Knowledge-Based Integration of Neuroscience Data Sources. - Amarnath Gupta; Bertram Ludäscher; Maryann E. Martone (SSDBM, 2000)

Model-Based Information Integration in a Neuroscience Mediator System. - Bertram Ludäscher; Amarnath Gupta; Maryann E. Martone (VLDB, 2000)

An Extensible Model-Based Mediatior System with Domain Maps. - Amarnath Gupta; Bertram Ludäscher; Maryann E. Martone (ICDE Demo Sessions, 2001)

Model-Based Mediation with Domain Maps. - Bertram Ludäscher; Amarnath Gupta; Maryann E. Martone (ICDE, 2001)

A System for Managing Alternate Models in Model-Based Mediation. - Amarnath Gupta; Bertram Ludäscher; Maryann E. Martone; Xufei Qian; Edward Ross; Joshua Tran; Ilya Zaslavsky (BNCOD, 2002)

Navigating Virtual Information Sources with Know-ME. - Xufei Qian; Bertram Ludäscher; Maryann E. Martone; Amarnath Gupta (EDBT, 2002)

Registering Scientific Information Sources for Semantic Mediation. - Amarnath Gupta; Bertram Ludäscher; Maryann E. Martone (ER, 2002)

A Model-Based Mediator System for Scientific Data Management. - Bertram Ludäscher; Amarnath Gupta; Maryann E. Martone (Bioinformatics, 2003)

BIRN-M: A Semantic Mediator for Solving Real-World Neuroscience Problems. - Amarnath Gupta; Bertram Ludäscher; Maryann E. Martone (SIGMOD Conference, 2003)

A Practical Approach for Microscopy Imaging Data Management (MIDM) in Neuroscience. - Shenglan Zhang; Xufei Qian; Amarnath Gupta; Maryann E. Martone (SSDBM, 2003)

The Telescience Portal for advanced tomography applications. - Steven Peltier; Abel W. Lin; David Lee; Stephen A. Mock; Stephan Lamont; Tomas E. Molina; Mona Wong; Lu Dai; Maryann E. Martone; Mark H. Ellisman (J. Parallel Distributed Comput., 2003)

The cell-centered database - A database for multiscale structural and protein localization data from light and electron microscopy. - Maryann E. Martone; Shenglan Zhang; Amarnath Gupta; Xufei Qian; Haiyun He; Diana L. Price; Mona Wong; Simone Santini; Mark H. Ellisman (Neuroinformatics, 2003)

Towards a formalization of disease-specific ontologies for neuroinformatics. - Amarnath Gupta; Bertram Ludäscher; Jeffrey S. Grethe; Maryann E. Martone (Neural Networks, 2003)

Integrating Brain Data Spatially: Spatial Data Infrastructure and Atlas Environment for Online Federation and Analysis of Brain Images. - Ilya Zaslavsky; Haiyun He; Joshua Tran; Maryann E. Martone; Amarnath Gupta (DEXA Workshops, 2004)

Biomedical Informatics Research Network: Building a National Collaboratory to Hasten the Derivation of New Understanding and Treatment of Disease. - Jeffrey S. Grethe; Chaitan Baru; Amarnath Gupta; Mark James; Bertram Ludäscher; Maryann E. Martone; Philip M. Papadopoulos; Steven Peltier; Arcot Rajasekar; Simone Santini; Ilya Zaslavsky; Mark H. Ellisman (HealthGrid, 2005)

Semantically Based Data Integration Environment for Biomedical Research. - Vadim Astakhov; Amarnath Gupta; Jeffrey S. Grethe; Edward Ross; David Little; Aylin Yilmaz; Xufei Qian; Simone Santini; Maryann E. Martone; Mark H. Ellisman (CBMS, 2006)

Imaging and visual analysis - Large image correction and warping in a cluster environment. - Vijay S. Kumar; Benjamin Rutt; Tahsin M. Kurç; Ümit V. Çatalyürek; Joel H. Saltz; Sunny K. Chow; Stephan Lamont; Maryann E. Martone (SC, 2006)

OntoQuest: Exploring Ontological Data Made Easy. - Li Chen 027; Maryann E. Martone; Amarnath Gupta; Lisa Fong; Mona Wong-Barnum (VLDB, 2006)

Real-time multi-scale brain data acquisition, assembly, and analysis using an end-to-end OptIPuter. - Rajvikram Singh; Nicholas Schwarz; Nut Taesombut; David Lee; Byungil Jeong; Luc Renambot; Abel W. Lin; Ruth West; Hiromu Otsuka; Sei Naito; Steven Peltier; Maryann E. Martone; et al. (Future Gener. Comput. Syst., 2006)

