DES-Amyloidoses “Amyloidoses through thelooking-glass”: A knowledgebase developedfor exploring and linking information relatedto human amyloid-related diseases
Само за регистроване кориснике
2022
Аутори
Bajić, Vladan P.Salhi, Adil
Lakota, Katja
Radovanović, Aleksandar
Razali, Rozaimi
Živković, Lada
Spremo-Potparević, Biljana
Uludag, Mahmut
Tifratene, Faroug
Motwalli, Olaa
Marchand, Benoit
Bajić, Vladimir
Gojobori, Takashi
Isenović, Esma R.
Essack, Magbubah
Чланак у часопису (Објављена верзија)
Метаподаци
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More than 30 types of amyloids are linked to close to 50 diseases in humans, the most prom- inent 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 net- work 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 rele- vant information regarding the biological network related to amyloid proteins/peptides and amyloid-related diseases. This KB contains information obtained through text and data min- ing 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 infor- mation 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.
Извор:
PLoS ONE, 2022, 17, 7Финансирање / пројекти:
- Ministry of Education, Science and Technological Development, Republic of Serbia
- KAUST [Grant No. OSR#4129]
- KAUST Base Research Fund [BAS/1/1606-01-01]
- KAUST Office of Sponsored Research (OSR) [Grant no. FCC/1/1976-20-01]
- (KAUST) Base Research Fund [BAS/1/1059-01-01]
DOI: 10.1371/journal.pone.0271737
ISSN: 1932-6203
PubMed: 35877764
Scopus: 2-s2.0-85135282245
Институција/група
VinčaTY - JOUR AU - Bajić, Vladan P. AU - Salhi, Adil AU - Lakota, Katja AU - Radovanović, Aleksandar AU - Razali, Rozaimi AU - Živković, Lada AU - Spremo-Potparević, Biljana AU - Uludag, Mahmut AU - Tifratene, Faroug AU - Motwalli, Olaa AU - Marchand, Benoit AU - Bajić, Vladimir AU - Gojobori, Takashi AU - Isenović, Esma R. AU - Essack, Magbubah PY - 2022 UR - https://vinar.vin.bg.ac.rs/handle/123456789/10387 AB - More than 30 types of amyloids are linked to close to 50 diseases in humans, the most prom- inent 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 net- work 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 rele- vant information regarding the biological network related to amyloid proteins/peptides and amyloid-related diseases. This KB contains information obtained through text and data min- ing 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 infor- mation 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. T2 - PLoS ONE T1 - DES-Amyloidoses “Amyloidoses through thelooking-glass”: A knowledgebase developedfor exploring and linking information relatedto human amyloid-related diseases VL - 17 IS - 7 DO - 10.1371/journal.pone.0271737 ER -
@article{ author = "Bajić, Vladan P. and Salhi, Adil and Lakota, Katja and Radovanović, Aleksandar and Razali, Rozaimi and Živković, Lada and Spremo-Potparević, Biljana and Uludag, Mahmut and Tifratene, Faroug and Motwalli, Olaa and Marchand, Benoit and Bajić, Vladimir and Gojobori, Takashi and Isenović, Esma R. and Essack, Magbubah", year = "2022", abstract = "More than 30 types of amyloids are linked to close to 50 diseases in humans, the most prom- inent 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 net- work 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 rele- vant information regarding the biological network related to amyloid proteins/peptides and amyloid-related diseases. This KB contains information obtained through text and data min- ing 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 infor- mation 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.", journal = "PLoS ONE", title = "DES-Amyloidoses “Amyloidoses through thelooking-glass”: A knowledgebase developedfor exploring and linking information relatedto human amyloid-related diseases", volume = "17", number = "7", doi = "10.1371/journal.pone.0271737" }
Bajić, V. P., Salhi, A., Lakota, K., Radovanović, A., Razali, R., Živković, L., Spremo-Potparević, B., Uludag, M., Tifratene, F., Motwalli, O., Marchand, B., Bajić, V., Gojobori, T., Isenović, E. R.,& Essack, M.. (2022). DES-Amyloidoses “Amyloidoses through thelooking-glass”: A knowledgebase developedfor exploring and linking information relatedto human amyloid-related diseases. in PLoS ONE, 17(7). https://doi.org/10.1371/journal.pone.0271737
Bajić VP, Salhi A, Lakota K, Radovanović A, Razali R, Živković L, Spremo-Potparević B, Uludag M, Tifratene F, Motwalli O, Marchand B, Bajić V, Gojobori T, Isenović ER, Essack M. DES-Amyloidoses “Amyloidoses through thelooking-glass”: A knowledgebase developedfor exploring and linking information relatedto human amyloid-related diseases. in PLoS ONE. 2022;17(7). doi:10.1371/journal.pone.0271737 .
Bajić, Vladan P., Salhi, Adil, Lakota, Katja, Radovanović, Aleksandar, Razali, Rozaimi, Živković, Lada, Spremo-Potparević, Biljana, Uludag, Mahmut, Tifratene, Faroug, Motwalli, Olaa, Marchand, Benoit, Bajić, Vladimir, Gojobori, Takashi, Isenović, Esma R., Essack, Magbubah, "DES-Amyloidoses “Amyloidoses through thelooking-glass”: A knowledgebase developedfor exploring and linking information relatedto human amyloid-related diseases" in PLoS ONE, 17, no. 7 (2022), https://doi.org/10.1371/journal.pone.0271737 . .