Results 31 to 40 of about 70,455 (289)

RDFScape: Semantic Web meets Systems Biology

BMC Bioinformatics, 2008
Background The recent availability of high-throughput data in molecular biology has increased the need for a formal representation of this knowledge domain. New ontologies are being developed to formalize knowledge, e.g.
Splendiani Andrea
doaj   +1 more source

Influence of lipopolysaccharide on proinflammatory gene expression in human corneal, conjunctival and meibomian gland epithelial cells [PDF]

, 2018
PURPOSE: Lipopolysaccharide (LPS), a bacterial endotoxin, is known to stimulate leuokotriene B4 (LTB4) secretion by human corneal (HCECs), conjunctival (HConjECs) and meibomian gland (HMGECs) epithelial cells.
Chen, Di, Darabad, Raheleh Rahimi, Kam, Wendy R., Liu, Yang, Sahin, Afsun, Sullivan, David A.   +5 more
core   +1 more source

Exploring biomedical ontology mappings with graph theory methods [PDF]

PeerJ, 2017
Background In the era of semantic web, life science ontologies play an important role in tasks such as annotating biological objects, linking relevant data pieces, and verifying data consistency.
Simon Kocbek, Jin-Dong Kim
doaj   +2 more sources

Ontology Design Patterns for bio-ontologies: a case study on the Cell Cycle Ontology

BMC Bioinformatics, 2008
Background Bio-ontologies are key elements of knowledge management in bioinformatics. Rich and rigorous bio-ontologies should represent biological knowledge with high fidelity and robustness.
Antezana Erick, Aranguren Mikel Egaña, Kuiper Martin, Stevens Robert   +3 more
doaj   +1 more source

Emerging semantics to link phenotype and environment [PDF]

PeerJ, 2015
Understanding the interplay between environmental conditions and phenotypes is a fundamental goal of biology. Unfortunately, data that include observations on phenotype and environment are highly heterogeneous and thus difficult to find and integrate ...
Anne E. Thessen, Daniel E. Bunker, Pier Luigi Buttigieg, Laurel D. Cooper, Wasila M. Dahdul, Sami Domisch, Nico M. Franz, Pankaj Jaiswal, Carolyn J. Lawrence-Dill, Peter E. Midford, Christopher J. Mungall, Martín J. Ramírez, Chelsea D. Specht, Lars Vogt, Rutger Aldo Vos, Ramona L. Walls, Jeffrey W. White, Guanyang Zhang, Andrew R. Deans, Eva Huala, Suzanna E. Lewis, Paula M. Mabee   +21 more
doaj   +2 more sources

Desiderata for an ontology of diseases for the annotation of biological datasets. [PDF]

, 2009
There is a plethora of disease ontologies available, all potentially useful for the annotation of biological datasets. We define seven desirable features for such ontologies and examine whether or not these features are supported by eleven disease ...
Anita Burgun, Olivier Bodenreider
core   +1 more source

Transcriptional network analysis of PTEN‐protein‐deficient prostate tumors reveals robust stromal reprogramming and signs of senescent paracrine communication

Molecular Oncology, EarlyView.
Combining PTEN protein assessment and transcriptomic profiling of prostate tumors, we uncovered a network enriched in senescence and extracellular matrix (ECM) programs associated with PTEN loss and conserved in a mouse model. We show that PTEN‐deficient cells trigger paracrine remodeling of the surrounding stroma and this information could help ...
Ivana Rondon‐Lorefice, Jose I. Lopez, Aitziber Ugalde‐Olano, Maite Zufiaurre, Ianire Astobiza, Natalia Martin‐Martin, Laura Bozal‐Basterra, Saioa Garcia‐Longarte, Amaia Zabala‐Letona, Sofia Rey, Aida Santos‐Martin, Miguel Unda, Ana Loizaga‐Iriarte, Mariona Graupera, Paolo Nuciforo, Arkaitz Carracedo, Isabel Mendizabal   +16 more
wiley   +1 more source

Improving the classification of cardinality phenotypes using collections

Journal of Biomedical Semantics, 2023
Motivation Phenotypes are observable characteristics of an organism and they can be highly variable. Information about phenotypes is collected in a clinical context to characterize disease, and is also collected in model organisms and stored in model ...
Sarah M. Alghamdi, Robert Hoehndorf
doaj   +1 more source

Plecstatin inhibits hepatocellular carcinoma tumorigenesis and invasion through cytolinker plectin

Molecular Oncology, EarlyView.
The ruthenium‐based metallodrug plecstatin exerts its anticancer effect in hepatocellular carcinoma (HCC) primarily through selective targeting of plectin. By disrupting plectin‐mediated cytoskeletal organization, plecstatin inhibits anchorage‐dependent growth, cell polarization, and tumor cell dissemination.
Zuzana Outla, Jan Kosla, Magdalena Prechova, Lukas Frick, Patricia Bortel, Yasmin Borutzki, Andrea Bileck, Christopher Gerner, Samuel M. Meier‐Menches, Selma Osmanagic‐Myers, Martin Gregor   +10 more
wiley   +1 more source

simona: a comprehensive R package for semantic similarity analysis on bio-ontologies

BMC Genomics
Background Bio-ontologies are keys in structuring complex biological information for effective data integration and knowledge representation. Semantic similarity analysis on bio-ontologies quantitatively assesses the degree of similarity between ...
Zuguang Gu
doaj   +1 more source