Multiple Ontologies for Integrating Complex Phenotype Datasets

There has been an emergence of multiple large scale phenotyping projects in the rat model organism community as well as renewed interest in the ongoing phenotype data generated by thousands of researchers using hundreds of rat strains worldwide. Unfortunately, this data is scattered and is neither described nor formatted in a standardized manner. A system to integrate complex phenotype data from multiple sources and facilitate data mining and analysis is being developed using multiple ontologies.

*Introduction*
The potential value of integrating phenotype data from multiple sources (different laboratories, varying techniques to measure similar phenotypes, multiple strains) is enormous. Presented here is a data integration system for complex phenotype data from both large-scale and individual experiments and the taxonomy and ontologies that provide the backbone of this format. RGD along with Mouse Genome Informatics (MGI) (Blake et al, 2009) and the Animal QTL Database (Hu and Reecy, 2007) is developing a Vertebrate Trait Ontology to represent morphological states and physiological processes to be used to annotate quantitative trait loci (QTL) and other data. RGD has also used the Mammalian Phenotype Ontology (Smith et al, 2005) for several years to indicate the relationship of genomic elements to abnormal phenotypes. The Vertebrate Trait Ontology represents what is being assessed, and the Mammalian Phenotype Ontology represents the conclusion that was made. The system presented here represents what was done to measure the trait in order to reach the conclusion. Because of the close relationship among these ontologies, care is being taken to ensure compatibility and similarity in structure using the phenotype properties in the Phenotypic Quality Ontology (PATO) for guidance. ("http://www.bioontology.org/wiki/index.php/PATO:Main_Page":http://www.bioontology.org/wiki/index.php/PATO:Main_Page) 

*Data Format and Ontologies*
Standardization of data types and relationships used to define the phenotype experiment and resulting data, and the ontologies to be used to standardize descriptive fields are being developed. For phenotype data, the major informational components include Researcher, Study, Experiment, Sample, Experimental Conditions and Clinical Measurement. A Rat Strain Taxonomy has been developed to standardize this information and provide the relationships among strains to allow investigators to retrieve and analyze phenotype data for strains that are related genetically. Two important aspects of a phenotype measurement include 1) what was measured and 2) how it was measured. The Clinical Measurement Ontology and the Measurement Method Ontology are being developed to standardize this information. In addition an Experimental Conditions ontology is under construction to allow integration of data measured under various conditions.

*Pilot Study Results*
Cardiovascular and biochemistry phenotype data from two major datasets have been integrated using the Rat Strain Taxonomy and the three phenotype related ontologies. A prototype data mining tool ("http://rgd.mcw.edu/rgdweb/":http://rgd.mcw.edu/rgdweb/) has also been developed that provides the user with options to begin a search with strains or any of the ontologies and make subsequent filter choices from the other ontologies. Choices presented to the user are restricted to those for which data is available and query tracking functions are provided to alert the user to the number of results being returned and the query choices made.

*References*
Blake JA, Bult CJ, Eppig JT, Kadin JA, Richardson JE; Mouse Genome Database Group, 2009 _Nucleic Acids Res_. Jan;37:D712-9.

HuZL, Reecy JM, Animal QTLdb: beyond a repository. A public platform for QTL comparisons and integration with diverse types of structural genomic information, 2007, _Mamm Genome_, Jan;18(1):1-4.

Smith CL, Goldsmith CA, Eppig JT. The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information, _Genome Biol_. 2005 6(1):R7.
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Evaluating Rice Straw as a Substitute for Barley Straw in Inhibiting Algal Growth in Farm Ponds

Algal blooms disrupt aquatic ecosystems and are more common in lakes, ponds, and rivers during the summer months due to nutrient pollution. Livestock production can contribute increased quantities of nutrients to water bodies from runoff of manure. Commonly used mechanical and chemical control methods may have limited success because algae are small and propagate quickly. Barley (Hordeum vulgare) straw has been shown to inhibit the growth of algae as the straw decomposes aerobically in ponds. Therefore, barley represents a natural option for algal biomass control. However, the small amount of barley production in Arkansas limits the availability of barley straw as a solution to control algal blooms locally. Other cereal grain straws may produce similar inhibitory effects during decomposition. Rice (Oryza sativa) is produced in large quantities in Arkansas, making rice straw a locally sourced straw product. The objective of this research was to determine the efficacy of using rice compared to barley straw to inhibit algal growth in freshwater ponds. Data were collected from nine farm ponds, three treated with rice straw, three treated with barley straw, and three without amendment to serve as the experimental control. Dissolved oxygen, pH, nitrate-nitrogen (NO3--N), dissolved phosphorus (P), temperature, and turbidity were measured for 14 weeks from June 12 to September 17, 2018. Algal biomass was measured as chlorophyll-a concentration to evaluate treatment effectiveness over time. Dissolved oxygen was significantly influenced by treatment and time. The NO3--N concentration in ponds treated with rice straw was significantly greater than the control and barley treatment. Chlorophyll-a concentrations were variable, and there were no consistent trends through time within a treatment. More research under controlled conditions to understand impacts of abiotic conditions, microbial and algal community compositions, and mode of action of algal inhibition is required before cereal straw can be a reliable, locally sourced method of algal control in farm ponds

Alien Registration- Jacob, Mary (Lewiston, Androscoggin County)

https://digitalmaine.com/alien_docs/27175/thumbnail.jp

Alien Registration- Jacob, Mary (Lewiston, Androscoggin County)

https://digitalmaine.com/alien_docs/27176/thumbnail.jp

Climate-Smart Agriculture: Farmer\u27s Bane Or Boon?

Climate-Smart Agriculture (CSA) is one of the solutions that simultaneously address the issues of food security, climate change and agricultural productivity. It has been gaining momentum in the last five years among policy circles and development organizations have prioritized CSA interventions in developing countries around the world. In this paper, CSA interventions are examined from the small farmer\u27s perspective and the purpose of this paper is to find out whether Climate-Smart Agriculture truly empowers the farmer in the face of climate change. Such a study emerged from the fact that in the past, agricultural interventions like the Green Revolution promised farmers food security but initiated practices that exacerbated their vulnerabilities and degraded the integrity of the ecosystem. The method involved assessing ongoing and completed projects of development agencies. These projects were examined based on the ease with which a small farmer could adopt such a practice and the ecological sustainability of the project. The results of this examination indicate that there are few interventions that have the potential to truly empower small farmers. Nevertheless, there are those interventions that are designed to be neither ecologically sustainable nor financially viable to the farmer. This implies an inherent flaw in the concept of CSA and sheds light on the vested agribusiness\u27 interest in this area

Efficient transport and economic development: A transport survey analysis

Efficient transport and economic growth in a city or country are inter-related. The overall focus of the survey conducted was to find the travel habits of the residents in the city of Kuching (Malaysia), so as to weigh the prospects of economic development in future. The three objectives were to evaluate the efficiency of the local bus transportation system, to confirm on the usage of car as the preferred mode of transport, and to identify areas of improvement to the system as well as analyzing the need for an alternative mode(s) of transportation. The quantitative and qualitative analysis is done on data to find the relationships between various variables measured. Car has been confirmed to be the popular mode of transport across the age groups, across the income groups and across the professions, whereas the bus transport was really not significant. The study identified the important characteristics and priorities in the travel behavior of Kuching residents. The results of the study will be significant in the planning of new economic developments that encourages the use of public transportation in Kuching city