Extracting Disease-Symptom Relationships by Learning Syntactic Patterns from Dependency Graphs

International audienceDisease-symptom relationships are of primary importance for biomedical informat-ics, but databases that catalog them are incomplete in comparison with the state of the art available in the scientific literature. We propose in this paper a novel method for automatically extracting disease-symptom relationships from text, called SPARE (standing for Syntactic PAttern for Relationship Extraction). This method is composed of 3 successive steps: first, we learn patterns from the dependency graphs; second, we select best patterns based on their respective quality and specificity (their ability to identify only disease-symptom relationships); finally, the patterns are used on new texts for extracting disease-symptom relationships. We experimented SPARE on a corpus of 121,796 abstracts of PubMed related to 457 rare diseases. The quality of the extraction has been evaluated depending on the pattern quality and specificity. The best F-measure obtained is 55.65% (for speci f icity ≥ 0.5 and quality ≥ 0.5). To provide an insight on the novelty of disease-symptom relationship extracted, we compare our results to the content of phenotype databases (OrphaData and OMIM). Our results show the feasibility of automatically extracting disease-symptom relationships, including true relationships that were not already referenced in phenotype databases and may involve complex symptom descriptions

Learning Subgraph Patterns from text for Extracting Disease–Symptom Relationships

International audienceTo some extent, texts can be represented in the form of graphs, such as dependency graphs in which nodes represent words and edges represent grammatical dependencies between words. Graph representation of texts is an interesting alternative to string representation because it provides an additional level of abstraction over the syntax that is sometime easier to compute. In this paper, we study the use of graph mining methods on texts represented as dependency graphs, for extracting relationships between pairs of annotated entities. We propose a three step approach that includes (1) the transformation of texts in a collection of dependency graphs; (2) the selection of frequent subgraphs, named hereafter patterns, on the basis of positive sentences; and (3) the extraction of relationships by searching for occurrences of patterns in novel sentences. Our method has been experimented by extracting disease–symptom relationships from a corpus of 51,292 PubMed abstracts (428,491 sentences)related to 50 rare diseases. The extraction of correct disease–symptom relationships has been evaluated on 565 sentences, showing a precision of 0.91 and a recall of 0.49 (F-Meaure is 0.63). These preliminary experiments show the feasibility of extracting good quality relationships using frequent subgraph mining

Leveraging graph-based semantic annotation for the identification of cause-effect relations

This research is related to language article in Indonesia that discuss about causality relationship research used as public health surveillance information monitoring system. Utilization of this research is suitability of feature selection, phrase annotation, paragraph annotation, medical element annotation and graph-based semantic annotation. Evaluation of system performance is done by intrinsic approach using the Naive Bayes Multinomial method. The results obtained sequentially for recall, precision and f-measure are 0.924, 0.905, and 0.910

KnowLife: A Versatile Approach for Constructing a Large Knowledge Graph for Biomedical Sciences

BACKGROUND: Biomedical knowledge bases (KB’s) have become important assets in life sciences. Prior work on KB construction has three major limitations. First, most biomedical KBs are manually built and curated, and cannot keep up with the rate at which new findings are published. Second, for automatic information extraction (IE), the text genre of choice has been scientific publications, neglecting sources like health portals and online communities. Third, most prior work on IE has focused on the molecular level or chemogenomics only, like protein-protein interactions or gene-drug relationships, or solely address highly specific topics such as drug effects. RESULTS: We address these three limitations by a versatile and scalable approach to automatic KB construction. Using a small number of seed facts for distant supervision of pattern-based extraction, we harvest a huge number of facts in an automated manner without requiring any explicit training. We extend previous techniques for pattern-based IE with confidence statistics, and we combine this recall-oriented stage with logical reasoning for consistency constraint checking to achieve high precision. To our knowledge, this is the first method that uses consistency checking for biomedical relations. Our approach can be easily extended to incorporate additional relations and constraints. We ran extensive experiments not only for scientific publications, but also for encyclopedic health portals and online communities, creating different KB’s based on different configurations. We assess the size and quality of each KB, in terms of number of facts and precision. The best configured KB, KnowLife, contains more than 500,000 facts at a precision of 93% for 13 relations covering genes, organs, diseases, symptoms, treatments, as well as environmental and lifestyle risk factors. CONCLUSION: KnowLife is a large knowledge base for health and life sciences, automatically constructed from different Web sources. As a unique feature, KnowLife is harvested from different text genres such as scientific publications, health portals, and online communities. Thus, it has the potential to serve as one-stop portal for a wide range of relations and use cases. To showcase the breadth and usefulness, we make the KnowLife KB accessible through the health portal (http://knowlife.mpi-inf.mpg.de). ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-015-0549-5) contains supplementary material, which is available to authorized users

Automated Extraction of Fragments of Bayesian Networks from Textual Sources

Mining large amounts of unstructured data for extracting meaningful, accurate, and actionable information, is at the core of a variety of research disciplines including computer science, mathematical and statistical modelling, as well as knowledge engineering. In particular, the ability to model complex scenarios based on unstructured datasets is an important step towards an integrated and accurate knowledge extraction approach. This would provide a significant insight in any decision making process driven by Big Data analysis activities. However, there are multiple challenges that need to be fully addressed in order to achieve this, especially when large and unstructured data sets are considered. In this article we propose and analyse a novel method to extract and build fragments of Bayesian networks (BNs) from unstructured large data sources. The results of our analysis show the potential of our approach, and highlight its accuracy and efficiency. More specifically, when compared with existing approaches, our method addresses specific challenges posed by the automated extraction of BNs with extensive applications to unstructured and highly dynamic data sources. The aim of this work is to advance the current state-of-the-art approaches to the automated extraction of BNs from unstructured datasets, which provide a versatile and powerful modelling framework to facilitate knowledge discovery in complex decision scenarios

From Text to Knowledge with Graphs: modelling, querying and exploiting textual content

This paper highlights the challenges, current trends, and open issues related to the representation, querying and analytics of content extracted from texts. The internet contains vast text-based information on various subjects, including commercial documents, medical records, scientific experiments, engineering tests, and events that impact urban and natural environments. Extracting knowledge from this text involves understanding the nuances of natural language and accurately representing the content without losing information. This allows knowledge to be accessed, inferred, or discovered. To achieve this, combining results from various fields, such as linguistics, natural language processing, knowledge representation, data storage, querying, and analytics, is necessary. The vision in this paper is that graphs can be a well-suited text content representation once annotated and the right querying and analytics techniques are applied. This paper discusses this hypothesis from the perspective of linguistics, natural language processing, graph models and databases and artificial intelligence provided by the panellists of the DOING session in the MADICS Symposium 2022