共查询到20条相似文献,搜索用时 46 毫秒
1.
Oliver Fiehn Don Robertson Jules Griffin Mariet van der Werf Basil Nikolau Norman Morrison Lloyd W. Sumner Roy Goodacre Nigel W. Hardy Chris Taylor Jennifer Fostel Bruce Kristal Rima Kaddurah-Daouk Pedro Mendes Ben van Ommen John C. Lindon Susanna-Assunta Sansone 《Metabolomics : Official journal of the Metabolomic Society》2007,3(3):175-178
In 2005, the Metabolomics Standards Initiative has been formed. An outline and general introduction is provided to inform
about the history, structure, working plan and intentions of this initiative. Comments on any of the suggested minimal reporting
standards are welcome to be sent to the open email list Msi-workgroups-feedback@lists.sourceforge.net 相似文献
2.
Christoph Steinbeck Pablo Conesa Kenneth Haug Tejasvi Mahendraker Mark Williams Eamonn Maguire Philippe Rocca-Serra Susanna-Assunta Sansone Reza M. Salek Julian L. Griffin 《Metabolomics : Official journal of the Metabolomic Society》2012,8(5):757-760
Exciting funding initiatives are emerging in Europe and the US for metabolomics data production, storage, dissemination and analysis. This is based on a rich ecosystem of resources around the world, which has been build during the past ten years, including but not limited to resources such as MassBank in Japan and the Human Metabolome Database in Canada. Now, the European Bioinformatics Institute has launched MetaboLights, a database for metabolomics experiments and the associated metadata (http://www.ebi.ac.uk/metabolights). It is the first comprehensive, cross-species, cross-platform metabolomics database maintained by one of the major open access data providers in molecular biology. In October, the European COSMOS consortium will start its work on Metabolomics data standardization, publication and dissemination workflows. The NIH in the US is establishing 6?C8 metabolomics services cores as well as a national metabolomics repository. This communication reports about MetaboLights as a new resource for Metabolomics research, summarises the related developments and outlines how they may consolidate the knowledge management in this third large omics field next to proteomics and genomics. 相似文献
3.
Fiehn O Wohlgemuth G Scholz M Kind T Lee do Y Lu Y Moon S Nikolau B 《The Plant journal : for cell and molecular biology》2008,53(4):691-704
The Metabolomics Standards Initiative (MSI) has recently released documents describing minimum parameters for reporting metabolomics experiments, in order to validate metabolomic studies and to facilitate data exchange. The reporting parameters encompassed by MSI include the biological study design, sample preparation, data acquisition, data processing, data analysis and interpretation relative to the biological hypotheses being evaluated. Herein we exemplify how such metadata can be reported by using a small case study – the metabolite profiling by GC-TOF mass spectrometry of Arabidopsis thaliana leaves from a knockout allele of the gene At1g08510 in the Wassilewskija ecotype. Pitfalls in quality control are highlighted that can invalidate results even if MSI reporting standards are fulfilled, including reliable compound identification and integration of unknown metabolites. Standardized data processing methods are proposed for consistent data storage and dissemination via databases. 相似文献
4.
Mariët J. van der Werf Ralf Takors Jørn Smedsgaard Jens Nielsen Tom Ferenci Jean Charles Portais Christoph Wittmann Mark Hooks Alberta Tomassini Marco Oldiges Jennifer Fostel Uwe Sauer 《Metabolomics : Official journal of the Metabolomic Society》2007,3(3):189-194
With the increasing use of metabolomics as a means to study a large number of different biological research questions, there
is a need for a minimal set of reporting standards that allow the scientific community to evaluate, understand, repeat, compare
and re-investigate metabolomics studies. Here we propose, a first draft of minimal requirements to effectively describe the
biological context of metabolomics studies that involve microbial or in vitro biological subjects. This recommendation has
been produced by the microbiology and in vitro biology working subgroup of the Metabolomics Standards Initiative in collaboration
with the yeast systems biology network as part of a wider standardization initiative led by the Metabolomics Society. Microbial
and in vitro biology metabolomics is defined by this sub-working group as studies with any cell or organism that require a
defined external medium to facilitate growth and propagation. Both a minimal set and a best practice set of reporting standards
for metabolomics experiments have been defined. The minimal set of reporting standards for microbial or in vitro biology metabolomics
experiments includes those factors that are specific for metabolomics experiments and that critically determine the outcome of the experiments. The best practice set of reporting
standards contains both the factors that are specific for metabolomics experiments and general aspects that critically determine the outcome of any microbial or in vitro biological experiment. 相似文献
5.