High-resolution large-scale mosaic imaging using multiphoton microscopy to characterize transgenic mouse models of human neurological disorders. - Diana L. Price; Sunny K. Chow; Natalie A. B. MacLean; Hiroyuki Hakozaki; Steven Peltier; Maryann E. Martone; Mark H. Ellisman (Neuroinformatics, 2006)

Toward an Ontological Database for Subcellular Neuroanatomy. - Amarnath Gupta; Stephen D. Larson; Christopher Condit; Sandeep Gupta; Lisa Fong; Li Chen 027; Maryann E. Martone (ER Workshops, 2007)

Data Integration in eHealth: A Domain/Disease Specific Roadmap. - Jenny Ure; Rob Procter; Maryann E. Martone; David Porteous; Sharon Lloyd; Stephen M. Lawrie; Dominic Job; Richard A. Baldock; Alistair Philp; Dave Liewald; Frank Rakebrandt; Alan Blaikie; et al. (HealthGrid, 2007)

Shape Priors by Kernel Density Modeling of PCA Residual Structure. - John P. Lewis; Iman Mostafavi; Gina E. Sosinsky; Maryann E. Martone; Ruth West (ICIP (4), 2007)

An Ontology-Driven Knowledge Environment For Subcellular Neuroanatomy. - Lisa Fong; Stephen D. Larson; Amarnath Gupta; Christopher Condit; William J. Bug; Li Chen 027; Ruth West; Stephan Lamont; Masako Terada; Maryann E. Martone (OWLED, 2007)

Rule-Based Reasoning With A Multi-Scale Neuroanatomical Ontology. - Stephen D. Larson; Maryann E. Martone (OWLED, 2007)

Bridging the resolution gap: superimposition of multiple multi-channel volumes. - Chih K. Liang; Jürgen P. Schulze; Ruth West; Maryann E. Martone; Matthias Zwicker (SIGGRAPH Posters, 2007)

A formal ontology of subcellular neuroanatomy. - Stephen D. Larson; Lisa Fong; Amarnath Gupta; Christopher Condit; William J. Bug; Maryann E. Martone (Frontiers Neuroinformatics, 2007)

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 L. Rubin; Gordon M. Shepherd; Jessica A. Turner; Maryann E. Martone (Neuroinformatics, 2008)

The Neuroscience Information Framework: A Data and Knowledge Environment for Neuroscience. - Daniel Gardner; Huda Akil; Giorgio A. Ascoli; Douglas M. Bowden; William J. Bug; Duncan E. Donohue; David H. Goldberg; Bernice Grafstein; Jeffrey S. Grethe; Amarnath Gupta; Maryam Halavi; David N. Kennedy; et al. (Neuroinformatics, 2008)

Federated Access to Heterogeneous Information Resources in the Neuroscience Information Framework (NIF). - Amarnath Gupta; William J. Bug; Luis N. Marenco; Xufei Qian; Christopher Condit; Arun Rangarajan; Hans-Michael Müller; Perry L. Miller; Brian Sanders; Jeffrey S. Grethe; Vadim Astakhov; Gordon M. Shepherd; et al. (Neuroinformatics, 2008)

The NIF LinkOut Broker: A Web Resource to Facilitate Federated Data Integration using NCBI Identifiers. - Luis N. Marenco; Giorgio A. Ascoli; Maryann E. Martone; Gordon M. Shepherd; Perry L. Miller (Neuroinformatics, 2008)

Issues in the Design of a Pilot Concept-Based Query Interface for the Neuroinformatics Information Framework. - Luis N. Marenco; Yuli Li; Maryann E. Martone; Paul W. Sternberg; Gordon M. Shepherd; Perry L. Miller (Neuroinformatics, 2008)

Large-Scale Biomedical Image Analysis in Grid Environments. - Vijay S. Kumar; Benjamin Rutt; Tahsin M. Kurç; Ümit V. Çatalyürek; Tony C. Pan; Sunny K. Chow; Stephan Lamont; Maryann E. Martone; Joel H. Saltz (IEEE Trans. Inf. Technol. Biomed., 2008)

The Smart Atlas: Spatial and Semantic Strategies for Multiscale Integration of Brain Data. - Maryann E. Martone; Ilya Zaslavsky; Amarnath Gupta; Asif Memon; Joshua Tran; Willy Wong; Lisa Fong; Stephen D. Larson; Mark H. Ellisman (Anatomy Ontologies for Bioinformatics, 2008)

