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* A Java open source library for gene normalization,
* a computer program for gene normalization
* A Java program for converting gene mentions to gene identifiers
* A Java program for converting gene identifiers to mentions
* Some utility programs for converting genes to sequences and other protein features
* An easy to use MySQL database for gene mentions
* A database for storing gene mentions, gene identifiers, their normalization, positions in texts and features
* A system for storing different types of training data in distinct databases, for training based on query gene mentions

With over 5,000 users a year, the SQL query tool is growing very fast as a result of the huge amount of data and advanced features it offers. Users can use basic SQL queries, advanced SQL queries, SQL union queries, stored procedures and SQL subqueries.
It is an ajax-based tool, which means it has a modern front-end and uses a back-end database server. The back-end is a MySQL server.

New features:
* Added ability to create index of a column for a given table
* Added ability to search on indices created by other tools
* Added ability to change password for a user
* Bug fixes

Mozenda is an open-source software for helping linguists, text analysts, software developers, and students of semantics, among others.

Mozenda Description:
* Mozenda is the Natural Language Toolkit that is recommended for linguistic processing that is robust, extensible, modular, and unencumbered. Mozenda has been adopted as one of the reference tools for natural language processing for many years.
* Mozenda consists of four main components: the linguistic library, the parser, the semantic annotation tool, and the natural language toolkit.
* The linguistic library is an open-source Java library that contains free open-source lexica and sets of grammars.
* The parser is an open-source Java library that represents the syntactic structure of a sentence. It also provides a parser description language (PDSL) for generating an efficient parser.
* The semantic annotation tool is a Java program that annotates a sentence and gives a semantic gloss of each word. It also allows automatic search for annotated words. The semantic gloss is based on the lexico-semantic model and the wordnet.
* The natural language toolkit is a collection of tools for linguistic processing and knowledge representation, which focuses on natural language applications.

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The main goal of Moara is to normalize mentions in the text and to identify and disambiguate gene and protein names. The “workbench” is easy to use and to understand. The source code is also easy to read and understand.
Module 1:…

FreeConceptParser for OpenCSG provides a set of utilities to work with concepts within OpenCSG ontologies, where the concepts can be logically associated with each other. The concepts can be represented as instances of pre-defined classes or can be defined using the user defined classes. The following utilities are available:
* Concept Cloner creates a…

Concept Classifier is a Java program to classify concepts and associates with them pre-defined classes. The classification is performed by using the Conceptual Schema, Ontologies and rules defined during the development stage.
Concept Classifier Description:
The Concept Classifier is a Java program which classifies concepts and associates them with pre-defined classes.

OpenCSG is an open-source, Web-based system for developing ontologies in the Open Source AYB (Ontology-driven) Way. It is being developed as an Eclipse-based tool and its GUI can be accessed on the web. OpenCSG allows users to create and edit OBO format ontologies as well as ontologies in the OWL format. It also provides ontology import tools for importing…

Relational Ontology Reasoning and Learning Tool (ROLEL) is a Java tool for learning and reasoning over general and domain-specific ontologies. The tool can be used to teach and learn about ontologies. The ontology learning tool is based on the SOL format.
ROLEL Description:
ROLEL is a tool for learning and reasoning over ontologies. It supports ontology learning and reasoning from a…

OntClassifier is a Java tool to perform classification on ontologies. The ontologies may be in the OBO or OWL format. OntClassifier also supports class-importation for converting an ontology from OBO to OWL, vice versa.
OntClassifier Description:
OntClassifier is a Java tool to perform classification on ontologies. The ontologies may be in the OBO or OWL format….

Grok is a Groovy package for dealing with JSON files. Grok automatically loads objects from JSON files, generates Java classes for these objects or imports them as needed, generates and outputs XML for the
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From a user’s perspective, Moara consists of three key components:

A Java library (Moara.jar) called Moara that is provided by the customer, and which contains all the Java classes and objects necessary for performing text mining. Moara is compiled into a Java Archive (JAR).

A database (Moara.db) that is provided by the customer, which contains the text data from the training and testing corpora. Moara automatically converts this database into the Moara.db.gz format, which can then be loaded into Moara for use during execution.

A MySQL database (Moara.MySQL) that is provided by the customer. This database stores all the extracted results.

Moara requires the use of a MySQL database for storing extracted results, due to limitations in the SQL capabilities of the Java library.

The Moara.MySQL database contains tables (Tables(1139) and Moara(1139)), both of which hold data extracted from the text. You can select data from the tables as easily as from a spreadsheet.

Usage

In order to use the software, the customer must make available a database from which Moara can extract content and classify it appropriately. These databases may be provided in the form of MySQL databases or relational databases in a format that can be loaded into Moara (Moara.db.gz and Moara.db). In some cases, pre-indexed databases may be available as well.

Moara automatically creates a database called Moara.db from any available database (Moara.db.gz or Moara.db) and an index. The index is a set of files, named Moara.xxx, which each contain a list of all the words in a database, in alphabetical order, with one word per line. Each Moara.xxx file contains the word along with the offset of each mention in the database.

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Moara is used for extracting the mentions from scientific text to build a training corpus for a new
[…More]
scientific text to build a training corpus for a new sentence.It’s also capable of extracting protein […Less]

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Moara is a simple and easy-to-use text mining system which extracts mentions from text written in English. The system supports gene / protein bi-directional text annotation.It has built in training corpus and several options for protein validation.
Moara uses basic string search engines such as Lucene and Perl-like regular expressions. Moara also allows users to train their own profile of mentions and error handling.
Mention notes, mention signals (descriptions / labels), disambiguation and text matching are available. It is easy to obtain results using simple URL protocol. Outputs of the system can be stored in the local database.
Moara Description:

moara-tools is a set of tools for automated gene / protein annotations that are needed for biological text mining. The tools aim at automatically annotating genes and proteins in text and thus generate a database of such annotations in the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) classification systems.
moara-tools is a set of tools for automated gene / protein annotations that are needed for biological text mining. The tools aim at automatically annotating genes and proteins in text and thus generate a database of such annotations in the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) classification systems.
moara-tools is a set of tools for automated gene / protein annotations that are needed for biological text mining. The tools aim at automatically annotating genes and proteins in text and thus generate a database

System Requirements For Moara:

Windows 7 x64
OS X 10.9.4 x64
Steam
4GB+ RAM
25GB hard drive space
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