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Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources

Sebastian Köhler, Leigh Carmody, Nicole Vasilevsky, Julius O B Jacobsen, Daniel Danis, Jean-Philippe Gourdine, Michael Gargano, Nomi L Harris, Nicolas Matentzoglu, Julie A McMurry, David Osumi-Sutherland, Valentina Cipriani (+57 others)
2018 Nucleic Acids Research  
The Human Phenotype Ontology (HPO)-a standardized vocabulary of phenotypic abnormalities associated with 7000+ diseases-is used by thousands of researchers, clinicians, informaticians and electronic health  ...  The newly redesigned HPO website ( simplifies browsing terms and exploring clinical features, diseases, and human genes.  ...  Members of the Monarch Initiative are contributing to community tools for pattern-based development using Dead Simple Ontology Design Patterns (DOSDP, (52) ) and the Ontology Development Kit (ODK).  ... 
doi:10.1093/nar/gky1105 pmid:30476213 pmcid:PMC6324074 fatcat:rsd6cv3i7jgjrgidg5ywtnxowa

The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species

2019 Nucleic Acids Research  
Our algorithms and tools are widely used to identify animal models of human disease through phenotypic similarity, for differential diagnostics and to facilitate translational research.  ...  The Monarch Initiative ( integrates information on genes, variants, genotypes, phenotypes and diseases in a variety of species, and allows powerful ontology-based search.  ...  ACKNOWLEDGEMENTS We would like to thank the many people who have contributed to the improvements and updates we have reported here, including (but not limited to) Donna Maglott, Anne Pariser and Janine  ... 
doi:10.1093/nar/gkz997 pmid:31701156 pmcid:PMC7056945 fatcat:tramusfgz5eufn2aguuzzasafi

The Human Phenotype Ontology in 2021

Sebastian Köhler, Michael Gargano, Nicolas Matentzoglu, Leigh C Carmody, David Lewis-Smith, Nicole A Vasilevsky, Daniel Danis, Ganna Balagura, Gareth Baynam, Amy M Brower, Tiffany J Callahan, Christopher G Chute (+39 others)
2020 Nucleic Acids Research  
The Human Phenotype Ontology (HPO, was launched in 2008 to provide a comprehensive logical standard to describe and computationally analyze phenotypic abnormalities found in human  ...  We present new efforts to harmonize computational definitions of phenotypic abnormalities across the HPO and multiple phenotype ontologies used for animal models of disease.  ...  Interoperability with other phenotype ontologies We have developed templated ontology design patterns to structure OWL definitions, encoded as Dead Simple OWL Design Patterns (DOSDPs) (44) .  ... 
doi:10.1093/nar/gkaa1043 pmid:33264411 pmcid:PMC7778952 fatcat:2lnshw3e7fcknncihgiqtfnc5y

Representing glycophenotypes: semantic unification of glycobiology resources for disease discovery

2019 Database: The Journal of Biological Databases and Curation  
Ontology (HPO), and model organism ontologies such as Mammalian Phenotype Ontology (MP) in the context of the Monarch Initiative.  ...  Diagnosis of rare diseases by computational cross-species comparison of genotype-phenotype data has been facilitated by leveraging ontological representations of clinical phenotypes, using Human Phenotype  ...  Acknowledgement We would like to thank our colleagues from the Monarch Initiative for comments and suggestions, KidsFirst (U2CHL138346) and Undiagnosed Disease Networks Metabolomics (U01-TR001395-02) for  ... 
doi:10.1093/database/baz114 pmid:31735951 pmcid:PMC6859258 fatcat:tg4c755iuzb35ct5be42k3xnp4

Using WormBase: A Genome Biology Resource for Caenorhabditis elegans and Related Nematodes [chapter]

Christian Grove, Scott Cain, Wen J. Chen, Paul Davis, Todd Harris, Kevin L. Howe, Ranjana Kishore, Raymond Lee, Michael Paulini, Daniela Raciti, Mary Ann Tuli, Kimberly Van Auken (+1 others)
2018 Msphere  
This chapter aims to provide an explanation of how to use basic features of WormBase, new features, and some commonly used tools and data queries.  ...  Explanations of the curated data and step-by-step instructions of how to access the data via the WormBase website and available data mining tools are provided.  ...  RESTful API The WormBase website implements a simple yet powerful Application Programming Interface (API) that follows the RESTful design pattern.  ... 
doi:10.1007/978-1-4939-7737-6_14 pmid:29761466 fatcat:pmvjwlblwrf6fkwid5fm272sfq

