Some proposed changes to PATO:

• Consolidate relational and monadic branches: One of the more major decisions was to remove the distinction between the “relational” and “monadic” branches of PATO. The relational terms can be descendants of the monadic terms which are pre-composed with a reference to a dependent entity. This change would be a major improvement helping to relate terms dealing with similar concepts and for inference using these concepts.
• Continuums: Add a relationship ‘ranges_from’ which can be used to specify a continuum of values between two indicated qualities.  Example: a color grading “from yellow to brown”.
• Position: Remove term ‘position’ after moving its children to more appropriate places.
• Enable directional references: Add classes describing directions a structure can be pointed.  These classes should include pre-composed logical definitions drawing on the spatial ontology. An example would be ‘directed posteriorly’.
• Spatial term review: Review all existing PATO terms referencing spatial aspects, and verify that they are based on logical definitions using the spatial ontology.
• Size vs. shape: Several children of ‘size’ were noted to actually be types of ‘shape’. Many of these were noted and several were immediately revised by George Gkoutos.  This discussion revealed that many free-text characters defined by biologists refer to size-sounding terms when they are actually describing changes in shape.
• Changes in various term definitions:
  • PATO:1485 should be obsoleted and two new separate terms, ‘condensed’ and ‘compressed’ (as a synonym of ‘flattened’) should be added. ‘Condensed’ is considered to be a type of ‘structure’, while ‘flattened’ is a ‘shape’ instead of a ‘curvature’. All children of ‘flattened’ should be reviewed to remove references to ‘curvature’.
  • Improved definition for ‘morphology’ referencing “shape or size or structure”.
  • Clarified terms ‘surface feature shape’ and ‘texture’. The parent term ‘surface shape’ was obsoleted while ‘surface feature shape’ is retained as a shape with a repeated feature on a surface. A ‘has_repeated_part’ relation should be added to be used in pre-composed subclasses of ‘surface feature shape’, linking them to specific shapes.
  • Add a term defining ‘spatial density’. The existing ‘density’ term refers to the physics concept.
• Spatial pattern: We proposed reworking the ‘spatial pattern’ term hierarchy to logically reference other terms which the given pattern is in respect to (structures, colors, etc.). The ‘color pattern’ term should be moved under ‘spatial pattern’.
• Synonyms: We discussed some community-specific term labels for various PATO classes.  There is an existing OBO standard for how to implement these as synonyms. Community-specific applications would need to support display of the appropriate synonym.
• Comparative relations: Generalize existing comparative relations in PATO.  For example, Instead of ‘increased_in_magnitude_relative_to’, it will be ‘increased_in_value_relative_to’.
• Qualitative branch: Clean up and better document ‘qualitative’ hierarchy (which is used for various logical “shortcuts”).

EQ representation issues:

• Size bins: Relative size characters (small, medium, large) can be represented by creating (within a given annotation application) anonymous subclasses of size which are related to each other in the appropriate way using relations such as ‘increased_in_magnitude_relative_to’.  This will provide the appropriate relative size inferencing for the given character states, but, as in the original paper, not be readily comparable to size classes created for characters in other studies.
• Negation: When describing a phenotype that is simply “not something else”, e.g. ‘not round’, the complement_of operator should be used in an OWL class expression.
• Comparative/relative qualities should not be conflated with relational (or, better, dependent) qualities. Comparative relations such as ‘increased_in_value_relative_to’ can be used to relate one EQ to another.
• Phenex and other annotation tools should provide enhanced interfaces for these special representation issues: creating comparative EQs by simply entering a relative entity or taxon, a simple means to say things like ‘not round’, and a way to create local groups of relatively ordered qualities for a given character (e.g. small, medium, large).

All Phenex users should replace their current copy of Phenex with the latest release. It can be downloaded from the Phenex homepage on the Phenoscape wiki.

The 1.0 release of Phenex includes features allowing it to be used for work with any taxonomic group. It can be configured to load any user-specified OBO ontologies, and users can specify the sets of ontology terms available within each type of entry field.  Also, this release uses the latest version of the NeXML schema for its file format, storing ontology annotations in an embedded RDFa-compliant format.

We look forward to working with anyone interested in making use of Phenex with their own data. Phenex is open source software, released under the MIT license.

This project also served as an important use-case for the NeXML phylogenetics exchange language.  Although Phenex has used NeXML for over a year, the annotations it generated were not readable by the NeXML package for Mesquite. During and after the database interoperability hackathon last spring, the NeXML developers worked out a standard for annotation and a common java library for parsing NeXML.  Kasia’s project served as a test of that interoperability, and the final product demonstrates that we have achieved it.

Although I was the primary mentor for this project, it would not have been possible without the contributions of Jim, who was co-mentor and who made some Phenex changes to support us, or of Rutger Vos, who pulled the annotation format together and provided us with lots of advice on the NeXML language and library implementation.

Finally, check out Kasia’s walk through of the project.  Her blog also traces the progress and frustrations of learning about ontologies, Mesquite, NeXML and the GraphViz Dot language, all in one summer.  Thank you Kasia!

This release has a few new features and a number of bug fixes:

Features:

Bugs fixed:

• Copy and paste of terms in the Phenotypes table works consistently now.
• The post-composition editor no longer disappears after tabbing out of the genus field when running on Java 6.
• The menubar no longer disappears after using the post-composition editor.

Phenex replaces Phenote as our data curation tool.  Phenote was developed by the Berkeley Bioinformatics and Ontologies Project to facilitate the annotation of biological phenotypes using ontologies.  By creating a custom configuration of Phenote to support our data requirements, we were able to immediately begin annotating phenotypes.  Because Phenote provides a flat table of annotations, it works well for curation of the prominent phenotypes of a few genotypes at a time, such as in model organism mutants.  However, evolutionary data is usually collected in the form of a character by taxon matrix, recording a value for each character for every taxon.  Over time we added several custom interface features to Phenote to better support annotation of evolutionary data.  However curation of data from real publications at our first Data Jamboree, in April 2008, revealed that our initial workflow was cumbersome and error prone.

Like Phenote, Phenex facilitates the construction of annotations using ontology terms.  In Phenex, however, the data model and interface are organized in a format that will be familiar to any evolutionary biologist who has used a character matrix.  The new design addresses several requirements highlighted by user testing at the April Data Jamboree:

• Manage independent lists of Taxa, Characters, and States, tied together via a data matrix.
• Facilitate entry of basic free text matrix data by undergraduate assistants.
• Allow morphology experts to focus on translating character state descriptions into ontology annotations without simultaneously managing unwieldy lists of taxa.
• Easily import data from published NEXUS matrix files.
• Include ontology annotations within a standard evolutionary data matrix file format.

We addressed this last requirement by adopting the new NeXML file format.  Being an XML schema, NeXML allows us to embed ontological annotations directly within standard evolutionary data.  Thus the standard data in Phenex documents should be usable in any evolutionary analysis software which supports NeXML.

Although Phenex began as an offshoot of Phenote, it is now a completely separate application hosted at the OBO project site.  Like Phenote, Phenex builds upon OBO-Edit as an application framework for working with ontologies.  While Phenex has been developed with the needs of Phenoscape in mind, it should be useful to anyone working with ontologies and evolutionary data.  We hope it can become a general tool for evolutionary biologists incorporating ontologies into their work.  More information about Phenex can be found on its homepage, including instructions for downloading the application and obtaining its source code.