Visualization Methods for the Ontology Development

Natural Language Processing and Computational Linguistics Research Group Tak-eun Kim CGV Lab Workshop (2007. 12. 20)

Ontology Development Natural Language Processing Visualization Logic

Term Finding

Word order variation

Concept Mapping

Relation Extraction

Event Extraction

…

Detection

Static/Dynamic Patterns

User Interface

Fast Development of Ontology

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Validation

Reasoning(Inference)

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Natural Language Processing Visualization Logic

Ontology Vis in the Process of Ontology Development Temporal Distribution of Terminologies Evolutionary Aspect of Ontologies Future Work & Conclusion

In philosophy

Ontology is the study of being or existence (from wikipedia)

In information science and artificial intelligence

The study of the categories of things that exist or may exist in some domain

In Information Science

Document Classification

Keyword Inference (search engine)

In Biology or Bioinformatics

Gene/Protein Classification

Named Entity Grounding

Drug Discovery

Information Classification & Knowledge Inference !!

Computer Company Motor Airplane part-of Apple Microsoft Dell Concepts (or class) represent a conceptualization Relations represent a relationship between concepts Instances represent a specific individual express a necessary fact holding between concepts and relationships e.g., If X is mortal then X will die one day Axioms

Determine the domain and scope of the ontology

Consider reusing existing ontologies

Enumerate important terms in the ontology

Define the classes and the class hierarchy

Define the properties of classes – slot

e.g., wine’s color, body, flavor, sugar contents, location of winery

Define the facets of the slots

slot cardinality, slot-value type (string, number, boolean, …)

Create instances

Natalya F. Noy et al., “ Ontology Development 101: A Guide To Creating Your First Ontology ”, Stanford Knowledge Systems Laboratory, 2001.

Reasoning

Maintaining

Automatic Extension

Alignment & Merging

Ontology Reuse

Term Finding

Collaborative Construction

…

Complexity of an Ontology

Number of GO terms Number of GO terms

Redundancy

Hierarchy

Patterns

e.g., Temporal Pattern

Date Frequency Date Frequency 2002. 5 2 2004. 10 4 2002. 7 1 2004. 11 7 2003.6 5 2006. 3 2003. 7 2

Jambalaya

DAG-Edit Protégé OntoEdit

Focus on “ PATTERN ”

Temporal Distribution of Terminologies

Research Patterns

Evolutionary Aspect of Ontologies

Changing Patterns of Concepts

“ Visualizing the Temporal Distribution of Terminologies for Biological Ontology Development”

Visualization and Data Analysis (VDA) 2008

Tak-eun Kim, Hodong Lee, Jinah Park and Jong C. Park

Problems in building biological ontologies

Biology is rapidly evolving field of science

new concepts are added, old concepts are removed, old concepts are changed into new concepts

Biological ontology developer should be skillful in keeping track of trend

Human can’t catch the speed of change

Number of biological literatures registered in PubMed over ten million

Human can’t deal with a massive number of literatures

Term Finding Temporal Pattern Search Interface Number of GO terms

Step 1

Step 2

Step 3 Proteins Evidence Abstracts

Step 4

Ontology Reuse

Use Gene Ontology’s concept & hierarchical information

Mapping each sentence in article to Gene Ontology / UMLS concept.

The identification of mutations in ABCA1 in patients with Tangier disease and familial HDL deficiency demonstrated that inadequate transport of phospholipid and cholesterol to the extracellular space results in the hypercatabolism of lipid-poor nascent HDL particles. [PMID:11714841]

tangier disease [CUI:C0039292]

familiar HDL deficiency [CUI:C1704429]

phospholipid transport [ GO:0015914]

cholesterol transport [GO:0030301]

extracellular transport [GO:0006858]

hypercatabolism [ CUI:C1704207]

More than 9,000 MEDLINE journal abstracts (which are E3 related)

Some scenarios

Evaluation Method?

Term Finding?

Visualization Technique?

To make a biological ontology building tool that can easily track temporal patterns of terminologies in literature, so that it can save a person much trouble in the biological ontology building process.

