We used the Synchronization Tool (an Obo-Edit plugin) to compare XAO to several external ontologies. The tool made it efficient to find and add missing cross-references and terms, and to resolve conflicting data (e.g., differing definitions). By the end of the week, we updated XAO with all relevant terms from the Amphibian Anatomy Ontology (AAO), Vertebrate Anatomy Ontology (VAO), Uber Ontology (UBERON), and Common Anatomy Reference Ontology (CARO).

Erik, VG, and Christina worked hard the rest of the week to make XAO is_a complete and to update definitions, relationships, and synonyms for existing terms. With XAO’s new release, the ontology is now 25% larger than before. The newest version of XAO will be available for downloaded soon from the OBO Foundry.

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 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.

This is a great improvement to our system of file management. We previously used a server for file sharing, which limited us to saving only the current version of each file.  Aside from version control, SVN has other nice features such as automatic file merging if a curator checks in a different version of a file (which might happen if the file on the repository has been updated by another user since the curator first updated their local copy).  Curators also utilize commit comments to document the edits made on a data file.

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.

A few weeks ago, from Sep 27 to Oct 1, we met in the Black Hills of South Dakota with a group of guest data curators and outside advisors to curate high priority papers, refine the curation workflow and Phenex interface, and evaluate the first prototypes for the web-based user interface to the database. Not only did the workshop end up highly productive (see below), we also had a chance to observe the annual roundup of the largest herd of buffalo in North America, swim in cold Sylvan lake, and see Mount Rushmore one evening.

After participant introductions, the day began with several presentations focused on the utility of synthetic research databases (Monte Westerfield) and the way that phenotype-genotype relationships are handled in model organism databases (Suzanna Lewis, Judy Blake) (for the curious, all presentations are available from the Jamboree agenda page). After a brief description of the Phenoscape data policy (Todd Vision), Jim Balhoff introduced the curation software tool, Phenex, which Wasila Dahdul followed with a hands-on curation exercise that involved using Phenex and associated ontologies to annotate phenotypes (characters) using EQ syntax.

We then paired up our guest data curators with project personnel and got them started.  In order to really focus them on EQ syntax and ontology development, we gave each of our guest curators pre-curated Phenex files containing taxon lists, character matrices and free text character and state descriptions from several important publications authored by the guest data curators themselves or within their area of specialty.

Inevitably, curators spent a significant portion of the time on ontology development.  Many new anatomical and quality entities, along with their relationships and definitions, needed to be added to either the Teleost Anatomy Ontology (TAO) or the Phenotype Ontology (PATO) before characters could be expressed in EQ syntax. In the process of training curators to submit new entities to the term trackers for these ontologies we recognized the need for small, dedicated ontology development meetings (e.g. focused on one anatomical region such as the lateral line system in fishes, or all geometrical or shape qualities).  The better the ontology, the more efficient curation will be.

The curation workflow itself is significantly different in Phenex from the Phenote tool, which we used in the first Data Jamboree. It were the issues brought up there that guided the development of Phenex, and indeed this time we noticed a significant improvement in curatorial efficiency.  We were very pleased that by the end of the workshop, the curators had curated 156 characters (~312 character states) for approximately 150 taxa, resulting in over 45,000 EQ annotations.

One frequent topic of discussion was the depth of annotation granularity to which characters should be curated. For example, many systematic characters pertain to shape, frequently with complex descriptors. These can be curated to a high level (e.g. fin: shape) or to a more granular level (e.g. fin: anterior margin rounded). Judy Blake, one of our outside advisors, pointed out that there is a continuum between use of a structured vocabulary and free text.  A reasonable guideline is to say that data specific to an individual study may not warrant the extra effort with granular annotation and should be left as free-text while data that can be compared across studies should be annotated with ontologies at a rather detailed level.

One observation was that the higher the level of granularity, the more often post-composition is required. The mechanics in using multiple post-composition windows in Phenex was somewhat confusing to guest curators. Another important topic involved the difficulty of not having a universal standard across systematic studies – e.g. descriptors pertaining to size and shape cannot easily be extended across systematic studies. This same issue came up at our previous data jamboree, too. John Lundberg suggested that for comparisons of size within a study, an internal grading of character states (a numbered scale from 1 for smallest and higher numbers corresponding to larger sizes) could be implemented, and this is something that we plan to try.

Following two days of curation, we conducted an experiment to assess curation consistency among our group of curators, and to identify areas where consistency can be improved, for example by better curator training, upfront ontology development, or user interface enhancements. We wanted to determine how often, and for what reasons, curators choose divergent EQ conceptualizations for the same character and character states. Five curators encoded EQ annotations for the same 10 character and state descriptions, using Phenex as the software tool. Immediately afterward we reviewed the results with the group. Notably, only two of the 10 characters were annotated identically among all curators. The reasons for why the other annotations differed revealed different interpretations of shape descriptors, inexperience and unfamiliarity with the ontologies and software, and lack of adequate terms in the ontologies (e.g. shape) as major hurdles towards consistency between curators. Identifying these hurdles helps us to prioritize efforts on visualization tools, ontology development and workflow and Phenex development.

