Gbrowse Moby: a Web-based browser for BioMoby Services

Background  

The BioMoby project aims to identify and deploy standards and conventions that aid in the discovery, execution, and pipelining of distributed bioinformatics Web Services. As of August, 2006, approximately 680 bioinformatics resources were available through the BioMoby interoperability platform. There are a variety of clients that can interact with BioMoby-style services. Here we describe a Web-based browser-style client – Gbrowse Moby – that allows users to discover and "surf" from one bioinformatics service to the next using a semantically-aided browsing interface.     

BioMoby extensions to the Taverna workflow management and enactment software

Background  

As biology becomes an increasingly computational science, it is critical that we develop software tools that support not only bioinformaticians, but also bench biologists in their exploration of the vast and complex data-sets that continue to build from international genomic, proteomic, and systems-biology projects. The BioMoby interoperability system was created with the goal of facilitating the movement of data from one Web-based resource to another to fulfill the requirements of non-expert bioinformaticians. In parallel with the development of BioMoby, the European myGrid project was designing Taverna, a bioinformatics workflow design and enactment tool. Here we describe the marriage of these two projects in the form of a Taverna plug-in that provides access to many of BioMoby's features through the Taverna interface.     

REMORA: a pilot in the ocean of BioMoby web-services

SUMMARY: Emerging web-services technology allows interoperability between multiple distributed architectures. Here, we present REMORA, a web server implemented according to the BioMoby web-service specifications, providing life science researchers with an easy-to-use workflow generator and launcher, a repository of predefined workflows and a survey system. CONTACT: Jerome.Gouzy@toulouse.inra.fr AVAILABILITY: The REMORA web server is freely available at http://bioinfo.genopole-toulouse.prd.fr/remora, sources are available upon request from the authors.     

Representing default knowledge in biomedical ontologies: application to the integration of anatomy and phenotype ontologies

Background  

Current efforts within the biomedical ontology community focus on achieving interoperability between various biomedical ontologies that cover a range of diverse domains. Achieving this interoperability will contribute to the creation of a rich knowledge base that can be used for querying, as well as generating and testing novel hypotheses. The OBO Foundry principles, as applied to a number of biomedical ontologies, are designed to facilitate this interoperability. However, semantic extensions are required to meet the OBO Foundry interoperability goals. Inconsistencies may arise when ontologies of properties – mostly phenotype ontologies – are combined with ontologies taking a canonical view of a domain – such as many anatomical ontologies. Currently, there is no support for a correct and consistent integration of such ontologies.     

DataBiNS: a BioMoby-based data-mining workflow for biological pathways and non-synonymous SNPs

DataBiNS is a custom-designed BioMoby Web Service workflow that integrates non-synonymous coding single nucleotide polymorphisms (nsSNPs) data with structure/function and pathway data for the relevant protein. A KEGG Pathway Identifier representing a specific human biological pathway initializes the DataBiNS workflow. The workflow retrieves a list of publications, gene ontology annotations and nsSNP information for each gene involved in the biological pathway. Manual inspection of output data from several trial runs confirms that all expected information is appropriately retrieved by the workflow services. The use of an automated BioMoby workflow, rather than manual 'surfing', to retrieve the necessary data, significantly reduces the effort required for functional interpretation of SNP data, and thus encourages more speculative investigation. Moreover, the modular nature of the individual BioMoby Services enables fine-grained reusing of each service in other workflows, thus reducing the effort required to achieve similar investigations in the future. AVAILABILITY: The workflow is freely available as a Taverna SCUFL XML document at the iCAPTURE Centre web site, http://www.mrl.ubc.ca/who/who_bios_scott_tebbutt.shtml.     

Towards a unified data infrastructure to support European and global microbiome research: a call to action

High-quality microbiome research relies on the integrity, management and quality of supporting data. Currently biobanks and culture collections have different formats and approaches to data management. This necessitates a standard data format to underpin research, particularly in line with the FAIR data standards of findability, accessibility, interoperability and reusability. We address the importance of a unified, coordinated approach that ensures compatibility of data between that needed by biobanks and culture collections, but also to ensure linkage between bioinformatic databases and the wider research community.     

Spatial and temporal variation of fish community biomass and energy flow throughout a tropical river network

