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Protein Ontology (PRO): enhancing and scaling up the representation of protein entities

Darren A. Natale, Cecilia N. Arighi, Judith A. Blake, Jonathan Bona, Chuming Chen, Sheng-Chih Chen, Karen R. Christie, Julie Cowart, Peter D'Eustachio, Alexander D. Diehl, Harold J. Drabkin, William D. Duncan (+10 others)
2016 Nucleic Acids Research  
The Protein Ontology (PRO; http://purl.obolibrary. org/obo/pr) formally defines and describes taxonspecific and taxon-neutral protein-related entities in three major areas: proteins related by evolution  ...  To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference  ...  ACKNOWLEDGEMENTS The authors thank the collaborating groups mentioned in this manuscript for their contribution to PRO and/or usage of PRO. Author contributions are as follows: Writing  ... 
doi:10.1093/nar/gkw1075 pmid:27899649 pmcid:PMC5210558 fatcat:xwzphiew4rcuzjmvb55fw4wf5i

The Protein Ontology: a structured representation of protein forms and complexes

D. A. Natale, C. N. Arighi, W. C. Barker, J. A. Blake, C. J. Bult, M. Caudy, H. J. Drabkin, P. D'Eustachio, A. V. Evsikov, H. Huang, J. Nchoutmboube, N. V. Roberts (+3 others)
2010 Nucleic Acids Research  
The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein  ...  The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms.  ...  ACKNOWLEDGEMENTS The authors thank PRO users, workshop attendees and other interested parties who have contributed terms, advice and stimulating discussions.  ... 
doi:10.1093/nar/gkq907 pmid:20935045 pmcid:PMC3013777 fatcat:ohpd42whsjblrdoipzc6tiyj4u

Dark kinase annotation, mining and visualization using the Protein Kinase Ontology [article]

Saber Soleymani, Nathan Gravel, Liang-Chin Huang, Wayland Yeung, Elika Bozorgi, Nathaniel G Bendzunas, Krzysztof J Kochut, Natarajan Kannan
2022 bioRxiv   pre-print
The Protein Kinase Ontology (ProKinO) is an integrated knowledge graph that conceptualizes the complex relationships connecting protein kinase sequence, structure, function, and disease in a human and  ...  The updated ontology browser and a web component, ProtVista, which allows interactive mining of kinase sequence annotations in 3D structures and Alphafold models, provide a valuable resource for the signaling  ...  ACKNOWLEDGEMENTS We thank members of the NK lab for feedback on the ProKinO browser and usage. FUNDING Funding from NIH (U01CA239106) is acknowledged  ... 
doi:10.1101/2022.02.25.482021 fatcat:d36wv3hcgvgsjfvxp6cweqor7a

Requirements and ontology for a G protein-coupled receptor oligomerization knowledge base

Lucy Skrabanek, Marta Murcia, Michel Bouvier, Lakshmi Devi, Susan R George, Martin J Lohse, Graeme Milligan, Richard Neubig, Krzysztof Palczewski, Marc Parmentier, Jean-Philippe Pin, Gerrit Vriend (+3 others)
2007 BMC Bioinformatics  
t Backg rou nd : G Protein-Coupled Receptors (GPCRs) are a large and diverse family of membrane proteins whose members participate in the regulation of most cellular and physiological processes and therefore  ...  The requirements and ontology described here will facilitate the development of future information systems for G PC R oligomers that contain both computational and experimental information about G P C  ...  Although there are other large-scale projects underway to define phenotype ontologies (i.e., the m am m alian phenotype ontology (MPO) [75] ), the phenotypic representation required by the GPCR oli gom  ... 
doi:10.1186/1471-2105-8-177 pmid:17537266 pmcid:PMC1904246 fatcat:nqs47qalkrgkxfxobvmakai4um

A chemogenomic screening identifies CK2 as a target for pro-senescence therapy in PTEN-deficient tumours

Madhuri Kalathur, Alberto Toso, Jingjing Chen, Ajinkya Revandkar, Claudia Danzer-Baltzer, Ilaria Guccini, Abdullah Alajati, Manuela Sarti, Sandra Pinton, Lara Brambilla, Diletta Di Mitri, Giuseppina Carbone (+14 others)
2015 Nature Communications  
Enhancement of cellular senescence in tumours triggers a stable cell growth arrest and activation of an antitumour immune response that can be exploited for cancer therapy.  ...  Currently, there are only a limited number of targeted therapies that act by increasing senescence in cancers, but the majority of them are not selective and also target healthy cells.  ...  DMSO DMSO Crystal violet staining OD Acknowledgements We thank members of the IRB animal core facility for technical assistance and the animal work.  ... 
doi:10.1038/ncomms8227 pmid:26085373 fatcat:opg2m7mjdjhm3mlhu3euysryea

