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Evolving BioAssay Ontology (BAO): modularization, integration and applications

Saminda Abeyruwan, Uma D Vempati, Hande Küçük-McGinty, Ubbo Visser, Amar Koleti, Ahsan Mir, Kunie Sakurai, Caty Chung, Joshua A Bittker, Paul A Clemons, Steve Brudz, Anosha Siripala (+6 others)
2014 Journal of Biomedical Semantics  
the integrity of the ontology and without creating redundancies.  ...  One of the critical questions in evolving BAO is the following: how can we provide a way to efficiently reuse and share among various research projects specific parts of our ontologies without violating  ...  Bixby and SCS ).  ... 
doi:10.1186/2041-1480-5-s1-s5 pmid:25093074 pmcid:PMC4108877 fatcat:pmnctn5bnjehxau63zbhci4bbi

Selected papers from the 16th Annual Bio-Ontologies Special Interest Group Meeting

Larisa N Soldatova, Philippe Rocca-Serra, Michel Dumontier, Nigam H Shah
2014 Journal of Biomedical Semantics  
The six papers selected for this supplement span a wide range of topics including: ontology-based data integration, ontology-based annotation of scientific literature, ontology and data model development  ...  Over the 16 years, the Bio-Ontologies SIG at ISMB has provided a forum for vibrant discussions of the latest and most innovative advances in the research area of bio-ontologies, its applications to biomedicine  ...  Acknowledgements As editors of this supplement, we thank all the authors who submitted papers, the Program Committee members and the reviewers for their excellent work.  ... 
doi:10.1186/2041-1480-5-s1-i1 pmcid:PMC4108850 fatcat:cyqs6udi2nbqfio3cj34qg7eq4

eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment

Janna Hastings, Nina Jeliazkova, Gareth Owen, Georgia Tsiliki, Cristian R Munteanu, Christoph Steinbeck, Egon Willighagen
2015 Journal of Biomedical Semantics  
We aim to make the re-use of external ontology content seamless and thus we have developed a library to automate the extraction of subsets of ontology content and the assembly of the subsets into an integrated  ...  Engineered nanomaterials (ENMs) are being developed to meet specific application needs in diverse domains across the engineering and biomedical sciences (e.g. drug delivery).  ...  , technological development and demonstration under grant agreement no 604134.  ... 
doi:10.1186/s13326-015-0005-5 pmid:25815161 pmcid:PMC4374589 fatcat:vnnndbjc3zemve5nss3veatyly

CLO: The cell line ontology

Sirarat Sarntivijai, Yu Lin, Zuoshuang Xiang, Terrence F Meehan, Alexander D Diehl, Uma D Vempati, Stephan C Schürer, Chao Pang, James Malone, Helen Parkinson, Yue Liu, Terue Takatsuki (+13 others)
2014 Journal of Biomedical Semantics  
Example case studies include annotation and analysis of EBI ArrayExpress data, bioassays, and host-vaccine/pathogen interaction. CLO's utility goes beyond a catalogue of cell line types.  ...  Ontology for Biomedical Investigation, and logical extensions.  ...  Acknowledgements The work described is funded in part by the National Institutes of Health (NIH) grants 1R01AI081062 (YH) from the National Institute of Allergy and  ... 
doi:10.1186/2041-1480-5-37 pmid:25852852 pmcid:PMC4387853 fatcat:ojqttwnoxjeedid4n7jzjsi3du

Drug target ontology to classify and integrate drug discovery data

Yu Lin, Saurabh Mehta, Hande Küçük-McGinty, John Paul Turner, Dusica Vidovic, Michele Forlin, Amar Koleti, Dac-Trung Nguyen, Lars Juhl Jensen, Rajarshi Guha, Stephen L. Mathias, Oleg Ursu (+10 others)
2017 Journal of Biomedical Semantics  
A modular, hierarchical implementation facilitate ontology development and maintenance and makes use of various external ontologies, thus integrating the DTO into the ecosystem of biomedical ontologies  ...  The long-term goal of DTO is to provide such an integrative framework and to populate the ontology with this information as a community resource.  ...  Availability of data and materials All materials related to this paper are stored and publicly available on GitHub, at:  ... 
doi:10.1186/s13326-017-0161-x pmid:29122012 pmcid:PMC5679337 fatcat:qpawvjwavbgkrlh5dn7as6g4ma

