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The cellular microscopy phenotype ontology

Simon Jupp, James Malone, Tony Burdett, Jean-Karim Heriche, Eleanor Williams, Jan Ellenberg, Helen Parkinson, Gabriella Rustici
2016 Journal of Biomedical Semantics  
Description: We present the Cellular Microscopy Phenotype Ontology (CMPO), a species neutral ontology for describing phenotypic observations relating to the whole cell, cellular components, cellular processes  ...  project database and the Cellular Phenotype Database to facilitate data browsing and discoverability.  ...  A subset of the phenotypic data used to build CMPO was provided by the EU-FP7-Systems Microscopy NoE, grant agreement no. 258068.  ... 
doi:10.1186/s13326-016-0074-0 pmid:27195102 pmcid:PMC4870745 fatcat:3su4umevqnedhdq6yn2d5p4xza

Development of Semantic Web-based Imaging Database for Biological Morphome [article]

Satoshi Kume, Hiroshi Masuya, Mitsuyo Maeda, Mitsuo Suga, Yosky Kataoka, Norio Kobayashi
2021 arXiv   pre-print
As a result, we have successfully managed vast numbers of images and their metadata, including the interpretation of morphological phenotypes occurring in sub-cellular components and biosamples captured  ...  We applied the database to accumulate comprehensive microstructural imaging data produced by automated scanning electron microscopy.  ...  This work was supported by the Management Expenses Grant for RIKEN CLST-JEOL Collaboration Center, the RIKEN Ageing project, and the RIKEN engineering network project.  ... 
arXiv:2110.12058v1 fatcat:37qzcxh76nfp3heaniazxf32c4

Cellular phenotype database: a repository for systems microscopy data

Catherine Kirsanova, Alvis Brazma, Gabriella Rustici, Ugis Sarkans
2015 Bioinformatics  
Motivation: The Cellular Phenotype Database (CPD) is a repository for data derived from highthroughput systems microscopy studies.  ...  The aims of this resource are: (i) to provide easy access to cellular phenotype and molecular localization data for the broader research community; (ii) to facilitate integration of independent phenotypic  ...  We are also grateful to Simon Jupp and EBI Samples, Phenotypes and Ontologies Team for providing us with the mapping of the original phenotype terms to the CMPO ontology.  ... 
doi:10.1093/bioinformatics/btv199 pmid:25861964 pmcid:PMC4528631 fatcat:r6b2cfe5wve7finlcj7uyaotni

Semantic integration of physiology phenotypes with an application to the Cellular Phenotype Ontology

Robert Hoehndorf, Midori A. Harris, Heinrich Herre, Gabriella Rustici, Georgios V. Gkoutos
2012 Computer applications in the biosciences : CABIOS  
The CPO can be used for the annotation of observed abnormalities in domains, such as systems microscopy, in which cellular abnormalities are observed and for which no phenotype ontology has been created  ...  The CPO is an ontology of morphological and physiological phenotypic characteristics of cells, cell components and cellular processes.  ...  ACKNOWLEDGEMENT We thank Michel Dumontier for valuable discussions about the formal representation of the axioms and the different possible interpretations of the regulates relation.  ... 
doi:10.1093/bioinformatics/bts250 pmid:22539675 pmcid:PMC3381966 fatcat:j5rixqrb4nas7hqmnp7mbkqyva

Development of an Ontology for an Integrated Image Analysis Platform to enable Global Sharing of Microscopy Imaging Data [article]

Satoshi Kume, Hiroshi Masuya, Yosky Kataoka, Norio Kobayashi
2021 arXiv   pre-print
In this ontology, we propose 18 upper-level concepts including missing concepts in OME such as electron microscopy, phenotype data, biosample, and imaging conditions.  ...  We translated the XML-based OME metadata into the base concept of RDF schema as a trial of developing microscopy ontology.  ...  Acknowledgments This work was supported by the Management Expenses Grant for RIKEN CLST-JEOL Collaboration Center.  ... 
arXiv:2110.10407v1 fatcat:j5v36egrhvdg7godnzqtodf7mq

