PhenDisco: phenotype discovery system for the database of genotypes and phenotypes.

The database of genotypes and phenotypes (dbGaP) developed by the National Center for Biotechnology Information (NCBI) is a resource that contains information on various genome-wide association studies (GWAS) and is currently available via NCBI's dbGaP Entrez interface. The database is an important resource, providing GWAS data that can be used for new exploratory research or cross-study validation by authorized users. However, finding studies relevant to a particular phenotype of interest is challenging, as phenotype information is presented in a non-standardized way. To address this issue, we developed PhenDisco (phenotype discoverer), a new information retrieval system for dbGaP. PhenDisco consists of two main components: (1) text processing tools that standardize phenotype variables and study metadata, and (2) information retrieval tools that support queries from users and return ranked results. In a preliminary comparison involving 18 search scenarios, PhenDisco showed promising performance for both unranked and ranked search comparisons with dbGaP's search engine Entrez. The system can be accessed at http://pfindr.net

Utilizing Knowledge Bases In Information Retrieval For Clinical Decision Support And Precision Medicine

Accurately answering queries that describe a clinical case and aim at finding articles in a collection of medical literature requires utilizing knowledge bases in capturing many explicit and latent aspects of such queries. Proper representation of these aspects needs knowledge-based query understanding methods that identify the most important query concepts as well as knowledge-based query reformulation methods that add new concepts to a query. In the tasks of Clinical Decision Support (CDS) and Precision Medicine (PM), the query and collection documents may have a complex structure with different components, such as disease and genetic variants that should be transformed to enable an effective information retrieval. In this work, we propose methods for representing domain-specific queries based on weighted concepts of different types whether exist in the query itself or extracted from the knowledge bases and top retrieved documents. Besides, we propose an optimization framework, which allows unifying query analysis and expansion by jointly determining the importance weights for the query and expansion concepts depending on their type and source. We also propose a probabilistic model to reformulate the query given genetic information in the query and collection documents. We observe significant improvement of retrieval accuracy will be obtained for our proposed methods over state-of-the-art baselines for the tasks of clinical decision support and precision medicine

People on Drugs: Credibility of User Statements in Health Communities

Online health communities are a valuable source of information for patients and physicians. However, such user-generated resources are often plagued by inaccuracies and misinformation. In this work we propose a method for automatically establishing the credibility of user-generated medical statements and the trustworthiness of their authors by exploiting linguistic cues and distant supervision from expert sources. To this end we introduce a probabilistic graphical model that jointly learns user trustworthiness, statement credibility, and language objectivity. We apply this methodology to the task of extracting rare or unknown side-effects of medical drugs --- this being one of the problems where large scale non-expert data has the potential to complement expert medical knowledge. We show that our method can reliably extract side-effects and filter out false statements, while identifying trustworthy users that are likely to contribute valuable medical information

Knowledge-based Biomedical Data Science 2019

Knowledge-based biomedical data science (KBDS) involves the design and implementation of computer systems that act as if they knew about biomedicine. Such systems depend on formally represented knowledge in computer systems, often in the form of knowledge graphs. Here we survey the progress in the last year in systems that use formally represented knowledge to address data science problems in both clinical and biological domains, as well as on approaches for creating knowledge graphs. Major themes include the relationships between knowledge graphs and machine learning, the use of natural language processing, and the expansion of knowledge-based approaches to novel domains, such as Chinese Traditional Medicine and biodiversity.Comment: Manuscript 43 pages with 3 tables; Supplemental material 43 pages with 3 table