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Prospects and Possibilities for Ontology Evaluation: The View from NCOR

Leo Obrst, Todd Hughes, Steve Ray
2006 The Web Conference  
In this position paper, we briefly describe the perspective of the US National Center for Ontological Research (NCOR, http://ncor.us) on ontology evaluation.  ...  This committee is charged with developing a plan for the evaluation of ontologies that is designed to transform ontological engineering into a true scientific and engineering discipline.  ...  Laboratories, the National Institute of Standards and Technology, the National Center for Ontological Research, or any other company or individual.  ... 
dblp:conf/www/ObrstHR06 fatcat:nwkv6sxwjjfh5adepocgn4ikle

The Interplay Between Ontology as Categorial Analysis and Ontology as Technology [chapter]

Roberto Poli, Leo Obrst
2010 Theory and Applications of Ontology: Computer Applications  
We note that the views expressed in this paper are those of the authors alone and do not reflect the official policy or position of any other organization or individual.  ...  Acknowledgments and Disclaimers One author's affiliation with The MITRE Corporation is provided for identification purposes only, and is not intended to convey or imply MITRE's concurrence with, or support  ...  effort would include strong evaluation criteria and possibly ontology certification.  ... 
doi:10.1007/978-90-481-8847-5_1 fatcat:tpvkq4djvjgxzcfvsouj4v4rgq

The Immediate Prospects for the Application of Ontologies in Digital Libraries

Jody L. DeRidder
2007 Knowledge organization  
The Immediate Prospects for the Application of Ontologies in Digital Libraries.  ...  DeRidder received her M.S. in Computer Science from the University of Tennessee in 2002, after developing repositories for the Open Archives Initiative in its alpha phases.  ...  ), LOA (Laboratory for Applied Ontology), and NCOR (National Center for Ontological Research).  ... 
doi:10.5771/0943-7444-2007-4-227 fatcat:ran32b7eajedzaxrtal7mdy4iq

Bio-ontologies: current trends and future directions

O. Bodenreider
2006 Briefings in Bioinformatics  
His other work includes the development of methodologies to migrate ontologies from the informal to formal and use reasoning to increase structural validity.  ...  He has co-chaired the annual bio-ontologies meeting at ISMB for many years and is a co-developer of a highly successful OWL training course.  ...  The National Center for Ontological Research (http://ncor.us/) (NCOR) was established in 2005 and is codirected by Barry Smith and Mark Musen.  ... 
doi:10.1093/bib/bbl027 pmid:16899495 pmcid:PMC1847325 fatcat:iwzoi4hqi5gmze6ekzwyugcfmy

Novel molecular players of X chromosome inactivation: new technologies and new insights

Piotr Przanowski, Urszula Waśko, Sanchita Bhatnagar
2018 Journal of Translational Genetics and Genomics  
XCI ensures equal gene dosage for X-linked genes between the two genders.  ...  interaction with chromatin, and structural organization of the Xi in the nuclei.  ...  Pathway based evaluation for 87 XCIFs identified through multiple genetic and proteomics screens were categorized according to biological process and molecular function using PANTHER protein class ontology  ... 
doi:10.20517/jtgg.2017.03 fatcat:ucieqvrlm5gploxl43kn6jmhci

Molecular Signatures of Self-Renewal, Differentiation, and Lineage Choice in Multipotential Hemopoietic Progenitor Cells In Vitro

L. Bruno, R. Hoffmann, F. McBlane, J. Brown, R. Gupta, C. Joshi, S. Pearson, T. Seidl, C. Heyworth, T. Enver
2003 Molecular and Cellular Biology  
The molecular mechanisms governing self-renewal, differentiation, and lineage specification remain unknown.  ...  These are likely to include genes important in self-renewal, the maintenance of multipotentiality, or the negative regulation of differentiation per se.  ...  ACKNOWLEDGMENTS We thank Gillian May and Mel Greaves for critical reading of the manuscript and Tim Dexter for technical assistance with the M-versus-A plots.  ... 
doi:10.1128/mcb.24.2.741-756.2004 pmid:14701746 pmcid:PMC343787 fatcat:6bnj6pk2mndrljtg3xkw6ul6ji

