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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 HPO's interoperability with other ontologies has enabled it to be used to improve diagnostic accuracy by incorporating model organism data.  ...  The Human Phenotype Ontology (HPO) provides the most comprehensive resource for computational deep phenotyping and has become the de facto standard for deep phenotyping in the field of rare disease--whether  ... 
doi:10.1093/nar/gky1105 pmid:30476213 pmcid:PMC6324074 fatcat:rsd6cv3i7jgjrgidg5ywtnxowa

An ontological foundation for ocular phenotypes and rare eye diseases

Panagiotis I. Sergouniotis, for the ERN-EYE Ontology Study Group, Emmanuel Maxime, Dorothée Leroux, Annie Olry, Rachel Thompson, Ana Rath, Peter N. Robinson, Hélène Dollfus
2019 Orphanet Journal of Rare Diseases  
Here, we discuss the development of the ophthalmology-related component of two well-established biomedical ontologies, the Human Phenotype Ontology (HPO; includes signs, symptoms and investigation findings  ...  They can be used to provide robust terminology standards and to enhance data interoperability.  ...  The ERN-EYE remains committed to further improving these resources and future plans include working on "layperson" terms for ocular phenotypes (so that patients can also use HPO) and on annotating each  ... 
doi:10.1186/s13023-018-0980-6 pmid:30626441 pmcid:PMC6327432 fatcat:sek4to3renftznolg2mkgat37y

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 (https://monarchinitiative.org) 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

Characterizing Long COVID: Deep Phenotype of a Complex Condition [article]

Rachel R Deer, Madeline A Rock, Nicole Vasilevsky, Leigh C Carmody, Halie M Rando, Alfred J Anzalone, Tiffany J Callahan, Carolyn T Bramante, Christopher G Chute, Casey S Greene, Joel J Gagnier, Haitao Chu (+40 others)
2021 medRxiv   pre-print
Phenotype Ontology (HPO) terms.  ...  the lack of a standard for denoting the many phenotypic manifestations of long COVID.  ...  In the field of rare disease, the Human Phenotype Ontology (HPO) has become an international standard for deep phenotyping that enables integrated computational analysis of genotype and phenotype for diagnostics  ... 
doi:10.1101/2021.06.23.21259416 fatcat:h7irfeu7uvgmfigektbjuoocby

The Sickle Cell Disease Ontology: enabling universal sickle cell-based knowledge representation

2019 Database: The Journal of Biological Databases and Curation  
The SCD Ontology (SCDO), which is a community-driven integrative and universal knowledge representation system for SCD, overcomes this issue by providing a controlled vocabulary developed by a group of  ...  Sickle cell disease (SCD) is one of the most common monogenic diseases in humans with multiple phenotypic expressions that can manifest as both acute and chronic complications.  ...  Acknowledgements The development of the SCDO is supported by the National Heart, Lung, and Blood Institute of the National Institutes of Health under  ... 
doi:10.1093/database/baz118 pmid:31769834 pmcid:PMC6878945 fatcat:ho4ie6nrxba27mbwhesu54khee

Race Differences in Intelligence: An Evolutionary Analysis. By Richard Lynn. Pp 322+xiii. (Washington Summit Publishers, Augusta, GA, USA, 2006.) $17.95, ISBN 978-1-59368-020-6, hardback; ISBN 978-1-59368-021-3, paperback

Maciej Henneberg
2006 Journal of Biosocial Science  
On the other hand, perhaps the book's title attracts mainly those who already long for a more open The Metaphysics of Apes: Negotiating the Animal-Human Boundary. By Raymond Corbey. Pp. 227.  ...  Metaphysics of apes here means that 'apes have always been assigned a certain metaphysical or ontological -these two terms are used synonymously -status in the grand scheme of things'.  ... 
doi:10.1017/s0021932006221539 fatcat:2dquvxgpovgcxbsdvw6v24sqny

Bias in ontologies – a preliminary assessment [article]

C. Maria Keet
2021 arXiv   pre-print
Logical theories in the form of ontologies and similar artefacts in computing and IT are used for structuring, annotating, and querying data, among others, and therewith influence data analytics regarding  ...  Algorithmic bias is a well-known notion, but what does bias mean in the context of ontologies that provide a structuring mechanism for an algorithm's input?  ...  With a benefit of the doubt, one might argue they may be layperson commonsense assumptions, but these would then be rather serious ones for an ontology for scientific literature.  ... 
arXiv:2101.08035v1 fatcat:qfrbjyoprbgg5gl26v3inscvoq

"Designer Babies" and "Playing God": Metaphor, Genome Editing, and Bioethics in Popular Science Texts

