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Claire O'Donovan

Publications and source records attributed to Claire O'Donovan.

18 recordsLinked to original sources
PubMed2026

Network-based integration of metabolomics data from large-scale repositories.

INTRODUCTION: Public metabolomics data repositories such as MetaboLights and Metabolomics Workbench host rapidly growing volumes of raw data, processed results, and metadata. As data deposition becomes a prerequisite for funding and publication, there is an increasing need for tools that enable integration and joint reanalysis of datasets across studies to maximise reuse and reproducibility. OBJECTIVES: This study aims to enable large-scale integrative meta-analysis of public metabolomics data, exploiting harmonised metabolite annotations to identify robust multi-study metabolite and pathway signatures and to provide global visual overviews of repository content. METHODS: We developed a network-based integration framework operating at both the study (dataset) level and the metabolite or pathway level. Metabolite-level meta-networks integrate studies with shared biological context using co-occurrences of differential metabolites represented as bipartite graphs. Study-level networks compare observed metabolites for overall repository exploration. Networks can be explored interactively using a dedicated Python Dash app available at https://github.com/EloisaRL/Metabolomic-data-analysis-app/tree/main . RESULTS: As an example, the approach was applied to six COVID-19 plasma datasets from MetaboLights generated using LC-MS and NMR. Ten metabolites were identified as differential in at least three studies, including consistently up-regulated pyroglutamic acid, in agreement with the literature. Pathway-level networks provided an overview of shared biological processes across studies. A global network of 1,181 studies in Metabolomics Workbench demonstrated clustering by assay coverage and associated metadata, as expected. CONCLUSION: Network-based integration of harmonised metabolomics data enables robust cross-study analyses and highlights the critical importance of standardised annotation pipelines. Such approaches enhance the reuse, reproducibility, and impact of public metabolomics datasets, accelerating biological discovery.

Metabolomics↗
PubMed2007

Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana.

We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates were manually curated. Functions were identified or inferred in 19,969 (70%) of the proteins, and 131 possible npRNAs (including 58 antisense transcripts) were found. Almost 5000 annotated protein-coding genes were found to be disrupted in insertional mutant lines, which will accelerate future experimental validation of the annotations. The rice loci were determined by using cDNA sequences obtained from rice and other representative cereals. Our conservative estimate based on these loci and an extrapolation suggested that the gene number of rice is approximately 32,000, which is smaller than previous estimates. We conducted comparative analyses between rice and Arabidopsis thaliana and found that both genomes possessed several lineage-specific genes, which might account for the observed differences between these species, while they had similar sets of predicted functional domains among the protein sequences. A system to control translational efficiency seems to be conserved across large evolutionary distances. Moreover, the evolutionary process of protein-coding genes was examined. Our results suggest that natural selection may have played a role for duplicated genes in both species, so that duplication was suppressed or favored in a manner that depended on the function of a gene.

Arabidopsis↗
PubMed2006

The Universal Protein Resource (UniProt): an expanding universe of protein information.

The Universal Protein Resource (UniProt) provides a central resource on protein sequences and functional annotation with three database components, each addressing a key need in protein bioinformatics. The UniProt Knowledgebase (UniProtKB), comprising the manually annotated UniProtKB/Swiss-Prot section and the automatically annotated UniProtKB/TrEMBL section, is the preeminent storehouse of protein annotation. The extensive cross-references, functional and feature annotations and literature-based evidence attribution enable scientists to analyse proteins and query across databases. The UniProt Reference Clusters (UniRef) speed similarity searches via sequence space compression by merging sequences that are 100% (UniRef100), 90% (UniRef90) or 50% (UniRef50) identical. Finally, the UniProt Archive (UniParc) stores all publicly available protein sequences, containing the history of sequence data with links to the source databases. UniProt databases continue to grow in size and in availability of information. Recent and upcoming changes to database contents, formats, controlled vocabularies and services are described. New download availability includes all major releases of UniProtKB, sequence collections by taxonomic division and complete proteomes. A bibliography mapping service has been added, and an ID mapping service will be available soon. UniProt databases can be accessed online at http://www.uniprot.org or downloaded at ftp://ftp.uniprot.org/pub/databases/.

Databases, Protein↗
PubMed2006

Canadian Network for Mood and Anxiety Treatments (CANMAT) guidelines for the management of patients with bipolar disorder: update 2007.

