We have also improved our software and data release processes so that the public Knowledgebase can easily keep up with new developments and the latest data updates from our curators. Looking forward, the next major feature to be added to the Knowledgebase is a faceted browsing interface which is currently under development. This interface should help provide an overview of how the data are organized within the various ontologies used in the Knowledgebase.

The first issue is that we are interested in changes in phenotype, not simply matching phenotypes.  For phenotypes associated with mutants of model organism mutants, it is understood that they vary with respect to the wild type.  For taxa, however, this means looking for taxonomic nodes where variation in a phenotype is observed among the children of the node.  For example, there are nine species within the genus Aspidoras with annotations for the shape of the opercle bone.  Of these, eight exhibit opercle bones with round shape, but the ninth (A. pauciradiatus) is annotated with a triangular opercle.  In contrast, all three annotated species of the related Hoplosternum are annotated with a triangular opercle.  Thus there is detectable variation in opercle shape within the children of Aspidoras, but not within  Hoplosternum - suggesting that change in opercle shape has occurred somewhere among the descendants of  Aspidoras. For our analysis, identifying variation among descendants is important.

Thus, our search for shared variation in phenotypes focuses on matching phenotypes associated with genes with phenotypes of taxa showing variation.  However we are looking for matches at a larger scale than single phenotypes; we are looking for matches across the set of phenotypes affected by a gene or the set of features that have changed among the descendants of a taxonomic node.   We refer to these sets of phenotypes as the ‘phenotypic profile’ of a gene or taxon, following a seminal paper by Washington et al. 2009.  Washington et al. propose four metrics (three based on ‘information content’) to score matches between the sets of phenotypes in a pair of profiles.

In the course of developing the search, we have encountered several important differences in curation approach between ZFIN and Phenoscape.  In some cases tehre are different uses of PATO to model the same phenotype, for example the absence of an entity.  In other cases ZFIN uses a quality ‘abnormal’ that applies to mutants, but not in a taxonomic, comparative sense, which means these phenotypes will be inaccessible to us.  Thus, implementing this search is helping us to better understand our data and our choices in modeling the data and how it interoperates with other ontology-based data.  Such reflection would have been difficult or impossible without the use of ontologies to represent the phenotypes.

Phenoscape KB integrates phenotypic data from genetic studies of zebrafish with evolutionarily variable phenotypes from the literature of fishes. It currently contains 333,987 phenotype statements about 2,310 taxa (mainly ostariophysan fishes), from 51 publications, and 11,267 phenotype statements about 2,953 genes retrieved from ZFIN (zfin.org). You can explore these data by searching for anatomical terms, taxa (by Latin name), or genes (by ZFIN gene symbol).

You will notice that entering search terms is simplified by auto-completion, so typing the first few letters of a term, taxon, or gene symbol often suffices. There is also a “tag cloud” on the front page that shows the terms most frequently occurring in the KB – click on a term to search for data relevant to that term.

The beta release was first announced at the ASIH meetings in Portland, Oregon this past summer in connection with “Ontologies for Ichthyology and Herpetology” workshop (https://www.phenoscape.org/wiki/ASIH09_workshop).

We expect to make a broader release announcement in February 2010, after we have incorporated the feedback from early users and implemented a number of important features that did not make it into the beta release.

So please take a few minutes to explore Phenoscape KB and send us your feedback and ideas (help@phenoscape.org).