Semantic Predications for Complex Information Needs in Biomedical Literature Delroy Cameron, Ramakanth Kavuluru, Pablo N. Mendes Amit P. Sheth, Krishnaprasad Thirunarayan Ohio Center for Excellence in Knowledge-enabled Computing kno.e.sis Center, Wright State University Dayton, OH 45435, USA Olivier Bodenreider National Library of Medicine Bethesda, MD 20894, USA 48 th ACM Southeast Conference. ACMSE 2010. Oxford, Mississippi. April 15-17, 2010. 2011 International Conference on Bioinformatics and Biomedicine (BIBM) 12-15 November, 2011 Atlanta, Georgia
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Semantic Predications for Complex Information Needs in Biomedical Literature
Delroy Cameron, Ramakanth Kavuluru, Pablo N. MendesAmit P. Sheth, Krishnaprasad Thirunarayan
Ohio Center for Excellence in Knowledge-enabled Computing kno.e.sis Center, Wright State University
Dayton, OH 45435, USA
Olivier BodenreiderNational Library of Medicine Bethesda, MD 20894, USA
“How do mutations in the Presenilin-1 (PS1) gene affect Alzheimer’s disease (AD)?”
. . . mutations in PS1 lead to Alzheimer’s disease by increasing the extracellular levels of [amyloid peptide 42] A42. (Source: PMID10652366)
. . . familial early onset Alzheimer’s disease is caused by point mutations in the amyloid precursor protein gene on chromosome 21, in the presenilin 2(PS2)1 gene on chromosome 1, or, most frequently, in the presenilin 1(PS1) gene on chromosome14. . . (Source:PMID9013610)chromosome14 finding_site_of presenilin1
PS1 associated_with Alzheimer’s Disease
Semantic Predications
COMPLEX INFO NEEDS
Literature-Based Discovery (LBD)Don R. Swanson’s Hypotheses
o Raynaud’s Syndrome-Dietary Fish Oilo Magnesium-Migraine
Absence of predications in text Predication extraction methods (SemRep) Absence of direct connections among text item Ambiguity in written language Abstractions may lead to information overflow Quality of background knowledge
“How do mutations in the Pes gene affect cell growth?”
G1_phase G2_phase
DNA Replication
• Novel Knowledge-driven framework • Semantic Predications to link scientific content• Alternative to Query reformulation• Background knowledge boost recall
• Effective at Coarse granularity• Poor at fine granularity
Human Performance & Cognition Ontology Project @knoesis
Cartic Ramakrishnan Michael Cooney Gary Alan Smith Paul Fultz II Jeffrey Ali Hyacinthe Thomas C. Rindflesch Mohamed Cyclegar Dongwook Shin John Nguyen May Cheh
21
QUESTIONS
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Topic ID Question
160 What is the role of PrnP in mad cow disease?
161 What is the role of IDE in Alzheimer's disease
163 What is the role of APC (adenomatous polyposis coli) in colon cancer?
165 How do Cathepsin D (CTSD) and apolipoprotein E (ApoE) interactions contribute to Alzheimer's disease?
167 How does nucleoside diphosphate kinase (NM23) contribute to tumor progression?
168 How does BARD1 regulate BRCA1 activity?
169 How does APC (adenomatous polyposis coli) protein affect actin assembly
170 How does COP2 contribute to CFTR export from the endoplasmic reticulum?
172 How does p53 affect apoptosis?
173 How do alpha7 nicotinic receptor subunits affect ethanol metabolism?
174 How does BRCA1 ubiquitinating activity contribute to cancer?
176 How does Sec61-mediated CFTR degradation contribute to cystic fibrosis?
177 How do Bop-Pes interactions affect cell growth?
178 How do interactions between insulin-like GFs and the insulin receptor affect skin biology?
179 How do interactions between HNF4 and COUP-TF1 suppress liver function?
180 How do Ret-GDNF interactions affect liver development?
184 How do mutations in the Pes gene affect cell growth?
185 How do mutations in the hypocretin receptor 2 gene affect narcolepsy?
186 How do mutations in the Presenilin-1 gene affect Alzheimer's disease?