DES-Amyloidoses "Amyloidoses through the looking-glass": A knowledgebase developed for exploring and linking information related to human amyloid-related diseases.
More than 30 types of amyloids are linked to close to 50 diseases in humans, the most prominent being Alzheimer's disease (AD). AD is brain-related local amyloidosis, while another amyloidosis, such as AA amyloidosis, tends to be more systemic. Therefore, we need to know more about the biologic...
| Main Authors: | , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2022-01-01
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| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0271737 |
| _version_ | 1828525160427159552 |
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| author | Vladan P Bajic Adil Salhi Katja Lakota Aleksandar Radovanovic Rozaimi Razali Lada Zivkovic Biljana Spremo-Potparevic Mahmut Uludag Faroug Tifratene Olaa Motwalli Benoit Marchand Vladimir B Bajic Takashi Gojobori Esma R Isenovic Magbubah Essack |
| author_facet | Vladan P Bajic Adil Salhi Katja Lakota Aleksandar Radovanovic Rozaimi Razali Lada Zivkovic Biljana Spremo-Potparevic Mahmut Uludag Faroug Tifratene Olaa Motwalli Benoit Marchand Vladimir B Bajic Takashi Gojobori Esma R Isenovic Magbubah Essack |
| author_sort | Vladan P Bajic |
| collection | DOAJ |
| description | More than 30 types of amyloids are linked to close to 50 diseases in humans, the most prominent being Alzheimer's disease (AD). AD is brain-related local amyloidosis, while another amyloidosis, such as AA amyloidosis, tends to be more systemic. Therefore, we need to know more about the biological entities' influencing these amyloidosis processes. However, there is currently no support system developed specifically to handle this extraordinarily complex and demanding task. To acquire a systematic view of amyloidosis and how this may be relevant to the brain and other organs, we needed a means to explore "amyloid network systems" that may underly processes that leads to an amyloid-related disease. In this regard, we developed the DES-Amyloidoses knowledgebase (KB) to obtain fast and relevant information regarding the biological network related to amyloid proteins/peptides and amyloid-related diseases. This KB contains information obtained through text and data mining of available scientific literature and other public repositories. The information compiled into the DES-Amyloidoses system based on 19 topic-specific dictionaries resulted in 796,409 associations between terms from these dictionaries. Users can explore this information through various options, including enriched concepts, enriched pairs, and semantic similarity. We show the usefulness of the KB using an example focused on inflammasome-amyloid associations. To our knowledge, this is the only KB dedicated to human amyloid-related diseases derived primarily through literature text mining and complemented by data mining that provides a novel way of exploring information relevant to amyloidoses. |
| first_indexed | 2024-12-11T21:02:08Z |
| format | Article |
| id | doaj.art-92711003c5a04d83af23b9d0a9ddebd4 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-11T21:02:08Z |
| publishDate | 2022-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-92711003c5a04d83af23b9d0a9ddebd42022-12-22T00:50:58ZengPublic Library of Science (PLoS)PLoS ONE1932-62032022-01-01177e027173710.1371/journal.pone.0271737DES-Amyloidoses "Amyloidoses through the looking-glass": A knowledgebase developed for exploring and linking information related to human amyloid-related diseases.Vladan P BajicAdil SalhiKatja LakotaAleksandar RadovanovicRozaimi RazaliLada ZivkovicBiljana Spremo-PotparevicMahmut UludagFaroug TifrateneOlaa MotwalliBenoit MarchandVladimir B BajicTakashi GojoboriEsma R IsenovicMagbubah EssackMore than 30 types of amyloids are linked to close to 50 diseases in humans, the most prominent being Alzheimer's disease (AD). AD is brain-related local amyloidosis, while another amyloidosis, such as AA amyloidosis, tends to be more systemic. Therefore, we need to know more about the biological entities' influencing these amyloidosis processes. However, there is currently no support system developed specifically to handle this extraordinarily complex and demanding task. To acquire a systematic view of amyloidosis and how this may be relevant to the brain and other organs, we needed a means to explore "amyloid network systems" that may underly processes that leads to an amyloid-related disease. In this regard, we developed the DES-Amyloidoses knowledgebase (KB) to obtain fast and relevant information regarding the biological network related to amyloid proteins/peptides and amyloid-related diseases. This KB contains information obtained through text and data mining of available scientific literature and other public repositories. The information compiled into the DES-Amyloidoses system based on 19 topic-specific dictionaries resulted in 796,409 associations between terms from these dictionaries. Users can explore this information through various options, including enriched concepts, enriched pairs, and semantic similarity. We show the usefulness of the KB using an example focused on inflammasome-amyloid associations. To our knowledge, this is the only KB dedicated to human amyloid-related diseases derived primarily through literature text mining and complemented by data mining that provides a novel way of exploring information relevant to amyloidoses.https://doi.org/10.1371/journal.pone.0271737 |
| spellingShingle | Vladan P Bajic Adil Salhi Katja Lakota Aleksandar Radovanovic Rozaimi Razali Lada Zivkovic Biljana Spremo-Potparevic Mahmut Uludag Faroug Tifratene Olaa Motwalli Benoit Marchand Vladimir B Bajic Takashi Gojobori Esma R Isenovic Magbubah Essack DES-Amyloidoses "Amyloidoses through the looking-glass": A knowledgebase developed for exploring and linking information related to human amyloid-related diseases. PLoS ONE |
| title | DES-Amyloidoses "Amyloidoses through the looking-glass": A knowledgebase developed for exploring and linking information related to human amyloid-related diseases. |
| title_full | DES-Amyloidoses "Amyloidoses through the looking-glass": A knowledgebase developed for exploring and linking information related to human amyloid-related diseases. |
| title_fullStr | DES-Amyloidoses "Amyloidoses through the looking-glass": A knowledgebase developed for exploring and linking information related to human amyloid-related diseases. |
| title_full_unstemmed | DES-Amyloidoses "Amyloidoses through the looking-glass": A knowledgebase developed for exploring and linking information related to human amyloid-related diseases. |
| title_short | DES-Amyloidoses "Amyloidoses through the looking-glass": A knowledgebase developed for exploring and linking information related to human amyloid-related diseases. |
| title_sort | des amyloidoses amyloidoses through the looking glass a knowledgebase developed for exploring and linking information related to human amyloid related diseases |
| url | https://doi.org/10.1371/journal.pone.0271737 |
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