The Gene Ontology Resource: 20 years and still GOing strong
The Gene Ontology resource (GO; http://geneontology.org) provides structured, computable knowledge regarding the functions of genes and gene products. Founded in 1998, GO has become widely adopted in the life sciences, and its contents are under continual improvement, both in quantity and in quality. Here, we report the major developments of the GO resource during the past two years. Each monthly release of the GO resource is now packaged and given a unique identifier (DOI), enabling GO-based analyses on a specific release to be reproduced in the future. The molecular function ontology has been refactored to better represent the overall activities of gene products, with a focus on transcription regulator activities. Quality assurance efforts have been ramped up to address potentially out-of-date or inaccurate annotations. New evidence codes for high-Throughput experiments now enable users to filter out annotations obtained from these sources. GO-CAM, a new framework for representing gene function that is more expressive than standard GO annotations, has been released, and users can now explore the growing repository of these models. We also provide the a GO ribbon' widget for visualizing GO annotations to a gene; the widget can be easily embedded in any web page.
Expansion of the gene ontology knowledgebase and resources: The gene ontology consortium
The Gene Ontology (GO) is a comprehensive resource of computable knowledge regarding the functions of genes and gene products. As such, it is extensively used by the biomedical research community for the analysis of-omics and related data. Our continued focus is on improving the quality and utility of the GO resources, and we welcome and encourage input from researchers in all areas of biology. In this update, we summarize the current contents of the GO knowledgebase, and present several new features and improvements that have been made to the ontology, the annotations and the tools. Among the highlights are 1) developments that facilitate access to, and application of, the GO knowledgebase, and 2) extensions to the resource as well as increasing support for descriptions of causal models of biological systems and network biology. To learn more, visit https://urldefense.proofpoint.com/v2/url?u=http- 3A__geneontology.org_&d=DQIBAg&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=vQfPybH YMptZTsGTKf8YZN_ho- QhkqmSqA9bfoe84p4&m=FWECBidVXo0ALQwQIUv7WM1GHzTeBIhQYi8nAqMZqzw&s=Bbv_JsLtuGTdO OEXNgUM5nbQSx8-Zf7uwXSJpJ2Najk&e= .
Gene Ontology Consortium: going forward
The Gene Ontology (GO; ext-link-type="uri" xlink:href="http://www.geneontology.org" xlink:type="simple">http://www.geneontology.org) is a community-based bioinformatics resource that supplies information about gene product function using ontologies to represent biological knowledge. Here we describe improvements and expansions to several branches of the ontology, as well as updates that have allowed us to more efficiently disseminate the GO and capture feedback from the research community. The Gene Ontology Consortium (GOC) has expanded areas of the ontology such as cilia-related terms, cell-cycle terms and multicellular organism processes. We have also implemented new tools for generating ontology terms based on a set of logical rules making use of templates, and we have made efforts to increase our use of logical definitions. The GOC has a new and improved web site summarizing new developments and documentation, serving as a portal to GO data. Users can perform GO enrichment analysis, and search the GO for terms, annotations to gene products, and associated metadata across multiple species using the all-new AmiGO 2 browser. We encourage and welcome the input of the research community in all biological areas in our continued effort to improve the Gene Ontology.
Severe Hypoglycemia as a Presenting Symptom of Celiac Disease in an Adolescent With Type 1 Diabetes [Meeting Abstract]
Gene Ontology annotations and resources
The Gene Ontology (GO) Consortium (GOC, http://www.geneontology.org) is a community-based bioinformatics resource that classifies gene product function through the use of structured, controlled vocabularies. Over the past year, the GOC has implemented several processes to increase the quantity, quality and specificity of GO annotations. First, the number of manual, literature-based annotations has grown at an increasing rate. Second, as a result of a new 'phylogenetic annotation' process, manually reviewed, homology-based annotations are becoming available for a broad range of species. Third, the quality of GO annotations has been improved through a streamlined process for, and automated quality checks of, GO annotations deposited by different annotation groups. Fourth, the consistency and correctness of the ontology itself has increased by using automated reasoning tools. Finally, the GO has been expanded not only to cover new areas of biology through focused interaction with experts, but also to capture greater specificity in all areas of the ontology using tools for adding new combinatorial terms. The GOC works closely with other ontology developers to support integrated use of terminologies. The GOC supports its user community through the use of e-mail lists, social media and web-based resources.
