Ontology Summit 2008 Communiqué: Towards an open ontology repository

Each annual Ontology Summit initiative makes a statement appropriate to each Summits theme as part of our general advocacy designed to bring ontology science and engineering into the mainstream. The theme this year is "Towards an Open Ontology Repository". This communiqué represents the joint position of those who were engaged in the year's summit discourse on an Open Ontology Repository (OOR) and of those who endorse below. In this discussion, we have agreed that an "ontology repository is a facility where ontologies and related information artifacts can be stored, retrieved and managed." We believe in the promise of semantic technologies based on logic, databases and the Semantic Web, a Web of exposed data and of interpretations of that data (i.e., of semantics), using common standards. Such technologies enable distinguishable, computable, reusable, and sharable meaning of Web and other artifacts, including data, documents, and services. We also believe that making that vision a reality requires additional supporting resources and these resources should be open, extensible, and provide common services over the ontologies

Inactivation of macrophage nitric oxide synthase activity by NG-Methyl-L-arginine

[middle dot]N=O synthase catalyzes the oxidation of one of the two chemically equivalent guanido nitrogens of L-arginine to nitric oxide ([middle dot]N=O). NG-Methyl-L-arginine has been previously characterized as a potent competitive inhibitor of both major types of [middle dot]N=O synthases. Initial rate kinetics were performed with a spectrophotometric assay based on the oxidation of oxy- to methemoglobin by [middle dot]N=O. NG-Methyl-L-arginine was a competitive inhibitor of [middle dot]N=O synthase activity derived from activated murine macrophages with a Ki of 6.2 [mu]M. When the enzyme was pre-incubated in the presence of the required cofactors NADPH and tetrahydrobiopterin, time- and concentration-dependent irreversible inactivation of the activity was observed. At 37[deg] C the kinact was 0.050 min-1. This inactivation process exhibited substrate protection, saturation kinetics and required the cofactors necessary for enzymatic turnover. These data indicate that NG-methyl-L-arginine asts as a mechanism-based enzyme inactivator of murine macrophage [middle dot]N=O synthase.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/29284/1/0000343.pd

Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to Hierarchical Modeling

The U.S. Department of Energy recently announced the first five grants for the Genomes to Life (GTL) Program. The goal of this program is to "achieve the most far-reaching of all biological goals: a fundamental, comprehensive, and systematic understanding of life." While more information about the program can be found at the GTL website (www.doegenomestolife.org), this paper provides an overview of one of the five GTL projects funded, "Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to Hierarchical Modeling." This project is a combined experimental and computational effort emphasizing developing, prototyping, and applying new computational tools and methods to ellucidate the biochemical mechanisms of the carbon sequestration of Synechococcus Sp., an abundant marine cyanobacteria known to play an important role in the global carbon cycle. Understanding, predicting, and perhaps manipulating carbon fixation in the oceans has long been a major focus of biological oceanography and has more recently been of interest to a broader audience of scientists and policy makers. It is clear that the oceanic sinks and sources of CO2 are important terms in the global environmental response to anthropogenic atmospheric inputs of CO2 and that oceanic microorganisms play a key role in this response. However, the relationship between this global phenomenon and the biochemical mechanisms of carbon fixation in these microorganisms is poorly understood. The project includes five subprojects: an experimental investigation, three computational biology efforts, and a fifth which deals with addressing computational infrastructure challenges of relevance to this project and the Genomes to Life program as a whole. Our experimental effort is designed to provide biology and data to drive the computational efforts and includes significant investment in developing new experimental methods for uncovering protein partners, characterizing protein complexes, identifying new binding domains. We will also develop and apply new data measurement and statistical methods for analyzing microarray experiments. Our computational efforts include coupling molecular simulation methods with knowledge discovery from diverse biological data sets for high-throughput discovery and characterization of protein-protein complexes and developing a set of novel capabilities for inference of regulatory pathways in microbial genomes across multiple sources of information through the integration of computational and experimental technologies. These capabilities will be applied to Synechococcus regulatory pathways to characterize their interaction map and identify component proteins in these pathways. We will also investigate methods for combining experimental and computational results with visualization and natural language tools to accelerate discovery of regulatory pathways. Furthermore, given that the ultimate goal of this effort is to develop a systems-level of understanding of how the Synechococcus genome affects carbon fixation at the global scale, we will develop and apply a set of tools for capturing the carbon fixation behavior of complex of Synechococcus at different levels of resolution. Finally, because the explosion of data being produced by high-throughput experiments requires data analysis and models which are more computationally complex, more heterogeneous, and require coupling to ever increasing amounts of experimentally obtained data in varying formats, we have also established a companion computational infrastructure to support this effort as well as the Genomes to Life program as a whole.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/63164/1/153623102321112746.pd