locate table values Find label/value associations

Recognize Tables Data Table Layout Tables (discard) Nested Data Tables

Locate Table Labels Examples: Identification.Gene model(s).Protein Identification.Gene model(s).2

Locate Table Labels Examples: Identification.Gene model(s).Gene Model Identification.Gene model(s)

Locate Table Values Value

Find Label/Value Associations Example: (Identification.Gene model(s).Protein, Identification.Gene model(s).2) = WP:CE

Interpretation Technique: Sibling Page Comparison

Same

Interpretation Technique: Sibling Page Comparison Almost Same

Interpretation Technique: Sibling Page Comparison Different Same

Technique Details Unnest tables Match tables in sibling pages – “Perfect” match (table for layout  discard ) – “Reasonable” match (sibling table) Determine & use table-structure pattern – Discover pattern – Pattern usage – Dynamic pattern adjustment

Generated RDF

WoK Demo (via TISP)

Semi-Automatic Annotation with TANGO (Table Analysis for Generating Ontologies) Recognize and normalize table information Construct mini-ontologies from tables Discover inter-ontology mappings Merge mini-ontologies into a growing ontology

Recognize Table Information Religion Population Albanian Roman Shi’a Sunni Country (July 2001 est.) Orthodox Muslim Catholic Muslim Muslim other Afganistan 26,813,057 15% 84% 1% Albania 3,510,484 20% 70% 10%

Construct Mini-Ontology Religion Population Albanian Roman Shi’a Sunni Country (July 2001 est.) Orthodox Muslim Catholic Muslim Muslim other Afganistan 26,813,057 15% 84% 1% Albania 3,510,484 20% 70% 10%

Discover Mappings

Merge

Build a page-layout, pattern-based annotator Automate layout recognition based on examples Auto-generate examples with extraction ontologies Synergistically run pattern-based annotator & extraction-ontology annotator Semi-Automatic Annotation via Synergistic Bootstrapping (Based on Nested Schemas with Regular Expressions)

Synergistic Execution Extraction Ontology Document Conceptual Annotator (ontology-based annotation) Partially Annotated Document Structural Annotator (layout-driven annotation) Annotated Document Layout Patterns Pattern Generation

Form-Based Information Harvesting Forms – General familiarity – Reasonable conceptual framework – Appropriate correspondence Transformable to ontological descriptions Capable of accepting source data Instance recognizers – Some pre-existing instance recognizers – Lexicons Automated extraction ontology creation?

Form Creation Basic form-construction facilities: single-entry field multiple-entry field nested form …

Created Sample Form

Generated Ontology View

Source-to-Form Mapping

Almost Ready to Harvest Need reading path: DOM-tree structure Need to resolve mapping problems – Split/Merge – Union/Selection

Almost Ready to Harvest … Need reading path: DOM-tree structure Need to resolve mapping problems – Split/Merge – Union/Selection Voltage-dependent anion-selective channel protein 3 VDAC-3 hVDAC3 Outer mitochondrial membrane Protein porin 3 Name

Almost Ready to Harvest … Need reading path: DOM-tree structure Need to resolve mapping problems – Split/Merge – Union/Selection Voltage-dependent anion-selective channel protein 3 VDAC-3 hVDAC3 Outer mitochondrial membrane Protein porin 3 Name

Almost Ready to Harvest … Need reading path: DOM-tree structure Need to resolve mapping problems – Split/Merge – Union/Selection Name T-complex protein 1 subunit theta TCP-1-theta CCT-theta Renal carcinoma antigen NY-REN-15

Almost Ready to Harvest … Need reading path: DOM-tree structure Need to resolve mapping problems – Split/Merge – Union/Selection Name T-complex protein 1 subunit theta TCP-1-theta CCT-theta Renal carcinoma antigen NY-REN-15

Can Now Harvest Name

Can Now Harvest Name protein epsilon Mitochondrial import stimulation factor Lsubunit Protein kinase C inhibitor protein-1 KCIP E

Can Now Harvest Name Voltage-dependent anion-selective channel protein 3 VDAC-3 hVDAC3 Outer mitochondrial membrane Protein porin 3

Can Now Harvest Name Tryptophanyl-tRNA synthetase, mitochondrial precursor EC Tryptophan—tRNA ligase TrpRS (Mt)TrpRS

Harvesting Populates Ontology

Also helps adjust ontology constraints

Can Harvest from Additional Sites Name T-complex protein 1 subunit theta TCP-1-theta CCT-theta Renal carcinoma antigen NY-REN-15

Automating Extraction Ontology Creation Lexicons Name protein epsilon Mitochondrial import stimulation factor Lsubunit Protein kinase C inhibitor protein-1 KCIP E Name T-complex protein 1 subunit theta TCP-1-theta CCT-theta Renal carcinoma antigen NY-REN-15 Name Tryptophanyl-tRNA synthetase, mitochondrial precursor EC Tryptophan—tRNA ligase TrpRS (Mt)TrpRS … protein epsilon Mitochondrial import stimulation factor Lsubunit Protein kinase C inhibitor protein-1 KCIP E … T-complex protein 1 subunit theta TCP-1-theta CCT-theta Renal carcinoma antigen NY-REN-15 … Tryptophanyl-tRNA synthetase, mitochondrial precursor EC Tryptophan—tRNA ligase TrpRS (Mt)TrpRS …

Automating Extraction Ontology Creation Instance Recognizers Number Patterns Context Keywords and Phrases

Automatic Source-to-Form Mapping

Automatic Semantic Annotation Recognize and annotate with respect to an ontology

Ontology Transformations Transformations to and from all

Advanced free-form queries with disjunction and negation Form-based query language Table-based query languages Graphical query languages Practicalities: WoK Query Interfaces (Future Work)

Won’t just happen without sufficient content Niche applications – Historical Data (e.g. Genealogy) – Topical Blogs Local WoKs – Intra-organizational effort – Individual interests Practicalities: Bootstrapping the WoK (Future Work)

Potential Rapid growth – Thousands of ontologies – Millions of simultaneous queries – Billions of annotated pages – Trillions of facts Search-engine-like caching & query processing Practicalities: Scalability (Future Work)

Automatic (or near automatic) creation of extraction ontologies Automatic (or near automatic) annotation of web pages Simple but accurate query specification without specialized training Key to Success: Simplicity via Automation