1. Source Page Understanding for Heterogeneous Molecular Biological Data
Cui Tao
Supported by NSF 1

2. Introduction Online biological data:
Highly diverse in both granularity and variety
In various formats
Uses different terminologies, ID systems, units, …
To automatically understand heterogeneous source pages is a challenge
Extraction ontology based source page understanding
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3. Extraction Ontology (Partial)
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4. Extraction Ontology (Partial)
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5. Extraction Ontology (Partial)
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6. Extraction Ontology (Partial)
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7. Extraction Ontology (Partial)
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8. Extraction Ontology Construction
Knowledge sources
Gene Ontology
Thousands of terms
All Species Toolkit
Total of 1,231,935 names
Protein databases
Thousands of protein names
Regular expressions, keywords
(Molecular Function, Biological Process,
Cellular Component)
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9. Source Page Understanding
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12. Source Page Understanding
Three steps:
Recognize attributes and values
Find attribute-value pairs
Map attribute-value pairs to target concepts
Two techniques:
Sibling page comparison
Seed ontology recognition
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13. Sibling Page Comparison
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14. Sibling Page Comparison
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15. Sibling Page Comparison
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16. Sibling Page Comparison
Attribute
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17. Sibling Page Comparison
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18. Sibling Page Comparison
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19. Seed Ontology Recognition
What is a seed ontology?
Why do we use a seed ontology?
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20. 2/23/2019 9 Homo sapiens; human; zinc ion binding;
nucleus;
zinc ion binding;
nucleic acid binding;
linear;
NP_079345;
9606;
Eukaryota; Metazoa;
Chorata;
Craniata;
Vertebrata;
Euteleostomi;
Mammalia;
Eutheria;
Primates;
Catarrhini;
Hominidae;
Homo;
Homo sapiens;
human;
GTTTTTGTGTT……….ATAAGTGCATTAACGGCCCACATG;
FLJ14299
msdspagsnprtpessgsgsgg………tagpyyspyalygqrlasasalgyq;
hypothetical protein FLJ14299; 8;
eight;
“8:?p\s?12”;
“8:?p11.2”;
“8:?p11.23”; :
“37,?612,?680”;
“37,?610,?585”;
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21. Seed Ontology Recognition
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22. 2/23/2019 11 Homo sapiens; human; nucleus; zinc ion binding;
nucleic acid binding;
9606;
Eukaryota; Metazoa;
Chorata;
Craniata;
Vertebrata;
Euteleostomi;
Mammalia;
Eutheria;
Primates;
Catarrhini;
Hominidae;
Homo;
zinc ion binding;
nucleic acid binding;
NP_079345;
nucleus;
linear;
NP_079345;
FLJ14299
GTTTTTGTGTT……….ATAAGTGCATTAACGGCCCACATG;
msdspagsnprtpessgsgsgg………tagpyyspyalygqrlasasalgyq; 8;
eight;
“8:?p\s?12”;
“8:?p11.2”;
“8:?p11.23”; :
hypothetical protein FLJ14299;
“37,?612,?680”;
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“37,?610,?585”; 11

23. Evaluation “Training”: Test: Determine thresholds
Set up rules for recognizing attribute-value patterns
Determine rules of combining different pair-wise comparisons
Refine Seed Ontologies
Test:
Structure recognition:
Test on column/row level
Measure Precision/Recall values
Mapping recognition:
Test on Concept level
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24. Contribution
Will contribute to both information extraction technology and bioinformatics
Can understand both structures and semantics of source pages in the molecular biology domain automatically
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