Genome sequencing and neurotoxin diversity of a wandering spider Pardosa pseudoannulata (pond wolf spider) [article]

Na Yu, Jingjing Li, Meng Liu, Lixin Huang, Haibo Bao, Zhiming Yang, Yixi Zhang, Haoli Gao, Zhaoying Wang, Yuanxue Yang, Thomas Van Leeuwen, Neil S. Millar (+1 others)
2019 bioRxiv   pre-print
We have generated a high-quality genome sequence of P. pseudoannulata and analysed genes associated with the production of silk and venom toxins.  ...  The presence of only 16 spidroin genes and four types of silk glands is consistent with the moderate use of silk and the lack of a prey-catching web.  ...  to integrated pest management 502 and other potential biomedical applications. 503Table S7-S9.  ... 
doi:10.1101/747147 fatcat:hjk7eqdlajfu3awfyt2a527bk4

A new wave of innovation in Semantic web tools for drug discovery

Samantha Kanza, Jeremy Graham Frey
2019 Expert Opinion on Drug Discovery  
Expert opinion: The increased availability of shared semantic resources (tools, data and importantly the communities) have enabled the application of semantic web technologies to facilitate semantic (context  ...  relevant compounds, or links between specific drugs and diseases).  ...  Acknowledgements The authors would like to thank Dr Colin Bird for his invaluable help with editing and reviewing the manuscript.  ... 
doi:10.1080/17460441.2019.1586880 pmid:30884989 fatcat:qsss5sv2jndo3dnlr7medsushy

Comparative analysis of functional assay evidence use by ClinGen Variant Curation Expert Panels [article]

Dona M. Kanavy, Shannon M. McNulty, Meera K. Jairath, Sarah E. Brnich, Chris Bizon, Bradford C. Powell, Jonathan S. Berg
2019 medRxiv   pre-print
However, our analysis suggests that further guidance is needed to standardize this process and ensure consistency in the application of functional evidence.  ...  The 2015 American College of Medical Genetics and Genomics (ACMG) and Association for Molecular Pathology (AMP) guidelines for clinical sequence variant interpretation state that well-established functional  ...  Evolving BioAssay Ontology (BAO): modularization, integration and applications. J Biomed Semantics. 2014;5(Suppl 1):S5. 15. Vempati UD, Przydzial MJ, Chung C, Abeyruwan S, Mir A, Sakurai K, et al.  ... 
doi:10.1101/19000661 fatcat:23whpowlabgl7p54aq7wvdi6je

Your Spreadsheets Can Be FAIR: A Tool and FAIRification Workflow for the eNanoMapper Database

Nikolay Kochev, Nina Jeliazkova, Vesselina Paskaleva, Gergana Tancheva, Luchesar Iliev, Peter Ritchie, Vedrin Jeliazkov
2020 Nanomaterials  
The NMDataParser is an open source Java library and application, making use of a JSON configuration to define the mapping.  ...  Safe by Design approaches are encouraged and promoted through regulatory initiatives and multiple scientific projects.  ...  The BioAssay Ontology (BAO) provides a foundation for standardizing assay descriptions and endpoints; high-throughput screening (HTS) data are represented using expressive description logic [13] with  ... 
doi:10.3390/nano10101908 pmid:32987901 fatcat:bboxevqba5ayhhjgdnx2ji3hji

Sustainable data and metadata management at the BD2K-LINCS Data Coordination and Integration Center

