Application of automatic mutation-gene pair extraction to diseases

Nowadays, it is known that several inherited genetic diseases? such as sickle cell anemia, are caused by mutations in genes. In order to find ways to prevent and even better to circumvent occurrence of these diseases, knowledge of mutations and the genes on which the mutations occur is of crucial importance. Information on disease related mutations and genes can be accessed through publicly available databases or biomedical literature sources. However, acquiring relevant information from such resources can be problematic because of two reasons. Firstly manually created databases are usually incomplete and not up to date. Secondly reading through vast amount of publicly available biomedical documents is very time consuming. Therefore, there is a need for systems that are capable of extracting relevant information from publicly available resources in an automated fashion. This thesis presents the design and implementation of a system, MuGeX, that automatically extracts mutationgene pairs from MEDLINE abstracts for a given disease. MuGeX performs mainly three tasks. First task is identification of mutations, applying pattern matching in conjunction with a machine learning algorithm. The second task is identification of gene names utilizing a dictionarybased method. The final task is building relations between genes and mutations based on proximity measures. Results of experiments indicate that MuGeX identifies 85.9% of mutations that are on experiment corpus at 95.9% precision. For mutationgene pair extraction, we focused on Alzheimer’s disease. We observed that 88.9% of mutationgene pairs retrieved by MuGeX for Alzheimer’s disease are correct

Improved mutation tagging with gene identifiers applied to membrane protein stability prediction

Background The automated retrieval and integration of information about protein point mutations in combination with structure, domain and interaction data from literature and databases promises to be a valuable approach to study structure-function relationships in biomedical data sets. Results We developed a rule- and regular expression-based protein point mutation retrieval pipeline for PubMed abstracts, which shows an F-measure of 87% for the mutation retrieval task on a benchmark dataset. In order to link mutations to their proteins, we utilize a named entity recognition algorithm for the identification of gene names co-occurring in the abstract, and establish links based on sequence checks. Vice versa, we could show that gene recognition improved from 77% to 91% F-measure when considering mutation information given in the text. To demonstrate practical relevance, we utilize mutation information from text to evaluate a novel solvation energy based model for the prediction of stabilizing regions in membrane proteins. For five G protein-coupled receptors we identified 35 relevant single mutations and associated phenotypes, of which none had been annotated in the UniProt or PDB database. In 71% reported phenotypes were in compliance with the model predictions, supporting a relation between mutations and stability issues in membrane proteins. Conclusion We present a reliable approach for the retrieval of protein mutations from PubMed abstracts for any set of genes or proteins of interest. We further demonstrate how amino acid substitution information from text can be utilized for protein structure stability studies on the basis of a novel energy model

Using Neural Networks for Relation Extraction from Biomedical Literature

Using different sources of information to support automated extracting of relations between biomedical concepts contributes to the development of our understanding of biological systems. The primary comprehensive source of these relations is biomedical literature. Several relation extraction approaches have been proposed to identify relations between concepts in biomedical literature, namely, using neural networks algorithms. The use of multichannel architectures composed of multiple data representations, as in deep neural networks, is leading to state-of-the-art results. The right combination of data representations can eventually lead us to even higher evaluation scores in relation extraction tasks. Thus, biomedical ontologies play a fundamental role by providing semantic and ancestry information about an entity. The incorporation of biomedical ontologies has already been proved to enhance previous state-of-the-art results.Comment: Artificial Neural Networks book (Springer) - Chapter 1

Mining clinical attributes of genomic variants through assisted literature curation in Egas

The veritable deluge of biological data over recent years has led to the establishment of a considerable number of knowledge resources that compile curated information extracted from the literature and store it in structured form, facilitating its use and exploitation. In this article, we focus on the curation of inherited genetic variants and associated clinical attributes, such as zygosity, penetrance or inheritance mode, and describe the use of Egas for this task. Egas is a web-based platform for text-mining assisted literature curation that focuses on usability through modern design solutions and simple user interactions. Egas offers a flexible and customizable tool that allows defining the concept types and relations of interest for a given annotation task, as well as the ontologies used for normalizing each concept type. Further, annotations may be performed on raw documents or on the results of automated concept identification and relation extraction tools. Users can inspect, correct or remove automatic text-mining results, manually add new annotations, and export the results to standard formats. Egas is compatible with the most recent versions of Google Chrome, Mozilla Firefox, Internet Explorer and Safari and is available for use at https://demo.bmd-software.com/egas/

A new unsupervised feature selection method for text clustering based on genetic algorithms

Nowadays a vast amount of textual information is collected and stored in various databases around the world, including the Internet as the largest database of all. This rapidly increasing growth of published text means that even the most avid reader cannot hope to keep up with all the reading in a field and consequently the nuggets of insight or new knowledge are at risk of languishing undiscovered in the literature. Text mining offers a solution to this problem by replacing or supplementing the human reader with automatic systems undeterred by the text explosion. It involves analyzing a large collection of documents to discover previously unknown information. Text clustering is one of the most important areas in text mining, which includes text preprocessing, dimension reduction by selecting some terms (features) and finally clustering using selected terms. Feature selection appears to be the most important step in the process. Conventional unsupervised feature selection methods define a measure of the discriminating power of terms to select proper terms from corpus. However up to now the valuation of terms in groups has not been investigated in reported works. In this paper a new and robust unsupervised feature selection approach is proposed that evaluates terms in groups. In addition a new Modified Term Variance measuring method is proposed for evaluating groups of terms. Furthermore a genetic based algorithm is designed and implemented for finding the most valuable groups of terms based on the new measure. These terms then will be utilized to generate the final feature vector for the clustering process . In order to evaluate and justify our approach the proposed method and also a conventional term variance method are implemented and tested using corpus collection Reuters-21578. For a more accurate comparison, methods have been tested on three corpuses and for each corpus clustering task has been done ten times and results are averaged. Results of comparing these two methods are very promising and show that our method produces better average accuracy and F1-measure than the conventional term variance method

The Curation of Genetic Variants: Difficulties and Possible Solutions

The curation of genetic variants from biomedical articles is required for various clinical and research purposes. Nowadays, establishment of variant databases that include overall information about variants is becoming quite popular. These databases have immense utility, serving as a user-friendly information storehouse of variants for information seekers. While manual curation is the gold standard method for curation of variants, it can turn out to be time-consuming on a large scale thus necessitating the need for automation. Curation of variants described in biomedical literature may not be straightforward mainly due to various nomenclature and expression issues. Though current trends in paper writing on variants is inclined to the standard nomenclature such that variants can easily be retrieved, we have a massive store of variants in the literature that are present as non-standard names and the online search engines that are predominantly used may not be capable of finding them. For effective curation of variants, knowledge about the overall process of curation, nature and types of difficulties in curation, and ways to tackle the difficulties during the task are crucial. Only by effective curation, can variants be correctly interpreted. This paper presents the process and difficulties of curation of genetic variants with possible solutions and suggestions from our work experience in the field including literature support. The paper also highlights aspects of interpretation of genetic variants and the importance of writing papers on variants following standard and retrievable methods. © 2012 Beijing Institute of Genomics, Chinese Academy of Sciences and Genetics Society of China