In parallel to the curation activities, we discussed the Teleost Taxonomy Ontology (TTO), taxon concepts, and intermediate synonyms.  Peter Midford has added the intermediate synonyms from the Catalog of Fishes (CoF), but many additional synonyms are present in the literature that must be added. We determined that the need to associate synonyms to their references/publications will require an OBO request for one or more database identifiers. At first we considered using the CoF publication database to generate dbxrefs rather than hunting for DOIs or generating our own, but CoF doesn’t contain many of our publications.  Thus we will need to maintain references and unique identifiers for them in our own database.

In another parallel activity, pairs of participants met with Jim Balhoff and Cartik Kothari  for demonstrations of the web user interface. Jim and Cartik are creating the database and web-application for the research community to explore and query the data. The central gateways for entering the database that emerged from those consultations are querying by gene, anatomy, taxon, or publication. The use case-level query to be implemented first is to find evolutionary phenotypes that match a mutant ZFIN phenotype, or, going in the reverse direction, to find ZFIN mutants for a set of phenotypes that differ between taxa. We plan to be able to demonstrate the first version of the interface at the educational outreach workshop at the SICB meeting on Jan. 6, where we also plan to conduct a first series of usability tests. (For those curious, there was much more feedback and suggestions we received, which we compiled all on the project wiki). 

Working our way towards that meeting over the coming months, we will put into place the first components of a production-level database and a fleshed out query interface. Aside from the software development efforts, we are planning ontology development workshops in small groups in the coming year, for example for TAO and for PATO, and we tentatively aim our next outreach workshop for ASIH 2009. In the meantime, we will need to review our data curation priorities in light of our high priority use cases and proof-of-concept experiments for queries across ZFIN and Phenoscape.

We need to especially thank all our speakers for their excellent presentations, They not only gave the audience a varied introduction to ontologies, but also a set of examples of the integrative questions that can be answered using them.   The slideshows for all of these talks are on our wiki but I thought I would provide a brief overview of each one right below as a summary of the workshop. The use of ontologies is just emerging in evolutionary biology, and it is an exciting time to be involved in this field.  As we move forward to use ontologies in evolutionary biology, we discover new requirements and challenges — for example, the challenge of how we create ontologies that are interoperable — so that we can ask big questions that span not only taxonomic groups (such as bees and fishes and mouse and fly) but different knowledge domains (such as phenotype, evolution, and genetics, genomics, medicine).

So here is an overview of each talk.

Barry Smith (NCBO and Univ. Buffalo) kicked off the workshop with “An Introduction to Ontology for Evolutionary Biology“.  He talked about the GO in relation to “doing biology across the genome”, and he described the domain coverage of the ontologies in the OBO foundry.  He introduced basic ontological concepts and relations, including several new ones that must be made in creating ontology resources for evolutionary biology.  He is currently working with a number of groups including EoL to develop an Environment Ontology (EnvO).

Chris Mungall (Lawrence Berkeley Labs) presented “PATO: The Phenotype and Trait Ontology“.  He focused on why we need ontologies (for example, to solve the data integration problem), introduced “phenotype” and the newly proposed Homologous_to relation. 

Monte Westerfield (Univ. Oregon, Zebrafish Information Network) talked about the use of ontologies in “Linking Animal Models and Human Diseases“.  Just as BLAST can be used to connect animal genes to human genes, shared ontologies and syntax can connect mutant phenotypes to candidate human disease genes. He talked about the importance of curation consistency and how it can be measured and increased.  His proof of principle example, comparing ontology-annotated phenotypes in human and zebrafish demonstrated that genes associated with human diseases can be identified.

It was then my turn to introduce Phenoscape in my talk “An Introduction to the Use of Ontologies in Linking Evolutionary Phenotypes to Genetics“.  Just as animal model phenotypes can be compared to human phenotypes using ontologies, so can animal model phenotypes be compared to phenotypes of multiple species – thus linking comparative evolutionary data to model organism genetics.  I presented several use cases for fishes and described the rapid progress that we have made in developing new ontologies, extending existing ones as well as some of the challenges involved in multispecies ontologies.

Jim Balhoff (NESCent, Phenoscape) presented the software that he has developed for curation of evolutionary phenotypes “Phenote: Curation Software for Evolutionary Phenotypes“.  Originally developed for ontology-based annotation of genetic mutant phenotypes and widely used by model organism curators, Jim described how he has extended and reconfigured Phenote to handle comparative evolutionary data, and he also spoke about his plans to integrate ontology-based phenotype descriptions into the NeXML file format.

Melissa Haendel (Zebrafish Information Network) presented “The Common Anatomy Reference Ontology (CARO) and queries across species“.  She described current anatomy ontologies and why we build them, and the standardization and integration of anatomy ontologies using CARO.  She explained how the issues created by homology can be addressed, including the draft definition of the Homologous_to relationship, and she described how homology data can be used with ontologies to query across species. 