Suppression of histone deacetylation promotes the differentiation of human pluripotent stem cells towards neural progenitor cells

Juan Yang, Yu Tang, Hui Liu, Fang Guo, Jun Ni, Weidong Le
2014 BMC Biology  
Emerging studies of human pluripotent stem cells (hPSCs) raise new prospects for neurodegenerative disease modeling and cell replacement therapies.  ...  Therefore, understanding the mechanisms underlying the commitment of neural progenitor cells (NPCs) is important for the application of hPSCs in neurodegenerative disease therapies.  ...  First, we treated H9 cells with NaB and VPA at various concentrations for 24 hours to evaluate the toxicity of those HDACi.  ... 
doi:10.1186/s12915-014-0095-z pmid:25406762 pmcid:PMC4254204 fatcat:yqlp6yhnhndwjpqbtvqww3drzi

Growth Factor Independence 1B-Mediated Transcriptional Repression and Lineage Allocation Require Lysine-Specific Demethylase 1-Dependent Recruitment of the BHC Complex

David McClellan, Mattie J. Casey, Diana Bareyan, Helena Lucente, Christopher Ours, Matthew Velinder, Jason Singer, Mehraju Din Lone, Wenxiang Sun, Yunuen Coria, Clinton C. Mason, Michael E. Engel
2019 Molecular and Cellular Biology  
We show that GFI1B preferentially recruits core and putative elements of the BRAF-histone deacetylase (HDAC) (BHC) chromatin-remodeling complex (LSD1, RCOR1, HMG20A, HMG20B, HDAC1, HDAC2, PHF21A, GSE1,  ...  These findings demonstrate the central role of the GFI1B-LSD1 interaction as a determinant of BHC complex recruitment to enable cell fate decisions driven by GFI1B.  ...  Components from several other complexes (NuRF, CHRAC, canonical and noncanonical PRC1, PRC2, SIN3A, and NCoR) were found, and for each, some elements were enriched, suggesting that they also contribute  ... 
doi:10.1128/mcb.00020-19 pmid:30988160 pmcid:PMC6580704 fatcat:euqixlcm5zcddkpfcw3vcppigi

Emerging functions of the nuclear receptor LRH-1 in liver physiology and pathology

Yu Sun, Hadrien Demagny, Kristina Schoonjans
2021 Biochimica et Biophysica Acta - Molecular Basis of Disease  
This review also focuses on the recent advances highlighting LRH-1 as an attractive target for liver-associated diseases, such as non-alcoholic fatty liver disease (NAFLD) and hepatocellular carcinoma  ...  In this review, we summarize the physiological and pathophysiological functions of LRH-1 in the liver, as well as the molecular mechanisms underlying these processes.  ...  This work was supported by funding from the Ecole Polytechnique Fédérale de Lausanne (EPFL), Switzerland, and the Swiss National Science Foundation (SNSF, No. 31003A_166695), Switzerland.  ... 
doi:10.1016/j.bbadis.2021.166145 pmid:33862147 fatcat:7hu3os436zffxeeyz6oi5bxhky

Integration of whole genome sequencing and transcriptomics reveals a complex picture of the reestablishment of insecticide resistance in the major malaria vector Anopheles coluzzii

Victoria A. Ingham, Jacob A. Tennessen, Eric R. Lucas, Sara Elg, Henrietta Carrington Yates, Jessica Carson, Wamdaogo Moussa Guelbeogo, N'Fale Sagnon, Grant L. Hughes, Eva Heinz, Daniel E. Neafsey, Hilary Ranson (+1 others)
2021 PLoS Genetics  
The original resistant, susceptible and re-selected colonies were subject to RNAseq and whole genome sequencing, which identified a number of changes across the transcriptome and genome linked with resistance  ...  In this study, we compare three populations of the major malaria vector An. coluzzii: a susceptible and two resistant colonies with the same genetic background.  ...  Acknowledgments The authors would like to thank Manuela Bernardi for graphical elements used to create Fig 7, Professor Joanne Knight, Lancaster Medical School, for input in the GWAS analysis and Ms  ... 
doi:10.1371/journal.pgen.1009970 pmid:34941884 pmcid:PMC8741062 fatcat:fel7nb3rgfb2ni5hamf3gsqtd4

