Obvio
Obvio (spanish for obvious) is the name of the project on the use of structured knowledge representation for Literature-Based Discovery (LBD) using Biomedical Literature. The goal of Obvio is to uncover hidden connections between concepts in biomedical texts, to facilitate hypothesis generation from publicly available scientific literature.
Contents
Overview
Obvio is driven by assertions extracted from structured text (called semantic predications) as well as assertions obtained from structured knowledge sources (such as the UMLS). The fundamental notion is that LBD could be greatly facilitated by the Semantic Integration of assertions extracted from scientific literature and well curated background knowledge from heterogeneous data sources.
People
Graduate Students: Delroy Cameron, Swapnil Soni, Nishita Jaykumar, Vishnu Bompally
External Collaborators: Olivier Bodenreider, Thomas C. Rindflesch, Ramakanth Kavuluru
Faculty: Krishnaprasad Thirunarayan, Amit P. Sheth (Advisor)
Past Members: Pablo N. Mendes, Tu Danh, Sreeram Vallabhaneni, Hima Yalamanchili, Drashti Dave
Applications
Reachability
We applied semantic predications to biomedical QA using data from the 2006 TREC Challenge using the notion of reachability to determine whether documents that answer complex biomedical questions could be connected through semantic predications, together with background knowledge<ref>D. Cameron, R. Kavuluru, O. Bodenreider, P. N. Mendes, A. P. Sheth, K. Thirunarayan, Semantic Predications for Complex Information Needs in Biomedical Literature, 5th International Conference on Bioinformatics and Biomedicine BIBM2011, Atlanta GA, November 12-15, 2011 (acceptance rate=19.4%)</ref>. The QA tasks put forth by the Text REtrieval Conferences (TREC) offer an opportunity to determine whether semantic predications and background knowledge can produce relevant information for complex biomedical questions and information needs. Below is our presentation from BIBM 2011 on our findings for the application of semantic predications and background knowledge to QA.
Rediscovery
A second application of semantic predications is to the field of Literature-based Discovery (LBD). LBD refers to uncovering conclusions that have never been made explicit before, but are implicit in publicly available literature. Semantic predications have been demonstrated to be important constructs in facilitating LBD by providing context among associated concepts.
RS-DFO Hypothesis
Much of the early research aimed at rediscovering Swanson's Hypotheses focused almost entirely on Information Retrieval (IR) techniques, such as term and concept co-occurrence. Only recently has significant attention been devoted to semantics-based techniques that exploit the meaning of associations between concepts. While generally more intuitive, the feasibility of such semantics-based approaches has not been fully established. It is reasonable to expect that if semantics-based techniques are adequate for discovering new knowledge, they ought to be sufficient for recovering existing knowledge.
In this work<ref>D. Cameron, O. Bodenreider, H. Yalamanchili, T. Danh, S. Vallabhaneni, K. Thirunarayan, A. P. Sheth, T. C. Rindflesch, A Graph-Based Recovery and Decomposition of Swanson’s Hypothesis using Semantic Predications, Journal of Biomedical Informatics 46(2) 238-251, (2013). ScienceDirect, PMID </ref> we investigate the applicability of semantics-based techniques for recovering and decomposing Swanson's Raynaud Syndrome--Fish Oil hypothesis using semantic predications, background knowledge and graph-based algorithms for path extraction and subgraph creation. Below is a presentation, and various datasets and experimental results for download and consumption based on our investigation.
Datasets and Experimental Results
- Dataset
- Baseline (B1)
- Original PDFs of the 65 articles cited by Swanson's RS-DFO paper (30.5MB)
- ASCII text with end-of-line text wrapping fixed
- Text in Medline format for parsing by SemRep
- SemRep Relations Output
- SemRep Relations Output (vascular reactivity)
- SemRep Extracted Predications
- Manually Identified Predications (vascular reactivity)
- Baseline (B2)
- Baseline (B1)
- Experimental Results
Automatic Subgraph Creation
In an evaluation of the context-driven subgraph model for LBD, 8 out of 9 existing discoveries were rediscovered using this approach. A manuscript detailing the approach is under preparation <ref>D. Cameron, R. Kavuluru, T. C. Rindflesch, A. P. Sheth, K. Thirunarayan, O. Bodenreider Context-Driven Automatic Subgraph Creation for Literature-Based Discovery (under preparation)</ref> The results of each scenario is detailed in the following table.
