BackgroundA quantitative trait locus (QTL) is a genomic region that correlates with a phenotype. Most of the experimental information about QTL mapping studies is described in tables of scientific publications. Traditional text mining techniques aim to extract information from unstructured text rather than from tables. We present QTLTableMiner++ (QTM), a table mining tool that extracts and semantically annotates QTL information buried in (heterogeneous) tables of plant science literature.QTM is a command line tool written in the Java programming language. This tool takes scientific articles from the Europe PMC repository as input, extracts QTL tables using keyword matching and ontology-based concept identification. The tables are further normalized using rules derived from table properties such as captions, column headers and table footers. Furthermore, table columns are classified into three categories namely column descriptors, properties and values based on column headers and data types of cell entries. Abbreviations found in the tables are expanded using the Schwartz and Hearst algorithm. Finally, the content of QTL tables is semantically enriched with domain-specific ontologies (e.g. Crop Ontology, Plant Ontology and Trait Ontology) using the Apache Solr search platform and the results are stored in a relational database and a text file.ResultsThe performance of the QTM tool was assessed by precision and recall based on the information retrieved from two manually annotated corpora of open access articles, i.e. QTL mapping studies in tomato (Solanum lycopersicum) and in potato (S. tuberosum). In summary, QTM detected QTL statements in tomato with 74.53% precision and 92.56% recall and in potato with 82.82% precision and 98.94% recall.ConclusionQTM is a unique tool that aids in providing QTL information in machine-readable and semantically interoperable formats.Electronic supplementary materialThe online version of this article (10.1186/s12859-018-2165-7) contains supplementary material, which is available to authorized users.
The genomes of thousands of individuals are profiled within Dutch healthcare and research each year. However, this valuable genomic data, associated clinical data and consent are captured in different ways and stored across many systems and organizations. This makes it difficult to discover rare disease patients, reuse data for personalized medicine and establish research cohorts based on specific parameters. FAIR Genomes aims to enable NGS data reuse by developing metadata standards for the data descriptions needed to FAIRify genomic data while also addressing ELSI issues. We developed a semantic schema of essential data elements harmonized with international FAIR initiatives. The FAIR Genomes schema v1.1 contains 110 elements in 9 modules. It reuses common ontologies such as NCIT, DUO and EDAM, only introducing new terms when necessary. The schema is represented by a YAML file that can be transformed into templates for data entry software (EDC) and programmatic interfaces (JSON, RDF) to ease genomic data sharing in research and healthcare. The schema, documentation and MOLGENIS reference implementation are available at https://fairgenomes.org.
Aim:The present study was undertaken to study the clinical and hemato-biochemical alterations, ultrasonography, and surgical treatment of bovine suffering from cecal dilatation and cecal impaction.Materials and Methods:The present study was conducted on 11 bovines (9 buffaloes and 2 cattle) suffering from cecal dilatation (n=6) and cecal impaction (n=5). The diagnosis of surgical affections of cecum was made on the basis of clinical examination, hematobiochemistry, ultrasonography, and exploratory laparotomy.Results:A marked decrease in serum total protein, albumin, chloride, potassium, and calcium levels while an increase in lactate concentrations was recorded. Peritoneal fluid examination revealed an increase in total protein concentration. Per rectal examination along with ultrasonography was used as a confirmatory diagnostic tool for cecal dilatation and cecal impaction. Ultrasonographic features of cecal dilatation and cecal impaction were recorded. Left flank laparorumenotomy was performed in six animals with dilated cecum along with colonic fecalith. Post-rumenotomy, these animals were treated with massage of cecum along with kneading of colonic fecalith. Right flank typhlotomy was done in the remaining five animals having impacted cecum for decompression of the dilated cecum. 9 of 11 animals survived which underwent surgery and remained healthy up to 3-month follow-up.Conclusion:Ultrasonography was reliable in the diagnosis of cecal dilatation and cecal impaction in bovine. Left flank exploration after laparorumenotomy is an ideal surgical technique for the management of cecal dilatation, while right flank typhlotomy is ideal for the management of cecal impaction in bovine.
between tuber flesh color and ZEP was experimentally substantiated later in the year 2011. The results illustrate that, indeed, supervised NLP shows a lot of promise to speed up knowledge discovery, data integration and hypothesis generation in scientific research.
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