Developmental microRNA expression profiling of murine embryonic orofacial tissue

Partha Mukhopadhyay, Guy Brock, Vasyl Pihur, Cynthia Webb, M. Michele Pisano, Robert M. Greene
2010 Birth defects research. Clinical and molecular teratology  
Quantitative real-time PCR was utilized for validation of gene expression changes. Cluster analysis of the microarray data was conducted with the clValid R package and the UPGMA clustering method.  ...  MicroRNA gene expression profiling is an effective means of acquiring novel and valuable information regarding the expression and regulation of genes, under the control of miRNA, involved in mammalian  ...  Acknowledgments This research was supported in part by NIH grants DE018215, HD053509, and P20 RR017702 from the COBRE program of the National Center for Research Resources and DOE grant 10EM00542.  ... 
doi:10.1002/bdra.20684 pmid:20589883 pmcid:PMC3146018 fatcat:34ezytnsb5a35jenqrmt6ov4li

Abstracts

2005 Oncology Research and Treatment  
These characteristics distinguish RG108 from other DNA methyltransferase inhibitors and will be important for further drug development.  ...  localization and those functional properties, identified to date, appear to differ from those of p220.  ...  The unifying concept behind our experimental strategy is the use of multiple experimental paradigms from genomics, proteomics and functional genomics for the prospective analysis of clinically relevant  ... 
doi:10.1159/000084411 pmid:15812902 fatcat:ijhzfgk4wffehcowkfzsgazrqy

pp. 1–87

2004 Oncology Research and Treatment  
assessment of drug sensitivity or resistance has been hampered by the lack of convenient methods for measurement of activated apoptosis signaling.  ...  We developed and characterized a flow cytometric method for combined measurement of caspase activation by cleavage of (Asp) 2rhodamine 110 (D 2 R) and mitochondrial membrane potential in living cells.  ...  Further evaluation of these mechanisms could possibly lead to new therapeutic options for the treatment of SCLC.  ... 
doi:10.1159/000081405 pmid:15521116 fatcat:itjq4ptvpbdlbncsoo2l2cpj7i

Targeting the Androgen Receptor in Breast Cancer

KeeMing Chia, Megan O'Brien, Myles Brown, Elgene Lim
2015 Current Oncology Reports  
Moreover, I identify AR-regulated genes from the global gene expression of an ER+AR+ endocrine-resistant PDX model treated with DHT and establish a highly prognostic AR gene signature based on primary  ...  As a result, there is an urgent medical need for novel therapeutic strategies capable of managing endocrine-resistant breast cancer.  ...  ., 2011) and hence it is possible that activation of AR signalling can reduce the activation of ER signalling through competition for the same pool of cofactors.  ... 
doi:10.1007/s11912-014-0427-8 pmid:25665553 fatcat:v3cenbehrvhqfluqu37mu6d6te

Setd5 haploinsufficiency alters neuronal network connectivity and leads to autistic-like behaviors in mice

Spencer M. Moore, Jason S. Seidman, Jacob Ellegood, Richard Gao, Alex Savchenko, Ty D. Troutman, Yohei Abe, Josh Stender, Daehoon Lee, Sicong Wang, Bradley Voytek, Jason P. Lerch (+3 others)
2019 Translational Psychiatry  
Setd5 is the highly conserved mouse homolog, and although the Setd5 null mouse is embryonic lethal, the heterozygote is viable.  ...  SETD5, a gene linked to intellectual disability (ID) and autism spectrum disorder (ASD), is a member of the SET-domain family and encodes a putative histone methyltransferase (HMT).  ...  Durigon and his group for the ZKV2015 aliquots, and P. Vasconcelos for providing a lyophilized ZKV2015 seed. Dr. Mesci and Dr. Macia drew the mouse schematics in the manuscript. Acknowledgements  ... 
doi:10.1038/s41398-018-0344-y pmid:30655503 pmcid:PMC6336863 fatcat:vrwhucnt4fdl7n2aqrvuv2qyt4
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