The Plant-Associated Microbe Gene Ontology (PAMGO) Consortium: community development of new Gene Ontology terms describing biological processes involved in microbe-host interactions

All microbes that form beneficial, neutral, or pathogenic associations with hosts face similar challenges. They must physically adhere to and/or gain entry to host tissues; they must avoid, suppress, or tolerate host defenses; they must acquire nutrients from the host and successfully multiply. Microbes that associate with hosts come from many kingdoms of life and include bacteria, fungi, oomycetes, and nematodes. The increasing numbers of full genome sequences from these diverse microbes provide the opportunity to discover common mechanisms by which the microbes forge and maintain intimate associations with host organisms. However, cross-genome analyses have been hindered by lack of a universal vocabulary for describing biological processes involved in the interplay between microbes and their hosts. The Plant-Associated Microbe Gene Ontology (PAMGO) Consortium has been working for three years as an official interest group of the Gene Ontology (GO) Consortium to develop well-defined GO terms that describe many of the biological processes common to diverse plant- and animal-associated microbes. Creating these terms, over 700 at this time, has required a synthesis of diverse points of view from many research communities. The use of these terms in genome annotation will allow cross-genome searches for genes with common function (without demand for sequence similarity) and also improve the interpretation of data from high-throughput microarray and proteomic analyses. This article, and the more focused mini-reviews that make up this supplement to BMC Microbiology, describe the development and use of these terms.     

Meeting report of the RNA Ontology Consortium January 8-9, 2011

This report summarizes the proceedings of the structure mapping working group meeting of the RNA Ontology Consortium (ROC), held in Kona, Hawaii on January 8-9, 2011. The ROC hosted this workshop to facilitate collaborations among those researchers formalizing concepts in RNA, those developing RNA-related software, and those performing genome annotation and standardization. The workshop included three software presentations, extended round-table discussions, and the constitution of two new working groups, the first to address the need for better software integration and the second to discuss standardization and benchmarking of existing RNA annotation pipelines. These working groups have subsequently pursued concrete implementation of actions suggested during the discussion. Further information about the ROC and its activities can be found at http://roc.bgsu.edu/.     

基于本体论的植物遗传资源数据整合研究

随着现代生物学的发展,全球范围内建立了大量的生物学数据共享中心,同时,在生物学发展的带动下,植物遗传资源数据变得更为复杂、异构化和海量。本文在分析国内外几大著名的数据整合共享中心的基础上,简要介绍了本体论的概念及其在生物学领域中的研究现状,提出了基于生物本体论将植物遗传数据、数据挖掘工具、科技文献和科技交流进行整合的设想,并对数据整合需要考虑的几个问题进行了讨论。     

Plant preference and plant succession

Summary The theory that early successional plants and annual plants will be less well defended against generalist herbivores than later successional plants and perennial plants, because they avoid herbivores by escaping in space and time, is evaluated. The theory is not supported in the ecosystem examined. The correlation between level of preference and the ability of plants to support growth and survival is examined and shown to be high.     

Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages

The Plant Ontology Consortium (POC) (www.plantontology.org) is a collaborative effort among several plant databases and experts in plant systematics, botany and genomics. A primary goal of the POC is to develop simple yet robust and extensible controlled vocabularies that accurately reflect the biology of plant structures and developmental stages. These provide a network of vocabularies linked by relationships (ontology) to facilitate queries that cut across datasets within a database or between multiple databases. The current version of the ontology integrates diverse vocabularies used to describe Arabidopsis, maize and rice (Oryza sp.) anatomy, morphology and growth stages. Using the ontology browser, over 3500 gene annotations from three species-specific databases, The Arabidopsis Information Resource (TAIR) for Arabidopsis, Gramene for rice and MaizeGDB for maize, can now be queried and retrieved.     