Ontology driven data integration for autism research. - Lynn Young; Samson W. Tu; Lakshika Tennakoon; David Vismer; Vadim Astakhov; Amarnath Gupta; Jeffrey S. Grethe; Maryann E. Martone; Amar K. Das; Matthew J. McAuliffe (CBMS, 2009)

NeuroLex.org - A semantic wiki for neuroinformatics based on the NIF Standard Ontology. - Stephen D. Larson; Sarah Maynard; Fahim T. Imam; Maryann E. Martone (SWAT4LS, 2009)

Multichannel transfer function with dimensionality reduction. - Han Suk Kim; Jürgen P. Schulze; Angela C. Cone; Gina E. Sosinsky; Maryann E. Martone (VDA, 2010)

Towards an ontology for psychosis. - Jay (Subbarao) Kola; Jonathan Harris; Stephen M. Lawrie; Alan L. Rector; Carole A. Goble; Maryann E. Martone (Cogn. Syst. Res., 2010)

Application of neuroanatomical ontologies for neuroimaging data annotation. - Jessica A. Turner; José L. V. Mejino Jr.; James F. Brinkley; Landon T. Detwiler; Hyo Jong Lee; Maryann E. Martone; Daniel L. Rubin (Frontiers Neuroinformatics, 2010)

Dimensionality reduction on multi-dimensional transfer functions for multi-channel volume data sets. - Han Suk Kim; Jürgen P. Schulze; Angela C. Cone; Gina E. Sosinsky; Maryann E. Martone (Inf. Vis., 2010)

NIFSTD and NeuroLex: Comprehensive Neuroscience Ontology Development Based on Multiple Biomedical Ontologies and Community Involvement. - Fahim T. Imam; Stephen D. Larson; Jeffrey S. Grethe; Amarnath Gupta; Anita E. Bandrowski; Maryann E. Martone (ICBO, 2011)

An Ontology-Based Approach to Linking Model Organisms and Resources to Human Diseases. - Chris Mungall; David Anderson; Anita E. Bandrowski; Brian A. Canada; Andrew Chatr-aryamontri; Keith C. Cheng; P. Michael Conn; Kara Dolinski; Mark H. Ellisman; Janan T. Eppig; Jeffrey S. Grethe; Joseph W. Kemnitz; et al. (ICBO, 2011)

Digital Atlasing and Standardization in the Mouse Brain. - Michael Hawrylycz; Richard A. Baldock; Albert Burger; Tsutomu Hashikawa; G. Allan Johnson; Maryann E. Martone; Lydia Ng; Christopher Lau; Stephen D. Larson; Jonathan Nissanov; Luis Puelles; Seth Ruffins; et al. (PLoS Comput. Biol., 2011)

Maturation of Neuroscience Information Framework: An Ontology Driven Information System for Neuroscience. - Fahim T. Imam; Stephen D. Larson; Anita E. Bandrowski; Jeffrey S. Grethe; Amarnath Gupta; Maryann E. Martone (FOIS, 2012)

Detecting and using document structure in scientific text. - Anita de Waard; Sophia Ananiadou; Maryann E. Martone; Ágnes Sándor; Hagit Shatkay (IHI, 2012)

A hybrid human and machine resource curation pipeline for the Neuroscience Information Framework. - Anita E. Bandrowski; Jonathan Cachat; Yuling Li 005; Hans-Michael Müller; Paul W. Sternberg; Paolo Ciccarese; Tim Clark; Luis N. Marenco; Rixin Wang; Vadim Astakhov; Jeffrey S. Grethe; Maryann E. Martone (Database J. Biol. Databases Curation, 2012)

Method: automatic segmentation of mitochondria utilizing patch classification, contour pair classification, and automatically seeded level sets. - Richard J. Giuly; Maryann E. Martone; Mark H. Ellisman (BMC Bioinform., 2012)

An ontological approach to describing neurons and their relationships. - David J. Hamilton; Gordon M. Shepherd; Maryann E. Martone; Giorgio A. Ascoli (Frontiers Neuroinformatics, 2012)

Prototype of Kepler Processing Workflows For Microscopy And Neuroinformatics. - Vadim Astakhov; Anita E. Bandrowski; Amarnath Gupta; A. W. Kulungowski; Jeffrey S. Grethe; James Bouwer; T. Molin; V. Rowley; S. Penticoff; Masako Terada; W. Wong; Hiroyuki Hakozaki; et al. (ICCS, 2012)