1. Accurately accounting for flows of energy through food webs is challenging because of the spatial and temporal variability associated with energy production and consumption. Wet–dry tropical rivers have a highly seasonal discharge regime where wet season flows allow access to energy sources (inundated wetlands) that are not available during the dry season when aquatic consumers are confined to disconnected waterholes.
2. We combined measures of fish community biomass with previously published feeding guild specific stable isotope analyses to explore how opposing wet- and dry-season habitat templates influence spatial and temporal trends in the sources of energy supporting fish biomass throughout a river network in the wet–dry tropics of northern Australia.
3. Accounting for the relative contribution of each feeding guild to fish community biomass was a critical component of our analyses, as a single feeding guild (invertivore/piscivore) influenced spatial and temporal patterns in the sources of energy supporting overall fish biomass. During the early dry season, the reliance of fish communities on autochthonous sources of energy (periphyton) decreased from the upper to lower reaches of the river network, which correlates with increasing floodplain area and wet season inundation times. These patterns disappeared by the late dry season as fish in both upper and lower reaches became increasingly reliant on autochthonous sources produced within waterholes over the course of the dry season, indicating that the large wet-season gains in fish biomass are maintained through the dry season by energy produced within waterhole refuges.
4. Collectively these results indicate that a combination of autochthonous and allochthonous sources of energy work in unison to support fish community biomass throughout the Mitchell River catchment and that access to these sources of energy is dictated by seasonal patterns in discharge interacting with spatial variability in river geomorphology (channel geometry and floodplain area).
5. Many rivers are experiencing decreased flows due to water resource development and more frequent and severe droughts. Thus, we suggest our study provides insight into how changes in discharge regime could influence food web energetics throughout river networks.

     

The ESF Programme on Functional Genomics Workshop on 'Data Integration in Functional Genomics: Application to Biological Pathways'

We report from the second ESF Programme on Functional Genomics workshop on Data Integration, which covered topics including the status of biological pathways databases in existing consortia; pathways as part of bioinformatics infrastructures; design, creation and formalization of biological pathways databases; generating and supporting pathway data and interoperability of databases with other external databases and standards. Key issues emerging from the discussions were the need for continued funding to cover maintenance and curation of databases, the importance of quality control of the data in these resources, and efforts to facilitate the exchange of data and to ensure the interoperability of databases.     

δ13C and δ15N indicators of fish and shrimp community diet and trophic structure in a mangrove ecosystem in Thailand

Stable carbon and nitrogen isotope ratios were used to elucidate primary carbon sources and trophic relationships of the fish and shrimp community in the Klong Ngao mangrove ecosystem, southern Thailand. There were no significant differences in isotopic compositions of biota between mangrove and offshore sites (Welch–Aspin test). The δ¹⁵N values of eight fish species and two shrimp species at both sites were also not significantly different by the test, meaning that at both sites they feed on the same diets due to the discharge of large quantities of mangrove sediments. The δ¹⁵N isotopic enrichment of consumers suggested that there are four trophic levels in the Klong Ngao food web, with at least two fish species capable of switching feeding strategies and thus altering their apparent trophic positions. Phytoplankton culture experiments indicated that mangrove-derived sediments could play an important role in stimulating phytoplankton growth for low turbidity offshore areas, thus providing an alternate food source. The isotopic associations among sources and consumers indicated that mangroves were the major carbon source supporting aquatic food webs in the Klong Ngao ecosystem.     

Comparison,alignment, and synchronization of cell line information between CLO and EFO

Background

The Experimental Factor Ontology (EFO) is an application ontology driven by experimental variables including cell lines to organize and describe the diverse experimental variables and data resided in the EMBL-EBI resources. The Cell Line Ontology (CLO) is an OBO community-based ontology that contains information of immortalized cell lines and relevant experimental components. EFO integrates and extends ontologies from the bio-ontology community to drive a number of practical applications. It is desirable that the community shares design patterns and therefore that EFO reuses the cell line representation from the Cell Line Ontology (CLO). There are, however, challenges to be addressed when developing a common ontology design pattern for representing cell lines in both EFO and CLO.

Results

In this study, we developed a strategy to compare and map cell line terms between EFO and CLO. We examined Cellosaurus resources for EFO-CLO cross-references. Text labels of cell lines from both ontologies were verified by biological information axiomatized in each source. The study resulted in the identification 873 EFO-CLO aligned and 344 EFO unique immortalized permanent cell lines. All of these cell lines were updated to CLO and the cell line related information was merged. A design pattern that integrates EFO and CLO was also developed.

Conclusion

Our study compared, aligned, and synchronized the cell line information between CLO and EFO. The final updated CLO will be examined as the candidate ontology to import and replace eligible EFO cell line classes thereby supporting the interoperability in the bio-ontology domain. Our mapping pipeline illustrates the use of ontology in aiding biological data standardization and integration through the biological and semantics content of cell lines.

     

Owner controlled data exchange in nutrigenomic collaborations: the NuGO information network

New ‘omics’ technologies are changing nutritional sciences research. They enable to tackle increasingly complex questions but also increase the need for collaboration between research groups. An important challenge for successful collaboration is the management and structured exchange of information that accompanies data-intense technologies. NuGO, the European Nutrigenomics Organization, the major collaborating network in molecular nutritional sciences, is supporting the application of modern information technologies in this area. We have developed and implemented a concept for data management and computing infrastructure that supports collaboration between nutrigenomics researchers. The system fills the gap between “private” storing with occasional file sharing by email and the use of centralized databases. It provides flexible tools to share data, also during experiments, while preserving ownership. The NuGO Information Network is a decentral, distributed system for data exchange based on standard web technology. Secure access to data, maintained by the individual researcher, is enabled by web services based on the the BioMoby framework. A central directory provides information about available web services. The flexibility of the infrastructure allows a wide variety of services for data processing and integration by combining several web services, including public services. Therefore, this integrated information system is suited for other research collaborations.     

MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology

Background  

The Minimal Information Requested In the Annotation of biochemical Models (MIRIAM) is a set of guidelines for the annotation and curation processes of computational models, in order to facilitate their exchange and reuse. An important part of the standard consists in the controlled annotation of model components, based on Uniform Resource Identifiers. In order to enable interoperability of this annotation, the community has to agree on a set of standard URIs, corresponding to recognised data types. MIRIAM Resources are being developed to support the use of those URIs.     

Temperature increase and fluctuation induce phytoplankton biodiversity loss – Evidence from a multi‐seasonal mesocosm experiment

Global climate change scenarios predict lake water temperatures to increase up to 4°C and extreme weather events, including heat waves and large temperature fluctuations, to occur more frequently. Such changes may result in a reorganization of the plankton community structure, causing shifts in diversity and structure toward a community dominated by fewer species that are more adapted to endure warmer and irregular temperature conditions. We designed a long‐term (8 months) mesocosm experiment to explore how ambient water temperature (C: control), induced increased temperature (T: +4°C), and temperature fluctuations (F: ±4°C relative to T) change phytoplankton phenology, taxonomical diversity, and community structure, and how such changes affected zooplankton abundance and composition. Synthesis. Our results show that T and F relative to C significantly decreased phytoplankton diversity. Moreover, there was a clear effect of the temperature treatments (T and F) on phytoplankton size structure that resulted in a significantly lower growth of large species (i.e., large Chlorophyta) compared to C. Decreased diversity and evenness in the T and F treatments pushed the community toward the dominance of only a few phytoplankton taxa (mainly Cyanobacteria and Chlorophyta) that are better adapted to endure warmer and more irregular temperature conditions. The observed shift toward Cyanobacteria dominance may affect trophic energy transfer along the aquatic food web.     

Food web of macroinvertebrate community in a Yangtze shallow lake: trophic basis and pathways

No detailed food web research on macroinvertebrate community of lacustrine ecosystem was reported in China. The present study is the first attempt on the subject in Lake Biandantang, a macrophytic lake in Hubei Province. Food webs of the macroinvertebrate community were compiled bimonthly from March, 2002 to March, 2003. Dietary information was obtained from gut analysis. Linkage strength was quantified by combining estimates of energy flow (secondary production) with data of gut analysis. The macroinvertebrate community of Lake Biandantang was based heavily on detritus. Quantitative food webs showed the total ingestion ranged from 6930 to 36,340 mg dry mass m⁻² bimonthly. The ingestion of macroinvertebrate community was higher in the months with optimum temperature than that in other periods with higher or lower temperature. Through comparison, many patterns in benthic food web of Lake Biandantang are consistent with other detritus-based webs, such as stream webs, but different greatly from those based on autochthonous primary production (e.g. pelagic systems). It suggests that the trophic basis of the web is essential in shaping food web structure. Electronic supplementary material Electronic supplementary material is available for this article at and accessible for authorised users.     

Informatics in neuroscience

The application of informatics to neuroscience goes far beyond 'traditional' bioinformatics modalities such as DNA sequences. In this review, we describe how informatics is being used to study the nervous system at multiple levels, spanning scales from molecules to behavior. The continuing development of standards for data exchange and interoperability, together with increasing awareness and acceptance of the importance of data sharing, are among the key efforts required to advance the field.     

Effects of nutrient supplementation on host‐pathogen dynamics of the amphibian chytrid fungus: a community approach

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Food Webs and Disease: Is Pathogen Diversity Limited by Vector Diversity?

Classical predator–prey and host–parasite systems have been extensively studied in a food web context. Less attention has been paid to communities that include pathogens and their vectors. We present a coarse-grained, pan-African analysis of the relationships between the abiotic environment (location, precipitation, temperature), the species richness and community composition of ixodid ticks, and the species richness and community composition of pathogens that ticks transmit to humans. We found strong correlations between the abiotic environment and tick species richness, and a weak but significant correlation between the abiotic environment and pathogen species richness. A substantial amount of variation in community composition of parasites and pathogens was not explained by the variables that we considered. A structural equation model that compensated for the indirect effects of climate on the pathogen community via tick community composition suggested that while the environment strongly regulates tick community composition and tick community composition strongly regulates pathogen community composition, abiotic influences on pathogen species richness and community composition are weak. Our results support the view that changes in the broader environment will influence tick-borne pathogens primarily via the influence of the environment on ticks. The interactions that regulate host–vector–pathogen dynamics are of particular relevance in understanding the relationships between environmental change and health concerns, such as the impact of climate change on the occurrence of vector-borne diseases.