Summary: The Quest for Orthologs (QfO) is an open collaboration framework for experts in comparative phylogenomics and related research areas who have an interest in highly accurate orthology predictions and their applications. We here report highlights and discussion points from the QfO meeting 2015 held in Barcelona. Achievements in recent years have established a basis to support developments for improved orthology prediction and to explore new approaches. Central to the QfO effort is proper benchmarking of methods and services, as well as design of standardized datasets and standardized formats to allow sharing and comparison of results. Simultaneously, analysis pipelines have been improved, evaluated and adapted to handle large datasets. All this would not have occurred without the long-term collaboration of Consortium members. Meeting regularly to review and coordinate complementary activities from a broad spectrum of innovative researchers clearly benefits the community. Highlights of the meeting include addressing sources of and legitimacy of disagreements between orthology calls, the context dependency of orthology definitions, special challenges encountered when analyzing very anciently rooted orthologies, orthology in the light of whole-genome duplications, and the concept of orthologous versus paralogous relationships at different levels, including domain-level orthology. Furthermore, particular needs for different applications (e.g. plant genomics, ancient gene families and others) and the infrastructure for making orthology inferences available (e.g. interfaces with model organism databases) were discussed, with several ongoing efforts that are expected to be reported on during the upcoming 2017 QfO meeting.

Accurate determination of the evolutionary relationships between genes is a foundational challenge in biology. Homology — evolutionary relatedness — is in many cases readily determined based on sequence similarity analysis. By contrast, whether or not two genes directly descended from a common ancestor by a speciation event (orthologs) or duplication event (paralogs) is more challenging, yet provides critical information on the history of a gene. Since 2009, this task has been the focus of the Quest for Orthologs (QFO) consortium. The 6th QFO meeting took place in Okazaki, Japan in conjunction with the 67th National Institute for Basic Biology conference. Here we report recent advances, applications, and oncoming challenges that were discussed during the conference. Steady progress has been made toward standardisation and scalability of new and existing tools. A feature of the conference was the presentation of a panel of accessible tools for phylogenetic profiling and several developments to bring orthology beyond the gene unit—from domains to networks. This meeting brought into light several challenges to come: leveraging orthology computations to get the most of the incoming avalanche of genomic data, integrating orthology from domain to biological network levels, building better gene models, and adapting orthology approaches to the broad evolutionary and genomic diversity recognized in different forms of life and viruses.

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Vast amounts of medical information reside within text documents, so that the automatic retrieval of such information would certainly be beneficial for clinical activities. The need for overcoming the bottleneck provoked by the manual construction of ontologies has generated several studies and research on obtaining semi-automatic methods to build ontologies. Most techniques for learning domain ontologies from free text have important limitations. Thus, they can extract concepts so that only taxonomies are generally produced although there are other types of semantic relations relevant in knowledge modelling. This paper presents a language-independent approach for extracting knowledge from medical natural language documents. The knowledge is represented by means of ontologies that can have multiple semantic relationships among concepts.

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