Vasileios Stathias, Amar Koleti, Dušica Vidović, Daniel J. Cooper, Kathleen M. Jagodnik, Raymond Terryn, Michele Forlin, Caty Chung, Denis Torre, Nagi Ayad, Mario Medvedovic, Avi Ma'ayan (+2 others)
2018 Scientific Data  
The large volume and variety of data necessitate rigorous data standards and effective data management including modular data processing pipelines and end-user interfaces to facilitate accurate and reliable  ...  data exchange, curation, validation, standardization, aggregation, integration, and end user access.  ...  Acknowledgements This work was supported by NIH grant U54HL127624 awarded by the National Heart, Lung, and Blood Institute through funds provided by the trans-NIH Library of Integrated Network-based Cellular  ... 
doi:10.1038/sdata.2018.117 pmid:29917015 pmcid:PMC6007090 fatcat:kssix6bcm5eppacpn7fngdwq5q

Eu Us Roadmap Nanoinformatics 2030 [article]

Haase, Klaessig
2018 Zenodo  
evolving field of "nanoinformatics".  ...  In particular it should be noted that some of the terms might be defined and used differently in the US versus the EU, also within different scientific disciplines and within different regulatory frameworks  ...  BioAssay Ontology (BAO) The BioAssay Ontology (BAO) aims to address the need for describing and annotating biological assays in a standardised way. Experimental data is organised in "measure groups".  ... 
doi:10.5281/zenodo.1486012 fatcat:yll2tsodjbgmlmyoyjfkcptxja

Mitochondrial Import [chapter]

2008 Encyclopedia of Genetics, Genomics, Proteomics and Informatics  
Molecular Genetics: The application of molecular biology to genetics. It is a somewhat unwarranted distinction because genetics as a basic science must always use all the best integrated approaches.  ...  One evolutionary advantage of the modular organization is that a mutation in a modular component may alter the function of that module without an upset in the whole system of the organism.  ...  Plasmids, S-1, and S-2 share 1.4-kb termini. These plasmids may integrate into the main mtDNA.  ... 
doi:10.1007/978-1-4020-6754-9_10535 fatcat:kablmiledvdx3lxxk4j3tsicca

MITE (mariner insect transposon-like element, miniature inverted-repeat transposable element) [chapter]

2008 Encyclopedia of Genetics, Genomics, Proteomics and Informatics  
Molecular Genetics: The application of molecular biology to genetics. It is a somewhat unwarranted distinction because genetics as a basic science must always use all the best integrated approaches.  ...  One evolutionary advantage of the modular organization is that a mutation in a modular component may alter the function of that module without an upset in the whole system of the organism.  ...  Plasmids, S-1, and S-2 share 1.4-kb termini. These plasmids may integrate into the main mtDNA.  ... 
doi:10.1007/978-1-4020-6754-9_10520 fatcat:tj67vdv34vc63hlfupk6xahu24

Integration and analysis of protein evolutionary relationships and small molecule bioactivity data

Felix Krüger, Apollo-University Of Cambridge Repository, Apollo-University Of Cambridge Repository
The mapping is now an integral part of the ChEMBL database and can be used to limit sequence-based queries to sequence partitions that are relevant to small molecule binding.  ...  The aim of my thesis was to integrate the ChEMBL database, a public repository of small molecule bioactivity measurements, with resources of protein evolutionary relationships, and exploit these new links  ...  One example in this context is the BioAssay ontology (BAO), which enables cross-analysis of diverse high-throughput screening data sets (Schürer et al., 2011) .  ... 
doi:10.17863/cam.15984 fatcat:yyvujkww35cvvg6s2cvy4uqdba

Comparative transcriptomics and network reconstruction with applications to auxin signaling [article]

Yvonne Pöschl, Universitäts- Und Landesbibliothek Sachsen-Anhalt, Martin-Luther Universität, Große, Ivo, Prof. Dr., Walther, Dirk, Dr.
This work aims at studying the molecular response of various ecotypes of the model plant Arabidopsis thaliana and the non-model plant Arabidopsis lyrata on treatment with Auxin, an essential plant hormone  ...  The PMP is designed in a modular fashion and can be applied to different use cases.  ...  We designed the PMP in a modular fashion that allows us to specifically address and solve all three mentioned problems.  ... 
doi:10.25673/1786 fatcat:dx37snqxivgprjt54rcxadhodi
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