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Terminology for Neuroscience Data Discovery: Multi-tree Syntax and Investigator-Derived Semantics

Daniel Gardner, David H. Goldberg, Bernice Grafstein, Adrian Robert, Esther P. Gardner
2008 Neuroinformatics  
Semantics enabling NIF data discovery were selected at one or more workshops by investigators expert in particular systems (vision, olfaction, behavioral neuroscience, neurodevelopment), brain areas (cerebellum  ...  Core NIF terminologies use a straightforward syntax designed for ease of use and for navigation by familiar web interfaces, and readily exportable to aid development of relational-model databases for neuroscience  ...  Early terminology meetings were funded by the Society for Neuroscience under a generous gift from Paul Allen and Jody Patton and under contract (NIH Order No. 263-MD-409125-1) from NIMH, NINDS, and NIDA  ... 
doi:10.1007/s12021-008-9029-7 pmid:18958630 pmcid:PMC2663521 fatcat:tmzuulzx3vdu3euurvy7hbqjea

Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related Ontologies

Ramona L. Walls, John Deck, Robert Guralnick, Steve Baskauf, Reed Beaman, Stanley Blum, Shawn Bowers, Pier Luigi Buttigieg, Neil Davies, Dag Endresen, Maria Alejandra Gandolfo, Robert Hanner (+14 others)
2014 PLoS ONE  
data in a semantically meaningful and computationally useful way.  ...  We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange  ...  , and GBIF to support the increased interoperability of molecular and biodiversity standards and syntax and thus enhance semantic interoperability of their data holdings.  ... 
doi:10.1371/journal.pone.0089606 pmid:24595056 pmcid:PMC3940615 fatcat:s5vf3qssfvdpndgipkhohuis2u

Explainable Machine Learning for Scientific Insights and Discoveries [article]

Ribana Roscher, Bastian Bohn, Marco F. Duarte, Jochen Garcke
2019 arXiv   pre-print
Machine learning methods have been remarkably successful for a wide range of application areas in the extraction of essential information from data.  ...  An exciting and relatively recent development is the uptake of machine learning in the natural sciences, where the major goal is to obtain novel scientific insights and discoveries from observational or  ...  Acknowledgements Part of the work was performed during the long-term program on "Science at Extreme Scales: Where Big Data Meets Large-Scale Computing" held at the Institute for Pure and Applied Mathematics  ... 
arXiv:1905.08883v2 fatcat:bwbkmljfljcpboqmppoemari64

Explainable Machine Learning for Scientific Insights and Discoveries

Ribana Roscher, Bastian Bohn, Marco F. Duarte, Jochen Garcke
2020 IEEE Access  
Machine learning methods have been remarkably successful for a wide range of application areas in the extraction of essential information from data.  ...  An exciting and relatively recent development is the uptake of machine learning in the natural sciences, where the major goal is to obtain novel scientific insights and discoveries from observational or  ...  ACKNOWLEDGMENT Part of the work was performed during the long-term program on ''Science at Extreme Scales: Where Big Data Meets Large-Scale Computing'' held at the Institute for Pure and Applied Mathematics  ... 
doi:10.1109/access.2020.2976199 fatcat:7wk6ljxlqrdwhpbv7xjk75buk4

The Fourth Paradigm – Data-Intensive Scientific Discovery [chapter]

Tony Hey
2012 Communications in Computer and Information Science  
The F o u r T H Data-In t e n s I v e scIen t I f I c DIs c o v e r y P a r a d i g m MiCroSoF T reSe arCH REDMOND, WASHINGTON  ...  And, of course, we thank Jim Gray, for inspiring us. ACKN OWLE DG M E NTS  ...  We also thank our families and colleagues for their support during the intensive editorial process.  ... 
doi:10.1007/978-3-642-33299-9_1 fatcat:etue636ubrandga5corvkx3d7u

Knowledge Discovery from Social Media using Big Data provided Sentiment Analysis (SoMABiT) [article]

Mahdi Bohlouli, Jens Dalter, Mareike Dornhöfer, Johannes Zenkert, Madjid Fathi
2020 arXiv   pre-print
But how traditional analytic algorithms and methods can scale up for such disparate and multi-structured data sources is the main challenge in this regard.  ...  The use of MapReduce and developing a distributed algorithm towards an integrated platform that can scale for any data volume and provide a social media-driven knowledge is the main novelty of the proposed  ...  deriving data.  ... 
arXiv:2001.05996v1 fatcat:q6fbnvhndjct5md4egj7eznh3m

Literature-related discovery: common factors for Parkinson's Disease and Crohn's Disease

Ronald N. Kostoff
2014 Scientometrics  
knowledge (i.e., potential discovery).  ...  ABSTRACT Literature-related discovery (LRD) is the linking of two or more literature concepts that have heretofore not been linked (i.e., disjoint), in order to produce novel, interesting, and intelligible  ...  Multi-organ, multi-lineage engraftment by a single bone marrow-derived stem cell.  ... 
doi:10.1007/s11192-014-1298-3 fatcat:jpfukiwcb5ggfexqsv2dfpvvqa

The NIFSTD and BIRNLex Vocabularies: Building Comprehensive Ontologies for Neuroscience

