Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection

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

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  • 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.