ArrayPlex is a software package that centrally provides a large number of flexible toolsets useful for functional genomics, including microarray data storage, quality assessments, data visualization, gene annotation retrieval, statistical tests, genomic sequence retrieval and motif analysis. It uses a client-server architecture based on open source components, provides graphical, command-line, and programmatic access to all needed resources, and is extensible by virtue of a documented application programming interface. ArrayPlex is available at http://sourceforge.net/projects/arrayplex/. 相似文献
6.
Djie Tjwan Thung Joep de Ligt Lisenka EM Vissers Marloes Steehouwer Mark Kroon Petra de Vries Eline P Slagboom Kai Ye Joris A Veltman Jayne Y Hehir-Kwa 《Genome biology》2014,15(10)
Mobile elements are major drivers in changing genomic architecture and can cause disease. The detection of mobile elements is hindered due to the low mappability of their highly repetitive sequences. We have developed an algorithm, called Mobster, to detect non-reference mobile element insertions in next generation sequencing data from both whole genome and whole exome studies. Mobster uses discordant read pairs and clipped reads in combination with consensus sequences of known active mobile elements. Mobster has a low false discovery rate and high recall rate for both L1 and Alu elements. Mobster is available at http://sourceforge.net/projects/mobster.
Electronic supplementary material
The online version of this article (doi:10.1186/s13059-014-0488-x) contains supplementary material, which is available to authorized users. 相似文献7.
8.
MOTIVATION: A Robot Scientist is a physically implemented robotic system that can automatically carry out cycles of scientific experimentation. We are commissioning a new Robot Scientist designed to investigate gene function in S. cerevisiae. This Robot Scientist will be capable of initiating >1,000 experiments, and making >200,000 observations a day. Robot Scientists provide a unique test bed for the development of methodologies for the curation and annotation of scientific experiments: because the experiments are conceived and executed automatically by computer, it is possible to completely capture and digitally curate all aspects of the scientific process. This new ability brings with it significant technical challenges. To meet these we apply an ontology driven approach to the representation of all the Robot Scientist's data and metadata. RESULTS: We demonstrate the utility of developing an ontology for our new Robot Scientist. This ontology is based on a general ontology of experiments. The ontology aids the curation and annotating of the experimental data and metadata, and the equipment metadata, and supports the design of database systems to hold the data and metadata. AVAILABILITY: EXPO in XML and OWL formats is at: http://sourceforge.net/projects/expo/. All materials about the Robot Scientist project are available at: http://www.aber.ac.uk/compsci/Research/bio/robotsci/. 相似文献
9.
Shyamashree Banerjee Parth Sarthi Sen Gupta Arnab Nayek Sunit Das Vishma Pratap Sur Pratyay Seth Rifat Nawaz Ul Islam Amal K Bandyopadhyay 《Bioinformation》2015,11(7):366-368
AvailabilityPHYSICO2: is freely available at http://sourceforge.net/projects/physico2/ along with its documentation at
https://sourceforge.net/projects/physico2/files/Documentation.pdf/download for all users. 相似文献
10.
Preeti Bais Stephanie M. Moon Kun He Ricardo Leitao Kate Dreher Tom Walk Yves Sucaet Lenore Barkan Gert Wohlgemuth Mary R. Roth Eve Syrkin Wurtele Philip Dixon Oliver Fiehn B. Markus Lange Vladimir Shulaev Lloyd W. Sumner Ruth Welti Basil J. Nikolau Seung Y. Rhee Julie A. Dickerson 《Plant physiology》2010,152(4):1807-1816
PlantMetabolomics.org (PM) is a web portal and database for exploring, visualizing, and downloading plant metabolomics data. Widespread public access to well-annotated metabolomics datasets is essential for establishing metabolomics as a functional genomics tool. PM integrates metabolomics data generated from different analytical platforms from multiple laboratories along with the key visualization tools such as ratio and error plots. Visualization tools can quickly show how one condition compares to another and which analytical platforms show the largest changes. The database tries to capture a complete annotation of the experiment metadata along with the metabolite abundance databased on the evolving Metabolomics Standards Initiative. PM can be used as a platform for deriving hypotheses by enabling metabolomic comparisons between genetically unique Arabidopsis (Arabidopsis thaliana) populations subjected to different environmental conditions. Each metabolite is linked to relevant experimental data and information from various annotation databases. The portal also provides detailed protocols and tutorials on conducting plant metabolomics experiments to promote metabolomics in the community. PM currently houses Arabidopsis metabolomics data generated by a consortium of laboratories utilizing metabolomics to help elucidate the functions of uncharacterized genes. PM is publicly available at http://www.plantmetabolomics.org.In the