The Gene Ontology knowledgebase in 2023.

The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products (proteins and noncoding RNAs). GO annotations cover genes from organisms across the tree of life as well as viruses, though most gene function knowledge currently derives from experiments carried out in a relatively small number of model organisms. Here, we provide an updated overview of the GO knowledgebase, as well as the efforts of the broad, international consortium of scientists that develops, maintains, and updates the GO knowledgebase. The GO knowledgebase consists of three components: (1) the GO-a computational knowledge structure describing the functional characteristics of genes; (2) GO annotations-evidence-supported statements asserting that a specific gene product has a particular functional characteristic; and (3) GO Causal Activity Models (GO-CAMs)-mechanistic models of molecular "pathways" (GO biological processes) created by linking multiple GO annotations using defined relations. Each of these components is continually expanded, revised, and updated in response to newly published discoveries and receives extensive QA checks, reviews, and user feedback. For each of these components, we provide a description of the current contents, recent developments to keep the knowledgebase up to date with new discoveries, and guidance on how users can best make use of the data that we provide. We conclude with future directions for the project.

Gene Ontology curation of the blood-brain barrier to improve the analysis of Alzheimer's and other neurological diseases.

The role of the blood-brain barrier (BBB) in Alzheimer's and other neurodegenerative diseases is still the subject of many studies. However, those studies using high-throughput methods have been compromised by the lack of Gene Ontology (GO) annotations describing the role of proteins in the normal function of the BBB. The GO Consortium provides a gold-standard bioinformatics resource used for analysis and interpretation of large biomedical data sets. However, the GO is also used by other research communities and, therefore, must meet a variety of demands on the breadth and depth of information that is provided. To meet the needs of the Alzheimer's research community we have focused on the GO annotation of the BBB, with over 100 transport or junctional proteins prioritized for annotation. This project has led to a substantial increase in the number of human proteins associated with BBB-relevant GO terms as well as more comprehensive annotation of these proteins in many other processes. Furthermore, data describing the microRNAs that regulate the expression of these priority proteins have also been curated. Thus, this project has increased both the breadth and depth of annotation for these prioritized BBB proteins. Database URLhttps://www.ebi.ac.uk/QuickGO/.

Gene Ontology Curation of Neuroinflammation Biology Improves the Interpretation of Alzheimer's Disease Gene Expression Data.

BACKGROUND: Gene Ontology (GO) is a major bioinformatic resource used for analysis of large biomedical datasets, for example from genome-wide association studies, applied universally across biological fields, including Alzheimer's disease (AD) research. OBJECTIVE: We aim to demonstrate the applicability of GO for interpretation of AD datasets to improve the understanding of the underlying molecular disease mechanisms, including the involvement of inflammatory pathways and dysregulated microRNAs (miRs). METHODS: We have undertaken a systematic full article GO annotation approach focused on microglial proteins implicated in AD and the miRs regulating their expression. PANTHER was used for enrichment analysis of previously published AD data. Cytoscape was used for visualizing and analyzing miR-target interactions captured from published experimental evidence. RESULTS: We contributed 3,084 new annotations for 494 entities, i.e., on average six new annotations per entity. This included a total of 1,352 annotations for 40 prioritized microglial proteins implicated in AD and 66 miRs regulating their expression, yielding an average of twelve annotations per prioritized entity. The updated GO resource was then used to re-analyze previously published data. The re-analysis showed novel processes associated with AD-related genes, not identified in the original study, such as 'gliogenesis', 'regulation of neuron projection development', or 'response to cytokine', demonstrating enhanced applicability of GO for neuroscience research. CONCLUSIONS: This study highlights ongoing development of the neurobiological aspects of GO and demonstrates the value of biocuration activities in the area, thus helping to delineate the molecular bases of AD to aid the development of diagnostic tools and treatments.

Evaluation of Prescribing Appropriateness and Initiatives to Improve Prescribing of Proton Pump Inhibitors at Vancouver General Hospital.

