TGF-beta signaling proteins and the Protein Ontology

The Protein Ontology (PRO) is designed as a formal and principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the homeomorphic level to the representation of the multiple protein forms of a gene, including those resulting from alternative splicing, cleavage and/or posttranslational modifications. Focusing specifically on the TGF-beta signaling proteins, we describe the building, curation, usage and dissemination of PRO. PRO provides a framework for the formal representation of protein classes and protein forms in the OBO Foundry. It is designed to enable data retrieval and integration and machine reasoning at the molecular level of proteins, thereby facilitating cross-species comparisons, pathway analysis, disease modeling and the generation of new hypotheses

Toll-like receptor signaling in vertebrates: Testing the integration of protein, complex, and pathway data in the Protein Ontology framework

The Protein Ontology (PRO) provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation of experimentally known forms and annotations thereof is expected to expose discrepancies, differences, and gaps in our knowledge. We have annotated the early events of innate immune signaling mediated by Toll-Like Receptor 3 and 4 complexes in human, mouse, and chicken. The resulting ontology and annotation data set has allowed us to identify species-specific gaps in experimental data and possible functional differences between species, and to employ inferred structural and functional relationships to suggest plausible resolutions of these discrepancies and gaps

A fast Peptide Match service for UniProt Knowledgebase

Summary: We have developed a new web application for peptide matching using Apache Lucene-based search engine. The Peptide Match service is designed to quickly retrieve all occurrences of a given query peptide from UniProt Knowledgebase (UniProtKB) with isoforms. The matched proteins are shown in summary tables with rich annotations, including matched sequence region(s) and links to corresponding proteins in a number of proteomic/peptide spectral databases. The results are grouped by taxonomy and can be browsed by organism, taxonomic group or taxonomy tree. The service supports queries where isobaric leucine and isoleucine are treated equivalent, and an option for searching UniRef100 representative sequences, as well as dynamic queries to major proteomic databases. In addition to the web interface, we also provide RESTful web services. The underlying data are updated every 4 weeks in accordance with the UniProt releases. Availability: http://proteininformationresource.org/peptide.shtml Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics onlin

The representation of protein complexes in the Protein Ontology

Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

Motivation: UniRef databases provide full-scale clustering of UniProtKB sequences and are utilized for a broad range of applications, particularly similarity-based functional annotation. Non-redundancy and intra-cluster homogeneity in UniRef were recently improved by adding a sequence length overlap threshold. Our hypothesis is that these improvements would enhance the speed and sensitivity of similarity searches and improve the consistency of annotation within clusters. Results: Intra-cluster molecular function consistency was examined by analysis of Gene Ontology terms. Results show that UniRef clusters bring together proteins of identical molecular function in more than 97% of the clusters, implying that clusters are useful for annotation and can also be used to detect annotation inconsistencies. To examine coverage in similarity results, BLASTP searches against UniRef50 followed by expansion of the hit lists with cluster members demonstrated advantages compared with searches against UniProtKB sequences; the searches are concise (∼7 times shorter hit list before expansion), faster (∼6 times) and more sensitive in detection of remote similarities (>96% recall at e-value <0.0001). Our results support the use of UniRef clusters as a comprehensive and scalable alternative to native sequence databases for similarity searches and reinforces its reliability for use in functional annotation. Availability and implementation: Web access and file download from UniProt website at http://www.uniprot.org/uniref and ftp://ftp.uniprot.org/pub/databases/uniprot/uniref. BLAST searches against UniRef are available at http://www.uniprot.org/blast/ Contact: [email protected]

A Bargaining Theory of US-China Economic Rivalry: Differentiating the Trade and Technology Wars

This article examines the outbreak and persistence of US–China economic war, which comprises both the trade war, featured with retaliatory tariffs, and the technology war, featured with restrictions on Chinese access to US technologies. Building on the analytical framework of bargaining and war, I argue that different components of the economic war emerged from distinct causes. The outbreak of the trade war was primarily driven by the information problem, characterized by mutual uncertainty and the lack of effective communications. The technology war was largely a result of the commitment problem driven by the existing power’s concern regarding potential future changes in the balance of power. After examining the initiation stage during the Trump era, I further analyze how the economic war has unfolded during the Biden administration. While the prospect of a new trade war seems unlikely as mutual uncertainty diminishes, existing tariffs remain as the commitment problem on trade issues has become more critical. The preventive technology war is expected to persist, reflecting Washington’s ongoing concerns over China’s growing leadership in technology

Examining How the Disclosure of IS Security Policies Affect IS Personnel Ethical Conducts

The issue of “professional ethics” in the workplace has been put under the spotlight in recent years; especially several scandals have involved questionable behaviour on the part of information systems (IS) professionals. In the past years, many countries have constructively paid attention to the rules of professional ethics. Among these efforts, many acts asked for corporate information disclosures, for example, the disclosure of IS security and privacy policies. In this study, two research questions are explored. The first of these investigates the disclosure of IS security policies and perception of codes in Taiwan IS corporations. The second empirically validates a research model to understand whether the disclosure of IS security policies have any influence on the IS professionals\u27 perceptions of codes, and in turn, how these perceptions impact their ethical and unethical conducts. Finally, the theoretical and practical implications to the management of ethics concerning information ethics are discussed

Raising Students\u27 Concept in Protecting Information Privacy through Information Ethics Education

The concept of privacy in Chinese context is a fragile perception. Under such a culture environment, the awareness of right of privacy raises late; therefore, it is of necessary raising people the concept of information privacy. To reach this purpose, this study adopts the theory of self-efficacy to examine factors that influence decisions related to information privacy. Further, a longitudinal model is explored whether information ethics education plays a role influencing students’ concept in protecting information privacy. A survey with senior-level undergraduate students is conducted to test the hypothesized model. The findings exhibit an important insight that through information ethics education, students demonstrate a significant change in their confidence of privacy self-efficacy; the increase of this concept noteworthy changes their behavior concerning information privacy protection. Finally, discussions and conclusions are discussed