Triage by ranking to support the curation of protein interactions

Today, molecular biology databases are the cornerstone of knowledge sharing for life and health sciences. The curation and maintenance of these resources are labour intensive. Although text mining is gaining impetus among curators, its integration in curation workflow has not yet been widely adopted. The Swiss Institute of Bioinformatics Text Mining and CALIPHO groups joined forces to design a new curation support system named nextA5. In this report, we explore the integration of novel triage services to support the curation of two types of biological data: protein–protein interactions (PPIs) and post-translational modifications (PTMs). The recognition of PPIs and PTMs poses a special challenge, as it not only requires the identification of biological entities (proteins or residues), but also that of particular relationships (e.g. binding or position). These relationships cannot be described with onto-terminological descriptors such as the Gene Ontology for molecular functions, which makes the triage task more challenging. Prioritizing papers for these tasks thus requires the development of different approaches. In this report, we propose a new method to prioritize articles containing information specific to PPIs and PTMs. The new resources (RESTful APIs, semantically annotated MEDLINE library) enrich the neXtA5 platform. We tuned the article prioritization model on a set of 100 proteins previously annotated by the CALIPHO group. The effectiveness of the triage service was tested with a dataset of 200 annotated proteins. We defined two sets of descriptors to support automatic triage: the first set to enrich for papers with PPI data, and the second for PTMs. All occurrences of these descriptors were marked-up in MEDLINE and indexed, thus constituting a semantically annotated version of MEDLINE. These annotations were then used to estimate the relevance of a particular article with respect to the chosen annotation type. This relevance score was combined with a local vector-space search engine to generate a ranked list of PMIDs. We also evaluated a query refinement strategy, which adds specific keywords (such as ‘binds’ or ‘interacts’) to the original query. Compared to PubMed, the search effectiveness of the nextA5 triage service is improved by 190% for the prioritization of papers with PPIs information and by 260% for papers with PTMs information. Combining advanced retrieval and query refinement strategies with automatically enriched MEDLINE contents is effective to improve triage in complex curation tasks such as the curation of protein PPIs and PTMs

The neXtProt knowledgebase on human proteins: current status

neXtProt (http://www.nextprot.org) is a human protein-centric knowledgebase developed at the SIB Swiss Institute of Bioinformatics. Focused solely on human proteins, neXtProt aims to provide a state of the art resource for the representation of human biology by capturing a wide range of data, precise annotations, fully traceable data provenance and a web interface which enables researchers to find and view information in a comprehensive manner. Since the introductory neXtProt publication, significant advances have been made on three main aspects: the representation of proteomics data, an extended representation of human variants and the development of an advanced search capability built around semantic technologies. These changes are presented in the current neXtProt update

The neXtProt knowledgebase on human proteins: 2017 update

The neXtProt human protein knowledgebase (https://www.nextprot.org) continues to add new content and tools, with a focus on proteomics and genetic variation data. neXtProt now has proteomics data for over 85% of the human proteins, as well as new tools tailored to the proteomics community.Moreover, the neXtProt release 2016-08-25 includes over 8000 phenotypic observations for over 4000 variations in a number of genes involved in hereditary cancers and channelopathies. These changes are presented in the current neXtProt update. All of the neXtProt data are available via our user interface and FTP site. We also provide an API access and a SPARQL endpoint for more technical applications

Unstable Jefferson fractures: Results of transoral osteosynthesis.

BACKGROUND: Majority of C1 fractures can be effectively treated conservatively by immobilization or traction unless there is an injury to the transverse ligament. Conservative treatment usually involves a long period of immobilization in a halo-vest. Surgical intervention generally involves fusion, eliminating the motion of the upper cervical spine. We describe the treatment of unstable Jefferson fractures designed to avoid these problems of both conservative and invasive methods. MATERIALS AND METHODS: A retrospective review of 12 patients with unstable Jefferson fractures treated with transoral osteosynthesis of C1 between July 2008 and December 2011 was performed. A steel plate and C1 lateral mass screw fixation were used to repair the unstable Jefferson fractures. Our study group included eight males and four females with an average age of 33 years (range 23-62 years). RESULTS: Patients were followed up for an average of 16 months after surgery. Range of motion of the cervical spine was by and large physiologic: Average flexion 35° (range 28-40°), average extension 42° (range 30-48°). Lateral bending to the right and left averaged 30° and 28° respectively (range 12-36° and 14-32° respectively). The average postoperative rotation of the atlantoaxial joint, evaluated by functional computed tomography scan was 60° (range 35-72°). Total average lateral displacement of the lateral masses was 7.0 mm before surgery (range 5-12 mm), which improved to 3.5 mm after surgery (range 1-6.5 mm). The total average difference of the atlanto-dens interval in flexion and extension after surgery was 1.0 mm (range 1-3 mm). CONCLUSIONS: Transoral osteosynthesis of the anterior ring using C1 lateral mass screws is a viable option for treating unstable Jefferson fractures, which allows maintenance of rotation at the C1-C2 joint and restoration of congruency of the atlanto-occipital and atlantoaxial joints