In 2005, the Canadian Network for Mood and Anxiety Treatments (CANMAT) published guidelines for the management of bipolar disorder. This update reviews new evidence since the previous publication and incorporates recommendations based on the most current evidence for treatment of various phases of bipolar disorder. It is designed to be used in conjunction with the 2005 CANMAT Guidelines. The recommendations for the management of acute mania remain mostly unchanged. Lithium, valproate and several atypical antipsychotics continue to be recommended as first-line treatments for acute mania. For the management of bipolar depression, new data support quetiapine monotherapy as a first-line option. Lithium and lamotrigine monotherapy, olanzapine plus selective serotonin reuptake inhibitors (SSRI), and lithium or divalproex plus SSRI/bupropion continue to remain the other first-line options. First-line options in the maintenance treatment of bipolar disorder continue to be lithium, lamotrigine, valproate and olanzapine. There is recent evidence to support the combination of olanzapine and fluoxetine as a second-line maintenance therapy for bipolar depression. New data also support quetiapine monotherapy as a second-line option for the management of acute bipolar II depression. The importance of comorbid psychiatric and medical conditions cannot be understated, and this update provides an expanded look at the prevalence, impact and management of comorbid conditions in patients with bipolar disorder.

Acute Disease↗
PubMed2005

The Universal Protein Resource (UniProt).

The Universal Protein Resource (UniProt) provides the scientific community with a single, centralized, authoritative resource for protein sequences and functional information. Formed by uniting the Swiss-Prot, TrEMBL and PIR protein database activities, the UniProt consortium produces three layers of protein sequence databases: the UniProt Archive (UniParc), the UniProt Knowledgebase (UniProt) and the UniProt Reference (UniRef) databases. The UniProt Knowledgebase is a comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase with extensive cross-references. This centrepiece consists of two sections: UniProt/Swiss-Prot, with fully, manually curated entries; and UniProt/TrEMBL, enriched with automated classification and annotation. During 2004, tens of thousands of Knowledgebase records got manually annotated or updated; we introduced a new comment line topic: TOXIC DOSE to store information on the acute toxicity of a toxin; the UniProt keyword list got augmented by additional keywords; we improved the documentation of the keywords and are continuously overhauling and standardizing the annotation of post-translational modifications. Furthermore, we introduced a new documentation file of the strains and their synonyms. Many new database cross-references were introduced and we started to make use of Digital Object Identifiers. We also achieved in collaboration with the Macromolecular Structure Database group at EBI an improved integration with structural databases by residue level mapping of sequences from the Protein Data Bank entries onto corresponding UniProt entries. For convenient sequence searches we provide the UniRef non-redundant sequence databases. The comprehensive UniParc database stores the complete body of publicly available protein sequence data. The UniProt databases can be accessed online (http://www.uniprot.org) or downloaded in several formats (ftp://ftp.uniprot.org/pub). New releases are published every two weeks.

Amino Acid Sequence↗
PubMed2005

Canadian Network for Mood and Anxiety Treatments (CANMAT) guidelines for the management of patients with bipolar disorder: consensus and controversies.

Since the previous publication of Canadian Network for Mood and Anxiety Treatments (CANMAT) guidelines in 1997, there has been a substantial increase in evidence-based treatment options for bipolar disorder. The present guidelines review the new evidence and use criteria to rate strength of evidence and incorporate effectiveness, safety, and tolerability data to determine global clinical recommendations for treatment of various phases of bipolar disorder. The guidelines suggest that although pharmacotherapy forms the cornerstone of management, utilization of adjunctive psychosocial treatments and incorporation of chronic disease management model involving a healthcare team are required in providing optimal management for patients with bipolar disorder. Lithium, valproate and several atypical antipsychotics are first-line treatments for acute mania. Bipolar depression and mixed states are frequently associated with suicidal acts; therefore assessment for suicide should always be an integral part of managing any bipolar patient. Lithium, lamotrigine or various combinations of antidepressant and mood-stabilizing agents are first-line treatments for bipolar depression. First-line options in the maintenance treatment of bipolar disorder are lithium, lamotrigine, valproate and olanzapine. Historical and symptom profiles help with treatment selection. With the growing recognition of bipolar II disorders, it is anticipated that a larger body of evidence will become available to guide treatment of this common and disabling condition. These guidelines also discuss issues related to bipolar disorder in women and those with comorbidity and include a section on safety and monitoring.

Adolescent↗
PubMed2004

Integrative annotation of 21,037 human genes validated by full-length cDNA clones.

The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates (1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for non-protein-coding RNA genes. In addition, among 72,027 uniquely mapped SNPs and insertions/deletions localized within human genes, 13,215 nonsynonymous SNPs, 315 nonsense SNPs, and 452 indels occurred in coding regions. Together with 25 polymorphic microsatellite repeats present in coding regions, they may alter protein structure, causing phenotypic effects or resulting in disease. The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology.

Alternative Splicing↗
PubMed2004

UniProt: the Universal Protein knowledgebase.

