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23041por Yu, Hua, Chen, Jianxin, Xu, Xue, Li, Yan, Zhao, Huihui, Fang, Yupeng, Li, Xiuxiu, Zhou, Wei, Wang, Wei, Wang, Yonghua“…In addition, the validated models were employed to systematically predict known/unknown drugs and targets involving the enzymes, ion channels, GPCRs, and nuclear receptors, which can be further mapped to functional ontologies such as target-disease associations and target-target interaction networks. …”
Publicado 2012
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23042“…Users can retrieve data for individual genes or for groups of genes belonging to the same or related ontological categories. Assistance in selecting valid search terms is provided by an Ajax ‘autosuggest’ facility that polls the database as the user types. …”
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23043por Hoehndorf, Robert, Hardy, Nigel W., Osumi-Sutherland, David, Tweedie, Susan, Schofield, Paul N., Gkoutos, Georgios V.“…We systematically analyze recorded phenotypes in animal models using the formal definitions created for phenotype ontologies. We evaluate the validity of the inferred functions manually and by demonstrating a significant improvement in predicting genetic interactions and protein-protein interactions based on functional similarity. …”
Publicado 2013
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23044por Zheng, Rena, Rebolledo-Jaramillo, Boris, Zong, Yiwei, Wang, Liqing, Russo, Pierre, Hancock, Wayne, Stanger, Ben Z., Hardison, Ross C., Blobel, Gerd A.“…GATA4 chromatin immunoprecipitation followed by high throughput sequencing (ChIP-seq) identified 4409 occupied sites, associated with genes enriched in ontologies related to liver function, including lipid and glucose metabolism. …”
Publicado 2013
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23045“…RESULTS: We utilized existing ontologies and standards for scientific data representation, measurement unit definition, and data manipulation to build a simple and flexible Semantic Web Service-based approach to measurement-unit harmonization. …”
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23046por van der Schyff, Dylan“…To conclude, I consider how an enactive-contemplative perspective may help students and teachers awaken to the possibilities of music education as ‘ontological education.’ That is, through a deeper understanding of ‘music as a manifestation of life’ rediscover their primordial nature as autopoietic and world-making creatures and thus engage more deeply with musicality as a means of forming richer and more compassionate relationships with their peers, their communities and the ‘natural’ and cultural worlds they inhabit.…”
Publicado 2015
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23047“…We found that (i) NOL scores reveal a sequence-based feature at the introns on both sides of the intron-exon boundary; (ii) this feature is not part of any recognizable consensus sequence; (iii) this feature is conserved throughout metazoa; (iv) this feature is enriched in genes sharing similar functions: ATPase activity, ATP binding, helicase activity, and motor activity; (v) genes with these functions exhibit different genomic characteristics; (vi) in vivo nucleosome positioning data confirm ontological enrichment at this feature; and (vii) genes with this feature exhibit unique dinucleotide distributions at the intron-exon boundary. …”
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23048por Chelliah, Vijayalakshmi, Juty, Nick, Ajmera, Ishan, Ali, Raza, Dumousseau, Marine, Glont, Mihai, Hucka, Michael, Jalowicki, Gaël, Keating, Sarah, Knight-Schrijver, Vincent, Lloret-Villas, Audald, Natarajan, Kedar Nath, Pettit, Jean-Baptiste, Rodriguez, Nicolas, Schubert, Michael, Wimalaratne, Sarala M., Zhao, Yangyang, Hermjakob, Henning, Le Novère, Nicolas, Laibe, Camille“…Many models submitted to the database are annotated, cross-referencing its components to external resources such as database records, and terms from controlled vocabularies and ontologies. BioModels comprises two main branches: one is composed of models derived from literature, while the second is generated through automated processes. …”
Publicado 2014
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23049“…We retrieve and aggregate knowledge from several open data sources, web services and biomedical ontologies. This knowledge is transformed to RDF, linked to the Bio2RDF datasets and made available through a SPARQL 1.1 Endpoint. …”
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23050por Sun, Celi, Molineros, Julio E., Looger, Loren L., Zhou, Xu-jie, Kim, Kwangwoo, Okada, Yukinori, Ma, Jianyang, Qi, Yuan-yuan, Kim-Howard, Xana, Motghare, Prasenjeet, Bhattarai, Krishna, Adler, Adam, Bang, So-Young, Lee, Hye-Soon, Kim, Tae-Hwan, Kang, Young Mo, Suh, Chang-Hee, Chung, Won Tae, Park, Yong-Beom, Choe, Jung-Yoon, Shim, Seung Cheol, Kochi, Yuta, Suzuki, Akari, Kubo, Michiaki, Sumida, Takayuki, Yamamoto, Kazuhiko, Lee, Shin-Seok, Kim, Young Jin, Han, Bok-Ghee, Dozmorov, Mikhail, Kaufman, Kenneth M., Wren, Jonathan D., Harley, John B., Shen, Nan, Chua, Kek Heng, Zhang, Hong, Bae, Sang-Cheol, Nath, Swapan K.“…Novel loci share functional and ontological characteristics with previously reported loci, and are possible drug targets for SLE therapeutics.…”