Introducing The Neuroscience Gateway. - Subhashini Sivagnanam; Amit Majumdar 001; Kenneth Yoshimoto; Vadim Astakhov; Anita E. Bandrowski; Maryann E. Martone; Nicholas T. Carnevale (IWSG, 2013)

Semantic query reformulation: the NIF experience. - Amarnath Gupta; Anita E. Bandrowski; Christopher Condit; Xufei Qian; Jeffrey S. Grethe; Maryann E. Martone (SSDBM, 2013)

A neuroscience gateway: software and implementation. - Subhashini Sivagnanam; Vadim Astakhov; Kenneth Yoshimoto; Ted Carnevale; Maryann E. Martone; Amitava Majumdar 001; Anita E. Bandrowski (XSEDE, 2013)

The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments. - Paola Roncaglia; Maryann E. Martone; David P. Hill; Tanya Z. Berardini; Rebecca E. Foulger; Fahim T. Imam; Harold J. Drabkin; Christopher J. Mungall; Jane Lomax (J. Biomed. Semant., 2013)

NeuroLex.org: an online framework for neuroscience knowledge. - Stephen D. Larson; Maryann E. Martone (Frontiers Neuroinformatics, 2013)

A knowledge based approach to matching human neurodegenerative disease and animal models. - Sarah Maynard; Christopher J. Mungall; Suzanna E. Lewis; Fahim T. Imam; Maryann E. Martone (Frontiers Neuroinformatics, 2013)

The cell: an image library-CCDB: a curated repository of microscopy data. - David N. Orloff; Janet H. Iwasa; Maryann E. Martone; Mark H. Ellisman; Caroline M. Kane (Nucleic Acids Res., 2013)

Connecting Connectomes. - Maryann E. Martone; Giorgio A. Ascoli (Neuroinformatics, 2013)

Automatic detection of mitochondria from electron microscope tomography images: a curve fitting approach. - Serdar F. Tasel; Reza Hassanpour; Erkan U. Mumcuoglu; Guy C. Perkins; Maryann E. Martone (Image Processing, 2014)

Comparative analysis of knowledge representation and reasoning requirements across a range of life sciences textbooks. - Vinay K. Chaudhri; Daniel Elenius; Andrew Goldenkranz; Allison Gong; Maryann E. Martone; William Webb; Neil Yorke-Smith (J. Biomed. Semant., 2014)

Neuroanatomical domain of the foundational model of anatomy ontology. - B. Nolan Nichols; José L. V. Mejino Jr.; Landon Detwiler; Trond T. Nilsen; Maryann E. Martone; Jessica A. Turner; Daniel L. Rubin; James F. Brinkley (J. Biomed. Semant., 2014)

Interdisciplinary perspectives on the development, integration, and application of cognitive ontologies. - Janna Hastings; Gwen A. Frishkoff; Barry Smith 001; Mark Jensen; Russell A. Poldrack; Jane Lomax; Anita E. Bandrowski; Fahim T. Imam; Jessica A. Turner; Maryann E. Martone (Frontiers Neuroinformatics, 2014)

Re-envisioning the business of information: Policies, practices and procedures. - Christopher Kenneally; October Ivins; Maryann E. Martone; Britt Mueller; William Trippe (Inf. Serv. Use, 2014)

Cell Centered Database. - Maryann E. Martone (Encyclopedia of Computational Neuroscience, 2014)

Neuroscience Information Framework (NIF). - Maryann E. Martone; Anita E. Bandrowski (Encyclopedia of Computational Neuroscience, 2014)

Early experiences in developing and managing the neuroscience gateway. - Subhashini Sivagnanam; Amit Majumdar 001; Kenneth Yoshimoto; Vadim Astakhov; Anita E. Bandrowski; Maryann E. Martone; Nicholas T. Carnevale (Concurr. Comput. Pract. Exp., 2015)

The Resource Identification Initiative: A Cultural Shift in Publishing. - Anita E. Bandrowski; Matthew H. Brush; Jeffrey S. Grethe; Melissa A. Haendel; David N. Kennedy; Sean L. Hill; Patrick R. Hof; Maryann E. Martone; Maaike Pols; Serena S. Tan; Nicole L. Washington; Elena V. Zudilova-Seinstra; et al. (Neuroinformatics, 2016)

