Ontologizer Crack For PC

The Ontologizer is a stand-alone Java application for exploration, visualization, and statistical analysis of biological data using Gene Ontology (GO).
Users can analyze large data sets such as those that typically arise from microarray experiments (among many other scenarios) for annotations to GO terms in order to gain an overview of the biological characteristics of the data they are analyzing.
Thanks to the fact that it is written in the Java programming language, you should have no problems in running Ontologizer on a variety of systems.

The Ontologizer is a tool that has been developed in order to help biologists rapidly find and visualize the biological processes, molecular functions and cellular components in which genes, proteins or other molecular entities of interest participate.
Moreover, the Ontologizer also enables the user to perform statistical data mining that would allow his to find significant enrichment of GO terms within a gene list and vice versa.
In order to perform statistics and visualization of the enriched GO terms, the Ontologizer combines the power and flexibility of the Java programming language with the R programming language, exploiting the underlying well-tested and stable infrastructure of the R software distribution, available for Windows as well as for Unix systems.
Ontologizer Features:
Support for the GO database (February 2004)
Support for the broad types of entities (genes, proteins, complexes, pathways, etc)
Support for annotations by various types of sources and retrieval methods
Support for statistical data mining via multiple linear regression and hierarchical clustering
Support for data retrieval in plain files, annotation in tables and annotation in flat files
Support for visualization of annotations in dot-connector diagrams
Support for statistics by various methods
Support for the GO database, DAG representation, RDF triples, and additional tools like BeGO 2.1
Support for data sets based on gene-to-gene comparison
Support for additional data sources
Support for the ABFO standard for the ontology fields of chemicals
Support for creation and annotation of new items from scratch
Support for customized data from any gene-to-gene comparison
Support for the generation of custom queries and reports
Support for batch data retrieval and analysis (easy to use)
Support for the RDF network of GO
Ability to export datasets and graphs to SVG
Supported platforms:
Windows
Linux and most Unix platforms including Mac OSX
Supported localisation:
English
German
Portuguese
Spanish

The Ontologizer is a stand-alone Java application for exploration, visualization, and statistical analysis of biological data using Gene Ontology (GO).
Users can analyze large data sets such as those that typically arise from microarray experiments (among many other scenarios) for annotations to GO terms in order to gain an overview of the biological characteristics of the data they are analyzing.
Thanks to the fact that it is written in the Java programming language, you should have no problems in running Ontologizer on a variety of systems.
Ontologizer Description:
The Ontologizer is a tool that

Ontologizer is a web-based tool for helping biologists explore, visualize, and analyze gene expression data (such as microarrays, but also other types of expression profiling experiments) in a gene ontology (GO) framework. It provides functions for exploring such data using matrix visualizations of annotation data; for extracting lists of the most significantly enriched GO terms in each of several gene list libraries; for finding the most significantly enriched GO terms of an input list of genes; and for computing hypergeometric statistics and comparing the statistics of various gene list libraries.

Ontologizer’s various functions are all based on a reference knowledge base of GO terms and their annotation to a large number of genes. Ontologizer is able to use a variety of knowledge bases to provide GO annotation for input gene lists.

Ontologizer’s web interface is generally flexible. It can be configured to always prompt the user for input parameters and for generating random lists (lists of input genes randomly selected with a limited range of values) that provide unbiased annotations to GO terms.

Special tabs are provided for computation of hypergeometric enrichment statistics and for comparison of statistical significance among different gene list libraries, which are all of arbitrary size. Ontologizer’s interface to the web also allows for simply editing knowledge bases and GO annotation files.

Ontologizer is completely free and open source software, available as a download from the web site at

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Ontologizer is a software environment for analyzing data annotated with Gene Ontology. Users can explore and visualize the annotated GO relationships between entities that were treated with experimental or computational methods. In addition, they can draw statistical analyses and exploit the GO database directly. Ontologizer is a flexible software environment that supports many types of data and can use other identifiers.
Using Ontologizer for Different Scenarios:
When used in its most basic form, Ontologizer supports analysis of microarray data. However, data can be manually converted to the appropriate format and uploaded directly, or the Ontologizer can be used in combination with other tools to process various file types.
Download Ontologizer
Ontologizer requires Java 1.5 or later. Java SE 6 or higher is recommended and is the version we have tested. You may also install Ontologizer on a computer with Java SE 7 (if your computer has this version of Java) but we don’t recommend it. (See section 5 for more information)
Note: For Windows users, we recommend and recommend the Oracle Java SE 6 update 16 (the 64-bit edition) or later. We have tested Ontologizer on Java SE 6 update 25 and JDK6u25.
The Ontologizer installer creates a file called Ontologizer.exe inside the Ontologizer zip file. Save this file on any Windows system (e.g., a USB stick or CD-ROM) and put it into your computer’s temporary directory (e.g., C:\Temp) before starting the Ontologizer application.
What makes Ontologizer different from other tools for manipulating data annotated with GO?
What makes Ontologizer different from other tools for manipulating data annotated with GO? Well, if you’ve ever tried to use other applications, such as Biomart or the GO Annotation Explorer, to analyze data annotated with GO you probably know that each is limited in a particular way. What they have in common is the standard representation of data annotated with GO and an interface for manipulating the data.
The Ontologizer, on the other hand, is an integrated, stand-alone tool with a built-in GO representation engine. The ontology and support code were developed for us and ported to Java. We use the entity annotation structure for representing data, thus facilitating the interaction with the GO database. Ontologizer handles the GO database queries itself and uses an in-house built inference engine to establish GO terms. The

– Download, install, and run Ontologizer.
– Run the Ontologizer main routine to analyze the content of your data set.
– Ontologizer includes built-in functions for visualization of your data in the bi-dimensional plane.
– It is easy to export your data into external bi-dimensional plots.
– As additional functions you can use the GO database for statistical analysis of the data you are analyzing.
– Ontologizer provides a powerful API, with which it is easy to access its functionality from other applications.
– Ontologizer supports the analysis of large data sets.
– Ontologizer can analyze data sets of up to 40 GB.
– It is also possible to create and perform the analysis of aggregate data sets from multiple data sets; e.g., data sets from multiple biological experiments.
– Ontologizer can perform a single analysis for genes, proteins, pathways, and GO data.
– Ontologizer can compare and contrast between different analyses of the same data set.
– It is easy to compare data from various platforms and analyze the gene sets and pathways that are shared between the various platforms.
– Ontologizer allows other applications to access its functionality via the Ontologizer API.

The Ontologizer is a stand-alone Java application for exploration, visualization, and statistical analysis of biological data using Gene Ontology (GO).
Users can analyze large data sets such as those that typically arise from microarray experiments (among many other scenarios) for annotations to GO terms in order to gain an overview of the biological characteristics of the data they are analyzing.
Thanks to the fact that it is written in the Java programming language, you should have no problems in running Ontologizer on a variety of systems.
Ontologizer Description:
– Download, install, and run Ontologizer.
– Run the Ontologizer main routine to analyze the content of your data set.
– Ontologizer includes built-in functions for visualization of your data in the bi-dimensional plane.
– It is easy to export your data into external bi-dimensional plots.
– As additional functions you can use the GO database for statistical analysis of the data you are analyzing.
– Ontologizer provides a powerful API, with which it is easy to access its functionality from other applications.
– Ontologizer supports the analysis of large data sets.
– Ontologizer can analyze data sets of up to 40 GB.
– It is

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