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Modeling biomedical experimental processes with OBI

Ryan R Brinkman, Mélanie Courtot, Dirk Derom, Jennifer M Fostel, Yongqun He, Phillip Lord, James Malone, Helen Parkinson, Bjoern Peters, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone (+4 others)
<span title="">2010</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/iasjcyzzyncgnohh3aitx65bhq" style="color: black;">Journal of Biomedical Semantics</a> </i> &nbsp;
Conclusion: We demonstrate how OBI can be applied to different biomedical investigations to both facilitate interpretation of the experimental process and increase the computational processing and integration  ...  Here we detail three real-world applications of OBI, provide detailed modeling information and explain how to use OBI.  ...  All authors contributed to the development of OBI. Competing interests The authors declare that they have no competing interests.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/2041-1480-1-s1-s7">doi:10.1186/2041-1480-1-s1-s7</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20626927">pmid:20626927</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2903726/">pmcid:PMC2903726</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/eoqof2hy4fcg3llyjuihqqhh2y">fatcat:eoqof2hy4fcg3llyjuihqqhh2y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170930234857/https://core.ac.uk/download/pdf/30713572.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/89/ff/89ffa0bb0f5520d672a479b466c5516cde1e9add.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/2041-1480-1-s1-s7"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2903726" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Selected papers from the 12th annual Bio-Ontologies meeting

Larisa N Soldatova, Phillip Lord, Susanna-Assunta Sansone, Susie M Stephens, Nigam H Shah
<span title="">2010</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/iasjcyzzyncgnohh3aitx65bhq" style="color: black;">Journal of Biomedical Semantics</a> </i> &nbsp;
The paper "Modeling biomedical experimental processes with OBI" presented by the OBI Consortiumwhich combines 19 biomedical communities from around the globereports the progress on the development of the  ...  The paper describes the key elements of OBI and explains how to use logically defined OBI descriptors to model experimental process.  ...  This article has been published as part of Journal of Biomedical Semantics Volume 1 Supplement 1, 2010: Proceedings of the Bio-Ontologies Special Interest Group Meeting 2009: Knowledge in Biology.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/2041-1480-1-s1-i1">doi:10.1186/2041-1480-1-s1-i1</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20626920">pmid:20626920</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2903719/">pmcid:PMC2903719</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rh62wecfifdnxgdrb2kx2v77xe">fatcat:rh62wecfifdnxgdrb2kx2v77xe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170811201715/http://cadair.aber.ac.uk/dspace/bitstream/handle/2160/14277/selected_papers_from_the_12th_annual_bio_ontologies_meeting.pdf?sequence=1" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ed/01/ed01b65cff4e3bec8f8ecb75070fc355f3a6d9fc.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/2041-1480-1-s1-i1"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2903719" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The representation of biomedical protocols

Larisa N. Soldatova, Ross D. King, Piyali S. Basu, Emma Haddi, Nigel Saunders
<span title="2013-10-14">2013</span> <i title="EMBnet Stichting"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/safaaq4uondrvmmn5dstg3qpp4" style="color: black;">EMBnet journal</a> </i> &nbsp;
The model we propose is based on the ontology of EXperimental ACTions (EXACT).  ...  The EXACT model has been harmonised with the OBI representations. Currently the EXACT model is being verified by experts, and we are checking how well it covers the domain (see the methods section).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.14806/ej.19.b.730">doi:10.14806/ej.19.b.730</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/niehbfm2xrdr5cogxjlvzds4qi">fatcat:niehbfm2xrdr5cogxjlvzds4qi</a> </span>
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EXACT2: the semantics of biomedical protocols

Larisa N Soldatova, Daniel Nadis, Ross D King, Piyali S Basu, Emma Haddi, Véronique Baumlé, Nigel J Saunders, Wolfgang Marwan, Brian B Rudkin
<span title="">2014</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
In this EXACT2 is used as a reference model for text mining tools to identify terms pertinent to experimental actions, and their properties, in biomedical protocols expressed in natural language.  ...  It can serve as a reference model for for the translation of biomedical protocols in natural language into a semantically-defined format.  ...  This article has been published as part of BMC Bioinformatics Volume 15 Supplement 14, 2014: Semantic, social, mobile applications for bioinformatics and biomedical laboratories: selected works from the  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-15-s14-s5">doi:10.1186/1471-2105-15-s14-s5</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25472549">pmid:25472549</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4255744/">pmcid:PMC4255744</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ao5hwxozczferfmkfqzfbd3n5e">fatcat:ao5hwxozczferfmkfqzfbd3n5e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170810152832/http://dspace.brunel.ac.uk/bitstream/2438/9597/1/Fulltext.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/12/c1/12c1a59009a23feed0dfc0951ac35cae72633f56.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-15-s14-s5"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4255744" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The Ontology of Biological and Clinical Statistics (OBCS)-based statistical method standardization and meta-analysis of host responses to yellow fever vaccines

