Software

This page provides a overview of our software development activities. Phenoscape supports open development processes and collaboration. All source code we create is available from open source repositories such as Github and Sourceforge, and we work with existing open-source projects whenever possible.

Phenoscape Knowledgebase

One of the chief objectives of the Phenoscape project is to present a centralized repository to store evolutionary phenotype annotations entered by curators and also integrate relevant data imported from partner projects. The Knowledgebase consists of a back-end semantic data store, web services which provide a query API for the data, a web application user interface allowing exploration of the Knowledgebase, and accessory tools for loading data. To meet requirements for scalability, reasoning expressivity, and support for linked data standards, we are developing a our Knowledgebase infrastructure using the RDF and OWL semantic web standards.

• phenoscape-owl-tools—build application for generating the RDF content for the Phenoscape KB, including utilities for converting datasets to OWL and running reasoning tasks
• phenoscape-kb-services—updated web services API for the Knowledgebase. Very early in development so far.
• phenoscape-data—document store for semantically annotated character matrix files. This is the evolutionary data content for the Phenoscape KB.
• owlet—integration of OWL reasoner queries within SPARQL. It parses embedded OWL class expressions and uses an OWL reasoner to either generate a new query by injecting FILTER statements containing the reasoner results, or instead return the reasoner results in SPARQL results format (for use in SPARQL federated queries). Owlet helps us query our database while making use of the full expressivity found in biological ontologies.
• owlery—web service interface for OWL API reasoner queries. In addition to direct DL queries, Owlery provides a SPARQL endpoint powered by Owlet.
• scowl—a Scala library allowing a declarative approach to composing OWL expressions and axioms using the OWL API.

Data curation tools

• Phenex—ontology annotation software tailored for phenotype annotation of evolutionary character matrices. It saves ontology annotations alongside traditional character matrix data using the NeXML format standard for evolutionary data. Also see the Phenex homepage.
• phenoscape-nlp—Phenoscape version of the CharaParser natural-language processing tool, which analyzes the text of character-state descriptions to produce a structured output used to generate proposals for ontological phenotype annotations. We are working to enhance the performance of CharaParser and also to integrate it with Phenex, so that data curators can take advantage of natural-language processing to accelerate their workflow. Developed and maintained by Hong Cui.
• charaparser-unsupervised—implementation of the CharaParser unsupervised learning algorithm in Java, to be incorporated into the main CharaParser code.

Other software products

VTOTool

The VTOTool assembles the VTO by starting from an initial taxonomy (NCBI) and deleting and splicing in group specific taxonomies (e.g., TTO, ATO). It will also add taxonomy from PaleoDB and synonyms from other taxonomic source (e.g., Catalog of Life).

TTOUpdate

This tool (legacy from Phenoscape I) builds the Teleost Taxonomy Ontology (TTO) from a download of the Catalog of Fishes.

Repositories no longer being used/maintained

Classic Phenoscape KB

The first edition of the Phenoscape Knowledgebase is still live at http://kb.phenoscape.org/. It makes use of the following software projects:

• OBD - an ontology-driven datastore developed by the Berkeley Bioinformatics Open-source Projects group. It provides a generic schema for storing ontologies and semantic data expressed with those ontologies. It also includes an automated reasoner used to materialize inferred knowledge into the datastore. The master build script for loading the Phenoscape Knowledgebase is included within the OBD source code.
• Phenoscape OBD data services - a suite of web services on top of OBD to serve as a data access API and foundation for our user-oriented Phenoscape web application. These web services present a RESTful service interface using the Restlet Java API. The specifications of these services are detailed in Data Services.
• Phenoscape web UI - a web application providing user-friendly interfaces for browsing and querying data and ontologies within the Knowledgebase.
• Phenoscape data loader - a Java library providing translations of various data inputs into the OBD model, used within the OBD build script.