Evolution of the Sequence Ontology terms and relationships

The Sequence Ontology is undergoing reform to meet the standards of the OBO Foundry. Here we report some of the incremental changes and improvements made to SO. We also propose new relationships to better define the mereological, spatial and temporal aspects of biological sequence

Numerical tidal models with unequal grid-spacing

Thesis (M.S.) University of Alaska Fairbanks, 2006A two-dimensional alternating-direction implicit numerical tidal model with unequal grid-spacing is developed and successfully tested. The method is essentially an extension into two dimensions of a one-dimensional implicit method in which tide heights and flow rates are evaluated on the same cross-sections, an approach which permits a river to be schematized into a number of sections of differing lengths. The two-dimensional scheme gives the user considerable control over the density of the computation points in a region by virtue of the fact that heights and depth-mean currents are evaluated midway between points of intersection of a grid constructed from orthogonal lines, the spacing between which may be chosed at will. The method is applied initially to the Irish Sea using a grid of constant spacing. The effects of increasing time step and friction on stability and accuracy are investigated, and the model is proved to be unconditionally stable. The results match those of previous investigators, and some new information on the M₂ currents of the region is obtained. The second application of the model is to a 'rectangular' North Sea, a favorable comparison being obtained when the region is schematized by two grids of equal and unequal spacing. Finally, the model is applied to Cook Inlet, Alaska, a region of complexity sufficient to warrant the use of a scheme possessing the unequal grid-spacing feature. Satisfactory results are obtained after tuning the model by adjustment of the friction coefficient. Movie films were made in order to conceptually clarify the tidal behaviors of the Irish Sea and Cook Inlet. Each film shows as functions of time, perspective views of the sea surface, and current vectors superimposed on a contour map of the sea surface.I. Introduction -- II. Hydraulic calculations using the harmonic method -- III. Hydraulic calculations using the one-dimensional implicit method -- IV. A two-dimensional model with unequal grid-spacing -- V. The finite-difference equations and their solution -- VI. Programming considerations -- VII. Application of the model to the Irish Sea -- VIII. Application of the model to a rectangular North Sea -- IX. Application of the model to Cook Inlet, Alaska -- X. Additional results of interest -- XI. Conclusions -- References -- Appendix I. The harmonic method : calculation of L,M,N, and O -- Appendix II. Example of branch-point solution for the harmonic method -- Appendix III. Analysis of stability and wave-deformation for the one-dimensional implicit method -- Appendix IV. Compact form of the finite-difference equations for the one-dimensional implicit method -- Appendix V. Example of branch-point solution for the one-dimensional implicit method -- Appendix VI. Compact form of the finite-difference equations for the two-dimensional implicit method

A variable-boundary numerical tidal model

Thesis (M.S.) University of Alaska Fairbanks, 1970A numerical tidal model using equations developed by Hansen (1952) and Yuen (1967) is automated to the point where a potential user need not undertake extensive reprogramming. The user adds to the program only those cards needed to specify tides at input points as a function of time; the application of the relevant calculations at each grid point being controlled by an integer matrix that corresponds to the inlet boundary. A sample problem is covered in detail and applications of the model to the M₂ tide of the Gulf of California, and to a hypothetical mean tide in Cook Inlet are shown.I. Introdution -- II. The calculation of tides in inlets -- III. The finite difference equations -- IV. Automation of the sequence of calculations -- V. Program arrangement -- VI. Grid selection and data arrangement -- VII. Computer outputs and data analysis -- VIII. A sample problem -- IX. Two applictations of the model -- Bibliography -- Appendix I. Listing of program for variable-boundary tidal model -- Appendix II. Listing of data compression subroutine -- Appendix III. Listing of height and current analysis programs -- Appendix IV. -- Appendix V

FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability.

The Immune Epitope Database (IEDB), at www.iedb.org, has the mission to make published experimental data relating to the recognition of immune epitopes easily available to the scientific public. By presenting curated data in a searchable database, we have liberated it from the tables and figures of journal articles, making it more accessible and usable by immunologists. Recently, the principles of Findability, Accessibility, Interoperability and Reusability have been formulated as goals that data repositories should meet to enhance the usefulness of their data holdings. We here examine how the IEDB complies with these principles and identify broad areas of success, but also areas for improvement. We describe short-term improvements to the IEDB that are being implemented now, as well as a long-term vision of true 'machine-actionable interoperability', which we believe will require community agreement on standardization of knowledge representation that can be built on top of the shared use of ontologies

A numerical tidal model and its application to Cook Inlet, Alaska

A numerical scheme for predicting tides and tidal currents has been designed for rapid application to new situations with a minimum of effort. The model is two-dimensional and includes Coriolis and fric tional terms. An application to Cook Inlet, Alaska, is described for a tide having a period of 12.42 hours and an amplitude of one half the mean tidal range...

Evolution of the Sequence Ontology terms and relationships

AbstractThe Sequence Ontology is an established ontology, with a large user community, for the purpose of genomic annotation. We are reforming the ontology to provide better terms and relationships to describe the features of biological sequence, for both genomic and derived sequence. The SO is working within the guidelines of the OBO Foundry to provide interoperability between SO and the other related OBO ontologies. Here, we report changes and improvements made to SO including new relationships to better define the mereological, spatial and temporal aspects of biological sequence

The NCBO OBOF to OWL Mapping

Two of the most significant formats for biomedical ontologies are the Open Biomedical Ontologies Format (OBOF) and the Web Ontology Language (OWL). To make it possible to translate ontologies between these two representation formats, the National Center for Biomedical Ontology (NCBO) has developed a mapping between the OBOF and OWL formats as well as inter-conversion software. The goal was to allow the sharing of tools, ontologies, and associated data between the OBOF and Semantic Web communities.

OBOF does not have a formal grammar, so the NCBO had to capture its intended semantics to map it to OWL.

This official NCBO mapping was used to make all OBO Foundry ontologies available in OWL. 

Availability: This mapping functionality can be embedded into OBO-Edit and Protégé-OWL ontology editors. This software is available at: http://bioontology.org/wiki/index.php/OboInOwl:Main_Pag

Modularization for the Cell Ontology

One of the premises of the OBO Foundry is that development of an orthogonal set of ontologies will increase domain expert contributions and logical interoperability, and decrease maintenance workload. For these reasons, the Cell Ontology (CL) is being re-engineered. This process requires the extraction of sub-modules from existing OBO ontologies, which presents a number of practical engineering challenges. These extracted modules may be intended to cover a narrow or a broad set of species. In addition, applications and resources that make use of the Cell Ontology have particular modularization requirements, such as the ability to extract custom subsets or unions of the Cell Ontology with other OBO ontologies. These extracted modules may be intended to cover a narrow or a broad set of species, which presents unique complications.

We discuss some of these requirements, and present our progress towards a customizable simple-to-use modularization tool that leverages existing OWL-based tools and opens up their use for the CL and other ontologies

Cross-Product Extensions of the Gene Ontology

The Gene Ontology is being normalized and extended to include computable logical definitions. These definitions are partitioned into mutually exclusive cross-product sets, many of which reference other OBO Foundry ontologies. The results can be used to reason over the ontology, and to make cross-ontology queries