The Gene Ontology: enhancements for 2011
The Gene Ontology (GO) (http://www.geneontology.org) is a community bioinformatics resource that represents gene product function through the use of structured, controlled vocabularies. The number of GO annotations of gene products has increased due to curation efforts among GO Consortium (GOC) groups, including focused literature-based annotation and ortholog-based functional inference. The GO ontologies continue to expand and improve as a result of targeted ontology development, including the introduction of computable logical definitions and development of new tools for the streamlined addition of terms to the ontology. The GOC continues to support its user community through the use of e-mail lists, social media and web-based resources.
ODS Score and Obstructed Defecation Reply [Letter]
Stapled transanal rectal resection vs. transvaginal rectocele repair for treatment of obstructive defecation syndrome
PURPOSE: Stapled transanal rectal resection has been introduced as a new technology for the management of obstructive defecation syndrome. In this study we observed the clinical outcomes for stapled transanal rectal resection as compared with transvaginal rectocele repair for obstructive defecation syndrome. METHODS: This study is a retrospective review of patients who received transvaginal rectocele repair for obstructive defecation syndrome from June 1997 to February 2002 as compared with patients who received stapled transanal rectal resection from June 2005 to August 2007. The clinical outcomes observed were operative time, estimated blood loss, length of stay, complication rate, procedure failure rate, recurrence rate, time to recurrence, and dyspareunia rate. RESULTS: Thirty-seven patients had transvaginal rectocele repair for management of obstructive defecation syndrome, and 36 patients had stapled transanal rectal resection. There was no difference in the age of patients receiving either procedure (transvaginal rectocele repair, 57.92 years old; stapled transanal rectal resection, 53.19 years old; P = 0.1096). Evaluation of the clinical outcomes showed that transvaginal rectocele repair had a longer operative time (transvaginal rectocele repair, 85 minutes; stapled transanal rectal resection, 52 minutes; P = or<0.0001), greater estimated blood loss (transvaginal rectocele repair, 108 ml; stapled transanal rectal resection, 43 ml; P = 0.0015), and a lower complication rate (transvaginal rectocele repair, 18.9 percent; stapled transanal rectal resection, 61.1 percent; P = 0.0001). CONCLUSION: The stapled transanal rectal resection procedure can be done with shorter operative times and less blood loss than transvaginal rectocele repair, however, it has a higher complication rate
Late presentation of a hepatic pseudoaneurysm with hemobilia after angioembolization for blunt hepatic trauma [Case Report]
Retroperitoneal perforation of the duodenum from biliary stent erosion [Case Report]
Endoscopically placed biliary stents have supplanted surgical decompression as the preferred treatment option for patients with obstructive jaundice from advanced pancreatic cancer. An unusual complication of indewelling biliary stents is duodenal perforation into the retroperitoneum. We describe the case of a patient with end-stage pancreatic cancer who presented with an acute abdomen from erosion of a previously placed bile duct stent through the wall of the second portion of the duodenum. Although our patient presented with advanced symptoms, clinical presentations can vary from mild abdominal discomfort and general malaise to overt septic shock. Definitive diagnosis is best made with computed tomography (CT) imaging, which can detect traces of retroperitoneal air and fluid. Treatment options vary from nonoperative management with antibiotics, bowel rest, and parenteral alimentation in the most stable patients to definitive surgery with complete diversion of gastric contents and biliary flow from the affected area in patients with clinical symptoms or radiologic evidence suggesting extensive contamination. Complications of management can include duodenal fistulization, residual retroperitoneal or intrabdominal abscess, and ongoing sepsis. This report highlights the salient issues in the presentation, diagnosis, and modern management of patients with this rare complication of indwelling biliary stents