Publicado 2016
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23051por Matos, Sérgio, Campos, David, Pinho, Renato, Silva, Raquel M., Mort, Matthew, Cooper, David N., Oliveira, José Luís“…Egas offers a flexible and customizable tool that allows defining the concept types and relations of interest for a given annotation task, as well as the ontologies used for normalizing each concept type. Further, annotations may be performed on raw documents or on the results of automated concept identification and relation extraction tools. …”
Publicado 2016
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23052por Piñero, Janet, Bravo, Àlex, Queralt-Rosinach, Núria, Gutiérrez-Sacristán, Alba, Deu-Pons, Jordi, Centeno, Emilio, García-García, Javier, Sanz, Ferran, Furlong, Laura I.“…DisGeNET data are homogeneously annotated with controlled vocabularies and community-driven ontologies. Additionally, several original metrics are provided to assist the prioritization of genotype–phenotype relationships. …”
Publicado 2017
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23053“…We highlighted how partners shared the impact of PD in their own ontological challenges. Further research with different types of families and in different situations is required to identify services required to facilitate the process of learning to live with PD. …”
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23054por Satou, Yorifumi, Katsuya, Hiroo, Fukuda, Asami, Misawa, Naoko, Ito, Jumpei, Uchiyama, Yoshikazu, Miyazato, Paola, Islam, Saiful, Fassati, Ariberto, Melamed, Anat, Bangham, Charles R. M., Koyanagi, Yoshio, Sato, Kei“…Expansion of HIV-1-infected clones was significantly more frequent when the provirus was integrated near host genes in specific gene ontological classes, including cell activation and chromatin regulation. …”
Publicado 2017
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23055“…First, the OGER entity recognizer, which has a bias towards high recall, annotates the terms that appear in selected domain ontologies. Subsequently, the Distiller framework uses this information as a feature for a machine learning algorithm to select the relevant entities only. …”
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23056por Zhan, Hao, Jiang, Jiahao, Sun, Qiman, Ke, Aiwu, Hu, Jinwu, Hu, Zhiqiang, Zhu, Kai, Luo, Chubin, Ren, Ning, Fan, Jia, Zhou, Jian, Huang, Xiaowu“…METHODS: We firstly sequenced the whole exomes of 5 paired hepatitis B virus-related early-stage HCC and peripheral blood samples, followed by gene ontological analysis and pathway analysis of the single-nucleotide variants discovered. …”
Publicado 2017
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23057por Jia, Jinmeng, An, Zhongxin, Ming, Yue, Guo, Yongli, Li, Wei, Li, Xin, Liang, Yunxiang, Guo, Dongming, Tai, Jun, Chen, Geng, Jin, Yaqiong, Liu, Zhimei, Ni, Xin, Shi, Tieliu“…It also uses disease-manifestation (D-M) integrated from existing biomedical ontologies as prior knowledge to automatically recognize text-mined, D-M-specific syntactic patterns from 774 514 full-text articles and 8 848 796 abstracts in MEDLINE. …”
Publicado 2018
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23058por Chen, Liang, Yuan, Lushun, Wang, Gang, Cao, Rui, Peng, Jianping, Shu, Bo, Qian, Guofeng, Wang, Xinghuan, Xiao, Yu“…To understand the function of dysregulated miRNAs in the development of MIBC, networks among miRNAs and genes, gene ontologies and pathways were built. The subsequent bioinformatics analysis indicated that the mitogen-associated protein kinase (MAPK) signaling pathway, apoptosis and pathways in cancer and the cell cycle, were significantly enriched Overall, these results provided comprehensive information on the biological function of dysregulated miRNAs in the development of MIBC. …”
Publicado 2017
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23059por Bekkar, Amel, Estreicher, Anne, Niknejad, Anne, Casals-Casas, Cristina, Bridge, Alan, Xenarios, Ioannis, Dorier, Julien, Crespo, Isaac“…Knowledgebases play an increasingly important role in scientific research, where the expert curation of biological knowledge in forms that are amenable to computational analysis (using ontologies for example)–provides a significant added value and enables new types of computational analyses for high throughput datasets. …”
Publicado 2018
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23060por Cano, Luis, Cerapio, Juan Pablo, Ruiz, Eloy, Marchio, Agnès, Turlin, Bruno, Casavilca, Sandro, Taxa, Luis, Marti, Guillaume, Deharo, Eric, Pineau, Pascal, Bertani, Stéphane“…Withal, liver clear cell foci of cellular alteration were genuinely associated with HCC and appended to some changes in immune and G protein-coupled receptor gene expression ontologies. Our findings confirm the occurrence of a particular setting of HCC in South America, a region where the pathophysiology of liver cancer remains largely unexplored.…”
Publicado 2018
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