To use visualization as a core module in the process of ontology development

“ Monitoring the Evolutionary Aspect of the Gene Ontology to Enhance Predictability and Usability”

The 2nd International Symposium on Languages in Biology and Medicine (LBM 2007)

BMC Bioinformatics Special Issues for LBM 2007

Jong C. Park, Tak-eun Kim and Jinah Park

Inherently Static! DAG-Edit AmiGO Protégé The need for an intuitive method to consult the timeline of changes to Gene Ontology

To present a method for tapping into an evolutionary aspect of Gene Ontology

By keeping track of temporal changes to any of the nodes and relations of GO

By consequently making it possible to anticipate and overcome such changes

GO term that is newly added to GO t2 (the more recent version) GO term that appears in GO t1 (the older version) but that does not appear in GO t2 (the more recent version) GO term that has different concept name but use the same GO identifier in the two versions of GO GO term that undergoes no changes in both concept name and GO identifier between the two versions of GO Added Node Removed Node Modified Node Static Node

DIFF Upward Graph Construction Diff Merging Colour Coding Modified Added Removed GO t1 GO t2 DIFF ∙∙∙ ∙∙∙ ROOT ROOT ROOT

PROCEDURE: UPWARD_GRAPH_CONSTRUCT(GO t1 , GO t2 ) - INPUT: GO t1 is GO version 1, GO t2 is GO version 2 - OUTPUT: colour-coded merged graph - CONSTRAINT: GO t1 temporally precedes GO t2 1 M, R, A = DIFF(GO t1 , GO t2 ) 2 upward_subgraphs ← NULL 3 for each GO_ID ∈ M ∪ A ∪ R 4 queue ← push GO_ID 5 edge ← NULL 6 while queue is not empty 7 current ← pop element in queue 8 if current ∈ M ∪ R 9 isa_parents ← { ‘isa’ parent GO_IDs in GO t1 } 10 partof_parents ← { ‘part-of’ parent GO_IDs in GO t1 } 11 else if current ∈ M ∪ A 12 isa_parents ← { ‘isa’ parent GO_IDs in GO t2 } 13 partof_parents ← { ‘part-of’ parent GO_IDs in GO t2 } 14 for each pGO_ID in isa_parents 15 queue ← push pGO_ID 16 edge ← edge ∪ (pGO_ID, current, ‘isa’) 17 for each pGO_ID in part of_parents 18 queue ← push pGO_ID 19 edge ← edge ∪ (pGO_ID, current, ‘partof’) 20 upward_subgraphs ← upward_subgraphs ∪ edge 21 G ← MERGE_SUBGRAPHS(upward_subgraphs) 22 return COLOUR_CODING(G, M, R, A)

DIFF DIFF Colour Coding DIFF Generating Sub-graphs Merging Modified Added Removed Initial Node Set Initial Node GO t1 GO t2 Initial Node Initial Node Initial Node

PROCEDURE: DOWNWARD_GRAPH_CONSTRUCT(GO t1 , GO t2 , INITIAL_GO_ID)

- INPUT: GO t1 , GO t2

OUTPUT: colour-coded merged graph

- CONSTRAINT: GO t1 temporally precedes GO t2

1 M, R, A = DIFF(GO t1 , GO t2 )

2 downward_subgraphs ← NULL

3 queue ← push INITIAL_GO_ID

4 for each GO_ID ∈ M ∪ A ∪ R

5 queue ← push GO_ID

6 edge ← NULL

7 while queue is not empty

8 current ← pop element in queue

9 if current ∈ M ∪ R

10 isa_children ← { ‘isa’ children GO_IDs in GO t1 }

11 partof_children ← { ‘part-of’ children GO_IDs in GO t1 }

12 else if current ∈ M ∪ A

13 isa_children ← { ‘isa’ children GO_IDs in GO t2 }

14 partof_children ← { ‘part-of’ children GO_IDs in GO t2 }

15 for each cGO_ID in isa_children

16 queue ← push cGO_ID

17 edge ← edge ∪ (cGO_ID, current, ‘isa’)

18 for each cGO_ID in partof_children

19 queue ← push cGO_ID

20 edge ← edge ∪ (cGO_ID, current, ‘partof’)

21 downward_subgraphs ← downward_subgraphs ∪ edge

22 G ← MERGE_SUBGRAPHS(downward_subgraphs)

23 return COLOUR_CODING(G, M, R, A)

Two possibilities for the reason that the node GO:0015196 is modified

When a blue node has a pink node as its parent

L-tryptophan transmembrane transporter activity Low-affinity tryptophan transmembrane transporter activity L-tryptophan transporter activity L-tryptophan permease activity Low-affinity tryptophan permease activity High-affinity tryptophan transporter activity Hypothesis #1