Intestinal progenitor P-bodies maintain stem cell identity by suppressing pro-differentiation factors [article]

Kasun Buddika, Yi-Ting Huang, Alex Butrum-Griffith, Sam A Norrell, Alex M OConnor, Viraj K Patel, Samuel A Rector, Mark Slovan, Mallory Sokolowski, Yasuko Kato, Akira Nakamura, Nicholas S Sokol
2020 bioRxiv   pre-print
We further demonstrate that this process is independent of well-known transcriptional repressor escargot, indicating P-body-dependent post-transcriptional regulation of pro-differentiation genes.  ...  However, the role of these mechanisms in cell fate transitions in adult stem cell populations remain poorly understood.  ...  review) is the author/funder.  ... 
doi:10.1101/2020.06.27.175398 fatcat:vpdq4ledfvbi7ndanflpcccwpe

Platelets supply p38 MAPK signaling that licenses pro-inflammatory cytokine responses of human monocytes [article]

Ibrahim Hawwari, Nathalia Sofia Rosero Reyes, Lucas S. Ribeiro, Agnieszka Demczuk, Lino L Teichmann, Lisa Meffert, Damien Bertheloot, Bernardo S. Franklin
2022 bioRxiv   pre-print
Here, we reveal a critical dependency on platelets for the pro-inflammatory cytokine responses of human monocytes.  ...  Mechanistically, we show that the trans-cellular propagation of platelet p38 MAPK signaling through platelet vesicles licences the full cytokine responses of human monocytes.  ...  The probability of a random intersection between a set of IDs in the target list with ontology entities is estimated in p value of hypergeometric intersection.  ... 
doi:10.1101/2022.08.10.503291 fatcat:daxiczkrfratvleqx5mca6rpou

WormBase: a modern Model Organism Information Resource

2019 Nucleic Acids Research  
In particular, we discuss the status of literature curation and recently added data, detail new features of the web interface and options for users wishing to conduct data mining workflows, and discuss  ...  We conclude with a description of WormBase's role as a founding member of the nascent Alliance of Genome Resources.  ...  ACKNOWLEDGEMENTS The authors wish to thank funding agencies for their ongoing support of WormBase and members of the C. elegans research community whose results form the foundation and purpose of WormBase  ... 
doi:10.1093/nar/gkz920 pmid:31642470 pmcid:PMC7145598 fatcat:6gcdoykkt5fmjji2i67akl3sw4

Reactome Knowledgebase of Human Biological Pathways and Processes [chapter]

Peter D'Eustachio
2010 Msphere  
ACKNOWLEDGEMENTS We are grateful to many scientists who collaborated with us as authors and reviewers to build the content of the knowledgebase, and for the helpful comments of the reviewers of this manscript  ...  In collaboration with the Protein Ontology group-PRO (8), Reactome annotations of complexes and physiological states of proteins are being applied to build a hierarchy of proteins and their functional  ...  The Reactome and PRO collaboration, as a source for curated annotations of proteins, extends the application of Reactome to a larger ontology community.  ... 
doi:10.1007/978-1-60761-977-2_4 pmid:21082427 fatcat:mrdugzz6zzal5e6guxopyt6dwe

Reactome knowledgebase of human biological pathways and processes

L. Matthews, G. Gopinath, M. Gillespie, M. Caudy, D. Croft, B. de Bono, P. Garapati, J. Hemish, H. Hermjakob, B. Jassal, A. Kanapin, S. Lewis (+8 others)
2009 Nucleic Acids Research  
Reactome (http://www.reactome.org) is an expertauthored, peer-reviewed knowledgebase of human reactions and pathways that functions as a data mining resource and electronic textbook. Its current  ...  ACKNOWLEDGEMENTS We are grateful to many scientists who collaborated with us as authors and reviewers to build the content of the knowledgebase, and for the helpful comments of the reviewers of this manscript  ...  In collaboration with the Protein Ontology group-PRO (8), Reactome annotations of complexes and physiological states of proteins are being applied to build a hierarchy of proteins and their functional  ... 
doi:10.1093/nar/gkn863 pmid:18981052 pmcid:PMC2686536 fatcat:6oo2ou6qabaexb4zwngwpgp27y

