1. Discovery of novel biomarkers with extended non-coding RNA interactor networks from genetic and protein biomarkersGregor Jezernik, Damjan Glavač, Pavel Skok, Martina Krušič, Uroš Potočnik, Mario Gorenjak, 2024, izvirni znanstveni članek Opis: Curated online interaction databases and gene ontology tools have streamlined the analysis of highly complex gene/protein networks. However, understanding of disease pathogenesis has gradually shifted from a protein-based core to complex interactive networks where non-coding RNA (ncRNA) is thought to play an essential role. As current gene ontology is based predominantly on protein-level information, there is a growing need to analyze networks with ncRNA. In this study, we propose a gene ontology workflow integrating ncRNA using the NPInter V5.0 database. To validate the proposed workflow, we analyzed our previously published curated biomarker datasets for hidden disease susceptibility processes and pharmacogenomics. Our results show a novel involvement of melanogenesis in psoriasis response to biological drugs in general. Hyperpigmentation has been previously observed in psoriasis following treatment with currently indicated biological drugs, thus calling attention to melanogenesis research as a response biomarker in psoriasis. Moreover, our proposed workflow highlights the need to critically evaluate computed ncRNA interactions within databases and a demand for gene ontology analysis of large miRNA blocks.
Ključne besede: gene ontology, non-coding RNA, disease pathogenesis
Objavljeno v DKUM: 06.12.2024; Ogledov: 0; Prenosov: 5
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2. Crosswalk of most used metadata schemes and guidelines for metadata interoperability (Version 1.0)Milan Ojsteršek, 2021, zaključena znanstvena zbirka raziskovalnih podatkov Opis: This resource provides crosswalks among the most commonly used metadata schemes and guidelines to describe digital objects in Open Science, including:
- RDA metadata IG recommendation of the metadata element set,
- EOSC Pilot - EDMI metadata set,
- Dublin CORE Metadata Terms,
- Datacite 4.3 metadata schema,
- DCAT 2.0 metadata schema and DCAT 2.0 application profile,
- EUDAT B2Find metadata recommendation,
- OpenAIRE Guidelines for Data Archives,
- OpenAire Guidelines for literature repositories 4.0,
- OpenAIRE Guidelines for Other Research Products,
- OpenAIRE Guidelines for Software Repository Managers,
- OpenAIRE Guidelines for CRIS Managers,
- Crossref 4.4.2 metadata XML schema,
- Harvard Dataverse metadata schema,
- DDI Codebook 2.5 metadata XML schema,
- Europeana EDM metadata schema,
- Schema.org,
- Bioschemas,
- The PROV Ontology.
Ključne besede: crosswalk, metadata, EDMI metadata set, Dublin CORE, Datacite 4.3 metadata schema, DCAT 2.0 metadata schema, UDAT B2Find metadata recommendation, OpenAIRE Guidelines for Data Archives, OpenAire Guidelines for literature repositories 4.0, OpenAIRE Guidelines for Other Research Products, OpenAIRE Guidelines for Software Repository Managers, OpenAIRE Guidelines for CRIS Managers, Crossref 4.4.2 metadata XML schema, Harvard Dataverse metadata schema, DDI Codebook 2.5 metadata XML schema, Europeana EDM metadata schema, Schema.org, Bioschemas, The PROV Ontology
Objavljeno v DKUM: 21.09.2021; Ogledov: 2030; Prenosov: 71
 Raziskovalni podatki (169,58 KB)
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3. Application of semantic technology for calculation of welding time in the development of new productsAmbrož Stropnik, Tomaž Vuherer, Ivan Samardžić, Milan Zorman, 2017, izvirni znanstveni članek Opis: Determining the time of execution is very important in the early stages of each project (e.g. making offers, design phase etc.), especially in the stage of planning. This paper presents our approach to estimating the welding time for the purposes of planning the manufacturing processes. The approach is based on the knowledge of welding experts from the Nieros metal d.o.o. company and standards of welding (international and internal). An expert system was developed based on semantic web technologies for calculating the welding time in the product design phase and it is strongly integrated with the main ERP system of the Nieros metal d.o.o. company. Test results are presented at the end of this article.
