Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection

Permanent URI for this collectionhttps://hdl.handle.net/11147/7148

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Now showing 1 - 4 of 4
  • Article
    The Architecture of Relational Materialism: a Categorial Formation of Onto-Epistemological Premises
    (Springer, 2025) Derin, Ozan Ekin; Baytas, Bekir
    This study formulates the basic premises of materialism, which has largely lost its visibility despite being one of the fundamental philosophical approaches that have been effective in the development of modern scientific practice and the construction of philosophy of science, in an alternative way, and aims to develop a new materialist interpretation of it that is non-reductive, pluralistic and open to the use of more than one scientific discipline. This interpretation, expressed with the term relational materialism, first addresses matter with the concept of signifier and foregrounds the concept of beable as the general philosophical category of matter. Secondly, it formulates the category of beable within the irreducible integrity of the categories of relationality, nonstaticity, and finitude; and positions knownability in terms of its correspondence to these general onto-epistemological categories. Thirdly, it clarifies the conditions of existence and knownability of particular entities under general categories based on specially corresponding onto-epistemological categories (interactability, structurability, contextuality, transformability, scale-dependency, actuality, contingency). In this respect, this study offers a pluralistic philosophical framework within which different methodological positions and scientific disciplines can be formulated and criticized based on combinations of different particular categories under general categories. In the conclusion of this article, the meaning and potential of relational materialism for the development of scientific research programs are evaluated.
  • Article
    Citation - WoS: 1
    Citation - Scopus: 1
    Dnmso; an Ontology for Representing De Novo Sequencing Results From Tandem-Ms Data
    (PeerJ Inc., 2020) Takan, Savaş; Allmer, Jens
    For the identification and sequencing of proteins, mass spectrometry (MS) has become the tool of choice and, as such, drives proteomics. MS/MS spectra need to be assigned a peptide sequence for which two strategies exist. Either database search or de novo sequencing can be employed to establish peptide spectrum matches. For database search, mzIdentML is the current community standard for data representation. There is no community standard for representing de novo sequencing results, but we previously proposed the de novo markup language (DNML). At the moment, each de novo sequencing solution uses different data representation, complicating downstream data integration, which is crucial since ensemble predictions may be more useful than predictions of a single tool. We here propose the de novo MS Ontology (DNMSO), which can, for example, provide many-to-many mappings between spectra and peptide predictions. Additionally, an application programming interface (API) that supports any file operation necessary for de novo sequencing from spectra input to reading, writing, creating, of the DNMSO format, as well as conversion from many other file formats, has been implemented. This API removes all overhead from the production of de novo sequencing tools and allows developers to concentrate on algorithm development completely. We make the API and formal descriptions of the format freely available at https://github.com/savastakan/dnmso.
  • Conference Object
    Citation - Scopus: 7
    From Requirements to Data Analytics Process: An Ontology-Based Approach
    (Springer International Publishing AG, 2019) Bandara, Madhushi; Behnaz, Ali; Rabhi, Fethi A.; Demirors, Onur
    Comprehensively describing data analytics requirements is becoming an integral part of developing enterprise information systems. It is a challenging task for analysts to completely elicit all requirements shared by the organization's decision makers. With a multitude of data available from e-commerce sites, social media and data warehouses selecting the correct set of data and suitable techniques for an analysis itself is difficult and time-consuming. The reason is that analysts have to comprehend multiple dimensions such as existing analytics techniques, background knowledge in the domain of interest and the quality of available data. In this paper, we propose to use semantic models to represent different spheres of knowledge related to data analytics space and use them to assist in analytics requirements definition. By following this approach users can create a sound analytics requirements specification, linked with concepts from the operation domain, available data, analytics techniques and their implementations. Such requirements specifications can be used to drive the creation and management of analytics solutions, well aligned with organizational objectives. We demonstrate the capabilities of the proposed method by applying on a data analytics project for house price prediction.
  • Conference Object
    Citation - Scopus: 4
    An Architecture for Verification of Access Control Policies With Multi Agent System Ontologies
    (Institute of Electrical and Electronics Engineers Inc., 2009) Tekbacak, Fatih; Tuğlular, Tuğkan; Dikenelli, Oğuz
    Multi-agent systems (MAS) which communicate with intra-domain and inter-domain agent platforms have access control requirements. Instead of a central mechanism, a fine-graned access control mechanism could have been applied to MAS platforms. This paper emphasizes MAS-based domain and security ontologies with XACML-based access control approach for MAS platforms. The domain dependent behaviour and access control parameters in agent ontologies could be combined within a common XACML policy document that is used through different MAS applications. Agent-based access control requirements and common XACML policy documents should be consistent to enforce policies for MAS. To obtain this condition, the translation of organizational policies and platform based policies have to be considered in detail and the verified policy features have to be enforced in MAS to provide access for resources.