Dataset Information

DISNET: a framework for extracting phenotypic disease information from public sources.

ABSTRACT: Background:Within the global endeavour of improving population health, one major challenge is the identification and integration of medical knowledge spread through several information sources. The creation of a comprehensive dataset of diseases and their clinical manifestations based on information from public sources is an interesting approach that allows one not only to complement and merge medical knowledge but also to increase it and thereby to interconnect existing data and analyse and relate diseases to each other. In this paper, we present DISNET (http://disnet.ctb.upm.es/), a web-based system designed to periodically extract the knowledge from signs and symptoms retrieved from medical databases, and to enable the creation of customisable disease networks. Methods:We here present the main features of the DISNET system. We describe how information on diseases and their phenotypic manifestations is extracted from Wikipedia and PubMed websites; specifically, texts from these sources are processed through a combination of text mining and natural language processing techniques. Results:We further present the validation of our system on Wikipedia and PubMed texts, obtaining the relevant accuracy. The final output includes the creation of a comprehensive symptoms-disease dataset, shared (free access) through the system's API. We finally describe, with some simple use cases, how a user can interact with it and extract information that could be used for subsequent analyses. Discussion:DISNET allows retrieving knowledge about the signs, symptoms and diagnostic tests associated with a disease. It is not limited to a specific category (all the categories that the selected sources of information offer us) and clinical diagnosis terms. It further allows to track the evolution of those terms through time, being thus an opportunity to analyse and observe the progress of human knowledge on diseases. We further discussed the validation of the system, suggesting that it is good enough to be used to extract diseases and diagnostically-relevant terms. At the same time, the evaluation also revealed that improvements could be introduced to enhance the system's reliability.

SUBMITTER: Lagunes-Garcia G

PROVIDER: S-EPMC7032061 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

DISNET: a framework for extracting phenotypic disease information from public sources.

Lagunes-García Gerardo G Rodríguez-González Alejandro A Prieto-Santamaría Lucía L García Del Valle Eduardo P EP Zanin Massimiliano M Menasalvas-Ruiz Ernestina E

PeerJ 20200217

<h4>Background</h4>Within the global endeavour of improving population health, one major challenge is the identification and integration of medical knowledge spread through several information sources. The creation of a comprehensive dataset of diseases and their clinical manifestations based on information from public sources is an interesting approach that allows one not only to complement and merge medical knowledge but also to increase it and thereby to interconnect existing data and analyse ...[more]

PMID: 32110491

Similar Datasets

Project description:BackgroundMisinformation about Lyme disease and other tick-transmitted pathogens circulates frequently on the internet and can compete with, or even overshadow, science-based guidance on tick-borne disease (TBD) prevention.ObjectiveWe surveyed internet users connected to academic tick-related resources to identify trusted sources of Lyme disease prevention information, explore confidence in tick bite prevention information, and examine associations of these responses with answers to commonly disputed issues.MethodsThe survey was conducted through social media and website pages for Western Connecticut State University Tickborne Disease Prevention Laboratory and the University of Rhode Island TickEncounter Resource Center.ResultsRespondents (N=1190) were predominantly female (903/1190, 76.3%), middle-aged (574/1182, 48.6%), and resided in New England states (663/1190, 55.7%). In total 984 of 1186 (83%) respondents identified conventional experts (eg, the Centers for Disease Control [CDC] or other government health agencies, physicians who follow Infectious Diseases Society of America guidelines for Lyme disease treatment guidelines, and academics) as trustworthy TBD prevention resources. However, nearly one-fourth of respondents would first consult personal contacts and web-based communities regarding prevention information before consulting conventional expert sources. The opinions of public health experts and physicians were rated among the top motivators underlying personal prevention decisions; yet, more than 50% of participants revealed distrustful attitudes toward, or were uncertain about, CDC-supported statements related to time to transmission of Lyme disease (708/1190, 59.5%), the safety of diethyltoluamide-based repellents for children (604/1183, 51.1%), and recommended use of antibiotic prophylaxis (773/1181, 65.4%). Multimodal regression models revealed that participants from high-Lyme-disease-incidence states were more likely to first seek TBD prevention information from personal networks and nontraditional sources before approaching conventional sources of TBD prevention information. We found that those reporting high rates of social media usage were more than twice as likely to first seek traditional expert sources of prevention information but were overall more likely to reject CDC-promoted Lyme disease information, in particular the established time to transmission of Lyme disease bacteria. Models also predicted that those participants who disagreed with the conventional scientific view on the antibiotic prophylaxis prevention statement were less likely to be confident in their ability to protect themselves from a tick bite. Overall, uncertainty in one's ability to protect oneself against tick bites was strongly associated with uncertainty about beliefs in CDC-promoted TBD prevention information. Self-reported trust in experts and frequency of social media use suggest that these platforms may provide opportunities to engage directly with the public about TBD prevention practices.ConclusionsUsing strategies to improve public trust and provide information where the public engages on social media may improve prevention communication and adoption of best practices.

Project description:BackgroundUnstructured data from clinical epidemiological studies can be valuable and easy to obtain. However, it requires further extraction and processing for data analysis. Doing this manually is labor-intensive, slow and subject to error. In this study, we propose an automation framework for extracting and processing unstructured data.MethodsThe proposed automation framework consisted of two natural language processing (NLP) based tools for unstructured text data for medications and reasons for medication use. We first checked spelling using a spell-check program trained on publicly available knowledge sources and then applied NLP techniques. We mapped medication names into generic names using vocabulary from publicly available knowledge sources. We used WHO's Anatomical Therapeutic Chemical (ATC) classification system to map generic medication names to medication classes. We processed the reasons for medication with the Lancaster stemmer method and then grouped and mapped to disease classes based on organ systems. Finally, we demonstrated this automation framework on two data sources for Mylagic Encephalomyelitis/ Chronic Fatigue Syndrome (ME/CFS): tertiary-based (n?=?378) and population-based (n?=?664) samples.ResultsA total of 8681 raw medication records were used for this demonstration. The 1266 distinct medication names (omitting supplements) were condensed to 89 ATC classification system categories. The 1432 distinct raw reasons for medication use were condensed to 65 categories via NLP. Compared to completion of the entire process manually, our automation process reduced the number of the terms requiring manual labor for mapping by 84.4% for medications and 59.4% for reasons for medication use. Additionally, this process improved the precision of the mapped results.ConclusionsOur automation framework demonstrates the usefulness of NLP strategies even when there is no established mapping database. For a less established database (e.g., reasons for medication use), the method is easily modifiable as new knowledge sources for mapping are introduced. The capability to condense large features into interpretable ones will be valuable for subsequent analytical studies involving techniques such as machine learning and data mining.

Dataset Information

DISNET: a framework for extracting phenotypic disease information from public sources.

Publications

DISNET: a framework for extracting phenotypic disease information from public sources.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets