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BackgroundLarge-scale mutagenesis projects are ongoing to improve our understanding about the pathology and subsequently the treatment of diseases. Such projects do not only record the genotype but also report phenotype descriptions of the genetically modified organisms under investigation. Thus far, phenotype data is stored in species-specific databases that lack coherence and interoperability in their phenotype representations. One suggestion to overcome the lack of integration are Entity-Quality (EQ) statements. However, a reliable automated transformation of the phenotype annotations from the databases into EQ statements is still missing.ResultsHere, we report on our ongoing efforts to develop a method (called EQ-liser) for the automated generation of EQ representations from phenotype ontology concept labels. We implemented the suggested method in a prototype and applied it to a subset of Mammalian and Human Phenotype Ontology concepts. In the case of MP, we were able to identify the correct EQ representation in over 52% of structure and process phenotypes. However, applying the EQ-liser prototype to the Human Phenotype Ontology yields a correct EQ representation in only 13.3% of the investigated cases.ConclusionsWith the application of the prototype to two phenotype ontologies, we were able to identify common patterns of mistakes when generating the EQ representation. Correcting these mistakes will pave the way to a species-independent solution to automatically derive EQ representations from phenotype ontology concept labels. Furthermore, we were able to identify inconsistencies in the existing manually defined EQ representations of current phenotype ontologies. Correcting these inconsistencies will improve the quality of the manually defined EQ statements.

The genome sequences of many important Triticeae species, including bread wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.), remained uncharacterized for a long time because their high repeat content, large sizes, and polyploidy. As a result of improvements in sequencing technologies and novel analyses strategies, several of these have recently been deciphered. These efforts have generated new insights into Triticeae biology and genome organization and have important implications for downstream usage by breeders, experimental biologists, and comparative genomicists. transPLANT (http://www.transplantdb.eu) is an EU-funded project aimed at constructing hardware, software, and data infrastructure for genome-scale research in the life sciences. Since the Triticeae data are intrinsically complex, heterogenous, and distributed, the transPLANT consortium has undertaken efforts to develop common data formats and tools that enable the exchange and integration of data from distributed resources. Here we present an overview of the individual Triticeae genome resources hosted by transPLANT partners, introduce the objectives of transPLANT, and outline common developments and interfaces supporting integrated data access.