Search Results for "annotation"

...The current version provides functionalities for both de-novo and reference guided analysis of sequencing data, including genome assembly, read mapping, variants detection and genotyping and de-novo analysis of data generated from reduced representation protocols. NGSEP also provides modules for analysis of genomic variation databases (VCF files), including functional annotation, filtering, format conversion, comparison, clustering, imputation, introgression analysis and different kinds of statistics. Since version 4, we provide functionalities for management of genomes and transcriptomes, including genome alignment and annotation of transposable elements. A complete list of functionalities is available in our wiki (https://sourceforge.net/p/ngsep/wiki/Home/). ...

...We have tested miRDP2 to analyze miRNA transcriptomes in such plants with gradually increased genome size as Arabidopsis, rice, tomato, maize and wheat. Compared with miRDeep-P and several other computational tools, miRDP2 processed NGS data with superior speed. By incorporating newly updated plant miRNA annotation criteria, the accuracy of miRDP2 is also markedly improved. Our results demonstrate miRDP2 as a fast and accurate tool for analyzing the miRNA transcriptome in plants. Reference: https://doi.org/10.1093/bioinformatics/bty972

The Phenoscape project attempts to formalize the description of evolutionary characters to make them interoperable and computable with the body of phenotype annotation being generated by model organism databases, and other biomedical research.

Network software for annotation and quality control of distributed data. Supported by NSF: DBI 0646266 and NSF: DBI 0960535. http://wiki.filteredpush.org

A minimalist approach to share text documents and data annotations. Allows a large number of different annotations to be represented. Project files contain: - simple code to hold/read/write data and perform sample processing. - BioC-formatted corpora - BioC tools that work with BioC corpora BioC goals - simplicity - interoperability - broad use - reuse There should be little investment required to learn to use a format or a software module to process that format. We are...

The BioNLP UIMA Component Repository provides UIMA wrappers for novel and well-known 3rd-party NLP tools used in biomedical text prosessing, such as tokenizers, parsers, named entity taggers, and tools for evaluation.

...Contact the developers to obtain them. Use http://www.integrativegenomics.org/ for the latest data and analyses. GenomeRunner is a tool for automating genome exploration. It performs annotation and enrichment analyses of user-provided genomic regions (SNPs, ChIP-seq binding sites etc.) against >6,000 (human genome) epigenomic features available from the UCSC genome browser. Input - any genome-wide data data in .bed format (tab-delimited text file with chrom, chromStart, chromEnd). Annotation analysis output - detailed annotation of each genomic region in input data. ...

The goal of this project is the extraction the information listed below from texts downloaded from the Federal Register (https://www.federalregister.gov). The texts are mainly applications for permits, notices about given permits, etc. This software tool is developed by the Max Planck Institute for the History of Science (http://www.mpiwg-berlin.mpg.de) in collaboration with Dirk Wintergrün and Etienne Benson.

Task of the project is a semantic annotation of Czech texts by using NLP tools.

Java & MPEG-7 based tools for annotation and retrieval of digital photos and images (Caliph & Emir). LIRE has moved to https://github.com/dermotte/lire. Caliph & Emir have moved to https://github.com/dermotte/CaliphEmir.

Research and development of an ontology for the analysis and representation of comparative data for use in evolutionary analysis. For more information, please see www.evolutionaryontology.org

Enrich and query corpora in the TEI-XML vocabulary. CorpusReader manage very large corpora and corpora containing milestone annotation. It provides tools for enriching corpora with output of linguistic parsers, and for extracting quantitative information

Ontea - Pattern based Semantic Annotation Platform. Ontea search or create semantic meta data from text or documents using pattern based approaches. Implementation currently includes regular expressions (regex) patterns

Annotate data sets that are stored in a Tranche repository. Administrators can maintain multiple versions of annotation standards - structured requested information. Supports controlled vocabularies.

This project provides bookmarklet-based web page overlays based on recognized terms from vocabulary servers. These overlays can be used to assist users with unfamiliar terminology or can be used for annotation of web-based data and literature.

LT4eL (Language Technology for e-Learning) develops a framework of multilingual language technology tools and semantic web techniques for improving the retrieval and the metadata annotation of learning material.

The Functional Annotation and Correlation Tool allows the meta-analysis of data from high-throughput experiments (typically microarrays) by annotating (clones, genes, GeneOntology, location, etc.) and correlating data sets to identify important patterns.

The ShapeAnnotator is an interactive GUI for the inspection, segmentation and semantic annotation of 3D surface meshes.

The Text Annotation Environment (tae) can be used to annotate natural language text manually or automatically (UIMA Annotator) with meta information (tokens, part-of-speech, named entities, ...). Tae is based on Eclipse and IBM's UIMA.

AmiGram is the AMI Graphical Representation and Annotation Module. It is a general-purpose tool for multimodal corpus annotation and allows the time line based annoation of NXT corpora in a layer based environment.

A tool for analyzing video data of human user studies. Allows playback of multiple video streams simultaneously, along with annotation capabilites and visualization of aggregated annotation categories. Written in C#, with c++ directX for video playback.

Thea, Tools for High-throughput Experiment Analysis, is an integrated information processing system dedicated to the annotation of data issued from classification systems with biological information coming from a knowledge base.

The Annotation Graph Schema API aims to aid developers in the creation and querying of Annotation bases where the use of XML-based tools is needed. It is easily integratable with any persistent representation and has a flexible in-memory model.

WordFreak is a java-based linguistic annotation tool designed to support human, and automatic annotation of linguistic data as well as employ active-learning for human correction of automatically annotated data.

A tool kit for multiplexing annotations and management of features for textual annotation.