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Time to change how we describe biodiversity

Andrew R. Deans, Matthew J. Yoder, James P. Balhoff
2012 Trends in Ecology & Evolution  
Encyclopedia of Life, and in rigorous conversation with participants of the Phenotype RCN (http://www.phenotypercn.org).  ...  Acknowledgments The ideas presented herein were developed during meetings funded by the US National Science Foundation (NSF; grants DBI-0850223, DEB-0956049) and the Biodiversity Synthesis Center of the  ...  I Infrastructure for semantic phenotype production.  ... 
doi:10.1016/j.tree.2011.11.007 pmid:22189359 fatcat:baoxrnvs2jfpplax6ix6br4hge

Species descriptions and digital environments: alternatives for accessibility of morphological data

Thiago Sanches Ranzani da Silva
2017 Revista Brasileira de Entomologia  
Considering this last aspect, web-based tools can be valuable to simplify the dissemination of the taxonomic product.  ...  products found in taxonomic works are commonly restricted to a small group of researchers, due to its low accessibility and specific language.  ...  Acknowledgements I am very grateful to Rodrigo Feitosa and John Lattke for reviewing preliminary versions of this manuscript, being also indebted to two anonymous reviewers, which gave valuable comments  ... 
doi:10.1016/j.rbe.2017.06.005 fatcat:fqdv33jggzgahl2w3yslrl4c2u

Common Agriculture Vocabulary for Enhancing Semantic-level Interoperability in Japan

Akane TAKEZAKI, Sungmin JOO, Hideaki TAKEDA, Tomokazu YOSHIDA
2020 JARQ - Japan Agricultural Research Quarterly  
We introduce the features of Common Agriculture Vocabulary (CAVOC) and CAVOC-based services, review other resources for standards in the domains of agriculture and food, and briefly discuss the future  ...  The extension of CAVOC coverage is important to unambiguously define objects and their relationships in the domains of agriculture and food.  ...  Acknowledgment This study was supported by the cross-ministerial Strategic Innovation Promotion Program of the Cabinet Office, Government of Japan, on "Technologies for creating next-generation agriculture  ... 
doi:10.6090/jarq.54.219 fatcat:2l5t4udomjdz3bsmxay62ov2ce

Incorporating ontology-driven similarity knowledge into functional genomics: an exploratory study

F. Azuaje, O. Bodenreider
2004 Proceedings. Fourth IEEE Symposium on Bioinformatics and Bioengineering  
Analyses of protein complex data show that, in general, there is a significant correlation between the semantic similarity exhibited by a pair of genes and the probability of finding them in the same complex  ...  These results can also be interpreted as an assessment of the quality and consistency of the information represented in the GO.  ...  Acknowledgements This research was partly supported by a visiting fellowship from the U.S-NLM. We thank Joaquin Dopazo (CNIO) and Mark Gerstein (Yale) for useful comments.  ... 
doi:10.1109/bibe.2004.1317360 pmid:25635264 pmcid:PMC4307019 dblp:conf/bibe/AzuajeB04 fatcat:cnpq56cp5rhajcqa26fa6hbpm4

AGINFRA PLUS D2.2 - Ontological Engineering Technologies

Panagis Katsivelis, Michail Papakonstantinou
2020 Zenodo  
Registry of Semantic Resources.  ...  In the last part of the document, a number of prominent ontologies and vocabularies are documented, made available for reference and curation to the project use-case partners, constituting the AGINFRA  ...  Agroknow's Hazard Taxonomy Semantic resource title Agroknow's Product Taxonomy (FDK_Hazards) Semantic resource description Another characteristic of food safety resources is the hazard that they indicate  ... 
doi:10.5281/zenodo.3634665 fatcat:yr2vm5eh25hs3p6ubkswux5lse

GOChase-II: correcting semantic inconsistencies from Gene Ontology-based annotations for gene products

Yu Rang Park, Jihun Kim, Hye Won Lee, Young Jo Yoon, Ju Han Kim
2011 BMC Bioinformatics  
Methods: To determine the semantic inconsistencies in GO annotation, we used the hierarchical structure of GO graph and tree structure of NCBI taxonomy.  ...  The numbers of gene products and species in a database that are related to the complexity of database management are also in correlation with the inconsistencies.  ...  Background The Gene Ontology (GO) project started to provide semantic standards for the annotation of molecular attributes of genes and gene products [1] .  ... 
doi:10.1186/1471-2105-12-s1-s40 pmid:21342572 pmcid:PMC3044297 fatcat:zqzlui5l6rd5nkksw3sq5nzhke

AGINFRA PLUS D2.2 - Ontological Engineering Technologies

Panagis Katsivelis, Nikos Manouselis
2019 Zenodo  
The present report is the first submitted iteration of a living document that will describe progress and evolvement of the AGINFRA PLUS ontology engineering components, i.e. the services that will be incorporated  ...  in the overall AGINFRA PLUS architecture and serve the conceptualization design, requirements of the involved research communities.  ...  Agroknow's Hazard Taxonomy Semantic resource title Agroknow's Product Taxonomy (FDK_Hazards) Semantic resource description Another characteristic of food safety resources is the hazard that they indicate  ... 
doi:10.5281/zenodo.3559768 fatcat:pichbd6nhzejxgalms2gcu75im

Scientific Discovery by Machine Intelligence: A New Avenue for Drug Research [article]

Carlo A. Trugenberger
2015 arXiv   pre-print
I will describe the methodology and a first successful experiment for the discovery of new biomarkers and phenotypes for diabetes and obesity on the basis of PubMed abstracts, public clinical trials and  ...  The majority of big data is unstructured and of this majority the largest chunk is text.  ...  semantic space, the reciprocal Kullback-Leibler distance [25] from the main topics, and the weighted score-sum of common synonyms, common hypernyms and common nodes on higher taxonomy levels.  ... 
arXiv:1506.07116v1 fatcat:ciuab5j5xbhknpdplkkg7cji7e