When some adjacent nodes are removed or modified

L-tryptophan transporter activity L-tryptophan permease activity Low-affinity tryptophan permease activity High-affinity tryptophan transporter activity L-tryptophan transmembrane transporter activity L-tryptophan permease activity Low-affinity tryptophan permease activity Hypothesis #1 Low-affinity tryptophan transmembrane transporter activity High-affinity tryptophan transmembrane transporter activity

When a blue node has a pink node as its parent

When some adjacent nodes are removed or modified

Hypothesis #1 In this case, it is likely that the changed content of the GO term is due to the blue node, not due to the red node

When a red node and a blue node share the same parent and the same child

Gap-junction forming channel activity Alpha-type channel activity Channel or pore class transporter activity Gap-junction channel activity Alpha-type channel activity Channel activity replace Hypothesis #2 Wide pore channel activity It is likely that the red node is replaced with the blue node

When a red node and a blue node share the same parent and the same child

replace Alpha-type channel activity Wide pore channel activity Hypothesis #2

When the parent node has a big fan-out

Similar number of red children nodes and blue children nodes

glucose permease activity galactosamine porter activity galactitol permease activity Protein-N(PI)-phosphohistidine-sugar phosphotransferase activity glucose permease activity galactosamine porter activity galactitol permease activity ~ Hypothesis #3 protein-N(PI)-phosphohistidine-glucose phosphotransferase system transporter activity protein-N(PI)-phosphohistidine-galactosamine phosphotransferase system transporter activity protein-N(PI)-phosphohistidine-galactitol phosphotransferase system transmembrane transporter activity It is likely that each red node has been replaced with a blue node

Hypothesis #3 OLD GO ID OLD CONCEPT NEW GO ID NEW CONCEPT GO:0015579 glucose permease activity GO:0022855 protein-N(PI)-phosphohistidine- glucose phosphotransferase system transporter activity GO:0019195 galactosamine porter activity GO:0022876 protein-N(PI)-phosphohistidine- galactosamine phosphotransferase system transporter activity GO:0015580 N-acetylglucosamine permease activity GO:0022880 protein-N(PI)-phosphohistidine- N-acetylglucosamine phosphotransferase system transporter activity GO:0015584 trehalose permease activity GO:0022879 protein-N(PI)-phosphohistidine- trehalose phosphotransferase system transporter activity GO:0015585 fructose permease activity GO:0022877 protein-N(PI)-phosphohistidine- fructose phosphotransferase system transporter activity GO:0019192 fructose porter activity GO:0019189 lactose permease activity GO:0022869 protein-N(PI)-phosphohistidine- lactose phosphotransferase system transporter activity GO:0019190 cellobiose permease activity GO:0022874 protein-N(PI)-phosphohistidine- cellobiose phosphotransferase system transporter activity GO:0015581 maltose porter activity GO:0022873 protein-N(PI)-phosphohistidine- maltose phosphotransferase system transporter activity GO:0015582 beta-glucoside permease activity GO:0022882 protein-N(PI)-phosphohistidine- beta-glucoside phosphotransferase system transporter activity GO:0015586 mannitol permease activity GO:0022872 protein-N(PI)-phosphohistidine- mannitol phosphotransferase system transmembrane transporter activity GO:0015587 sorbitol permease activity GO:0022856 protein-N(PI)-phosphohistidine- sorbitol phosphotransferase system transporter activity GO:0015588 galactitol permease activity GO:0022875 protein-N(PI)-phosphohistidine- galactitol phosphotransferase system transmembrane transporter activity GO:0022870 protein-N(PI)-phosphohistidine-mannose phosphotransferase system transporter activity

The Evolutionary behavior of the node GO:0031399 (regulation of protein modification) Before 2005.4.18 2005.4.18 – 2005.5.16 2005.11.20 – 2005.12.18 2007.2.18 – 2007.2.25 2007.5.27 – 2007.6.3

GO t1 : 2005. 4. 18 GO t2 : 2005. 5. 16 regulation of protein modification negative regulation of protein modification regulation of protein ubiquitination positive regulation of protein modification negative regulation of protein ubiquitination positive regulation of protein ubiquitination The level of detail for the terms do not appear overall quite adequate. negative positive Naming Convention