Concept annotation in the CRAFT corpus

Michael Bada, Miriam Eckert, Donald Evans, Kristin Garcia, Krista Shipley, Dmitry Sitnikov, William A Baumgartner, K Cohen, Karin Verspoor, Judith A Blake, Lawrence E Hunter
2012 BMC Bioinformatics  
Taxonomy, the Protein Ontology, the Sequence Ontology, the entries of the Entrez Gene database, and the three subontologies of the Gene Ontology.  ...  CRAFT identifies all mentions of nearly all concepts from nine prominent biomedical ontologies and terminologies: the Cell Type Ontology, the Chemical Entities of Biological Interest ontology, the NCBI  ...  Acknowledgements The authors gratefully acknowledge their support from NIH, 5R01 LM008111, 2R01 LM009254, 5 T15 LM009451, and 3 T15 LM009451.  ... 
doi:10.1186/1471-2105-13-161 pmid:22776079 pmcid:PMC3476437 fatcat:kuulhujx4ratnkoywafxggkhmi

Evaluating a variety of text-mined features for automatic protein function prediction with GOstruct

Christopher S Funk, Indika Kahanda, Asa Ben-Hur, Karin M Verspoor
2015 Journal of Biomedical Semantics  
In this work we evaluate both ontology term co-mention and bag-of-words features mined from the biomedical literature and analyze their impact in the context of a structured output support vector machine  ...  Additionally, we present a "medium-throughput" pipeline that was used to annotate a large subset of co-mentions; we suggest that this strategy could help to speed up the rate at which proteins are curated  ...  KV was partially supported by NICTA, which is funded by the Australian Government as represented by the Department of Broadband, Communications and the Digital Economy and the Australian Research Council  ... 
doi:10.1186/s13326-015-0006-4 pmid:26005564 pmcid:PMC4441003 fatcat:pz7pgludtjgm3ndkcl56ir26am

Building an effective Semantic Web for health care and the life sciences

Michel Dumontier
2010 Semantic Web Journal  
Second, significant challenges remain in the development and adoption of a well founded, intuitive and coherent knowledge representation for general use.  ...  Health Care and the Life Sciences (HCLS) are at the leading edge of applying advanced information technologies for the purpose of knowledge management and knowledge discovery.  ...  Current stand-alone solutions appear to scale up into hundreds of millions of triples, wh ile cluster-based solutions (Virtuoso Cluster Edition; BigOW LIM; BigData) appear to scale into the tens or hundreds  ... 
doi:10.3233/sw-2010-0018 fatcat:m3pcjcvq3nerljd54bhjasg6my

Deep Learning meets Semantic Web: A feasibility study with the Cardiovascular Disease Ontology and PubMed citations

Mercedes Argüello Casteleiro, George Demetriou, Warren J. Read, Maria Jesus Fernandez Prieto, Diego Maseda-Fernandez, Goran Nenadic, Julie Klein, John A. Keane, Robert Stevens
2016 Workshop on Ontologies and Data in Life Sciences  
Automatic identification of gene and protein names from biomedical publications can help curators and researchers to keep up with the findings published in the scientific literature.  ...  /expanded the annotated terms using terms from the human-readable labels of key classes (gene/proteins) from the CVDO ontology.  ...  ACKNOWLEDGEMENTS To Prof Iain Buchan and Stephen Walker for useful discussions; and to Timothy Furmston for helping with the software and einfrastructure.  ... 
dblp:conf/odls/CasteleiroDRPMN16 fatcat:gxdpzlhwfjeu7kwzkk5y6v3bve

MecCog: A knowledge representation framework for genetic disease mechanism [article]

Kunal Kundu, Lindley Darden, John Moult
2020 bioRxiv   pre-print
evidence tagging, a mechanism ontology, and depiction of knowledge gaps, ambiguities, and uncertainties.  ...  Integration and structuring of such mechanistic information will greatly enhance its utility.  ...  We thank Lipika Ray, Yizhou Yin, Maya Zuhl, Christian Presley, and undergraduate students in the University of Maryland Human Genetic course for many useful suggestions and comments on  ... 
doi:10.1101/2020.09.03.282012 fatcat:7sbeyumlivetthixvvyguedy7i
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