Ključne besede: expert systems, new product development, ontology, welding of steels
Objavljeno v DKUM: 23.08.2017; Ogledov: 1173; Prenosov: 408
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4. Ontology driven development of domain-specific languagesInes Čeh, Matej Črepinšek, Tomaž Kosar, Marjan Mernik, 2011, izvirni znanstveni članek Opis: Domain-specific languages (DSLs) are computer (programming, modeling, specification) languages devoted to solving problems in a specific domain. Thedevelopment of a DSL includes the following phases: decision, analysis, design, implementation, testing, deployment, and maintenance. The least-known and least examined are analysis and design. Although various formal methodologies exist, domain analysis is still done informally most of the time. A common reason why formal methodologies are not used as often as they could be is that they are very demanding. Instead of developing a new, less complex methodology, we propose that domain analysis could be replaced with a previously existing analysis in another form. A particularly suitable form is the use of ontologies. This paper focuses on ontology-based domain analysis and how it can be incorporated into the DSL design phase. We will present the preliminary results of the Ontology2DSL framework, which can be used to help transform ontology to a DSL grammar incorporating concepts from a domain.
Ključne besede: domain specific language, domain analysis, ontology
Objavljeno v DKUM: 06.07.2017; Ogledov: 1617; Prenosov: 553
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5. A question-based design pattern advisement approachLuka Pavlič, Vili Podgorelec, Marjan Heričko, 2014, izvirni znanstveni članek Opis: Design patterns are a proven way to build flexible software architectures. But the selection of an appropriate design pattern is a difficult task in practice, particularly for less experienced developers. In this paper, a question based design pattern advisement approach will be proposed. This approach primarily assists developers in identifying and selecting the most suitable design pattern for a given problem. We will also propose certain extensions to the existing Object-Oriented Design Ontology (ODOL). In addition to the advisement procedure, a new design pattern advisement ontology will be defined. We have also developed a tool that supports the proposed ontology and question-based advisement (OQBA) approach. The conducted controlled experiment and two surveys have shown that the proposed approach is beneficial to all software developers, especially to those who have less experience with design patterns.
Ključne besede: design patterns, pattern selection, ontology, semantic web, selection algorithm
Objavljeno v DKUM: 06.07.2017; Ogledov: 1721; Prenosov: 430
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6. BIOINFORMATSKA ANALIZA MOLEKULARNO BIOLOŠKIH POTI RAKA MATERNIČNEGA VRATUMaja Ferlež, 2016, diplomsko delo Opis: Rak je kompleksna genetska bolezen. Na nastanek in razvoj raka vplivajo tako okoljski dejavniki kot tudi sama genetika. Med vrste raka spada tudi rak materničnega vratu. V diplomski nalogi smo se opredelili na RMV in njegove podoblike ( SCC, AC, ASC, MM). RMV je eden od najpogostejših vzrokov smrti zaradi raka pri ženskah. Pojavlja se v različnih oblikah in je zelo heterogena bolezen. Glavni namen diplomske naloge je bil s podatkovnimi zbirkami genske ontologije in ustreznimi bioinformatskimi orodji ( DAVID 6.7, BioMart) identificirati oziroma raziskati genetiko posamezne podoblike RMV in na podlagi dobljenih zadetkov predpostaviti molekularno biološko pot nastanka različnih oblik RMV. Nadaljnji namen naloge je bil z bioinformatskimi orodji poiskati skupne gene in biološke mehanizme, ki vodijo do nastanka različnih oblik RMV. S pomočjo GWA študij smo dobili 6 skupnih genov in 4 biološke poti. Zaradi pomanjkanj raziskav RMV pa smo se opredelili tudi na gene, ki sodelujejo pri somatskih mutacijah. S pomočjo podatkovnih zbirk in orodij genske ontologije smo dobili 6 skupnih genov in 16 bioloških poti. Ti rezultati naj bi nam dali boljši vpogled v sam nastanek in razvoj te bolezni ter napredek pri iskanju novih možnosti za zdravljenje te bolezni.
Ključne besede: Rak materničnega vratu ( RMV), ploščatocelični karcinom ( SCC), adenokarcinom ( AC), ploščatocelični adenokarcinom ( ASC), maligni melanom ( MM), Gene Ontology (GO), DAVID 6.7, biološka pot, asociacijska študija ( GWA)
Objavljeno v DKUM: 04.10.2016; Ogledov: 2050; Prenosov: 125
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7. A question answering system on domain specific knowledge with semantic web supportBorut Gorenjak, Marko Ferme, Milan Ojsteršek, 2011, izvirni znanstveni članek Opis: In today's world the majority of information is accessible via the World Wide Web. A common way to access this information is through information retrieval applications like web search engines. We already know that web search engines flood their users with enormous amount of data from which they cannot figure out the essential and most important information. These disadvantages can be reduced with question answering systems. The basic idea of question answering systems is to be able to provide answers to a specific question written in natural language. The main goal of question answering systems is to find a specific answer. This paper presents an architecture of our ontology-driven system that uses semantic description of the processes, databases and web services for question answering system in the Slovenian language.
