The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013

The PRoteomics IDEntifications (PRIDE, http://www.ebi.ac.uk/pride) database at the European Bioinformatics Institute is one of the most prominent data repositories of mass spectrometry (MS)-based proteomics data. Here, we summarize recent developments in the PRIDE database and related tools. First, we provide up-to-date statistics in data content, splitting the figures by groups of organisms and species, including peptide and protein identifications, and post-translational modifications. We then describe the tools that are part of the PRIDE submission pipeline, especially the recently developed PRIDE Converter 2 (new submission tool) and PRIDE Inspector (visualization and analysis tool). We also give an update about the integration of PRIDE with other MS proteomics resources in the context of the ProteomeXchange consortium. Finally, we briefly review the quality control efforts that are ongoing at present and outline our future plans.

Reactome: a database of reactions, pathways and biological processes

Reactome (http://www.reactome.org) is a collaboration among groups at the Ontario Institute for Cancer Research, Cold Spring Harbor Laboratory, New York University School of Medicine and The European Bioinformatics Institute, to develop an open source curated bioinformatics database of human pathways and reactions. Recently, we developed a new web site with improved tools for pathway browsing and data analysis. The Pathway Browser is an Systems Biology Graphical Notation (SBGN)-based visualization system that supports zooming, scrolling and event highlighting. It exploits PSIQUIC web services to overlay our curated pathways with molecular interaction data from the Reactome Functional Interaction Network and external interaction databases such as IntAct, BioGRID, ChEMBL, iRefIndex, MINT and STRING. Our Pathway and Expression Analysis tools enable ID mapping, pathway assignment and overrepresentation analysis of user-supplied data sets. To support pathway annotation and analysis in other species, we continue to make orthology-based inferences of pathways in non-human species, applying Ensembl Compara to identify orthologs of curated human proteins in each of 20 other species. The resulting inferred pathway sets can be browsed and analyzed with our Species Comparison tool. Collaborations are also underway to create manually curated data sets on the Reactome framework for chicken, Drosophila and rice.

Innate Immune Signaling Pathways in Reactome (94.13)

Toll-like receptors (TLR) play a key role in the innate immune system, providing vertebrates with a critical first line of defense against invading microbial pathogens. With the increasing body of molecular data relating to TLR function, organizing this information is useful to biologists and immunologists. We have used Reactome (www.reactome.org), a manually curated pathway database, to organize TLR data so that it can be viewed like an electronic textbook. TLR signaling cascades were authored by experts, maintained by the Reactome editorial staff and cross-referenced to publicly available bioinformatics resources. The Reactome data model generalizes the concept of a biochemical reaction to encompass any transformation of an input set of physical entities into an output set, and thus allows us to integrate TLR cascades with other innate immune processes, adaptive immunity, metabolic pathways, and other signaling processes. Since TLR-signaling molecules and pathways and the signaling pathways they initiate are highly conserved, Reactome provides pathway inference for 22 species based upon improved orthology prediction methods. A new entity-level pathway viewer and pathway analysis tools facilitate searching and visualizing pathway data and the analysis of user-supplied high-throughput data sets. All data content and software can be freely used and redistributed under open source terms.

Countertransference in the nurse-patient relationship: a review of the literature

Countertransference is a psychoanalytical concept which, when applied to nursing, refers to the unconscious response of the nurse to the patient. Psychoanalytical concepts such as the unconscious are infrequently mentioned in the nursing literature and have received little research attention. In this paper the literature about the nurse's countertransference is reviewed. In order that the psychodynamic aspects of this phenomenon are more fully appreciated, both the concepts of the unconscious and transference are first described. The nurse's countertransference has many expressions. The literature under review has highlighted the expression of countertransference through physical symptoms, through the nurse's level of involvement with the patient and through the nurse's positive and negative descriptions of patients. The value of recognizing countertransference is universally acknowledged. It is suggested that countertransference in the nurse-patient relationship should be explored further. The knowledge provided would help provide greater insights into the nurse-patient relationship, and ultimately will be reflected in the quality of care which the patient receives.