post genomics era, metabolomics is fast emerging as a vital source of information to aid in solving systems biology puzzles with an emphasis on metabolic solutions. Metabolomics is the science of measuring the pool sizes of metabolites (small molecules of Mr ≤ 1,000 D), which collectively define the metabolome of a biological sample (Fiehn et al., 2000; Hall et al., 2002). Coverage of the entire plant metabolome is a daunting task as it is estimated that there are over 200,000 different metabolites within the plant kingdom (Goodacre et al., 2004). Although technology is rapidly advancing, there are still large gaps in our knowledge of the plant metabolome.Despite this lack of complete knowledge and the immense metabolic diversity among plants, metabolomics has become a key analytical tool in the plant community (Hall et al., 2002). This has led to the emergence of multiple experimental and analytical platforms that collectively generate millions of metabolite data points. Because of this vast amount of data, the development of public databases to capture information from metabolomics experiments is vital to provide the scientific community with comprehensive knowledge about metabolite data generation, annotation, and integration with metabolic pathway data. Some examples of these public databases are given below. The Human Metabolome Project contains comprehensive data for more than 2,000 metabolites found within the human body (Wishart et al., 2007). The Golm Database is a repository that provides access to mass spectrometry (MS) libraries, metabolite profiling experiments, and related information from gas chromatography (GC)-MS experimental platforms, along with tools to integrate this information with other systems biology knowledge (Kopka et al., 2005). The Madison Metabolomics Consortium Database contains primarily NMR spectra for Arabidopsis (Arabidopsis thaliana) and features thorough NMR search tools (Cui et al., 2008). SetupX and Binbase provide a framework that combines MS data and biological metadata for steering laboratory work flows and employs automated metabolite annotation (Scholz and Fiehn, 2007).A single analytical technique cannot identify and quantify all the metabolites found in plants. Thus, PlantMetabolomics.org (PM) was developed to provide a portal for accessing publicly available MS-based plant metabolomics experimental results from multiple analytical and separation techniques. PM also follows the emerging metabolomics standards for experiment annotation. PM has extensive annotation links between the identified metabolites and metabolic pathways in AraCyc (Mueller et al., 2003) at The Arabidopsis Information Resource (Rhee et al., 2003) and the Plant Metabolic Network (www.plantcyc.org), the Kyoto Encyclopedia of Genes and Genomes (KEGG; Kanehisa et al., 2004), and MetNetDB (Wurtele et al., 2007).Standards for the annotation of metabolomics experiments are still under active development and the metadata types collected in PM are based on the recommendations of the Metabolomics Standards Initiative (MSI; Fiehn et al., 2007a) and the Minimal Information for a Metabolomic Experiment (Bino et al., 2004) standards. MSI attempts to capture the complete annotation of metabolomics experiments and includes metadata of the experiments along with the metabolite abundance data. The initial database schema design was guided by the schema proposed in the Architecture for Metabolomics project (Jenkins et al., 2004). 相似文献
11.
Angelica Dessì Laura Corona Roberta Pintus Vassilios Fanos 《Expert review of proteomics》2018,15(8):647-656
Introduction: The exposure to tobacco smoke during pregnancy is one of the leading causes of perinatal adverse outcomes such as stillbirth, intrauterine growth restriction (IUGR), and low birth weight, but the underlying biological mechanisms are still unclear. The incidence of this phenomenon maybe largely underestimated since the evaluation is made mainly by self-assessment questionnaires rather than measuring nicotine metabolites (such as cotinine) in biological fluids. In this context metabolomics may be useful to assess the actual number of pregnant women and to highlight the pathophysiological mechanisms that lead to the abovementioned adverse outcomes.
Areas covered: The aims of this review are to analyze the literature and the application of the omics sciences, such as genomics and metabolomics concerning the negative effects of smoking during pregnancy in order to give a comprehensive picture of all the study made so far and to point out the potential of metabolomics as an investigative, predictive, and diagnostic tool.
Expert commentary: Metabolomics in recent years has proved an excellent tool to try to understand the problems in perinatal medicine. With the increase in the number of studies we are convinced that it can be a useful instrument of investigation in this field. 相似文献
12.
Arnab Nayek Parth Sarthi Sen Gupta Shyamashree Banerjee Vishma Pratap Sur Pratyay Seth Sunit Das Rifat Nawaz Ul Islam Amal Kumar Bandyopadhyay 《Bioinformation》2015,11(8):413-415
AvailabilityADSBET2 is freely available at http://sourceforge.net/projects/ADSBET2/ for all users. 相似文献
13.
