RDFizing the biosynthetic pathway of E.coli O-antigen to enable semantic sharing of microbiology data

Background The abundance of glycomics data that have accumulated has led to the development of many useful databases to aid in the understanding of the function of the glycans and their impact on cellular activity. At the same time, the endeavor for data sharing between glycomics databases with other biological databases have contributed to the creation of new knowledgebases. However, different data types in data description have impeded the data sharing for knowledge integration. To solve this matter, Semantic Web techniques including Resource Description Framework (RDF) and ontology development have been adopted by various groups to standardize the format for data exchange. These semantic data have contributed to the expansion of knowledgebases and hold promises of providing data that can be intelligently processed. On the other hand, bench biologists who are experts in experimental finding are end users and data producers. Therefore, it is indispensable to reduce the technical barrier required for bench biologists to manipulate their experimental data to be compatible with standard formats for data sharing. Results There are many essential concepts and practical techniques for data integration but there is no method to enable researchers to easily apply Semantic Web techniques to their experimental data. We implemented our procedure on unformatted information of E.coli O-antigen structures collected from the web and show how this information can be expressed as formatted data applicable to Semantic Web standards. In particular, we described the E-coli O-antigen biosynthesis pathway using the BioPAX ontology developed to support data exchange between pathway databases. Conclusions The method we implemented to semantically describe O-antigen biosynthesis should be helpful for biologists to understand how glycan information, including relevant pathway reaction data, can be easily shared. We hope this method can contribute to lower the technical barrier that is required when experimental findings are formulated into formal representations and can lead bench scientists to readily participate in the construction of new knowledgebases that are integrated with existing ones. Such integration over the Semantic Web will enable future work in artificial intelligence and machine learning to enable computers to infer new relationships and hypotheses in the life sciences.

Sequencing-Based Transcriptome-Wide Targeted Genotyping for Evolutionary and Ecological Studies

Transcriptome-wide targeted genotyping is highly attractive for evolutionary and ecological studies but, until recently, accomplishing this goal presented a major technical barrier for the study of non-model organisms. Our group has recently developed a high-throughput targeted genotyping approach (called HD-Marker) based on the high specificity and accuracy of oligo extension-ligation assays that facilitates the design of assays tailored to meet specific genotyping needs. HD-Marker allows for targeted genotyping of over 10 000 genes in a single tube, with strikingly high capture rate (98%-99%) and genotyping accuracy (97%-99%). With the remarkable advantages of cost-effectiveness and flexibility, we envision that HD-Marker has broad application potential in evolutionary and ecological studies.

PEMASYARAKATAN DAUR ULANG AIR LIMBAH UNTUK MENGANTISIPASI KELANGKAAN AIR AKIBAT PERUBAHAN IKLIM GLOBAL

Climate change has impact on many sectors in the earth such as on the water resources sector. For example, the occurrence of floods and droughts in Indonesia that needs to be anticipated. In the Technology Needs Assessment document of the Republic of Indonesia, there are three priorities technology of the water sector to anticipate the climate change. One of the technologies is recycling domestic wastewater. The recycling of waste water can be done through two consecutive stages. First, wastewater treatment processes itself to produce the quality standard limits allowed to be discharged into the environment. Second is processing the treated wastewater till the product water can be used for particular purpose. There are many technologies can be used for water recycling process. Selection of technology depends on the type of waste water and product water quality targets. The utilization of recycled water in the community is still very little due to the barriers of technical and non-technical factors (social, economic, regulatory and others) which need to be anticipated along. Technical barrier include technology that is relatively more expensive to treat wastewater into products that can be utilized. While the non-technical barrier is many people are still reluctant to use the recycled water due to psychological factors. Therefore sosialization of waste water recycling to be expected can eliminate such barriers. Keywords: Water recycling, domestic waste, global climate change.

Impact of Non Tariff Measure on Indonesian Cacao Exports

Increased awareness of food safety issues has resulted in non-tariff measure in the form of sanitary and phytosanitary, technical barrier to trade applied to various importing countries. The policy is widely applied by various countries on agricultural commodities, especially Cocoa. Cocoa is Indonesia's flagship commodity exported to many countries. The purpose of this research is to analyze the implementation and impact of non tariff measure on Indonesian cocoa exports. The model used in this research is to estimate the result of inventory approach in gravity model. The results show that Sanitary and Phytosanitary policy has an effect on decreasing export value of Indonesian Cocoa while Technical Barrier to Trade has no significant effect. SPS policy is mostly applied to Cocoa Beans while TBT is more applied to processed cocoa. So, Indonesia needs to improve the processing of cocoa beans such as cacao shells, cacao paste, cacao butter, cacao powder, chocolate and other preparations. The government needs to provide socialization to Indonesian cocoa agribusiness entrepreneurs in the implementation of sanitary and phytosanitary policy. Government programs or policies are designed according to the characteristics of SPS and TBT.

Perlindungan Lingkungan Hidup dalam Perdagangan Internasional

Isu lingkungan hidup tidak dapat dipisahkan dari perdagangan intemasional. Dalam sejarahpembentukan GATT pada tahun 1947 isu lingkungan hidup telah dimuat dalam artikel XX tentang "General Exception ". Aturan dasar ini kemudian disepakati dalam "Tokyo Round"menjadi "Agreement on Technical Barrier to Trade" dan disempumakan dalam "Uruguay Round". Melalui perjanjian ini GATT/WTO kemudian mengakui keberadaan "International Organization for Standarization (ISO)". Dengan demikian melahirkan pengakuan keterkaitan antara perdagangan intemasional dengan isu lingkungan hidup.