Scenario 1 | Intermediate | Association | Status | ||||
---|---|---|---|---|---|---|---|
Source | Target | Cut-off Date | Researcher | ||||
Dietary Fish Oils | Raynaud Syndrome | November 1985 | Don R. Swanson (PubMed) | Blood Viscosity | Dietary Fish Oils INHIBITS Blood Viscosity | Blood Viscosity CAUSES Raynaud Syndrome | zero rarity singleton |
Platelet Aggregation | Dietary Fish Oils INHIBITS Platelet Aggregation | Platelet Aggregation CAUSES Raynaud Syndrome | subgraph1 | ||||
Vascular Reactivity (Vasoconstriction) | Dietary Fish Oils INHIBITS Vasoconstriction | Vasoconstriction CAUSES Raynaud Syndrome |
Scenario 2 | Intermediate | Association | Status | ||||
---|---|---|---|---|---|---|---|
Source | Target | Cut-off Date | Researcher | ||||
Magnesium | Migraine | April 1987 | Don R. Swanson | ||||
Calcium Channel Blockers | Magnesium ISA Calcium Channel Blocker | Calcium Channel Blockers TREATS Migraine | subgraph22 | ||||
Epilepsy | subgraph9 | ||||||
Hypoxia | |||||||
Inflammation | zero rarity | ||||||
Platelet Activity | Magnesium INHIBITS Platelet Aggregation | Platelet Aggregation CAUSES Migraine | subgraph1 | ||||
Prostaglandins | Magnesium STIMULATES Prostaglandins | Prostaglandins DISRUPTS Migraine Disorders | subgraph4 | ||||
Type A Personality | |||||||
Serotonin | Magnesium INHIBITS Serotonin | Serotonin CAUSES Migraine | subgraph1 | ||||
Cortical Depression | |||||||
Substance P | |||||||
Vascular Mechanisms | Magnesium INHIBITS Vasoconstriction | Vasoconstriction CAUSES Migraine | subgraph9 |
Scenario 3 | Intermediate | Association | Status | ||||
---|---|---|---|---|---|---|---|
Source | Target | Cut-off Date | Researcher | ||||
Somatomedin C | Arginine | April 1989 | Don R. Swanson | Growth Hormone | Arginine STIMULATES Growth Hormone | Growth Hormone STIMULATES Somatomedins | subgraph1 |
Body Weight | Somatomedins (IGF1) STIMULATES Growth (body mass) | Arginine STIMULATES Growth (body mass) | subgraph1 | ||||
Somatomedins | Arginine TREATS Malnutrition | Arginine TREATS Malnutrition | |||||
Wound Healing | Somatomedin STIMULATES Wound Healing (NK activity) | Arginine STIMULATES Wound Healing (NK activity) |
Scenario 4 | Intermediate | Association | Status | ||||
---|---|---|---|---|---|---|---|
Source | Target | Cut-off Date | Researcher | ||||
Indomethacin | Alzheimer’s Disease | July 1995 | Neil R. Smalheiser/Don R. Swanson | Acetylcholine | Indomethacin INHIBITS Acetylcholine | Acetylcholine CAUSES Alzheimer's Disease | subgraph4 |
Lipid peroxidation | Indomethacin INHIBITS Lipid peroxidation | Lipid peroxidation CAUSES Alzheimer's Disease | subgraph2 | ||||
M2-muscarinic | Indomethacin INHIBITS M2-muscarinic | M2-muscarinic CAUSES Alzheimer's Disease | |||||
Membrane Fluidity | Indomethacin INHIBITS Membrane Fluidity | Membrane Fluidity CAUSES Alzheimer's Disease | |||||
Lymphocytes | Indomethacin STIMULATES natural killer T-Cell Activity | T-Cell Activity INHIBITS Alzheimer's Disease | subgraph14 | ||||
Thyrotropin | Indomethacin STIMULATES Thyrotropin | Thyrotropin AFFECTS Alzheimer's Disease | zero rarity | ||||
T-lymphocytes (T-Cells) | Indomethacin STIMULATES T-lymphocytes | T-lymphocytes Activity INHIBITS Alzheimer's Disease | subgraph3 | ||||
Signal Transduction | subgraph14 |