The PlaNet Consortium: a network of European plant databases connecting plant genome data in an integrated biological knowledge resource

The completion of the Arabidopsis genome and the large collections of other plant sequences generated in recent years have sparked extensive functional genomics efforts. However, the utilization of this data is inefficient, as data sources are distributed and heterogeneous and efforts at data integration are lagging behind. PlaNet aims to overcome the limitations of individual efforts as well as the limitations of heterogeneous, independent data collections. PlaNet is a distributed effort among European bioinformatics groups and plant molecular biologists to establish a comprehensive integrated database in a collaborative network. Objectives are the implementation of infrastructure and data sources to capture plant genomic information into a comprehensive, integrated platform. This will facilitate the systematic exploration of Arabidopsis and other plants. New methods for data exchange, database integration and access are being developed to create a highly integrated, federated data resource for research. The connection between the individual resources is realized with BioMOBY. BioMOBY provides an architecture for the discovery and distribution of biological data through web services. While knowledge is centralized, data is maintained at its primary source without a need for warehousing. To standardize nomenclature and data representation, ontologies and generic data models are defined in interaction with the relevant communities.Minimal data models should make it simple to allow broad integration, while inheritance allows detail and depth to be added to more complex data objects without losing integration. To allow expert annotation and keep databases curated, local and remote annotation interfaces are provided. Easy and direct access to all data is key to the project.     

The Genomic Standards Consortium

A vast and rich body of information has grown up as a result of the world's enthusiasm for 'omics technologies. Finding ways to describe and make available this information that maximise its usefulness has become a major effort across the 'omics world. At the heart of this effort is the Genomic Standards Consortium (GSC), an open-membership organization that drives community-based standardization activities, Here we provide a short history of the GSC, provide an overview of its range of current activities, and make a call for the scientific community to join forces to improve the quality and quantity of contextual information about our public collections of genomes, metagenomes, and marker gene sequences.     

Interoperability between biomedical ontologies through relation expansion, upper-level ontologies and automatic reasoning

Researchers design ontologies as a means to accurately annotate and integrate experimental data across heterogeneous and disparate data- and knowledge bases. Formal ontologies make the semantics of terms and relations explicit such that automated reasoning can be used to verify the consistency of knowledge. However, many biomedical ontologies do not sufficiently formalize the semantics of their relations and are therefore limited with respect to automated reasoning for large scale data integration and knowledge discovery. We describe a method to improve automated reasoning over biomedical ontologies and identify several thousand contradictory class definitions. Our approach aligns terms in biomedical ontologies with foundational classes in a top-level ontology and formalizes composite relations as class expressions. We describe the semi-automated repair of contradictions and demonstrate expressive queries over interoperable ontologies. Our work forms an important cornerstone for data integration, automatic inference and knowledge discovery based on formal representations of knowledge. Our results and analysis software are available at http://bioonto.de/pmwiki.php/Main/ReasonableOntologies.     

Plant hormones and plant growth regulators in plant tissue culture

Summary This is a short review of the classical and new, natural and synthetic plant hormones and growth regulators (phytohormones) and highlights some of their uses in plant tissue culture. Plant hormones rarely act alone, and for most processes— at least those that are observed at the organ level—many of these regulators have interacted in order to produce the final effect. The following substances are discussed: (a) Classical plant hormones (auxins, cytokinins, gibberellins, abscisic acid, ethylene and growth regulatory substances with similar biological effects. New, naturally occurring substances in these categories are still being discovered. At the same time, novel structurally related compounds are constantly being synthesized. There are also many new but chemically unrelated compounds with similar hormone-like activity being produced. A better knowledge of the uptake, transport, metabolism, and mode of action of phytohormones and the appearance of chemicals that inhibit synthesis, transport, and action of the native plant hormones has increased our knowledge of the role of these hormones in growth and development. (b) More recently discovered natural growth substances that have phytohormonal-like regulatory roles (polyamines, oligosaccharins, salicylates, jasmonates, sterols, brassinosteroids, dehydrodiconiferyl alcohol glucosides, turgorins, systemin, unrelated natural stimulators and inhibitors), as well as myoinositol. Many of these growth active substances have not yet been examined in relation to growth and organized developmentin vitro.     

