Mining the Web: Discovering New Biomedical KnowledgeAly Khan

The Human Genome ProjectGoal: Sequence the human DNACompleted in 2003Joint effort between National Institutes of Health and Celera Genomics.~25,000 genes

25,000 GenesWhat do they do?How do they interact?

Finding contextUse vast amounts of published works to find novel relationships between genes

17,000,000 records from more than 5,000 biomedical journals

On searchingBiomedical literature unboundedUnstructured text in biomedical publications

Example record

XML record

ApplicationsNLPParse text for matches using POS tags:[Query noun phrase term] is a [noun phrase class]hiv is a virus[Noun phrase class] is a [Query noun phrase term]genes such as 4fgf

ApplicationsPath1: KaiC nsubj interacts obj SasAPath2: KaiC nsubj interacts obj SasA conj_and KaiAPath3: KaiC nsubj interacts obj - SasA conj_and KaiBPath4: SasA conj_and KaiAPath5: SasA conj_and KaiBPath6: KaiA - prep_with - SasA conj_and KaiBThe results demonstrated that KaiC interacts rhythmically with KaiA, KaiB, and SasA.Ozgur et al.

Contextual representationPTEN is transcriptionally regulated by transcription factors such as p53 and Egr-1.In response to DNA damage, the cell-cycle checkpoint kinase CHEK2 can be activated by ATM kinase to phosphorylate p53 and BRCA1, which are involved in cell-cycle control and apoptosis.

GoalsCreating a global ontology for genes, diseases, etc. Automated discovery of relationships.