Scenario 5 | Intermediate | Association | Status | ||||
---|---|---|---|---|---|---|---|
Source | Target | Cut-off Date | Researcher | ||||
Estrogen | Alzheimer’s Disease | July 1995 | Neil R. Smalheiser/Don R. Swanson | Antioxidant activity | Estrogen INHIBITS Antioxidant activity | Antioxidant activity CAUSES Alzheimer's Disease | subgraph5 |
AlipoproteinE (ApoE) | Estrogen INHIBITS ApoE | ApoE CAUSES Alzheimer's Disease | subgraph3 | ||||
Calbindin D28k | Estrogen REGULATES Calbindin D28k | Calbindin D28k AFFECTS Alzheimer's Disease | subgraph5 | ||||
Cathepsin D | Estrogen STIMULATES Cathepsin D | Cathepsin D PREVENTS Alzheimer's Disease | |||||
Cytochrome C oxidase subunit III | Estrogen STIMULATES Cytochrome Coxidase subunit III | Cytochrome Coxidase subunit III AFFECTS Alzheimer's Disease | |||||
Glutamate | Estrogen STIMULATES Glutamate | Glutamate AFFECTS Alzheimer's Disease | |||||
Receptor Polymorphism | Estrogen PRODUCES Receptor Polymorphism | Receptor Polymorphism AFFECTS Alzheimer's Disease |
Scenario 6 | Intermediate | Association | Status | ||||
---|---|---|---|---|---|---|---|
Source | Target | Cut-off Date | Researcher | ||||
Calcium-Independent PLA2 | Schizophrenia | 1997 | Neil R. Smalheiser/Don R. Swanson | Oxidative stress | Oxidative Stress INHIBITS Calcium-Independent PLA2 | Oxidative stress CAUSES Schizophrenia | subgraph3 |
Selenium | Selenium INHIBITS Calcium-Independent PLA2 | Selenium PREVENTS Schizophrenia | subgraph3 | ||||
Vitamin E | Vitamin E STIMULATES Calcium-Independent PLA2 | Vitamin E PREVENTS Schizophrenia | subgraph3 |
Scenario 7 | Intermediate | Association | Status | ||||
---|---|---|---|---|---|---|---|
Source | Target | Cut-off Date | Researcher | ||||
Chlorpromazine | Cardiac Hypertrophy (Cardiomegaly) | 2002 | Jonathan D. Wren (PubMed) | Calcineurin | Chlorpromazine INHIBITS Calcineurin | Calcineurin CAUSES Cardiac Hypertrophy | subgraph5 |
Isoproterenol | Chlorpromazine INHIBITS Isoproterenol | Isoproterenol CAUSES Cardiomegaly | subgraph14 |
Scenario 8 | Intermediate | Association | Status | ||||
---|---|---|---|---|---|---|---|
Source | Target | Cut-off Date | Researcher | ||||
Testosterone | Sleep | 2011 | Christopher M. Miller/Thomas C. Rindflesch (PubMed) | Cortisol/Hydrocortisone | Testosterone INHIBITS Hydrocortisone | Hydrocortisone DISRUPTS Sleep | subgraph10 |
Scenario 9 | Intermediate | Association | Status | ||||
---|---|---|---|---|---|---|---|
Source | Target | Cut-off Date | Researcher | ||||
Diethylhexyl phthalate (DEHP) | Sepsis | 2013 | Michael J. Cairelli/Thomas C. Rindflesch (PubMed Central) | PParGamma | DEHP STIMULATES PParGamma | PParGamma INHIBITS Sepsis |
Publications
<references/>
SWLBD Workshop
Kno.e.sis and the National Library of Medicine (NLM) organized The First International Workshop on the role of Semantic Web in Literature-Based Discovery (SWLBD2012) in conjunction with The IEEE Conference on Bioinformatics and Biomedicine (BIBM2012) in Philadelphia PA, USA.
- Due date for full workshop papers submission: Aug 6, 2012
- Notification of paper acceptance to authors: August 28, 2012
- Camera-ready version of accepted papers: September 4, 2012
- Workshop: October 4, 2012
Internal
Obvio Web App
Automatic Subgraph Creation
Recovery and Decomposition
Reachability
Contact: Delroy Cameron