Relation extraction software tools | Biomedication text mining
Rapidly evolving sequencing technologies have led to a dramatic rise in the number of published articles reporting associations between genomic variations and diseases. There is an estimate that over 10,000 articles are published each year mentioning such associations. Manually collecting this information is both expensive and time consuming. To assist this manual curation, several text-mining (TM) efforts have been attempted. However, most of these efforts are limited to identifying mutation mentions only. The majority utilize regular expressions to detect mutations, although there are some, like tmVar, that use conditional random fields (CRFs), and SETH, which implements an Extended Backus-Naur Form (EBNF) grammar. Only a few of these efforts extend the mutation detection method to associate the mutation with a disease phenotype. Most of these are search based TM tools that do not employ automatic extraction of the mutation-disease relationships expressed in articles.
Allows probabilistic record linkages. Link Plus is a record linkage tool for cancer registries. The software can run in two modes corresponding to two usages: (1) linking a cancer registry file to external files or (2) detecting duplicates in the cancer registry database.
A product of the PubGene Company designed to be used by anyone seeking information on health, medicine and biology. It is ideal for those seeking an overview of a complex subject while allowing the possibility to "drill down" to specific details. Search results are presented in a dashboard format comprised of panels containing various categories of information ranging from introductory sources to the latest scientific articles.
Creates expert candidate gene lists. GLAD4U is a web-based gene retrieval and prioritization tool. It uses NCBI eSearch API to find publications related to a user query and on the gene-to-publication link table to identify genes from the retrieved publications. It also provides additional functionalities such as sending queries towards WebGestalt for analyzing functional enrichment, or provides a direct link to visualize interactions among the protein products of the genes based on the Cytoscape Web utility.
A tool developed for the reconstruction of molecular genetic networks. ANDSystem is based on an automated text- and data-mining techniques. It provides detailed description of the various types of interactions between genes, proteins, microRNAs, metabolites, cellular components, pathways and diseases, taking into account the specificity of cell lines and organisms. Although the accuracy of ANDSystem is comparable to other well known text-mining tools, such as Pathway Studio and STRING, it outperforms them in having the ability to identify an increased number of interaction types.
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