About Site Map Submit Contact Us Log in | Create an account
Create an account Log In
Average Rating
User Rating:
Visitors Rating:
My rating:

Write review
  • Last update: 5 years ago
  • Total downloads: 77
  • Operating system: Win All
  • Publisher: Biopax.org
See full specifications

windows default iconpaxtools Publisher's description

Paxtools is a Java library specially designed for accessing and manipulating data in BioPAX format.

Paxtools is a Java library specially designed for accessing and manipulating data in BioPAX format. It is also runnable as console application that can execute several commands:

--validate [xml|html]
--integrate (experimental)
--to-GSEA " converts level 1 or 2 or 3 to GSEA output. Searches database for participant id or uses biopax rdf id if database is NONE. Cross species check ensures participant protein is from same species as pathway (set to true or false).

Paxtools Features

A complete and consistent implementation of BioPAX specification: BioPAX elements in Paxtools are plain Java beans which provide methods to access the properties described in BioPAX, and a model, acting as a container for all BioPAX elements, provides querying facilities for them. Users can either read a BioPAX model from a file or create an empty one from the scratch. Methods to add new elements to a model and to remove elements from a model are also provided.

Support for OWL properties and additional inverse links: Owl properties can be symmetric, transient or subtyped into other properties. These semantics can not be represented directly in an object oriented programming language. Paxtools implements these additional semantics and automatically update the fields of objects. For example, since property “standardName” is a subproperty of “name”, updating the standardName of a protein will also update its list of names. Similarly since “component” is a transient property, a query for the components of a complex will not only list its immediate components but also the components of the subcomplexes inside this complex. In the BioPAX specification properties are unidirectional for brevity. For example, “participant” property links interactions to physical entities. Paxtools provides additional “inverse” links that allows efficient navigation from a physical entity to the all interactions that it participates.

Syntactic validation: Each operation that modifies the model is internally validated by Paxtools to comply with BioPAX syntax, including RDF well-formedness, domain and range restrictions, bidirectional links, and redundancies.(BioPAX Validator project provides a much more detailed validation and also checks for best practices.)

Seamless handling of different BioPAX levels: Recently released BioPAX Level 3 introduced significant improvements to the naming and structure of the BioPAX at some cost of backwards compatibility. Paxtools supports all three BioPAX levels and provides facilities for upgrading older BioPAX models to Level 3, reducing the burden of working with different BioPAX levels for developers.

Converting to and from different formats: Paxtools can convert PSI-MI models to BioPAX Level 3. In addition, BioPAX models can be exported back to OWL and several other useful formats, including SIF (Simple Interaction Format) and GSEA gene sets.

Efficient traversal and editing via reflection: Paxtools implements the Property Editor design pattern to allow tools to manipulate BioPAX models without actually hard coding property and class names. This pattern considerably simplifies development of BioPAX exporters and other tools and makes it easier to extend and update them to support future changes in the BioPAX specification.

Modular and lightweight structure: Paxtools is currently distributed as a Maven project in a modular structure which allows developers to easily select just the parts of PaxTools they need in their application.

A platform for development of BioPAX software infrastructure: Some projects built on top of Paxtools include: a state-of-the-art persistence system using Java Persistence API integrated with the querying facilities, an advanced validator that allows checking complex rules and the best practices using an extensible framework, an integrator that detects and merges interactions that are equivalent based on their participants, and a graph theoretic query engine for finding biologically relevant connections and subnetworks. These software tools are available as a part of Pathway Commons project. Software that uses Paxtools can natively interact with these tools.

System Requirements:

Program Release Status: Major Update
Program Install Support: Install and Uninstall

Is paxtools your software?

Manage your software

Most Popular

windows default icon Bill Scale and Balance Wedge Keyboard 6.0B
Inputs scale and balance data directly into any Windows programs
windows default icon P7S Viewer 3.1
P7S Signer is a standards-based electronic signature solution Signing electronic documents with P7S Signer
windows default icon English to Hindi Character Converter 9.0
English to Hindi typing software. Its works as you speak Hindi language.
windows default icon TickNTick for Windows
TickNTick (Windows Based) Application is a powerful analytical tool with advanced charting features.
windows default icon Multilizer PDF Translator 2.0
Multilizer translates PDF documents automatically and preserves the layout.