Janos X. Binder

Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data

The current version of the Human Disease Ontology (DO) (http://www.disease-ontology.org) database expands the utility of the ontology for the examination and comparison of genetic variation, phenotype, protein, drug and epitope data through the lens of human disease. DO is a biomedical resource of standardized common and rare disease concepts with stable identifiers organized by disease etiology. The content of DO has had 192 revisions since 2012, including the addition of 760 terms. Thirty-two percent of all terms now include definitions. DO has expanded the number and diversity of research communities and community members by 50+ during the past two years. These community members actively submit term requests, coordinate biomedical resource disease representation and provide expert curation guidance. Since the DO 2012 NAR paper, there have been hundreds of term requests and a steady increase in the number of DO listserv members, twitter followers and DO website usage. DO is moving to a multi-editor model utilizing Protégé to curate DO in web ontology language. This will enable closer collaboration with the Human Phenotype Ontology, EBIs Ontology Working Group, Mouse Genome Informatics and the Monarch Initiative among others, and enhance DOs current asserted view and multiple inferred views through reasoning.

DISEASES: text mining and data integration of disease-gene associations.

Text mining is a flexible technology that can be applied to numerous different tasks in biology and medicine. We present a system for extracting disease-gene associations from biomedical abstracts. The system consists of a highly efficient dictionary-based tagger for named entity recognition of human genes and diseases, which we combine with a scoring scheme that takes into account co-occurrences both within and between sentences. We show that this approach is able to extract half of all manually curated associations with a false positive rate of only 0.16%. Nonetheless, text mining should not stand alone, but be combined with other types of evidence. For this reason, we have developed the DISEASES resource, which integrates the results from text mining with manually curated disease-gene associations, cancer mutation data, and genome-wide association studies from existing databases. The DISEASES resource is accessible through a web interface at http://diseases.jensenlab.org/, where the text-mining software and all associations are also freely available for download.

COMPARTMENTS: unification and visualization of protein subcellular localization evidence.

Information on protein subcellular localization is important to understand the cellular functions of proteins. Currently, such information is manually curated from the literature, obtained from high-throughput microscopy-based screens and predicted from primary sequence. To get a comprehensive view of the localization of a protein, it is thus necessary to consult multiple databases and prediction tools. To address this, we present the COMPARTMENTS resource, which integrates all sources listed above as well as the results of automatic text mining. The resource is automatically kept up to date with source databases, and all localization evidence is mapped onto common protein identifiers and Gene Ontology terms. We further assign confidence scores to the localization evidence to facilitate comparison of different types and sources of evidence. To further improve the comparability, we assign confidence scores based on the type and source of the localization evidence. Finally, we visualize the unified localization evidence for a protein on a schematic cell to provide a simple overview. Database URL: http://compartments.jensenlab.org

Ten simple rules for organizing an unconference.

An academic conference is a traditional platform for researchers and professionals to network and learn about recent developments and trends in a particular academic field [1–4]. Typically, the organizing committees and sponsors decide the main theme and sub-topics of the conference and select the presenters based on peer-reviewed papers [5]. The selected speakers usually share their research with a large audience by means of presentations and posters. However, the most stimulating discussions generally take place over coffee breaks when attendees can interact with each other and discuss various topics, including their own research interests, in a more informal manner [1, 6, 7], while expanding their own professional networks. An emphasis on facilitating such informal/networking interactions is a central focus of “unconventional conferences”—or “unconferences.” While many people may not yet have taken part in an unconference, the concept has been around for more than two decades. Events with unconference formats, beginning as early as 1985, include Open Space Technology, Foo Camp, BarCamp, Birds of a Feather, EdCamp, ScienceOnline, and many others. The success of these events has made the unconference format increasingly popular and widely known [8–11]. Unlike traditional conferences, an unconference is a participant-oriented meeting where the attendees decide on the agenda, discussion topics, workshops, and, often, even the time and venues. The informal and flexible program allows participants to suggest topics of their own interest and choose sessions accordingly. The format provides an excellent opportunity for researchers from diverse disciplines to work collaboratively on topics of common interest. The overarching goal for most unconferences is to prioritize conversation over presentation. In other words, the content for a session does not come from a select number of individuals at the front of the room, but is generated by all the attendees within the room, and, as such, every participant has an important role. Advantages of the unconference format include: a focus on topics that are relevant to the attendees (because they suggested them), an opportunity for teamwork development, flexibility of schedule, and an emphasis on contributions from every participant. The relationships built during an unconference often continue well past the event. The interactions can lead to productive collaborations, professional development opportunities, and a network of resources and are very effective at building a community amongst participants. The unconference format, therefore, gives participants experience in working together, and this can change how they think about their day-to-day work. A range of articles offer tips and advice for organizing and delivering aspects of scientific conferences and meetings or observations on features of successful meetings [5, 12, 13], including several from the PLOS Computational Biology “Ten Simple Rules” collection [14–16]. While the rules presented in this article are of particular relevance to the organization of unconferences, several of these points are also useful and complementary guidelines for organizing other kinds of events.