GO t1 : 2007. 5. 27 GO t2 : 2007. 6. 3 regulation of protein modification negative regulation of protein modification regulation of protein ubiquitination positive regulation of protein modification negative regulation of protein ubiquitination positive regulation of protein ubiquitination 11-beta-hydroxysteroid dehydrogenase (NAD+) activity positive regulation of protein sumoylation regulation of protein sumoylation negative regulation of protein amino acid glycosylation positive regulation of protein amino acid glycosylation regulation of protein amino acid glycosylation regulation of actin phosphorylation Positive & Negative Positive & Negative Positive & Negative? It does not follow the naming convention which involves the qualifies positive and negative. Naming Convention

The Evolutionary behavior of the node GO:0048622 (reproductive sporulation) Before 2005.6.19 2005.6.19 – 2005.7.17 2005.11.20 – 2005.12.18 2005.12.18 – 2006.7.23 2006.7.23 – 2007.1.23

A Large Fan-out It is the usual tendency to put all the related but unrefined nodes as the children nodes of a certain parent node until the classification method matures.

Restructuring of Child Nodes Restructuring the graph with additions and updates of the children nodes of the node GO:0030437

When the fan-out of a certain node is 1

GO t1 : 2006. 7. 23 GO t2 : 2007. 1. 23 1 Fan-out spore development (sensu Magnoliophyta) microsporogenesis megasporogenesis reproductive sporulation sporulation (sensu Fungi) spore wall assembly (sensu Fungi) prospore formation conidium formation prospore membrane formation prospore-specific spindle pole body modification microsporogenesis megasporogenesis spore development (sensu Magnoliophyta) The node would be merged into another node ? Another node is added to it as its child node

To make available a means for monitoring changes of GO over time, so that both developers and users of GO may understand the full impact of such changes on the larger scale

Ontology Reduction 1 Ontology-change Map 2 Ontology-change Animation 3

Number of Nodes & Edges (GO version: 20070916)

24,931 nodes

37,997 edges

DAG(Directed Acyclic Graph) structure

We simply cannot determine the level of concept

It is hard to recognize the difference of the level of detail between two concepts

Level is 1? or 2?

Focus on concepts which contain Positive/Negative qualifiers , and their hierarchical relationships

To reduce complexity of Gene Ontology

By removing unnecessary nodes and edges

To restore removed nodes and edges

Build an inference rules on Gene Ontology by using word combination rules (positive/negative + word pattern) and graph search algorithm

GO:0031399 regulation of protein modification GO:0031396 regulation of protein ubiquitination GO:0031397 negative regulation of protein ubiquitination GO:0031400 negative regulation of protein modification GO:0033233 regulation of protein sumoylation GO:0033234 negative regulation of protein sumoylation GO:0031398 positive regulation of protein ubiquitination GO:0033235 positive regulation of protein sumoylation GO:0031401 positive regulation of protein modification GO:0060051 negative regulation of protein amino acid glycosylation GO:0060050 positive regulation of protein amino acid glycosylation GO:0060049 regulation of protein amino acid glycosylation GO:0043538 regulation of actin phosphorylation 13 nodes 18 edges Case #1

GO:0031399 regulation of protein modification GO:0031396 regulation of protein ubiquitination GO:0031397 negative regulation of protein ubiquitination GO:0031400 negative regulation of protein modification GO:0033233 regulation of protein sumoylation GO:0033234 negative regulation of protein sumoylation GO:0031398 positive regulation of protein ubiquitination GO:0033235 positive regulation of protein sumoylation GO:0031401 positive regulation of protein modification GO:0060051 negative regulation of protein amino acid glycosylation GO:0060050 positive regulation of protein amino acid glycosylation GO:0060049 regulation of protein amino acid glycosylation GO:0043538 regulation of actin phosphorylation 11 nodes (-15%) 10 edges (-44%) Case #1

GO:0002911 regulation of lymphocyte anergy GO:0002912 negative regulation of lymphocyte anergy GO:0002667 regulation of T cell anergy GO:0002670 regulation of B cell anergy GO:0031401 positive regulation of lymphocyte anergy GO:0002668 negative regulation of T cell anergy GO:0002671 negative regulation of B cell anergy GO:0002914 regulation of central B cell anergy GO:0002669 positive regulation of T cell anergy GO:0002917 regulation of peripheral B cell anergy GO:0002672 positive regulation of B cell anergy GO:0002915 negative regulation of central B cell anergy GO:0002918 negative regulation of peripheral B cell anergy GO:0002916 positive regulation of central B cell anergy GO:0002919 positive regulation of peripheral B cell anergy 15 nodes 22 edges Case #2