William J. Bug, Giorgio A. Ascoli, Jeffrey S. Grethe, Amarnath Gupta, Christine Fennema-Notestine, Angela R. Laird, Stephen D. Larson, Daniel Rubin, Gordon M. Shepherd, Jessica A. Turner, Maryann E. Martone
2008 Neuroinformatics  
A critical component of the Neuroscience Information Framework (NIF) project is a consistent, flexible terminology for describing and retrieving neurosciencerelevant resources.  ...  ontology for neuroscience with sufficient granularity to describe and access a diverse collection of information became obvious.  ...  the original author(s) and source are credited.  ... 
doi:10.1007/s12021-008-9032-z pmid:18975148 pmcid:PMC2743139 fatcat:5xu3gqt2hndotmmjru4xwnwaqu

Development and use of Ontologies Inside the Neuroscience Information Framework: A Practical Approach

Fahim T. Imam, Stephen D. Larson, Anita Bandrowski, Jeffery S. Grethe, Amarnath Gupta, Maryann E. Martone
2012 Frontiers in Genetics  
Information Framework (NIF) project advances neuroscience by enabling discovery and access to public research data and tools worldwide through an open source, semantically enhanced search portal.  ...  One of the critical components for the overall NIF system, the NIF Standardized Ontologies (NIFSTD), provides an extensive collection of standard neuroscience concepts along with their synonyms and relationships  ...  ACKNOWLEDGMENTS Supported for NIF is provided by a contract from the NIH Neuroscience Blueprint HHSN271200800035C via the National Institute on Drug Abuse.  ... 
doi:10.3389/fgene.2012.00111 pmid:22737162 pmcid:PMC3381282 fatcat:5d6g6al7gnbxpgkqpqoyaswscy

Bioinformatics

2008 Biophysical Journal  
This error analyses will be used for error analysis of rate constants determined using NMM from experimental Fluorescence Correlation Spectroscopy data.  ...  Data Discovery: Multi-Tree Syntax and Investigator-Derived Semantics Daniel Gardner NIF Consortium, Lab of Neuroinformatics, Weill Cornell Medical College, New York, NY, USA.  ...  Other NIF components supply and relate complementary terminologies; one such literature-derived thrust is at http://textpresso.org/neuroscience.  ... 
doi:10.1016/s0006-3495(08)79198-7 fatcat:btwp2htzmnhrjblcyn4bb2kk6a

Twenty Questions for Neuroscience Metadata

Giorgio A. Ascoli
2012 Neuroinformatics  
Many of the helpful terms to identify relevant data, for example, appear in the Materials and Methods sections of published articles rather than in their titles, abstracts, and keywords.  ...  Textpresso: an ontology-based information retrieval and extraction system for biological literature.  ...  Terminology for neuroscience data discovery: Multi-tree syntax and investigator-derived semantics. Neuroinformatics, 6, 161-174. 5 Bowden, D. M., Song, E., Kosheleva, J., & Dubach, M. F. (2012).  ... 
doi:10.1007/s12021-012-9143-4 pmid:22354746 fatcat:cxx4zomgkjd77i3uwaag3gg4ay

The Evolution of Syntax: An Exaptationist Perspective

W. Tecumseh Fitch
2011 Frontiers in Evolutionary Neuroscience  
The evolution of language required elaboration of a number of independent mechanisms in the hominin lineage, including systems involved in signaling, semantics, and syntax.  ...  I conclude by illustrating the importance of both homology (studied via primates) and convergence (typically analyzed in birds) for testing such evolutionary hypotheses.  ...  , syntax, and semantics (cf.  ... 
doi:10.3389/fnevo.2011.00009 pmid:22207847 pmcid:PMC3245538 fatcat:pq5ngakedvajjnzuwtnvkhzut4

Scientific modelling in generative grammar and the dynamic turn in syntax

Ryan M. Nefdt
2016 Linguistics and Philosophy  
the University of Newcastle and friends and colleagues at the Arché Research Centre in St Andrews for helpful discussion concerning many of the ideas presented here.  ...  Acknowledgments I am indebted to Reinhard Blutner, Josh Dever, Ephraim Glick, Patrick Greenough, Geoff Poole, Geoff Pullum and Zoltan Szabó for looking at various drafts of this research and offering insightful  ...  descriptions since they miss out on relevant and systematic data found in corpora and multi-person discourse.  ... 
doi:10.1007/s10988-016-9193-4 fatcat:afeb3lx5ybcllbnsctsrcc6bpm

Précis of Foundations of Language: Brain, Meaning, Grammar, Evolution,

Ray Jackendoff
2003 Behavioral and Brain Sciences  
The proper approach is a parallel architecture, in which phonology, syntax, and semantics are autonomous generative systems linked by interface components.  ...  The parallel architecture leads to an integration within linguistics, and to a far better integration with the rest of cognitive neuroscience.  ...  required no change in brain structure for their discovery and cultural transmission.  ... 
doi:10.1017/s0140525x03000153 fatcat:eewzkvv7wjc4tnn4okt7cbui64

Précis of Foundations of language: brain, meaning, grammar, evolution

Ray Jackendoff
2003 Behavioral and Brain Sciences  
The proper approach is a parallel architecture, in which phonology, syntax, and semantics are autonomous generative systems linked by interface components.  ...  The parallel architecture leads to an integration within linguistics, and to a far better integration with the rest of cognitive neuroscience.  ...  required no change in brain structure for their discovery and cultural transmission.  ... 
pmid:15377127 fatcat:bzensiywbngxjlsooeenx3czpm
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