DES-Tcell is a knowledgebase for exploring immunology-related literature

Abstract T-cells are a subtype of white blood cells circulating throughout the body, searching for infected and abnormal cells. They have multifaceted functions that include scanning for and directly killing cells infected with intracellular pathogens, eradicating abnormal cells, orchestrating immun...

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Autores principales:	Ahdab AlSaieedi, Adil Salhi, Faroug Tifratene, Arwa Bin Raies, Arnaud Hungler, Mahmut Uludag, Christophe Van Neste, Vladimir B. Bajic, Takashi Gojobori, Magbubah Essack
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/cbfc89cb4e3b4eabbabf16b40d6f1942
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spelling	oai:doaj.org-article:cbfc89cb4e3b4eabbabf16b40d6f19422021-12-02T16:14:16ZDES-Tcell is a knowledgebase for exploring immunology-related literature10.1038/s41598-021-93809-12045-2322https://doaj.org/article/cbfc89cb4e3b4eabbabf16b40d6f19422021-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-93809-1https://doaj.org/toc/2045-2322Abstract T-cells are a subtype of white blood cells circulating throughout the body, searching for infected and abnormal cells. They have multifaceted functions that include scanning for and directly killing cells infected with intracellular pathogens, eradicating abnormal cells, orchestrating immune response by activating and helping other immune cells, memorizing encountered pathogens, and providing long-lasting protection upon recurrent infections. However, T-cells are also involved in immune responses that result in organ transplant rejection, autoimmune diseases, and some allergic diseases. To support T-cell research, we developed the DES-Tcell knowledgebase (KB). This KB incorporates text- and data-mined information that can expedite retrieval and exploration of T-cell relevant information from the large volume of published T-cell-related research. This KB enables exploration of data through concepts from 15 topic-specific dictionaries, including immunology-related genes, mutations, pathogens, and pathways. We developed three case studies using DES-Tcell, one of which validates effective retrieval of known associations by DES-Tcell. The second and third case studies focuses on concepts that are common to Grave’s disease (GD) and Hashimoto’s thyroiditis (HT). Several reports have shown that up to 20% of GD patients treated with antithyroid medication develop HT, thus suggesting a possible conversion or shift from GD to HT disease. DES-Tcell found miR-4442 links to both GD and HT, and that miR-4442 possibly targets the autoimmune disease risk factor CD6, which provides potential new knowledge derived through the use of DES-Tcell. According to our understanding, DES-Tcell is the first KB dedicated to exploring T-cell-relevant information via literature-mining, data-mining, and topic-specific dictionaries.Ahdab AlSaieediAdil SalhiFaroug TifrateneArwa Bin RaiesArnaud HunglerMahmut UludagChristophe Van NesteVladimir B. BajicTakashi GojoboriMagbubah EssackNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Ahdab AlSaieedi Adil Salhi Faroug Tifratene Arwa Bin Raies Arnaud Hungler Mahmut Uludag Christophe Van Neste Vladimir B. Bajic Takashi Gojobori Magbubah Essack DES-Tcell is a knowledgebase for exploring immunology-related literature
description	Abstract T-cells are a subtype of white blood cells circulating throughout the body, searching for infected and abnormal cells. They have multifaceted functions that include scanning for and directly killing cells infected with intracellular pathogens, eradicating abnormal cells, orchestrating immune response by activating and helping other immune cells, memorizing encountered pathogens, and providing long-lasting protection upon recurrent infections. However, T-cells are also involved in immune responses that result in organ transplant rejection, autoimmune diseases, and some allergic diseases. To support T-cell research, we developed the DES-Tcell knowledgebase (KB). This KB incorporates text- and data-mined information that can expedite retrieval and exploration of T-cell relevant information from the large volume of published T-cell-related research. This KB enables exploration of data through concepts from 15 topic-specific dictionaries, including immunology-related genes, mutations, pathogens, and pathways. We developed three case studies using DES-Tcell, one of which validates effective retrieval of known associations by DES-Tcell. The second and third case studies focuses on concepts that are common to Grave’s disease (GD) and Hashimoto’s thyroiditis (HT). Several reports have shown that up to 20% of GD patients treated with antithyroid medication develop HT, thus suggesting a possible conversion or shift from GD to HT disease. DES-Tcell found miR-4442 links to both GD and HT, and that miR-4442 possibly targets the autoimmune disease risk factor CD6, which provides potential new knowledge derived through the use of DES-Tcell. According to our understanding, DES-Tcell is the first KB dedicated to exploring T-cell-relevant information via literature-mining, data-mining, and topic-specific dictionaries.
format	article
author	Ahdab AlSaieedi Adil Salhi Faroug Tifratene Arwa Bin Raies Arnaud Hungler Mahmut Uludag Christophe Van Neste Vladimir B. Bajic Takashi Gojobori Magbubah Essack
author_facet	Ahdab AlSaieedi Adil Salhi Faroug Tifratene Arwa Bin Raies Arnaud Hungler Mahmut Uludag Christophe Van Neste Vladimir B. Bajic Takashi Gojobori Magbubah Essack
author_sort	Ahdab AlSaieedi
title	DES-Tcell is a knowledgebase for exploring immunology-related literature
title_short	DES-Tcell is a knowledgebase for exploring immunology-related literature
title_full	DES-Tcell is a knowledgebase for exploring immunology-related literature
title_fullStr	DES-Tcell is a knowledgebase for exploring immunology-related literature
title_full_unstemmed	DES-Tcell is a knowledgebase for exploring immunology-related literature
title_sort	des-tcell is a knowledgebase for exploring immunology-related literature
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/cbfc89cb4e3b4eabbabf16b40d6f1942
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DES-Tcell is a knowledgebase for exploring immunology-related literature

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