Jie Zheng, Huan Li, Qingzhi Liu, Yongqun He
<span title="2017-11-12">2017</span> <i title="Springer-Verlag"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rs7kqbk47nd3nbcl32zad56uv4" style="color: black;">Quantitative Biology</a> </i> &nbsp;
Our ontology-based meta-analysis showed that different experimental results might be due to different experimental assays and conditions, sample variations, and data analysis methods.  ...  The study represents the first single use case of applying OBCS ontology to standardize, integrate, and use biomedical data and statistical methods.  ...  Acknowledgments The development of VO and OBCS and the vaccine modeling research was supported by a grant from the USA National Institute of Allergy and Infectious Diseases (NIAID) (R01AI081062).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30034908">pmid:30034908</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6054478/">pmcid:PMC6054478</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/35ydwdx2xbdgdkb52osnx6acxu">fatcat:35ydwdx2xbdgdkb52osnx6acxu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200207172129/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC6054478&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ae/f2/aef2a6b9f0729fb2bd3d768488641bb4b0a119fb.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6054478" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Minimum Information about a Genotyping Experiment (MIGEN)

Jie Huang, Daniel Mirel, Elizabeth Pugh, Chao Xing, Peter N. Robinson, Alexander Pertsemlidis, LiangHao Ding, Julia Kozlitina, Joseph Maher, Jonathan Rios, Michael Story, Nishanth Marthandan (+1 others)
<span title="2011-11-22">2011</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/5xcscx7glffihaolts5vo2ioaa" style="color: black;">Standards in Genomic Sciences</a> </i> &nbsp;
(OBI) for the description of the various types of planned processes and implements a hierarchical document structure.  ...  MIGen standard covers experimental design, subject description, genotyping procedure, quality control and data analysis.  ...  Planned Processes With the application of OBI concepts in MIGen, genotyping procedure and data analysis components of a genotyping experiment are considered as a sequence of planned processes, each of  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4056/sigs.1994602">doi:10.4056/sigs.1994602</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22180825">pmid:22180825</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3235517/">pmcid:PMC3235517</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/eimzzyng6zgy5haev3ybvtkvtu">fatcat:eimzzyng6zgy5haev3ybvtkvtu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171114110909/http://publisher-connector.core.ac.uk/resourcesync/data/Springer-OA/pdf/ca4/aHR0cDovL2xpbmsuc3ByaW5nZXIuY29tLzEwLjQwNTYvc2lncy4xOTk0NjAyLnBkZg%3D%3D.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/83/14/831402119bc52f7b041eedb333018168d0d4a61f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4056/sigs.1994602"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3235517" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The Ontology for Biomedical Investigations

Anita Bandrowski, Ryan Brinkman, Mathias Brochhausen, Matthew H. Brush, Bill Bug, Marcus C. Chibucos, Kevin Clancy, Mélanie Courtot, Dirk Derom, Michel Dumontier, Liju Fan, Jennifer Fostel (+33 others)
<span title="2016-04-29">2016</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3gm7274mfe6fcs7e3jterqlri" style="color: black;">PLoS ONE</a> </i> &nbsp;
The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are  ...  OBI covers all phases of the investigation process, such as planning, execution and reporting.  ...  The key planned processes used to model this case are genetic transformation and assay (both drawn from OBI).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0154556">doi:10.1371/journal.pone.0154556</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27128319">pmid:27128319</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4851331/">pmcid:PMC4851331</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/cxeglm5tynfszjthzt7ebbsjhe">fatcat:cxeglm5tynfszjthzt7ebbsjhe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171011193639/http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0154556&amp;type=printable" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/1b/8b/1b8b5ee6074a04b68fdabb5412249ac7d56286ef.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0154556"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4851331" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The Ontology of Biological and Clinical Statistics (OBCS)-based statistical method standardization and meta-analysis of host responses to yellow fever vaccines