BACKGROUND: Proton pump inhibitors (PPIs) have proven clinical efficacy for a variety of indications. However, there is emerging evidence of adverse events associated with their long-term use. The emergence of these adverse events has reinforced the need to regularly evaluate the appropriateness of continuing PPI therapy, and to use only the lowest effective dose for the minimally indicated duration. OBJECTIVES: To characterize the appropriateness of PPI orders continued or initiated in the internal medicine and family practice units of Vancouver General Hospital, to detect adverse events associated with PPI use, and to explore the impact of multidisciplinary teaching and provision of educational resources on health care practitioners' views about PPI use. METHODS: A chart review was conducted for patients admitted (for at least 24 hours) between January 1 and December 31, 2015, for whom a hospital formulary PPI was prescribed. An educational initiative, which included interprofessional in-service sessions, a PPI prescribing infographic, a PPI prescribing card, and a patient counselling sheet, was implemented. The impact of these interventions was assessed using a qualitative survey of health care practitioners. RESULTS: Of the 258 patients whose charts were reviewed, 175 had a PPI prescription before hospital admission, and 83 were initiated on PPI therapy during their hospital stay. Overall, 94 (36%) of the patients were receiving PPIs without an appropriate indication. Community-acquired pneumonia and Clostridium difficile infections were the most common adverse events potentially associated with PPI use. In-service sessions and educational resources on PPI prescribing were reported to affect the clinical practice of 24 (52%) of the 46 survey respondents. CONCLUSIONS: The results of this study emphasize the need for ongoing re-evaluation of long-term PPI therapy at the time of admission, during the hospital stay, and upon discharge. Implementing multidisciplinary teaching and providing educational resources may encourage more appropriate prescribing.

CONTEXTE: Les inhibiteurs de la pompe à protons (IPP) ont prouvé leur efficacité clinique pour une gamme d'indications. Cependant, de nouvelles données sur leur utilisation à long terme leur imputent des événements indésirables. L'émergence de ces événements indésirables a renforcé l'idée qu'il est nécessaire d'évaluer régulièrement la pertinence d'un traitement prolongé par IPP et d'employer seulement la plus faible dose efficace pendant la durée indiquée la plus courte. OBJECTIFS: Offrir un portrait de la pertinence des ordonnances d'IPP, renouvelées ou nouvelles, dans les services de médecine interne et de médecine familiale de l'Hôpital général de Vancouver, détecter les événements indésirables liés à l'utilisation des IPP et étudier l'effet qu'ont une formation multidisciplinaire et une fourniture de ressources éducatives sur les points de vue des professionnels de la santé à propos des IPP. MÉTHODES: Une analyse rétrospective de dossiers médicaux a été menée auprès de patients qui ont été admis (pendant au moins 24 heures) entre le 1er janvier et le 31 décembre 2015 et qui se sont vu prescrire un IPP inscrit sur la liste des médicaments de l'hôpital. On a mis en place un programme éducatif comprenant des séances de formation interprofessionnelles internes, un document infographique de prescription des IPP, une carte de prescription des IPP et une fiche de conseils aux patients. L'effet de ces interventions a été évalué à l'aide d'une enquête qualitative auprès des professionnels de la santé. RÉSULTATS: Parmi les 258 patients dont le dossier a été examiné, 175 avaient une ordonnance d'IPP avant l'admission à l'hôpital et 83 ont amorcé un traitement par IPP pendant leur séjour. Dans l'ensemble, 94 (36 %) des patients recevaient un IPP sans indication pertinente. Les infections à Clostridium difficile et les pneumonies extra-hospitalières représentaient les événements indésirables les plus courants potentiellement liés à l'utilisation des IPP. On a signalé que les séances de formation interne et les ressources éducatives sur la prescription des IPP avaient eu un effet sur la pratique clinique de 24 (52 %) des 46 participants à l'enquête. CONCLUSIONS: Les résultats de l'étude font ressortir la nécessité d'une réévaluation continuelle des traitements à long terme par IPP au moment de l'admission, pendant le séjour et lors du congé. La mise en place de formation multidisciplinaire et l'offre de ressources éducatives pourraient favoriser des pratiques de prescription plus adéquates.