Alliance of Genome Resources Portal: unified model organism research platform

2019 Nucleic Acids Research  
The Alliance of Genome Resources (Alliance) is a consortium of the major model organism databases and the Gene Ontology that is guided by the vision of facilitating exploration of related genes in human  ...  Initiated in 2016, the Alliance is building a central portal ( for access to data for the primary model organisms along with gene ontology data and human data.  ...  ACKNOWLEDGEMENTS The Alliance platform is designed and implemented by a core group of developers and curators at SGD, Worm-Base, ZFIN, RGD, MGD, FlyBase and the GOC.  ... 
doi:10.1093/nar/gkz813 pmid:31552413 pmcid:PMC6943066 fatcat:kfgyjj7jybclndvfjbk5s53wci

Comparative analyses of histone H3K9 trimethylations in the heart and spleen of normal humans

W. Sui, C. Cao, W. Che, J. Chen, W. Xue, P. Liu, L. Guo, Y. Dai
2014 Genetics and Molecular Research  
Research supported by grants from the Key Project for Science and Technology of Guangxi (#2012GXNSFDA053017), the Construction Projects Planned Mission Statement of Guangxi Science and Technology Infrastructure  ...  (Key Laboratory, #11-031-33), and the Construction Projects Planned Mission Statement of Guangxi Key Laboratory (#12-071-32).  ...  A simple effective technique for the analysis of eukaryotes, MACS was designed to identify transcription factor binding sites and histone modification-enriched regions in ChIP-seq datasets, with or without  ... 
doi:10.4238/2014.january.14.5 pmid:24446338 fatcat:oujljaxkprervpzmwcwbfq4rv4

Inactivation of Zeb1 in GRHL2-deficient mouse embryos rescues mid-gestation viability and secondary palate closure

Marina R. Carpinelli, Michael E. de Vries, Alana Auden, Tariq Butt, Zihao Deng, Darren D. Partridge, Lee B. Miles, Smitha R. Georgy, Jody J. Haigh, Charbel Darido, Simone Brabletz, Thomas Brabletz (+3 others)
2020 Disease Models & Mechanisms  
The mammalian grainyhead-like (Grhl1-3) genes play key roles in a number of tissue fusion processes including neurulation, epidermal wound healing and eyelid fusion.  ...  Grhl2-null mice die at E11.5 with neural tube defects and a cleft face phenotype, precluding analysis of palatal fusion at a later stage of development.  ...  and the Monash Bioinformatics Platform.  ... 
doi:10.1242/dmm.042218 pmid:32005677 pmcid:PMC7104862 fatcat:bwzgoheh5bdghe32sqfxcmiuiu

BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services

Toshiaki Katayama, Shuichi Kawashima, Gos Micklem, Shin Kawano, Jin-Dong Kim, Simon Kocbek, Shinobu Okamoto, Yue Wang, Hongyan Wu, Atsuko Yamaguchi, Yasunori Yamamoto, Erick Antezana (+64 others)
2019 F1000Research  
The first section describes how we developed RDF data, ontologies and tools in genomics, proteomics, metabolomics, glycomics and by literature text mining.  ...  , and the service quality of SPARQL Protocol and RDF Query Language (SPARQL) endpoints.  ...  Acknowledgements BioHackathon 2013 and 2014 are supported by the Integrated Database Project (Ministry of Education, Culture, Sports, Science and Technology of Japan) and hosted by the National Bioscience  ... 
doi:10.12688/f1000research.18238.1 fatcat:mdt6bijqlveanplh4bmca5towu

Bloomsbury report on mouse embryo phenotyping: recommendations from the IMPC workshop on embryonic lethal screening

D. Adams, R. Baldock, S. Bhattacharya, A. J. Copp, M. Dickinson, N. D. E. Greene, M. Henkelman, M. Justice, T. Mohun, S. A. Murray, E. Pauws, M. Raess (+3 others)
2013 Disease Models & Mechanisms  
ACKNOWLEDGEMENTS We would like to acknowledge contributions from the following representatives of the International Mouse Phenotyping Consortium towards the proposals summarised in this paper: Jim Battey  ...  using internationally defined mouse anatomy and phenotype ontologies.  ...  All phenotypes will be captured using standard annotation and vocabularies [Mouse Phenotype Ontology (MP) terms; see below].  ... 
doi:10.1242/dmm.011833 pmid:23519032 pmcid:PMC3634642 fatcat:qg7fx5zeh5euthdbbpnwrefc3u