To provide the scientific community with a single, centralized, authoritative resource for protein sequences and functional information, the Swiss-Prot, TrEMBL and PIR protein database activities have united to form the Universal Protein Knowledgebase (UniProt) consortium. Our mission is to provide a comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and query interfaces. The central database will have two sections, corresponding to the familiar Swiss-Prot (fully manually curated entries) and TrEMBL (enriched with automated classification, annotation and extensive cross-references). For convenient sequence searches, UniProt also provides several non-redundant sequence databases. The UniProt NREF (UniRef) databases provide representative subsets of the knowledgebase suitable for efficient searching. The comprehensive UniProt Archive (UniParc) is updated daily from many public source databases. The UniProt databases can be accessed online (http://www.uniprot.org) or downloaded in several formats (ftp://ftp.uniprot.org/pub). The scientific community is encouraged to submit data for inclusion in UniProt.

Animals↗
PubMed2004

The human cost of not achieving full remission in depression.

Depression is among the most disabling and costly illnesses in the world. Despite good short-term efficacy outcomes in the treatment of depression, long-term outcomes remain disappointing. Depression continues to be missed or underdiagnosed and undertreated, and comorbidities are frequently not identified. Of particular concern is the low rate of depression treated to full remission. Treating only to response leaves patients with residual depressive symptoms and an increased risk of a recurrent or chronic course. Anything less than full remission should be considered a treatment failure. This article examines the substantial psychiatric, medical, functional, and economic costs associated with not achieving remission. Available pharmacoeconomic data and randomized, controlled clinical trials published in the last 5 years identified through Medline searches with terms including burden, cost, economics, serotonin reuptake inhibitors (also, specific agents), venlafaxine, nefazadone, mirtazapine, psychotherapy, remission, and depression were reviewed. One of the limiting factors to this review is that few trials have compared the effects of various antidepressant strategies on clinically relevant outcomes such as depression-free days and patient productivity, making the full benefit of remission more difficult to measure. Patients who fail to achieve a full remission have a more recurrent and chronic course, increased medical and psychiatric comorbidities, greater functional burden, and increased social and economic costs. Cost-effective treatment for depression includes antidepressant therapies with higher remission rates. Antidepressants with a dual mechanism of action and combination therapies are associated with higher remission rates, more depression-free days, reduced pain-symptom morbidity, reduced health service utilization, and improved productivity.

Achievement↗
PubMed2003

The European Bioinformatics Institute's data resources.

As the amount of biological data grows, so does the need for biologists to store and access this information in central repositories in a free and unambiguous manner. The European Bioinformatics Institute (EBI) hosts six core databases, which store information on DNA sequences (EMBL-Bank), protein sequences (SWISS-PROT and TrEMBL), protein structure (MSD), whole genomes (Ensembl) and gene expression (ArrayExpress). But just as a cell would be useless if it couldn't transcribe DNA or translate RNA, our resources would be compromised if each existed in isolation. We have therefore developed a range of tools that not only facilitate the deposition and retrieval of biological information, but also allow users to carry out searches that reflect the interconnectedness of biological information. The EBI's databases and tools are all available on our website at www.ebi.ac.uk.

Animals↗
PubMed2003

The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003.

The SWISS-PROT protein knowledgebase (http://www.expasy.org/sprot/ and http://www.ebi.ac.uk/swissprot/) connects amino acid sequences with the current knowledge in the Life Sciences. Each protein entry provides an interdisciplinary overview of relevant information by bringing together experimental results, computed features and sometimes even contradictory conclusions. Detailed expertise that goes beyond the scope of SWISS-PROT is made available via direct links to specialised databases. SWISS-PROT provides annotated entries for all species, but concentrates on the annotation of entries from human (the HPI project) and other model organisms to ensure the presence of high quality annotation for representative members of all protein families. Part of the annotation can be transferred to other family members, as is already done for microbes by the High-quality Automated and Manual Annotation of microbial Proteomes (HAMAP) project. Protein families and groups of proteins are regularly reviewed to keep up with current scientific findings. Complementarily, TrEMBL strives to comprise all protein sequences that are not yet represented in SWISS-PROT, by incorporating a perpetually increasing level of mostly automated annotation. Researchers are welcome to contribute their knowledge to the scientific community by submitting relevant findings to SWISS-PROT at swiss-prot@expasy.org.

Animals↗
PubMed2003

Managing core resources for genomics and proteomics.

Recent years have seen an explosive growth in biological data, which is often not published in a conventional sense but rather deposited in a database. This trend and the need for computational analyses of the data make databases essential tools for biological research. Data from a variety of sources, covering a wide range of biological information, are stored in different, often quite specialized, databases. The provision of such databases as useful resources for the scientific community is a demanding task since the data not only have to be stored in a consistent way, but also have to be easily accessible and highly integrated with other databases. Furthermore, it is necessary to provide users with effective tools to search the databases and to analyze the data. At the European Bioinformatics Institute (EBI), we develop and maintain a number of biological databases and provide a variety of bioinformatics tools to facilitate database and similarity searches and data analysis. In this review, we will provide examples of the core resources maintained at the EBI and summarize important issues of database management of such resources.