Ključne besede: ontology, natural language processing, question answering system, semantic web, web ontology language
Objavljeno v DKUM: 01.06.2012; Ogledov: 3263; Prenosov: 68
Celotno besedilo (807,82 KB) |
8. Using ontologies in the domain analysis of domain-specific languagesRobert Tairas, Marjan Mernik, Jeffrey G. Gray, 2008, objavljeni znanstveni prispevek na konferenci Opis: The design stage of domain-specific language development, which includes domain analysis, has not received as much attention compared to the subsequentstage of language implementation. This paper investigates the use of ontology in domain analysis for the development of a domain-specific language. The standard process of ontology development is investigated as an aid to determine the pertinent information regarding the domain (e.g., the conceptualization of the domain and the common and variable elements of the domain) that should be modeled in a language for the domain. Our observations suggest that ontology assists in the initial phase of domain understanding and can be combined with further formal domain analysis methods during the development of a domain-specific language.
Ključne besede: domain-specific languages, programming languages, ontology, domain analysis
Objavljeno v DKUM: 31.05.2012; Ogledov: 1688; Prenosov: 161
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9. Asociacijska analiza nekaterih genov vključenih v regulacijo aktivacije T celic pri bolnikih s kronično vnetno črevesno boleznijo Andrej Sovec, 2011, magistrsko delo/naloga Opis: Kronično vnetna črevesna bolezen (KVČB) je kompleksna genetska bolezen. Dva glavna tipa KVČB sta Crohnova bolezen (CB) in ulcerozni kolitis (UC). Za Crohnovo bolezen je značilno, da je vnetje razširjeno po celotni prebavni cevi, pri ulceroznem kolitisu pa je omejeno na debelo črevo in danko. Namen magistrskega dela je bil s podatkovnimi zbirkami genske ontologije in ustreznimi bioinformatskimi orodji ugotoviti najpomembnejše biološke procese in poti, v katerih sodelujejo geni, ki so jih v asociacijskih študijah statistično značilno povezali s KVČB; ugotoviti, v katerih molekularnih funkcijah sodelujejo ti geni in katere celične komponente sestavljajo proteini, ki jih kodirajo ti geni; s podatkovnimi zbirkami genske ontologije poiskati gene, ki so vključeni v biološki proces Regulacija aktivacije T celic in jih analizirati kot kandidatne gene za asociacijsko študijo pri slovenskih bolnikih s KVČB. S pomočjo podatkovne zbirke HuGE Navigator smo izdelali seznam 180 genov, ki so jih v asociacijskih študijah na podlagi polimorfizmov posameznega nukleotida (SNP) statistično značilno povezali s KVČB, in ga uporabili za identifikacijo najpomembnejših bioloških procesov, molekularnih funkcij, celičnih komponent in bioloških poti v patogenezi KVČB. S pomočjo podatkovnih zbirk genske ontologije (DAVID 6.7, Gene Ontology, KEGG in BioCarta) in ustreznih bioinformatskih orodij ter seznama KVČB genov smo najprej identificirali 380 bioloških procesov, 18 molekularnih funkcij, 10 celičnih komponent in 15 bioloških poti v KEGG in 12 bioloških poti v BioCarti. Med njimi smo v nadaljnji raziskavi z uporabo istih podatkovnih zbirk in bioinformatskih orodij kot najpomembnejše v patogenezi KVČB identificirali 12 bioloških procesov, 2 molekularni funkciji, 2 celični komponenti in 10 bioloških poti. Z uporabo podatkovnih zbirk Gene Ontology in HuGE Navigator smo v biološkem procesu Regulacija aktivacije T celic izbrali 5 kandidatnih genov in 2 izmed njih, IL10 in IL12A, na podlagi SNP-jev (rs3024505 in rs17810546), statistično značilno povezali, P<0,05, s fenotipskimi podtipi slovenskih bolnikov s KVČB.
Ključne besede: Kronično vnetna črevesna bolezen (KVČB), Gene Ontology (GO), DAVID 6.7, biološki proces, biološka pot, molekularna funkcija, celična komponenta, asociacijska študija, BioCarta, KEGG, HuGE Navigator, ulcerozni kolitis (UC), Crohnova bolezen (CB)
Objavljeno v DKUM: 06.01.2012; Ogledov: 3653; Prenosov: 339
Celotno besedilo (1,77 MB) |