The complexity of the gene and the precision of CRISPR

Esha Shah, David Ludwig, Phil Macnaghten
2021 Elementa: Science of the Anthropocene  
By tracing the considerably destabilized scientific understanding of the gene in genomics and postgenomics, this article highlights that this publicly mediated ontology strategically avoids positioning  ...  of the scientific literature in promoting or opposing the commercial use of the gene-editing technology.  ...  Thaler and one anonymous reviewer, which greatly strengthened our article as well as the guidance and support from the editorial team at Elementa and in particular Alastair Iles and Maywa Montenegro de  ... 
doi:10.1525/elementa.2020.00072 fatcat:qqtitkbba5gq5h4gvkbmoljpnq

Contents list

2018 Soft Matter  
Genetic determinism of cranial morphology is complex and largely unknown in humans. Animal models such as mice may be useful in identifying genes influencing skull morphogenesis.  ...  This study demonstrates that genetic control of bone shape can be efficiently dissected in the mouse using appropriate tools.  ...  Use of structured vocabularies for anatomy, gene function (GO), phenotypes (Mammalian Phenotype Ontology), and diseases (OMIM); and adherence to nomenclature standards enables rich annotation.  ... 
doi:10.1039/c8sm90107d fatcat:tko5byj5izccvgfzmdsssx4mgm

The novel lncRNA lnc-NR2F1 is pro-neurogenic and mutated in human neurodevelopmental disorders

Cheen Euong Ang, Qing Ma, Orly L Wapinski, ShengHua Fan, Ryan A Flynn, Qian Yi Lee, Bradley Coe, Masahiro Onoguchi, Victor Hipolito Olmos, Brian T Do, Lynn Dukes-Rimsky, Jin Xu (+10 others)
2019 eLife  
Thus, integrating human genetics and functional testing in neuronal lineage induction is a promising approach for discovering candidate lncRNAs involved in neurodevelopmental diseases.  ...  We further show that lnc-NR2F1 is an evolutionarily conserved lncRNA functionally enhances induced neuronal cell maturation and directly occupies and regulates transcription of neuronal genes including  ...  UE is supported by the Austrian Academy of Sciences, the Austrian National Bank (OeNB), and is a Wittgenstein Prize fellow. JMP is supported by an Advanced ERC grant and an Era of Hope/DoD grant.  ... 
doi:10.7554/elife.41770 pmid:30628890 pmcid:PMC6380841 fatcat:jqifusgwendqvmxmu44h74biye

Homeostatic maintenance and age-related functional decline in the Drosophila ear [article]

Alyona Keder, Camille Tardieu, Liza Malong, Anastasia Filia, Assel Kashkenbayeva, Jonathan E Gale, Mike Lovett, Andrew P Jarman, Joerg T Albert
2019 biorxiv/medrxiv   pre-print
The widespread loss of hearing is one of the major threats to future wellbeing in ageing human societies.  ...  The transcription factors Onecut (closest human orthologues: ONECUT2, ONECUT3), Optix (SIX3, SIX6), Worniu (SNAI2) and Amos (ATOH1, ATOH7, NEUROD1) emerged as key regulators acting upstream of core sensory  ...  , within the list originally submitted to 649 iRegulon. 650 651 Gene ontology analysis -GORILLA 652 The online interface GOrilla (Gene Ontology enRIchment anaLysis and visuaLizAtion tool) 653 was used  ... 
doi:10.1101/764670 fatcat:fprrhpowpfdqrplews6o4ukaga

Diversification of retinoblastoma protein function associated with cis and trans adaptations [article]

Rima Mouawad, Jaideep Prasad, Dominic Thorley, Pamela Himadewi, Dhruva Kadiyala, Nathan Wilson, Philipp Kapranov, David N. Arnosti
2018 bioRxiv   pre-print
Structurally, Rbf1 resembles p107 and p130 most closely, and mutation of the gene is lethal, while Rbf2 is more divergent, and is not essential for development.  ...  separately in the Drosophila lineage an ancestral Rbf1 gene and a derived Rbf2 gene.  ...  Wei and members of the Arnosti lab for technical assistance and advice.  ... 
doi:10.1101/501866 fatcat:exxtg3c3v5afhcedufqpk56ti4
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