Elisa Mattiello
2019 Lingue Culture Mediazioni  
group would also have to wrestle with where to draw the line between ethically acceptable and unacceptable uses genetic enhancement as just the latest step in the struggle to improve human life  ...  As for the method, the articles making up the corpus were initially found by using the advanced search tool of both websites, and looking for the key words gene, genetic, genetics, and genome.  ... 
doi:10.7358/lcm-2019-001-matt fatcat:7kd47rv5yzgunlcf4zmspdroti

Implications: Human Cognition and Communication and the Emergence of the Cognitive Society [chapter]

James L. Olds, Philip Rubin, Donald MacGregor, Marc Madou, Anne McLaughlin, Aude Oliva, Brian Scassellati, H.-S. Philip Wong
2013 Science Policy Reports  
Use of molecular and personalized information to enhance treatment of disease and improve human cognition 2.  ...  , while at the same time offering up new potential for an enhanced human response to global challenges.  ... 
doi:10.1007/978-3-319-02204-8_6 fatcat:ffdach5nbbbl5ohds3u44qr3oe

Towards standardization guidelines for in silico approaches in personalized medicine

Søren Brunak, Catherine Bjerre Collin, Katharina Eva Ó Cathaoir, Martin Golebiewski, Marc Kirschner, Ingrid Kockum, Heike Moser, Dagmar Waltemath
2020 Journal of Integrative Bioinformatics  
Further hurdles are associated with legal and ethical issues surrounding the use of personal/patient data across disciplines and borders.  ...  Reasons for this obstacle are the inherent heterogeneity of data sources and the lack of broadly accepted standards.  ...  The primary labels use medical terminology used by clinicians and researchers. These are complemented with laypersons synonyms.  ... 
doi:10.1515/jib-2020-0006 pmid:32827396 pmcid:PMC7756614 fatcat:c4vye52o7rcu5bayint423gwki

Critical Essay: Organizational cognitive neuroscience drives theoretical progress, or: The curious case of the straw man murder

Michael JR Butler, Nick Lee, Carl Senior
2017 Human Relations  
We put forward a more positive case for OCN methodologies and data, as well as clarifying exactly what OCN really means, and its consequences for the development of strong management theory.  ...  We also find his distinction between demand and supply side forces helpful as an analytical framework identifying the momentum for the contemporary production of management theory.  ...  Further details of the various activities that are delivered by the International Neuroethics Society can be found here: http://www.neuroethicssociety.org/.  ... 
doi:10.1177/0018726716684381 fatcat:fu27lhnxdbbgdp3gtpa5lup5ea

An ontological foundation for ocular phenotypes and rare eye diseases

Panagiotis I Sergouniotis, Emmanuel Maxime, Dorothée Leroux, Annie Olry, Rachel Thompson, Ana Rath, Peter N Robinson, Hélène Dollfus, ERN-EYE Ontology Study Group, Apollo-University Of Cambridge Repository, Apollo-University Of Cambridge Repository
2019
Here, we discuss the development of the ophthalmology-related component of two well-established biomedical ontologies, the Human Phenotype Ontology (HPO; includes signs, symptoms and investigation findings  ...  They can be used to provide robust terminology standards and to enhance data interoperability.  ...  The ERN-EYE remains committed to further improving these resources and future plans include working on "layperson" terms for ocular phenotypes (so that patients can also use HPO) and on annotating each  ... 
doi:10.17863/cam.36727 fatcat:szyfsgnvvbgulhgvy3rgzq3oqi

The ontogenetic evolution of verbal behavior

Carsta Simon
2020 European Journal of Behavior Analysis  
Merging and enhancing Skinner's work on selection as a cause of behavior change on the one hand and his work on verbal behavior on the other provides a theoretical basis for placing verbal behavior in  ...  The article proposes a framework that helps us understand selection processes in conversations.  ...  useful feedback during the editorial process.  ... 
doi:10.1080/15021149.2019.1710034 fatcat:2dzvfe7my5bbjcmhnewfwrtkf4

When CRISPR Meets Art: The Experience of Relationality Through the Affective Agency of Matter

Lotte Pet
2018 Leonardo: Journal of the International Society for the Arts, Sciences and Technology  
While the visible veins in the flower petals are inherent to the plant's phenotype, by drawing attention to the relation between Kac's own blood -the expression of his used genetic sequence is part of  ...  sense of its ontology.  ...  For that matter, the notion of posthuman is a material agent reconfiguring the world.  ... 
doi:10.1162/leon_a_01665 fatcat:k7kjhmaowzcytigaqa4ypkciia

Justice from an Interdisciplinary Perspective: The Impact of the Revolution in Human Sciences on Peace Research and International Relations [chapter]

Harald Müller
2019 Justice and Peace  
We are confronted with an ontological revolution that forces us to reconstruct our image of the human (Crawford 2011) .  ...  They cannot be used as ontological templates to decipher the empirical world.  ...  If material is not included in the chapter's Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly  ... 
doi:10.1007/978-3-658-25196-3_2 fatcat:iyxr3ju5o5ao7m2bsgtobstpgi
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