Transcript Gene Regulation, Cancer, Rules

FP7 meeting - Gent - Carlos Rodríguez - April 18
WP4: Conceptual Mining from Text
for Knowledge Engineering
State of the Art
WP Coordinators:
Alfonso Valencia
Carlos Rodriguez
FP7 meeting - Gent - Carlos Rodríguez - April 18
Why Concept/Semantic Mining?
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Knowledge Acquisition Bottleneck
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Top-Down, manually-designed Ontologies are:
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sparse (non-exhaustive)
shallow (not fine-grained)
not mappable (to terms or other ontologies)
not easily updated or customized
Text-based ontologies reflect better diversity
in knowledge as reflected by the literature
and domain terminology
FP7 meeting - Gent - Carlos Rodríguez - April 18
Information for Ontology Learning
FP7 meeting - Gent - Carlos Rodríguez - April 18
State of the Art Methods
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implicit relations
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explicit relations
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Corpus Distribuition
Machine Learning Algorithms
Symbolic (rule and syntax-based)
Hybrid, combining some or all
Bootstrap the ontology-learning process
using existing resources
FP7 meeting - Gent - Carlos Rodríguez - April 18
An example
Meiosis
Cyclin
Checkpoint
Interphase
Nucleoplasma
Division
Histone
Replication
Chromatid
Blaschke, et al., Funct. Integ. Genomics 2001
Cell
cycle
17 genes
PCNA
CDC2
MSH2
LBR
TOP2A
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GO codes
DNA replication
DNA metabolism
Cell Cycle control
PCNA-MSH2
The binding of PCNA to MSH2 may
reflect linkage between mismatch repair
and replication.
LBR-CDC2
LBR undergoes mitotic phosphorylation
mediated by p34(cdc2) protein kinase.
24 genes
ABCA5
CAT
ELF2
PIM1
WNT2
...
Words
Unknown
Dipeptidyl
Prolyl
nmr
Collagen-binding
FP7 meeting - Gent - Carlos Rodríguez - April 18
Induce rules at different linguistic levels
FP7 meeting - Gent - Carlos Rodríguez - April 18
Lexical- and syntax-derived relationships from text
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Complex relationships in CCO
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degradates
participate_in
catalyses
adjacent_to
agent_in
What new ones can be learnt?
LBR undergoes mitotic phosphorylation
mediated by p34(cdc2) protein kinase.
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mitotic phosphorylation mediated_by protein kinase
Can it be subsumed by others?
Are there other subcategories?
FP7 meeting - Gent - Carlos Rodríguez - April 18
Beyond the State of the Art
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Optimal hybrid methodology for:
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Extracting entities
Discovering relations
Providing ontology-relevant information
(But what and how ?)
Comparing top-down with bottom-up ontologies
Providing definitional information
Application to CC-cancer domains
(and possibly to gene regulation)
FP7 meeting - Gent - Carlos Rodríguez - April 18
In the context of project and other WPs…
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Reasoning with text-generated ontologies:
competing or complementing?
Reduction of lexical and semantic relationships to
ontological relation inventory
How to present and use Text-Mined information for
ontology design (especially for database
annotation)?
How to curate, evaluate and compare ontologies?
FP7 meeting - Gent - Carlos Rodríguez - April 18
Information for Ontology Engineers
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New Classes (ontology) and Instances (KB)
Definitions and glosses
Concept usage and entity examples
Terms and synonyms
Hierarchical and non-hierarchical relations
Possible reasoning rules
FP7 meeting - Gent - Carlos Rodríguez - April 18
To and Fro other WPs
WP
To
from
1: CCO extension
New entities, terms,
definitions and relations
Seeds for learning and
ontology curation
2.- Ontology Engineering
Integration of text-mining
into ontology design
methods
Ontology evaluation
3.- Corpus Processing and Curation
Subcorpus and term
inventories
Annotated corpus
5.- Knowledge Base Population
New entities, terms
definitions and relations
Ontology evaluation and
curation
6.- Reasoning
New relations and
inference rules from text
Evaluation of mappings
and reasoning