Search Results - "Database : the journal of biological databases and curation"

A comprehensive aligned nifH gene database: a multipurpose tool for studies of nitrogen-fixing bacteria by Gaby, John Christian, Buckley, Daniel H.

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BelSmile: a biomedical semantic role labeling approach for extracting biological expression language from text by Lai, Po-Ting, Lo, Yu-Yan, Huang, Ming-Siang, Hsiao, Yu-Cheng, Tsai, Richard Tzong-Han

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Building deep learning models for evidence classification from the open access biomedical literature by Burns, Gully A, Li, Xiangci, Peng, Nanyun

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BioMart: a data federation framework for large collaborative projects by Zhang, J., Haider, S., Baran, J., Cros, A., Guberman, J. M., Hsu, J., Liang, Y., Yao, L., Kasprzyk, A.

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NBDC RDF portal: a comprehensive repository for semantic data in life sciences by Kawashima, Shuichi, Katayama, Toshiaki, Hatanaka, Hideki, Kushida, Tatsuya, Takagi, Toshihisa

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WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions by Karr, J. R., Phillips, N. C., Covert, M. W.

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Maser: one-stop platform for NGS big data from analysis to visualization by Kinjo, Sonoko, Monma, Norikazu, Misu, Sadahiko, Kitamura, Norikazu, Imoto, Junichi, Yoshitake, Kazutoshi, Gojobori, Takashi, Ikeo, Kazuho

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RetrogeneDB-a database of plant and animal retrocopies by Rosikiewicz, Wojciech, Kabza, Michal, Kosinski, Jan G, Ciomborowska-Basheer, Joanna, Kubiak, Magdalena R, Makalowska, Izabela

“…http://yeti.amu.edu.pl/retrogenedb. http://rhesus.amu.edu.pl/retrogenedb…”
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Comparison of human cell signaling pathway databases--evolution, drawbacks and challenges by Chowdhury, Saikat, Sarkar, Ram Rup

“…Elucidating the complexities of cell signaling pathways is of immense importance to gain understanding about various biological phenomenon, such as dynamics of…”
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Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat by Babbitt, Patricia C, Bagos, Pantelis G, Bairoch, Amos, Bateman, Alex, Chatonnet, Arnaud, Chen, Mark Jinan, Craik, David J, Finn, Robert D, Gloriam, David, Haft, Daniel H, Henrissat, Bernard, Holliday, Gemma L, Isberg, Vignir, Kaas, Quentin, Landsman, David, Lenfant, Nicolas, Manning, Gerard, Nagano, Nozomi, Srinivasan, Narayanaswamy, O'Donovan, Claire, Pruitt, Kim D, Sowdhamini, Ramanathan, Rawlings, Neil D, Saier, Jr, Milton H, Sharman, Joanna L, Spedding, Michael, Tsirigos, Konstantinos D, Vastermark, Ake, Vriend, Gerrit

“…During 11-12 August 2014, a Protein Bioinformatics and Community Resources Retreat was held at the Wellcome Trust Genome Campus in Hinxton, UK. This meeting…”
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NCBI Taxonomy: a comprehensive update on curation, resources and tools by Schoch, Conrad L, Ciufo, Stacy, Domrachev, Mikhail, Hotton, Carol L, Kannan, Sivakumar, Khovanskaya, Rogneda, Leipe, Detlef, Mcveigh, Richard, O’Neill, Kathleen, Robbertse, Barbara, Sharma, Shobha, Soussov, Vladimir, Sullivan, John P, Sun, Lu, Turner, Seán, Karsch-Mizrachi, Ilene

“…Abstract The National Center for Biotechnology Information (NCBI) Taxonomy includes organism names and classifications for every sequence in the nucleotide and…”
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OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies by Jackson, Rebecca, Matentzoglu, Nicolas, Overton, James A, Vita, Randi, Balhoff, James P, Buttigieg, Pier Luigi, Carbon, Seth, Courtot, Melanie, Diehl, Alexander D, Dooley, Damion M, Duncan, William D, Harris, Nomi L, Haendel, Melissa A, Lewis, Suzanna E, Natale, Darren A, Osumi-Sutherland, David, Ruttenberg, Alan, Schriml, Lynn M, Smith, Barry, Stoeckert, Jr, Christian J, Vasilevsky, Nicole A, Walls, Ramona L, Zheng, Jie, Mungall, Christopher J, Peters, Bjoern

“…Biological ontologies are used to organize, curate and interpret the vast quantities of data arising from biological experiments. While this works well when…”
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Post-translational modifications in proteins: resources, tools and prediction methods by Ramazi, Shahin, Zahiri, Javad

“…Abstract Posttranslational modifications (PTMs) refer to amino acid side chain modification in some proteins after their biosynthesis. There are more than 400…”
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FerrDb: a manually curated resource for regulators and markers of ferroptosis and ferroptosis-disease associations by Zhou, Nan, Bao, Jinku

“…Abstract Ferroptosis is a mode of regulated cell death that depends on iron. Cells die from the toxic accumulation of lipid reactive oxygen species…”
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ScaleNet: a literature-based model of scale insect biology and systematics by García Morales, Mayrolin, Denno, Barbara D, Miller, Douglass R, Miller, Gary L, Ben-Dov, Yair, Hardy, Nate B

“…Scale insects (Hemiptera: Coccoidea) are small herbivorous insects found on all continents except Antarctica. They are extremely invasive, and many species are…”
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PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data by Franzén, Oscar, Gan, Li-Ming, Björkegren, Johan L M

“…Single-cell RNA sequencing is an increasingly used method to measure gene expression at the single cell level and build cell-type atlases of tissues. Hundreds…”
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bc-GenExMiner 4.5: new mining module computes breast cancer differential gene expression analyses by Jézéquel, Pascal, Gouraud, Wilfried, Ben Azzouz, Fadoua, Guérin-Charbonnel, Catherine, Juin, Philippe P, Lasla, Hamza, Campone, Mario

“…'Breast cancer gene-expression miner' (bc-GenExMiner) is a breast cancer-associated web portal (http://bcgenex.ico.unicancer.fr). Here, we describe the…”
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Artificial intelligence with multi-functional machine learning platform development for better healthcare and precision medicine by Ahmed, Zeeshan, Mohamed, Khalid, Zeeshan, Saman, Dong, XinQi

“…Abstract Precision medicine is one of the recent and powerful developments in medical care, which has the potential to improve the traditional symptom-driven…”
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PlasticDB: a database of microorganisms and proteins linked to plastic biodegradation by Gambarini, Victor, Pantos, Olga, Kingsbury, Joanne M, Weaver, Louise, Handley, Kim M, Lear, Gavin

“…The number of publications reporting putative plastic-degrading microbes and proteins is continuously increasing, necessitating the compilation of these data…”
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Enhancing a Pathway-Genome Database (PGDB) to capture subcellular localization of metabolites and enzymes: the nucleotide-sugar biosynthetic pathways of Populus trichocarpa by Nag, Ambarish, Karpinets, Tatiana V, Chang, Christopher H, Bar-Peled, Maor

“…Understanding how cellular metabolism works and is regulated requires that the underlying biochemical pathways be adequately represented and integrated with…”
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