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.
The live KB can be accessed at http://kb.phenoscape.org/. For more
information on the Phenoscape Knowledgebase see these wiki pages:
Software components:
- 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. Written in Scala using the OWL API.
- phenoscape-kb-services—updated
web services API for the Knowledgebase. Written in Scala using
Spray web services.
- phenoscape-kb-ui—Phenoscape
KB web user interface. A client-side web application using AngularJS.
- phenoscape-data—document
store for semantically annotated character matrix files. This is the
evolutionary data content for the Phenoscape KB. NeXML.
- 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). Written in
Scala using OWL API and Jena.
- owlery—web service interface
for OWL API reasoner queries. In addition to direct DL queries, Owlery
provides a SPARQL endpoint powered by Owlet. Written in Scala using
Spray web services.
- scowl—a Scala library allowing a
declarative approach to composing OWL expressions and axioms using the
OWL API. Written in Scala.
- RPhenoscape— R package that
facilitates interfacing with the Phenoscape Knowledgebase for
searching ontology terms, querying data matrices, obtaining dependency
matrices, and computing semantic similarity metrics.
- OntoTrace — tool used to
query the KB for a synthetic character matrix of asserted and inferred
presence/absence characters for anatomical structures. OntoTrace is
also accessible by using
RPhenoscape to query the web
services API.
- 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 active projects
- presence-absence-matrix—tool
for querying a local copy of the Phenoscape KB and generating a
synthetic presence/absence character matrix using anatomical
reasoning.
- kb-sparql-queries—miscellaneous
queries for use with the Phenoscape KB SPARQL endpoint. Used for
reports and may also aid in navigating the KB RDF datamodel.
- phenoscape.github.com—source
for Phenoscape public website
- phenoscape-ontologies—ontologies
developed internally for the Phenoscape project. Currently contains
only a demonstration ontology for presence/absence reasoning.
- Taxonomy-Ontology-Tool—tool
used to assemble the VTO by starting from an initial taxonomy (NCBI)
and deleting and splicing in group specific taxonomies (e.g., TTO,
ATO).
- phenoday-reasoning-paper—Demonstration
code for paper
submission to the
Bio-ontologies SIG Phenotype Day
at ISMB 2014.
Exploratory projects
These are in a state of preliminary development or just for
exploration/testing.
- vue2owl—Convert a VUE document
to an OWL ontology. Scala.
Repositories no longer being used/maintained
Classic Phenoscape KB
The first edition of the Phenoscape Knowledgebase is still live at
http://fish.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.
- PhenoscapeOBD-WS - 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.
- PhenoscapeWeb - a web
application providing user-friendly interfaces for browsing and
querying data and ontologies within the Knowledgebase, written using
Ruby on Rails.
- PhenoscapeDataLoader -
a Java library providing translations of various data inputs into the
OBD model, used within the OBD build script.
Others