GO:0002911 regulation of lymphocyte anergy GO:0002912 negative regulation of lymphocyte anergy GO:0002667 regulation of T cell anergy GO:0002670 regulation of B cell anergy GO:0031401 positive regulation of lymphocyte anergy GO:0002668 negative regulation of T cell anergy GO:0002671 negative regulation of B cell anergy GO:0002914 regulation of central B cell anergy GO:0002669 positive regulation of T cell anergy GO:0002917 regulation of peripheral B cell anergy GO:0002672 positive regulation of B cell anergy GO:0002915 negative regulation of central B cell anergy GO:0002918 negative regulation of peripheral B cell anergy GO:0002916 positive regulation of central B cell anergy GO:0002919 positive regulation of peripheral B cell anergy 11 nodes (-26%) 10 edges (-54%) Case #2

GO:0002805 regulation of antimicrobial peptide biosynthetic process GO:0002806 negative regulation of antimicrobial peptide biosynthetic process GO:0002807 positive regulation of antimicrobial peptide biosynthetic process GO:0002808 regulation of antibacterial peptide biosynthetic process GO:0002810 regulation of antifungal peptide biosynthetic process GO:0002809 negative regulation of antibacterial peptide biosynthetic process GO:0002813 regulation of biosynthetic process of antibacterial peptides active against Gram-negative bacteria GO:0002816 regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria GO:0006963 positive regulation of antibacterial peptide biosynthetic process GO:0002811 negative regulation of antifungal peptide biosynthetic process GO:0006967 positive regulation of antifungal peptide biosynthetic process GO:0002814 negative regulation of biosynthetic process of antibacterial peptides active against Gram-negative bacteria GO:0006964 positive regulation of biosynthetic process of antibacterial peptides active against Gram-negative bacteria GO:0002817 negative regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria GO:0006965 positive regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria 15 nodes 22 edges Case #3

GO:0002805 regulation of antimicrobial peptide biosynthetic process GO:0002806 negative regulation of antimicrobial peptide biosynthetic process GO:0002807 positive regulation of antimicrobial peptide biosynthetic process GO:0002808 regulation of antibacterial peptide biosynthetic process GO:0002810 regulation of antifungal peptide biosynthetic process GO:0002809 negative regulation of antibacterial peptide biosynthetic process GO:0002813 regulation of biosynthetic process of antibacterial peptides active against Gram-negative bacteria GO:0002816 regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria GO:0006963 positive regulation of antibacterial peptide biosynthetic process GO:0002811 negative regulation of antifungal peptide biosynthetic process GO:0006967 positive regulation of antifungal peptide biosynthetic process GO:0002814 negative regulation of biosynthetic process of antibacterial peptides active against Gram-negative bacteria GO:0006964 positive regulation of biosynthetic process of antibacterial peptides active against Gram-negative bacteria GO:0002817 negative regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria GO:0006965 positive regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria 11 nodes (-26%) 10 edges (-54%) Case #3

GO:0050854 regulation of antigen receptor-mediated signaling pathway GO:0050858 negative regulation of antigen receptor-mediated signaling pathway GO:0050857 positive regulation of antigen receptor-mediated signaling pathway GO:0050856 regulation of T cell receptor signaling pathway GO:0050861 positive regulation of B cell receptor signaling pathway GO:0050862 positive regulation of T cell receptor signaling pathway GO:0050860 negative regulation of T cell receptor signaling pathway GO:0050859 negative regulation of B cell receptor signaling pathway 8 nodes 9 edges Case #4

GO:0050854 regulation of antigen receptor-mediated signaling pathway GO:0050858 negative regulation of antigen receptor-mediated signaling pathway GO:0050857 positive regulation of antigen receptor-mediated signaling pathway GO:0050856 regulation of T cell receptor signaling pathway GO:0050861 positive regulation of B cell receptor signaling pathway GO:0050862 positive regulation of T cell receptor signaling pathway GO:0050860 negative regulation of T cell receptor signaling pathway GO:0050859 negative regulation of B cell receptor signaling pathway GO:??????? regulation of B cell receptor signaling pathway 7 nodes (12%) 6 edges (33%) Case #4

