Annotation of epidemiological information in animal disease-related news articles: guidelines and manually labelled corpus

PADI-web (Platform for Automated extraction of animal Disease Information from the web) is a biosurveillance system dedicated to monitoring online news sources for the detection of emerging animal infectious diseases. PADI-web has collected more than 380,000 news articles since 2016. Compared to other existing biosurveillance tools, PADI-web focuses specifically on animal health and has a fully automated pipeline based on machine-learning methods. This paper presents the new functionalities of PADI-web based on the integration of: (i) a new fine-grained classification system, (ii) automatic methods to extract terms and named entities with text-mining approaches, (iii) semantic resources for indexing keywords and (iv) a notification system for end-users. Compared to other biosurveillance tools, PADI-web, which is integrated in the French Platform for Animal Health Surveillance (ESA Platform), offers strong coverage of the animal sector, a multilingual approach, an automated information extraction module and a notification tool configurable according to end-user needs.

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“…training data). For the proposed fine-grained classification, a dedicated corpus has been built [ 40 ]. This one is summarized below.…”

Section: Methodsmentioning

confidence: 99%

“…This one is summarized below. A detailed version of the guidelines and the labeled corpus are publicly available in a Dataverse repository [ 40 ]. For each sentence, two labeling approaches are proposed: event and information types.…”

Section: Methodsmentioning

confidence: 99%

PADI-web 3.0: A new framework for extracting and disseminating fine-grained information from the news for animal disease surveillance

et al. 2021

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Elaboration of a new framework for fine-grained epidemiological annotation

et al. 2022

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Event-based surveillance (EBS) gathers information from a variety of data sources, including online news articles. Unlike the data from formal reporting, the EBS data are not structured, and their interpretation can overwhelm epidemic intelligence (EI) capacities in terms of available human resources. Therefore, diverse EBS systems that automatically process (all or part of) the acquired nonstructured data from online news articles have been developed. These EBS systems (e.g., GPHIN, HealthMap, MedISys, ProMED, PADI-web) can use annotated data to improve the surveillance systems. This paper describes a framework for the annotation of epidemiological information in animal disease-related news articles. We provide annotation guidelines that are generic and applicable to both animal and zoonotic infectious diseases, regardless of the pathogen involved or its mode of transmission (e.g., vector-borne, airborne, by contact). The framework relies on the successive annotation of all the sentences from a news article. The annotator evaluates the sentences in a specific epidemiological context, corresponding to the publication date of the news article.

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Information retrieval for animal disease surveillance: a pattern-based approach.

Valentin¹,

Roche²,

Lancelot³

2020

Proceedings of the 11th International Workshop on Health Text Mining and Information Analysis

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Animal diseases-related news articles are rich in information useful for risk assessment. In this paper, we explore a method to automatically retrieve sentence-level epidemiological information. Our method is an incremental approach to create and expand patterns at both lexical and syntactic levels. Expert knowledge input are used at different steps of the approach. Distributed vector representations (word embedding) were used to expand the patterns at the lexical level, thus alleviating manual curation. We showed that expert validation was crucial to improve the precision of automatically generated patterns.

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Annotation of epidemiological information in animal disease-related news articles: guidelines and manually labelled corpus

Cited by 3 publications

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PADI-web 3.0: A new framework for extracting and disseminating fine-grained information from the news for animal disease surveillance

PADI-web 3.0: A new framework for extracting and disseminating fine-grained information from the news for animal disease surveillance

Elaboration of a new framework for fine-grained epidemiological annotation

Information retrieval for animal disease surveillance: a pattern-based approach.

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