As the biomedical impact of small RNAs grows, so does the need to understand competing structural alternatives for regions of functional interest. Suboptimal structure analysis provides significantly more RNA base pairing information than a single minimum free energy prediction. Yet computational enhancements like Boltzmann sampling have not been fully adopted by experimentalists since identifying meaningful patterns in this data can be challenging. Profiling is a novel approach to mining RNA suboptimal structure data which makes the power of ensemble-based analysis accessible in a stable and reliable way. Balancing abstraction and specificity, profiling identifies significant combinations of base pairs which dominate low-energy RNA secondary structures. By design, critical similarities and differences are highlighted, yielding crucial information for molecular biologists. The code is freely available via http://gtfold.sourceforge.net/profiling.html. 相似文献
14.
Parth Sarthi Sen Gupta Arnab Nayek Shyamashree Banerjee Pratyay Seth Sunit Das Vishma Pratap Sur Chittran Roy Amal Kumar Bandyopadhyay 《Bioinformation》2015,11(1):39-42
AvailabilitySBION2 is freely available at http://sourceforge.net/projects/sbion2/ for academic users 相似文献
15.
Metabolomics or the large-scale phytochemical analysis of plants is reviewed in relation to functional genomics and systems biology. A historical account of the introduction and evolution of metabolite profiling into today's modern comprehensive metabolomics approach is provided. Many of the technologies used in metabolomics, including optical spectroscopy, nuclear magnetic resonance, and mass spectrometry are surveyed. The critical role of bioinformatics and various methods of data visualization are summarized and the future role of metabolomics in plant science assessed. 相似文献
16.
The MGED Ontology: a resource for semantics-based description of microarray experiments 总被引:5,自引:0,他引:5
Whetzel PL Parkinson H Causton HC Fan L Fostel J Fragoso G Game L Heiskanen M Morrison N Rocca-Serra P Sansone SA Taylor C White J Stoeckert CJ 《Bioinformatics (Oxford, England)》2006,22(7):866-873
MOTIVATION: The generation of large amounts of microarray data and the need to share these data bring challenges for both data management and annotation and highlights the need for standards. MIAME specifies the minimum information needed to describe a microarray experiment and the Microarray Gene Expression Object Model (MAGE-OM) and resulting MAGE-ML provide a mechanism to standardize data representation for data exchange, however a common terminology for data annotation is needed to support these standards. RESULTS: Here we describe the MGED Ontology (MO) developed by the Ontology Working Group of the Microarray Gene Expression Data (MGED) Society. The MO provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data. The MO was developed to provide terms for annotating experiments in line with the MIAME guidelines, i.e. to provide the semantics to describe a microarray experiment according to the concepts specified in MIAME. The MO does not attempt to incorporate terms from existing ontologies, e.g. those that deal with anatomical parts or developmental stages terms, but provides a framework to reference terms in other ontologies and therefore facilitates the use of ontologies in microarray data annotation. AVAILABILITY: The MGED Ontology version.1.2.0 is available as a file in both DAML and OWL formats at http://mged.sourceforge.net/ontologies/index.php. Release notes and annotation examples are provided. The MO is also provided via the NCICB's Enterprise Vocabulary System (http://nciterms.nci.nih.gov/NCIBrowser/Dictionary.do). CONTACT: Stoeckrt@pcbi.upenn.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. 相似文献
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Cyclone aims at facilitating the use of BioCyc, a collection of Pathway/Genome Databases (PGDBs). Cyclone provides a fully extensible Java Object API to analyze and visualize these data. Cyclone can read and write PGDBs, and can write its own data in the CycloneML format. This format is automatically generated from the BioCyc ontology by Cyclone itself, ensuring continued compatibility. Cyclone objects can also be stored in a relational database CycloneDB. Queries can be written in SQL, and in an intuitive and concise object-oriented query language, Hibernate Query Language (HQL). In addition, Cyclone interfaces easily with Java software including the Eclipse IDE for HQL edition, the Jung API for graph algorithms or Cytoscape for graph visualization. AVAILABILITY: Cyclone is freely available under an open source license at: http://sourceforge.net/projects/nemo-cyclone. SUPPLEMENTARY INFORMATION: For download and installation instructions, tutorials, use cases and examples, see http://nemo-cyclone.sourceforge.net. 相似文献
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20.
We describe PerlMAT, a Perl microarray toolkit providing easy to use object-oriented methods for the simplified manipulation, management and analysis of microarray data. The toolkit provides objects for the encapsulation of microarray spots and reporters, several common microarray data file formats and GAL files. In addition, an analysis object provides methods for data processing, and an image object enables the visualisation of microarray data. This important addition to the Perl developer's library will facilitate more widespread use of Perl for microarray application development within the bioinformatics community. The coherent interface and well-documented code enables rapid analysis by even inexperienced Perl developers. AVAILABILITY: Software is available at http://sourceforge.net/projects/perlmat 相似文献