Ontology-based prediction of cancer driver genes [article]

Sara Althubaiti, Andreas Karwath, Ashraf Dallol, Adeeb Noor, Shadi Salem Alkhayyat, Rolina Alwassia, Katsuhiko Mineta, Takashi Gojobori, Andrew D Beggs, Paul N Schofield, Georgios V Gkoutos, Robert Hoehndorf
2019 bioRxiv   pre-print
Our approach utilizes multiple complementary types of information, specifically cellular phenotypes, cellular locations, functions, and whole body physiological phenotypes as features.  ...  We demonstrate the utility of our method by validating its predictions in nasopharyngeal cancer and colorectal cancer using whole exome and whole genome sequencing.  ...  microscopy studies and recorded using the Cellular Microscopy 84 Phenotype Ontology (CMPO) [16] ; gene functions and cellular locations recorded by 85 Uniprot [12] and encoded using the Gene Ontology  ... 
doi:10.1101/561480 fatcat:fbh7qv6x5bfaxb2nwcnh6vpnoa

Ontology-based prediction of cancer driver genes

Sara Althubaiti, Andreas Karwath, Ashraf Dallol, Adeeb Noor, Shadi Salem Alkhayyat, Rolina Alwassia, Katsuhiko Mineta, Takashi Gojobori, Andrew D. Beggs, Paul N. Schofield, Georgios V. Gkoutos, Robert Hoehndorf
2019 Scientific Reports  
Our approach utilizes multiple complementary types of information, specifically cellular phenotypes, cellular locations, functions, and whole body physiological phenotypes as features.  ...  We demonstrate the utility of our method by validating its predictions in nasopharyngeal cancer and colorectal cancer using whole exome and whole genome sequencing.  ...  We use three types of information associated with genes: cellular phenotypes observed in large-scale microscopy studies and recorded using the Cellular Microscopy Phenotype Ontology (CMPO) 16 ; gene  ... 
doi:10.1038/s41598-019-53454-1 pmid:31757986 pmcid:PMC6874647 fatcat:lfrtketkjfdodhs3zf7blq7gam

How can functional annotations be derived from profiles of phenotypic annotations?

Beatriz Serrano-Solano, Antonio Díaz Ramos, Jean-Karim Hériché, Juan A. G. Ranea
2017 BMC Bioinformatics  
Results: We explored the relation between cellular phenotypes from RNAi-based screens in human cells and gene annotations of cellular functions as provided by the Gene Ontology (GO).  ...  However, phenotypic similarities did not map to the Gene Ontology organization of gene function but to functions defined as groups of GO terms with shared gene annotations.  ...  Funding This work was supported by the European Commission, EU-FP7-Systems Microscopy Network of Excellence (grant agreement number 258068) and FP7-INFRASTRUCTURES-BioMedBridges (grant agreement number  ... 
doi:10.1186/s12859-017-1503-5 pmid:28183267 pmcid:PMC5304448 fatcat:oidegkar65fd5d4sddjdoxaqwm

Open source tools and standardized data in cancer systems biology [article]

Paul Macklin, Samuel H. Friedman
2018 bioRxiv   pre-print
We review the state-of-the-art in open source software and data standards in multicellular systems biology, and point out areas of needed growth to move beyond isolated models to community-driven frameworks  ...  To reach the full potential of multicellular systems biology, mathematical and computational modelers must pool their efforts to share and curate biophysical measurements, create and combine mathematical  ...  More recently, the Cell Behavior Ontology (CBO) [7] emerged to annotate key cellular processes (e.g., division). See [3] for more discussion.  ... 
doi:10.1101/244319 fatcat:633fy4f76bfxde3yy3gjjkkjcq