Tripartite Flavour Model: Food Phenotype, Sensory and Interpretative Matrices

Tarini Naravane, Matthew Lange
2018 International Semantic Web Conference  
Together these three matrices represent an initial ontological model for the flavor and sensory experience portion of the emerging semantic web of food.  ...  Flavor, and the pleasure it engenders, is the primary driver of food choice.  ...  Conclusion The semantic web of food critically depends on digital models of flavour for enabling predictive outcomes from food production, transformation, and ingredient combination processes relative  ... 
dblp:conf/semweb/NaravaneL18 fatcat:53lbk5rwfbelvojpvpxhhwy5hy

Text mining tools for extracting information about microbial biodiversity in food

Estelle Chaix, Louise Deléger, Robert Bossy, Claire Nédellec
2018 Food microbiology  
We would like to express our gratitude to Philippe Bessi eres, who is deceased, and who contributed to the preliminary studies of this work.  ...  We would like to thank biologists from the French National Institute for Agricultural Research (Inra) Floril ege working group and Food Microbiome project, for their participation in the enrichment of  ...  Taxonomy We use the taxonomy of the NCBI 2 to detect mentions of microorganisms in the documents and assign them a reference taxon.  ... 
doi:10.1016/j.fm.2018.04.011 fatcat:n3poizfyhbbeddt3alpthkydqm

Omnicrobe, an open-access database of microbial habitats and phenotypes using a comprehensive text mining and data fusion approach [article]

Sandra Dérozier, Robert Bossy, Louise Deléger, Mouhamadou Ba, Estelle Chaix, Olivier Harlé, Valentin Loux, Hélène Falentin, Claire Nédellec
2022 bioRxiv   pre-print
ontology-based representation and normalization of the textual descriptions by semantic analysis.  ...  It provides an easy-to-use support in the resolution of scientific questions related to the habitats, phenotypes and uses of microbes through simple and complex ontology-based queries.  ...  Acknowledgements The authors thank the Migale platform for providing the resources to run Omnicrobe  ... 
doi:10.1101/2022.07.21.500958 fatcat:sak4uhbqmzefhaepzv74swq3ii

PathoPhenoDB, linking human pathogens to their phenotypes in support of infectious disease research

Şenay Kafkas, Marwa Abdelhakim, Yasmeen Hashish, Maxat Kulmanov, Marwa Abdellatif, Paul N. Schofield, Robert Hoehndorf
2019 Scientific Data  
Provision of a comprehensive and integrated disease phenotype knowledgebase has the potential to provide novel and orthogonal sources of information for the understanding of infectious agent pathogenesis  ...  Using Semantic Web technologies, PathoPhenoDB also links to knowledge about drug resistance mechanisms and drugs used in the treatment of infectious diseases.  ...  and its NCBI Taxonomy identifier.  ... 
doi:10.1038/s41597-019-0090-x pmid:31160594 pmcid:PMC6546783 fatcat:bdbrndyb7jeifittr247642eme

Phenotypes in insect biodiversity research [article]

Andrew R Deans, Istvan Miko
2015 bioRxiv   pre-print
In this chapter we describe the philosophy behind these new tools, the mechanisms by which they operate, and the real and future benefits of the semantic representation of phenotype data (e.g., standardization  ...  We provide examples using real data and describe some limitations of semantic phenotype annotations.  ...  Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. James P.  ... 
doi:10.1101/032425 fatcat:4at5vgjms5czjf44x4tta53qke

Transforming the study of organisms: Phenomic data models and knowledge bases

Anne E. Thessen, Ramona L. Walls, Lars Vogt, Jessica Singer, Robert Warren, Pier Luigi Buttigieg, James P. Balhoff, Christopher J. Mungall, Deborah L. McGuinness, Brian J. Stucky, Matthew J. Yoder, Melissa A. Haendel (+1 others)
2020 PLoS Computational Biology  
We discuss barriers to integration of phenotypic data and make recommendations for developing an operationally useful, semantically interoperable phenotypic data ecosystem.  ...  One powerful solution is to represent phenotypic data using data models with precise, computable semantics, but adoption of semantic standards for representing phenotypic data has been slow, especially  ...  Acknowledgments The authors would like to acknowledge the organizers and sponsors of the 2019 US2TS Conference held at Duke University who created space for this discussion.  ... 
doi:10.1371/journal.pcbi.1008376 pmid:33232313 pmcid:PMC7685442 fatcat:d36yhdezgnbblbj4sy62jiqw3m

DNA Data Bank of Japan

Jun Mashima, Yuichi Kodama, Takatomo Fujisawa, Toshiaki Katayama, Yoshihiro Okuda, Eli Kaminuma, Osamu Ogasawara, Kousaku Okubo, Yasukazu Nakamura, Toshihisa Takagi
2016 Nucleic Acids Research  
The DNA Data Bank of Japan (DDBJ) (http://www. ddbj.nig.ac.jp) has been providing public data services for thirty years (since 1987).  ...  We are collecting nucleotide sequence data from researchers as a member of the International Nucleotide Sequence Database Collaboration (INSDC, http://www.insdc. org), in collaboration with the  ...  ACKNOWLEDGEMENTS We gratefully acknowledge the support of Koji Watanabe, Chiharu Kawagoe, and all members of DDBJ Center for  ... 
doi:10.1093/nar/gkw1001 pmid:27924010 pmcid:PMC5210514 fatcat:sbslos5mnbgnpfurvzabh2svki
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