The Childhood Leukemia International Consortium

Background: Acute leukemia is the most common cancer in children under 15 years of age; 80% are acute lymphoblastic leukemia (ALL) and 17% are acute myeloid leukemia (AML). Childhood leukemia shows further diversity based on cytogenetic and molecular characteristics, which may relate to distinct etiologies. Case–control studies conducted worldwide, particularly of ALL, have collected a wealth of data on potential risk factors and in some studies, biospecimens. There is growing evidence for the role of infectious/immunologic factors, fetal growth, and several environmental factors in the etiology of childhood ALL. The risk of childhood leukemia, like other complex diseases, is likely to be influenced both by independent and interactive effects of genes and environmental exposures. While some studies have analyzed the role of genetic variants, few have been sufficiently powered to investigate gene–environment interactions. Objectives: The Childhood Leukemia International Consortium (CLIC) was established in 2007 to promote investigations of rarer exposures, gene–environment interactions and subtype-specific associations through the pooling of data from independent studies. Methods: By September 2012, CLIC included 22 studies (recruitment period: 1962–present) from 12 countries, totaling approximately 31 000 cases and 50 000 controls. Of these, 19 case–control studies have collected detailed epidemiologic data, and DNA samples have been collected from children and child–parent trios in 15 and 13 of these studies, respectively. Two registry-based studies and one study comprising hospital records routinely obtained at birth and/or diagnosis have limited interview data or biospecimens. Conclusions: CLIC provides a unique opportunity to fill gaps in knowledge about the role of environmental and genetic risk factors, critical windows of exposure, the effects of gene–environment interactions and associations among specific leukemia subtypes in different ethnic groups.     

Plant polyploidy and insect/plant interactions

We used flow cytometry and extensive geographic surveys of herbivore attack to test whether repeated evolution of autotetraploidy in the perennial herb Heuchera grossulariifolia Rydb. (Saxifragaceae) has created evolutionary barriers to attack by the specialist moth herbivore Greya politella (Prodoxidae). We found that the moth has colonized tetraploid as well as diploid populations, has colonized tetraploids of separate evolutionary origin, and, at least under some conditions, is more likely to attack tetraploids than diploids. Plant polyploidy therefore provides a potential route out of specialization as an evolutionary dead end in phytophagous insect taxa as well as a potentially important route to subsequent phylogenetic and geographic diversification of plant/insect interactions.     

植物糖生物学与糖链植物疫苗

植物糖生物学是研究植物与糖类互作机制、植物体内糖链与糖缀合物结构及生物学功能的科学,具体涉及糖信号、糖蛋白及其糖链功能、糖基转移酶及植物凝集素等研究方向。依据相关文献及实际研究经验,简要综述植物糖生物学的最新研究进展,其中重点介绍糖链植物疫苗并阐述其应用情况及作用机制。     

The qualitative and time-dependent character of spatial relations in biomedical ontologies

MOTIVATION: The formal representation of mereological aspects of canonical anatomy (parthood relations) is relatively well understood. The formal representation of other aspects of canonical anatomy, such as connectedness and adjacency relations between anatomical parts, their shape and size as well as the spatial arrangement of anatomical parts within larger anatomical structures are, however, much less well understood and represented in existing computational anatomical and bio-medical ontologies only insufficiently. RESULTS: In this article, we provide a methodology of how to incorporate this kind of information into anatomical and bio-medical ontologies by applying techniques of representing qualitative spatial information from Artificial Intelligence. In particular, we focus on how to explicitly take into account the qualitative and time-dependent character of these relations. As a running example, we use the human temporomandibular joint (TMJ). AVAILABILITY: Using the presented methodology, a formal ontology was developed which is accessible on http://www.ifomis.org/bfo/fol. This ontology may help to improve the logical and ontological rigor of bio-medical ontologies such as the OBO relation ontology.