Informatics

PhenoScape Software Components

We are building the following database and software components for this project.

• An editor to create, maintain, and manage the taxonomy of Ostariophysi. We will focus on a reference taxonomy derived from the Catalog of Fishes.
  A taxonomy is a hypothesis about the phylogeny of clades of organisms, and as such we need to allow ultimately for different taxonomies that a user can choose from.
• An editor to create, maintain, and manage the anatomical ontology for Ostariophysi (TAO).
• An editor to create, maintain, and manage phenotype annotations in EQ syntax ("EQ Editor"). This editor needs to tightly integrate with the character annotation workflow that morphologists collaborating in the project will follow.
• A database and web-application to store the taxonomies, ontologies, and phenotype data. The web-application will allow scientists to browse and query the ontologies as well as the phenotype data.
  Initially, the query capabilities will concentrate on implementing a select set of "use-cases", research questions that show the utility of the approach. Ultimately, we will build interfaces that allow researchers to ask open-ended questions of the data.

All software and database developments will be made freely available as open-source software, and we will make use of existing open-source projects as much as possible. For example, the ontology editor is being built on top of OBO-Edit, and the EQ Editor will be based on, or synergize with, Phenote.

Software roadmap

At present, we have implemented

1. A relational database to hold ontological definitions of concepts from ontologies such as the TTO, TAO, and PATO, and curated data from NeXML files
2. A reasoner to extract implicit information by combining user assertions and inference rules such as transitive relations
3. A query API to extract assertions from the database using combinations of taxon, entity, and quality parameters
4. A front end application to query the database by Entity Quality (EQ) combinations

APIs

Proposals

• Ontology Data Service API Description