After lunch we had about a ½ hour of “Lightning Talks” during which workshop attendees had an opportunity to introduce themselves and give brief (2-3 minutes) descriptions of their interest in ontologies.  Several attendees seized the chance and made the audience aware of their ontology building efforts.

After that, Ann Maglia (Missouri Univ. of Science and Technology, AmphibAnat) resumed the regular talks and spoke about her group’s work in the “Development of the Amphibian Anatomical Ontology“.  This ontology was driven by the need of the amphibian community to standardize their terminology and thus integrate their comparative work.  She is exploring automated techniques to reduce manual efforts and enhance existing, manually created ontologies.  Ann also described the relational database (RDBOM), the modularization, and web-based community curation methods built by her group and community. 

Martin Ramirez (Museo Argentino de Ciencias Naturales) in his talk “Ontologies, Image Databases, and Evolutionary Biology” described the use of the spider ontology to link images from the spider Tree of Life project to a phylogenetic dataset and a body of image annotation.  He discussed a series of challenges, such as issues involving the alignment of ontologies using homology relations and the “combinability” of ontologies.

Todd Vision (Univ. North Carolina, NESCent), presented “Ontologies and the Identification of Candidate Genes for Complex Traits“.  He considered the qualities of “good” candidate genes and how they are typically discovered and ranked, and then described a test case where ontology terms were used in picking candidate genes computationally (using an approach named CAESAR) for Type 2 Diabetes.  This approach has a promising application for evolutionary traits in non-model organisms.

Peter Midford (Univ. Kansas, Phenoscape) introduced taxonomy ontologies with his talk “Names, Ranks, Clades, and Taxonomy Ontologies” — what’s in them, how they are built and why one would use one.  The issue of what species are ontologically, more specifically whether species are classes or instances or both, impacts not only the way an ontology is built but also what kinds of assertions can be inferred or not.

Suzanna Lewis (Lawrence Berkeley Lab, BBOP) and I wrapped up by listing some of the challenges for the evolutionary biology community that became apparent over the day. 

Especially prominent was the need for communication among evolutionary biologists developing ontologies so that they can be developed from the outset to be interoperable.  This and many related comments from attendees suggested that an NSF-RCN (Research Coordination Network) proposal might be the best next step and an effective mechanism to fund and promote communication among and between evolutionary biologists, ontologists, and model organism biologists.

As a result, we are now beginning to gather ideas, objectives, and possible participants for an RCN proposal. If you have thoughts on this, or if you are interested in participating, we would love to hear from you – leave a comment here, or email me (pmabee{at}usd{dot}edu).

• Changed version scheme again, hopefully for the last time
• Bug fixes to in-table editing
• Added TAO to the Quality field for use in post-composition
• Included built-in Phenoscape interface layout
• Re-ordered input fields to better match curation workflow

• Annotations can now be edited directly in the table

• Changed version back to 1.6 beta to be inline with NCBO versioning
• Term info panel now shows information for terms selected in Complete Ontology Tree View
• Window close button now works on specimen picker window
• User can turn off table sorting by clicking again on a reverse-sorted table column
• Rows can be dragged from Taxon list into any other table
• Dropped rows are selected in target table
• Fixed bug where dragged rows were not being copied as new rows (editing would screw up original)
• Editor fields no longer grow wider than the panel they’re in
• Selected rows attempt to stay visible when table is re-sorted
• Added updated collection code ontology

This is also the first release uploaded to and downloadable from the OBO SourceForge site as a file release, and can therefore be linked to indefinitely. Previously we were putting up the updated downloads on the Phenoscape wiki, which had the nasty effect that upon every update all earlier links no longer pointed to the correct version (but simply always to the latest).  

• New feature – “Scratch lists” (see below)
• Browse all the ontologies using a tree view, select terms, and drag them onto fields to use them as values
• New, clean, interface look

You can open Scratch lists from the View menu. First you will see a blank table.  You can add rows to the table and give them whatever name you want.  Select a row and press the table-looking button in the component’s toolbar.  A character table will open somewhere with that name.  You can make new annotation rows in this table and then drag them into the main annotation table.  You might want to make a couple different scratch lists that have particular values pre-filled in that you want to use again and again.  This makes life a lot easier for Wasila, our data curator,  when particular species always use the same voucher evidence. The caveat is that right now the scratch tables aren’t saved. That will require data adapter work.

• Museum collection code name completion when entering specimens for a taxon.
• Separate editable table for entering specimens for a taxon.
• Field for spatial ontology.
• Post-composition enabled for PATO fields.

• Taxon Comments field
• Publication Name field
• changed Taxon field to Valid Name
• write out starter NEXUS file for Taxon List (in phylogeny window)
• press Cmd-Return to enter current value and advance to next character while editing the same field
• in-progress Save (Cmd-S)
• simultaneous save of main document and taxon list files
• lock layout of interface panels (look in the Settings menu – Nicole Washington added this, it’s really handy)