Methotrexate in chronic active Crohn's disease: a double-blind, randomized, Israeli multicenter trial.

BACKGROUND: At present only one large controlled study has indicated that parenteral methotrexate may be effective in chronic active Crohn's disease (CD). AIM: To evaluate the effectiveness of oral methotrexate in chronic steroid-dependent CD. PATIENTS: Patients with active CD, who have received steroids and/or immunosuppressives for at least 4 months during the preceding 12 months and with a current Harvey-Bradshaw index of > or = 7 were studied. METHODS: Methotrexate (12.5 mg weekly) or 6-mercaptopurine (50 mg daily), or placebo were given during the 9 months of the trial in addition to steroids and 5-aminosalicylic acid as clinically indicated. RESULTS: Eighty-four patients were included (methotrexate, 26 patients; 6-mercaptopurine, 32 patients; placebo, 26 patients). The proportion of patients entering first remission as well as the proportions of patients relapsing after first remission were not significantly different between the groups. The mean Harvey-Bradshaw index and the mean monthly steroid dose were also similar. However, when each patient was evaluated as his or her own control, the reduction in steroid dose, the general well being, and the reduction in abdominal pain were significantly better in the methotrexate treated patients. CONCLUSIONS: Methotrexate at a weekly oral dose of 12.5 mg was found to be moderately better than 6-mercaptopurine and placebo in patients with chronic active CD.

Metabolism of guanine and guanine nucleotides in primary rat cardiomyocyte cultures.

The metabolic fate of labeled guanine and of prelabeled guanine nucleotides (GuRN) was studied in cultured rat cardiomyocytes. Special attention was given to guanine salvage in comparison to degradation; to the contribution of GuRN to adenine nucleotides (AdRN); to the fluxes from GMP to IMP and from IMP to GMP; and to the degradation pathways of GuRN. In accordance with the 3- to 4-fold higher activity of guanine deaminase (guanase), in comparison to that of hypoxanthine-guanine phosphoribosyltransferase (HGPRT), the rate of guanine deamination to xanthine exceeded that of guanine incorporation into nucleotides (at 4 microM) by 13.2-fold. The label from guanine incorporated into nucleotides was found mainly (81%) in GuRN, but also in IMP and AdRN. The prelabeled GuRN lost 43% of the label in 4 h, reflecting mainly degradation to xanthine (and uric acid) and synthesis of nucleic acids. Blocking nucleoside degradation was associated with a marked accumulation of label in guanosine and inosine (guanosine/inosine labeling ratio is 1.25). The results indicate that in the myocardium guanine is a poor substrate for salvage synthesis of GuRN and that its contribution to the homeostasis of adenine nucleotides is negligible; that GMP degradation to xanthine proceeds through both guanosine and IMP; and that the cardiomyocytes contain the activity of GMP reductase and of the enzymes converting IMP to GMP.

Metabolic fate of hypoxanthine and inosine in cultured cardiomyocytes.

The metabolic fate of labeled hypoxanthine and inosine, degradation products of adenine nucleotides, was studied in cultured beating cardiomyocytes, in order to assess the physiological significance of their contribution to salvage nucleotide synthesis in the heart. Inosine and hypoxanthine were found to be incorporated into nucleotides by a similar rate, but in the presence of 8-aminoguanosine, a potent inhibitor of purine nucleoside phosphorylase (EC 2.4.2.1), the rate of inosine incorporation into nucleotides was markedly reduced (by 75%), indicating that inosine incorporation to IMP (inosinic acid) occurs following its degradation to hypoxanthine. The proportion of hypoxanthine converted to IMP by hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) is markedly greater than that degraded to xanthine and uric acid by xanthine oxidase (EC 1.3.2.3). However, close to 50% of the IMP formed was degraded to inosine by IMP 5'-nucleotidase (EC 3.1.3.5). The results demonstrate the activity of the following futile cycle in the cardiomyocytes: hypoxanthine----IMP----inosine----hypoxanthine. The rational for the activity of this energy consuming cycle is yet unclear.