Jie Zheng, Huan Li, Qingzhi Liu, Yongqun He
<span title="2017-11-23">2017</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rs7kqbk47nd3nbcl32zad56uv4" style="color: black;">Quantitative Biology</a> </i> &nbsp;
Our ontology-based meta-analysis showed that different experimental results might be due to different experimental assays and conditions, sample variations, and data analysis methods.  ...  Conclusions: The study represents the first single use case of applying OBCS ontology to standardize, integrate, and use biomedical data and statistical methods.  ...  ACKNOWLEDGEMENTS The development of VO and OBCS and the vaccine modeling research was supported by a grant from the USA National Institute of Allergy and Infectious Diseases (NIAID) (R01AI081062).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s40484-017-0122-5">doi:10.1007/s40484-017-0122-5</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ax6kb4mdarfl5kaisvehcvkgiu">fatcat:ax6kb4mdarfl5kaisvehcvkgiu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180727134459/https://link.springer.com/content/pdf/10.1007%2Fs40484-017-0122-5.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/0c/06/0c06fae98b1b96b082b6a4e0ac972957f6100f3f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s40484-017-0122-5"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Towards an Ontology of Biomodelling [chapter]

Larisa Soldatova, Qian Gao, David Gilbert
<span title="">2012</span> <i title="Springer Berlin Heidelberg"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2w3awgokqne6te4nvlofavy5a4" style="color: black;">Lecture Notes in Computer Science</a> </i> &nbsp;
GO, SBML, ChEBI, and the recording of biomodelling knowledge with Ontology of Biomedical investigations (OBI) ensures efficient sharing and re-use of information, reproducibility of developed biomodels  ...  models.  ...  OBM employs standard upper level classes and relations where possible to ensure full interoperability with key biomedical ontologies and other resources, i.e. ChEBI, GO, OBI.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-642-33636-2_28">doi:10.1007/978-3-642-33636-2_28</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/nc6yt2jqzrahnp5ugw7uz5qedq">fatcat:nc6yt2jqzrahnp5ugw7uz5qedq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20121114205915/http://people.brunel.ac.uk/~csstdrg/publications/conferences/cmsb2012OBM.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c7/83/c7836d33722dc7ca23a91954414e0cd6fa854d55.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-642-33636-2_28"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Query enhancement through the practical application of ontology: the IEDB and OBI

Randi Vita, James A Overton, Jason A Greenbaum, Alessandro Sette, Bjoern Peters
<span title="">2013</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/iasjcyzzyncgnohh3aitx65bhq" style="color: black;">Journal of Biomedical Semantics</a> </i> &nbsp;
The Immune Epitope Database (IEDB, www.iedb.org) utilizes the Ontology for Biomedical Investigations (OBI) and several additional ontologies to represent immune epitope mapping experiments.  ...  We applied a simple approach to incorporate the benefits of the information captured in a formal ontology directly into the user web interface, resulting in an improved user experience with minimal changes  ...  OBI represents the experimental design, protocols, materials, and instruments used in biomedical investigations, the data generated and the type of analyses performed.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/2041-1480-4-s1-s6">doi:10.1186/2041-1480-4-s1-s6</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23734660">pmid:23734660</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3633001/">pmcid:PMC3633001</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zey6o3na6fbhjnfegxanr6yuwq">fatcat:zey6o3na6fbhjnfegxanr6yuwq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170706103233/http://jbiomedsem.biomedcentral.com/track/pdf/10.1186/2041-1480-4-S1-S6?site=jbiomedsem.biomedcentral.com" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/8b/2a/8b2ad8dbb5e66445b47cde2831aed0e237d8224b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/2041-1480-4-s1-s6"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3633001" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis

Jie Zheng, Marcelline R. Harris, Anna Maria Masci, Yu Lin, Alfred Hero, Barry Smith, Yongqun He
<span title="2016-09-14">2016</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/iasjcyzzyncgnohh3aitx65bhq" style="color: black;">Journal of Biomedical Semantics</a> </i> &nbsp;
OBCS is aligned with the Basic Formal Ontology (BFO) and extends the Ontology of Biomedical Investigations (OBI), an OBO (Open Biological and Biomedical Ontologies) Foundry ontology supported by over 20  ...  Currently, OBCS comprehends 878 terms, representing 20 BFO classes, 403 OBI classes, 229 OBCS specific classes, and 122 classes imported from ten other OBO ontologies.  ...  ., and the OBI Consortium for their valuable discussions and feedback.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13326-016-0100-2">doi:10.1186/s13326-016-0100-2</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27627881">pmid:27627881</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5024438/">pmcid:PMC5024438</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6tbrilbh4nd27o57n7rpqxt3oe">fatcat:6tbrilbh4nd27o57n7rpqxt3oe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170921234709/https://jbiomedsem.biomedcentral.com/track/pdf/10.1186/s13326-016-0100-2?site=jbiomedsem.biomedcentral.com" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/78/fb/78fba716eb0e5bb075e563e667dab0b3799ee879.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13326-016-0100-2"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5024438" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Using semantics for representing experimental protocols

