Search Results for "database language"

polyglot framework using Python/C++/JavaScript to fast develop applications to analyze biological sequences

GNAT is a BioNLP/text mining tool to recognize and identify gene/protein names in natural language text. It will detect mentions of genes in text, such as PubMed/Medline abstracts, and disambiguate them to remove false positives and map them to the correct entry in the NCBI Entrez Gene database by gene ID. March 2017: We started to upload GNAT output on Medline. See files/results/medline/.

JBioFramework (JBF) is a set of two different chemical separations simulations (2D Electrophoresis and Mass Spectrometry) that are frequently used in chemistry, biochemistry and proteomics research. It is written in the Java programming language and will run on any and all systems that have the JVM installed. As we continue to develop the software over the coming months/years and attempt to quantify the success of our efforts with testing and reviews, user input is very important. Please...

This is a Java-based project for complex event extraction from text and co-reference resolution. Currently the code can read BioNLP shared task format (http://2011.bionlp-st.org/) and i2b2 Natural Language Processing for Clinical Data shared task format (https://www.i2b2.org/NLP/DataSets/Main.php). Event extraction includes finding events and the parameters for an event in a text. The method is based on SVM but other ML algorithms can be adopted. The method details are explained in the...

Ruby Research Wiki (RRiki) can be used to keep notes and organize references for research. It uses a browser interface, an intuitive plain text formatting language (markdown), and facilities to cross-reference and hierarchically organize notes

This project supports ASTM E13.15 "Analytical Data Magement" in its work defining AnIML, an XML standard for representing, managing and interchanging analytical chemistry and biology data.

A dialect of XUL implementing most of Mozilla XUL's Fourth Draft. XML User Interface Language (XUL) is a method for easily creating GUI applications. Lux XUL supports Python scripting via Jython 2.1.

Talisman is an interpreter for a logical markup language. This language contains the content and logic of a web (or, in the future, Java Swing) based user interface, including arbitrary datatypes and processing actions.

UIMA-compliant text analytics using a rule language in which to express context-sensitive constraints on syntactic and semantic text elements.