Computational Biology↗
PubMed2002

High-quality protein knowledge resource: SWISS-PROT and TrEMBL.

SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domain structure, post-translational modifications, variants, etc.), a minimal level of redundancy and a high level of integration with other databases. Together with its automatically annotated supplement TrEMBL, it provides a comprehensive and high-quality view of the current state of knowledge about proteins. Ongoing developments include the further improvement of functional and automatic annotation in the databases including evidence attribution with particular emphasis on the human, archaeal and bacterial proteomes and the provision of additional resources such as the International Protein Index (IPI) and XML format of SWISS-PROT and TrEMBL to the user community.

Amino Acid Sequence↗
PubMed2002

Menstrual abnormalities and polycystic ovary syndrome in women taking valproate for bipolar mood disorder.

BACKGROUND: Valproate treatment has been associated with high rates of menstrual abnormalities, hyperandrogenism, and polycystic ovaries in women with epilepsy. This pilot study investigated whether valproate treatment had the same associations in women with bipolar disorder. METHOD: One hundred forty outpatient women with a DSM-IV diagnosis of bipolar disorder (aged 15-45 years) were surveyed on their medical, psychiatric, and reproductive health history. Thirty-two women met entry criteria for the study and were divided into 2 groups: (1) those currently receiving valproate (valproate, N = 17) and (2) those who were not currently taking valproate (nonvalproate, N = 15). These 2 groups were compared with a normal (never diagnosed with a psychiatric disorder) control group of 22 women. Women in the valproate group with current menstrual problems (N = 7) underwent further assessment for the presence of polycystic ovaries and hyperandrogenism. RESULTS: The age at onset of menses, mean length of menstrual cycle, and mean length of menses were not significantly different between the groups. Significantly more women reported menstrual abnormalities in the valproate group (47%) than women not receiving valproate (13%) and controls (0%). Forty-one percent of women with bipolar disorder taking valproate had polycystic ovary syndrome. CONCLUSION: These results suggest high rates of menstrual disturbances and polycystic ovary syndrome in women with bipolar disorder currently receiving valproate.

Adolescent↗
PubMed2002

Is response to prophylactic lithium a familial trait?

BACKGROUND: Selecting a drug according to the treatment response in a relative has been widely accepted advice in the management of mood disorders. However, this recommendation has not been adequately substantiated in the literature. We tested the hypothesis that response to long-term lithium treatment is a familial trait. METHOD: We compared response to long-term lithium treatment in bipolar relatives of bipolar lithium responders and bipolar controls. Twenty-four relatives with bipolar disorder (as determined using the Schedule for Affective Disorders and Schizophrenia-Lifetime version [SADS-L] and Research Diagnostic Criteria [RDC]) were identified in families of 106 patients with lithium-responsive bipolar disorder. A consecutive series of 40 lithium-treated patients in a bipolar clinic (meeting RDC and DSM-IV criteria for bipolar disorder) served as a comparison group. Lithium response was evaluated on a rating scale reflecting the quality and quantity of available data. RESULTS: The prevalence of unequivocal response among the relatives was 67%, as compared with the response rate of 35% in the comparison group (chi2 = 6.04, df = 1, p = .014). CONCLUSION: This highly significant difference in response between relatives and the control group supports the view that the response to lithium prophylaxis clusters in families.

Adult↗
PubMed2002

Prevalence and outcome of partial remission in depression.

The goal of treatment of major depression should be full remission. Many patients, however, fail to achieve or maintain symptom-free status. Residual depressive symptoms are common, even where there has been a robust response to antidepressant therapy. In clinical studies, approximately one-third of patients achieve a full remission, one-third experience a response and one-third are nonresponders. Partial remission is characterized by the presence of poorly defined residual symptoms. These symptoms typically include depressed mood, psychic anxiety, sleep disturbance, fatigue and diminished interest or pleasure. It is currently unclear which factors predict partial remission. However, it is clear that residual symptoms are powerful predictors of relapse, with relapse rates 3-6 times higher in patients with residual symptoms than in those who experience full remission. Residual symptoms are also associated with more medical and psychiatric visits, increased public assistance, disability benefits, thoughts of and attempts at suicide and chronicity. The risk of stroke and coronary events is also higher in patients with residual depressive symptoms. The substantial proportion of patients who achieve only partial remission has traditionally been neglected in antidepressant trials. Given that residual symptoms may relate, in part, to an incompatibility between patient and treatment, further research is needed to predict a better match. These symptoms are a clinically relevant state of illness, and the correct choice of initial antidepressant treatment should offer the greatest chance of achieving full remission.

Adult↗