Olga Giraldo, Alexander García, Federico López, Oscar Corcho
<span title="2017-11-13">2017</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/iasjcyzzyncgnohh3aitx65bhq" style="color: black;">Journal of Biomedical Semantics</a> </i> &nbsp;
By combining comprehensive vocabularies with NLP rules and gazetteers we identify meaningful parts of speech in experimental protocols.  ...  In this paper we present "SMART Protocols", a semantic and NLP-based infrastructure for processing and enacting experimental protocols.  ...  Experimental protocols are fundamental information structures that support the description of the processes by means of which results are generated in experimental research [6] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13326-017-0160-y">doi:10.1186/s13326-017-0160-y</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29132408">pmid:29132408</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5683383/">pmcid:PMC5683383</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/a6ghxhrzgfgmfh35kziugpedkm">fatcat:a6ghxhrzgfgmfh35kziugpedkm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170822000723/http://www.swat4ls.org:80/wp-content/uploads/2015/10/SWAT4LS_2015_paper_15.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/72/79/7279aa16c05b84abc0e2e47ff21c2e734351b257.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13326-017-0160-y"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5683383" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Towards an Ontology of Data Mining Investigations [chapter]

Panče Panov, Larisa N. Soldatova, Sašo Džeroski
<span title="">2009</span> <i title="Springer Berlin Heidelberg"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2w3awgokqne6te4nvlofavy5a4" style="color: black;">Lecture Notes in Computer Science</a> </i> &nbsp;
(OBI) .  ...  In this paper we present an updated version of the OntoDM ontology, that is based on a recent proposal of a general framework for data mining and it is aligned with the ontology of biomedical investigations  ...  OBI is fully compliant with the existing formalisms in biomedical domains.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-642-04747-3_21">doi:10.1007/978-3-642-04747-3_21</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/udpyd7id4bbpbkinidhnpn5b3a">fatcat:udpyd7id4bbpbkinidhnpn5b3a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170808132032/http://kt.ijs.si/panovp/Default_files/DS_09_PanovEtAl.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f7/08/f708841277f031b99548f08abf46ac26a3461474.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-642-04747-3_21"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Representation of research hypotheses

Larisa N Soldatova, Andrey Rzhetsky
<span title="">2011</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/iasjcyzzyncgnohh3aitx65bhq" style="color: black;">Journal of Biomedical Semantics</a> </i> &nbsp;
We thank members of the OBI Consortium for the fruitful discussions.  ...  This article has been published as part of Journal of Biomedical Semantics Volume 2 Supplement 2, 2011: Proceedings of the Bio-Ontologies Special Interest Group Meeting 2010.  ...  OBI intends to serve as the standard for the recording of biomedical investigations.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/2041-1480-2-s2-s9">doi:10.1186/2041-1480-2-s2-s9</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21624164">pmid:21624164</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3102898/">pmcid:PMC3102898</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/bnkpbaniyzgippz3yr3nlrggou">fatcat:bnkpbaniyzgippz3yr3nlrggou</a> </span>
<a target="_blank" rel="noopener" href="https://archive.org/download/pubmed-PMC3102898/PMC3102898-2041-1480-2-S2-S9.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> File Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/0f/d2/0fd2a292bac6d330f52001fa04051d964a26c1b7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/2041-1480-2-s2-s9"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3102898" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

An ontology for description of drug discovery investigations

Da Qi, Ross D King, Andrew L Hopkins, G Richard J Bickerton, Larisa N Soldatova
<span title="2010-03-25">2010</span> <i title="Walter de Gruyter GmbH"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fvl4m6o2tre4pcvl4ljymxu4ly" style="color: black;">Journal of Integrative Bioinformatics</a> </i> &nbsp;
DDI is highly transferable and extendable due to its adherence to accepted standards, and compliance with existing ontology resources.  ...  This enables DDI to be integrated with such related ontologies as the Vaccine Ontology, the Advancing Clinico-Genomic Trials on Cancer Master Ontology, etc.  ...  We employ the same methodology which we used for the description of investigations in LABORS [8] and for modelling the experimental processes in OBI.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2390/biecoll-jib-2010-126">doi:10.2390/biecoll-jib-2010-126</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20375446">pmid:20375446</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mdkaqhaymzeibogp7do5cpht6i">fatcat:mdkaqhaymzeibogp7do5cpht6i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200225081352/https://www.degruyter.com/downloadpdf/j/jib.2010.7.issue-3/biecoll-jib-2010-126/biecoll-jib-2010-126.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2390/biecoll-jib-2010-126"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a>
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