GO:0051709 regulation of killing of cells of another organism GO:0001899 negative regulation by symbiont of cytolysis of host cells GO:0051841 positive regulation by host of cytolysis of symbiont cells GO:0051710 regulation of cytolysis of cells of another organism GO:0051802 regulation of cytolysis of cells in other organism during symbiotic interaction GO:0051839 regulation by host of cytolysis of symbiont cells GO:0001898 regulation by symbiont of cytolysis of host cells GO:0001900 positive regulation by symbiont of cytolysis of host cells GO:0051804 positive regulation of cytolysis of cells in other organism during symbiotic interaction GO:0051714 positive regulation of cytolysis of cells of another organism GO:0051712 positive regulation of killing of cells of another organism GO:0051840 negative regulation by host of cytolysis of symbiont cells GO:0051803 negative regulation of cytolysis of cells in other organism during symbiotic interaction GO:0051713 negative regulation of cytolysis of cells of another organism GO:0051711 negative regulation of killing of cells of another organism Case #1

GO:0051709 regulation of killing of cells of another organism GO:0001899 negative regulation by symbiont of cytolysis of host cells GO:0051841 positive regulation by host of cytolysis of symbiont cells GO:0051710 regulation of cytolysis of cells of another organism GO:0051802 regulation of cytolysis of cells in other organism during symbiotic interaction GO:0051839 regulation by host of cytolysis of symbiont cells GO:0001898 regulation by symbiont of cytolysis of host cells GO:0001900 positive regulation by symbiont of cytolysis of host cells GO:0051804 positive regulation of cytolysis of cells in other organism during symbiotic interaction GO:0051714 positive regulation of cytolysis of cells of another organism GO:0051712 positive regulation of killing of cells of another organism GO:0051840 negative regulation by host of cytolysis of symbiont cells GO:0051803 negative regulation of cytolysis of cells in other organism during symbiotic interaction GO:0051713 negative regulation of cytolysis of cells of another organism GO:0051711 negative regulation of killing of cells of another organism GO:0051803 negative regulation of cytolysis of cells in other organism during symbiotic interaction GO:0051713 negative regulation of cytolysis of cells of another organism GO:0051711 negative regulation of killing of cells of another organism Case #2

GO:0008361 regulation of cell size GO:0051712 positive regulation of cell size GO:0045792 negative regulation of cell size GO:0016049 cell growth GO:0030308 negative regulation of cell growth GO:0030307 positive regulation of cell growth GO:0001558 regulation of cell growth GO:0001560 regulation of cell growth by extracellular stimulus Case #2

GO:0008361 regulation of cell size GO:0051712 positive regulation of cell size GO:0045792 negative regulation of cell size GO:0016049 cell growth GO:0030308 negative regulation of cell growth GO:0030307 positive regulation of cell growth GO:0001558 regulation of cell growth GO:0001560 regulation of cell growth by extracellular stimulus GO:??????? negative cell growth GO:??????? positive cell growth GO:??????? negative regulation of cell size GO:??????? positive regulation of cell size Positive/Negative qualifiers should not be combined with keyword “cell” GO Version: 20070916 Case #2 keyword frequency keyword Frequency regulation 957 chemotaxis 7 T cell 1 energy 7 thymic 1 gravitaxis 1 extrathymic 1 aerotaxis 7 gravitropism 1 phototaxis 1

Reduce the number of nodes and edges

In GO version 20070916, 984 concepts have positive/negative qualifiers in each concept name (3%)

Among 3%, 20% nodes & 50% edges are removed

Restore remove nodes and edges

By using inference rules and keyword combination rules

Future Work

Various antonyms (e.g., decrease/increase)

Ontology Reduction 1 Ontology-change Map 2 Ontology-change Animation 3

Before 2005.6.19 2005.6.19 – 2005.7.17 2005.11.20 – 2005.12.18 2005.12.18 – 2006.7.23 2006.7.23 – 2007.1.23

Evolutionary Aspect of ontologies Temporal Distribution of Terminologies Ontology-change Animation Ontology-change Map Ontology Reduction Semi-Automatic Ontology Development Visualization

Automatic Ontology Development Natural Language Processing Visualization Logic