Siri of the Cell: What Biology Could Learn from the iPhone

Anne-Ruxandra Carvunis, Trey Ideker
2014 Cell  
Recent progress in computer science, embodied by intelligent agents such as Siri, inspires an approach for moving from networks to multiscale models able to predict a range of cellular phenotypes and answer  ...  Modern genomics is very efficient at mapping genes and gene networks, but how to transform these maps into predictive models of the cell remains unclear.  ...  This work was supported by the National Institutes of General Medical Sciences grants P41 GM103504 and P50 GM085764.  ... 
doi:10.1016/j.cell.2014.03.009 pmid:24766803 pmcid:PMC4154484 fatcat:hippczsqvzaxbhab6prdvryrom

Human fibroblasts display a differential focal adhesion phenotype relative to chimpanzee

Alexander S. Advani, Annie Y. Chen, Courtney C. Babbitt
2016 Evolution, Medicine and Public Health  
expression changes and the role they play in influencing phenotype.  ...  Additionally, we see that adhesion related gene ontology categories are some of the most differentially expressed between human and chimpanzee in normal fibroblast cells.  ...  It will be important to understand how these cellular phenotypes functionally link changes from gene expression to organismal phenotype, and how that might assist in our understanding of susceptibilities  ... 
doi:10.1093/emph/eow010 pmid:26971204 pmcid:PMC4804348 fatcat:fj2q6cld4rebjppiylj2lifvui

Modelling data across labs, genomes, space and time

Jason R. Swedlow, Suzanna E. Lewis, Ilya G. Goldberg
2006 Nature Cell Biology  
-the contextual descriptors that define the primary data.  ...  Here, we use imaging applications to illustrate the purpose of the various implementations of data specifications and the requirement for open, standardized, data formats to facilitate the sharing of critical  ...  ACKNOWLEDGEMENTS Work in the authors' laboratories is supported by grants from the Wellcome Trust, the Biotechnology and Biological Sciences Research Council (BBSRC) and Cancer Research UK (J.R.S.) and  ... 
doi:10.1038/ncb1496 pmid:17060903 fatcat:56mgnnajazgl5bqxuwoiadhyny

Building bridges between cellular and molecular structural biology

Ardan Patwardhan, Robert Brandt, Sarah J Butcher, Lucy Collinson, David Gault, Kay Grünewald, Corey Hecksel, Juha T Huiskonen, Andrii Iudin, Martin L Jones, Paul K Korir, Abraham J Koster (+15 others)
2017 eLife  
The integration of cellular and molecular structural data is key to understanding the function of macromolecular assemblies and complexes in their in vivo context.  ...  with defined objects), and the development of tools to support the annotation of biological structures.  ...  The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.  ... 
doi:10.7554/elife.25835 pmid:28682240 pmcid:PMC5524535 fatcat:aknpnuuiyfcx3h4xau6ffhiu6u

A pattern-based approach to a cell tracking ontology

Patryk Burek, Nico Scherf, Heinrich Herre
2019 Procedia Computer Science  
As a first step we integrate the Phenotype and Trait Ontology (PATO) as one of the most relevant ontologies to annotate cell tracking experiments.  ...  As a first step we integrate the Phenotype and Trait Ontology (PATO) as one of the most relevant ontologies to annotate cell tracking experiments.  ...  Cell Ontology [22] , and cell characteristics and behaviors, e.g. Phenotype and Trait Ontology (PATO) [23] or Cell Behavior Ontology [24] .  ... 
doi:10.1016/j.procs.2019.09.237 fatcat:ij54lx7sbveglivh422uhp24ni

Deep Collection of Quantitative Nuclear Division Dynamics Data in RNAi-treated Caenorhabditis elegans Embryos [article]

Koji Kyoda, Hatsumi Okada, Hiroya Itoga, Shuichi Onami
2020 bioRxiv   pre-print
Application of a two-sample t-test identified 8660 reproducible RNAi-induced phenotypes for 421 phenotypic characters.  ...  Recent advances in bioimage informatics techniques have yielded quantitative data on multicellular dynamics from microscopy images of animal development.  ...  However, we can use the microscopy images to check the phenotypes detected from the collection of quantitative data.  ... 
doi:10.1101/2020.10.04.325761 fatcat:5tnyrhf3sfhh7cjsamymuqzvmu
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