Assessing value of biomedical digital repositories. - Chun-Nan Hsu; Anita E. Bandrowski; Jeffrey S. Grethe; Maryann E. Martone (PeerJ Prepr., 2017)

Research Resource IDentifiers for Key Biological Resources. - Anita E. Bandrowski; Tom Gillespie; Maryann E. Martone (RO, 2018)

How BIDs and BIDs validator has informed the data aggregation needs of the Stimulating Peripheral Activity to Relieve Conditions, SPARC, consortium. - Anita E. Bandrowski; Tom Gillespie; Monique Surles-Zeigler; Gabrielle Pine; Jeffrey S. Grethe; Maryann E. Martone (RO, 2019)

Everything Matters: The ReproNim Perspective on Reproducible Neuroimaging. - David N. Kennedy; Sanu Ann Abraham; Julianna F. Bates; Albert Crowley; Satrajit S. Ghosh; Tom Gillespie; Mathias Goncalves; Jeffrey S. Grethe; Yaroslav O. Halchenko; Michael Hanke; Christian Haselgrove; Steven M. Hodge; et al. (Frontiers Neuroinformatics, 2019)

Comparing the Use of Research Resource Identifiers and Natural Language Processing for Citation of Databases, Software, and Other Digital Artifacts. - Chun-Nan Hsu; Anita E. Bandrowski; Tom Gillespie; Jon Udell; Ko-Wei Lin; Ibrahim Burak Özyurt; Jeffrey S. Grethe; Maryann E. Martone (Comput. Sci. Eng., 2020)

Software and Data Citation. - Daniel S. Katz; Neil P. Chue Hong; Tim Clark; Martin Fenner; Maryann E. Martone (Comput. Sci. Eng., 2020)

Antibody Watch: Text mining antibody specificity from the literature. - Chun-Nan Hsu; Chia-Hui Chang; Thamolwan Poopradubsil; Amanda Lo; Karen A. William; Ko-Wei Lin; Anita E. Bandrowski; Ibrahim Burak Özyurt; Jeffrey S. Grethe; Maryann E. Martone (PLoS Comput. Biol., 2021)

Extending and using anatomical vocabularies in the stimulating peripheral activity to relieve conditions project. - Monique Surles-Zeigler; Troy Sincomb; Thomas H. Gillespie; Bernard de Bono; Jacqueline Bresnahan; Gary M. Mawe; Jeffrey S. Grethe; Susan J. Tappan; Maci L. Heal; Maryann E. Martone (Frontiers Neuroinformatics, 2022)

A Standards Organization for Open and FAIR Neuroscience: the International Neuroinformatics Coordinating Facility. - Mathew Birdsall Abrams; Jan G. Bjaalie; Samir Das; Gary F. Egan; Satrajit S. Ghosh; Wojtek James Goscinski; Jeffrey S. Grethe; Jeanette Hellgren Kotaleski; Eric Tatt Wei Ho; David N. Kennedy; Linda J. Lanyon; Trygve B. Leergaard; et al. (Neuroinformatics, 2022)

Correction to: A Standards Organization for Open and FAIR Neuroscience: the International Neuroinformatics Coordinating Facility. - Mathew Birdsall Abrams; Jan G. Bjaalie; Samir Das; Gary F. Egan; Satrajit S. Ghosh; Wojtek James Goscinski; Jeffrey S. Grethe; Jeanette Hellgren Kotaleski; Eric Tatt Wei Ho; David N. Kennedy; Linda J. Lanyon; Trygve B. Leergaard; et al. (Neuroinformatics, 2022)

The Neuron Phenotype Ontology: A FAIR Approach to Proposing and Classifying Neuronal Types. - Thomas H. Gillespie; Shreejoy J. Tripathy; Mohameth-François Sy; Maryann E. Martone; Sean L. Hill (Neuroinformatics, 2022)

Is Neuroscience FAIR? A Call for Collaborative Standardisation of Neuroscience Data. - Jean-Baptiste Poline; David N. Kennedy; Friedrich T. Sommer; Giorgio A. Ascoli; David C. Van Essen; Adam R. Ferguson; Jeffrey S. Grethe; Michael Hawrylycz; Paul M. Thompson; Russell A. Poldrack; Satrajit S. Ghosh; David B. Keator; et al. (Neuroinformatics, 2022)

Promoting FAIR Data Through Community-driven Agile Design: the Open Data Commons for Spinal Cord Injury (odc-sci.org). - Abel Torres-Espin; Carlos A. Almeida; Austin Chou; J. Russell Huie; Michael Chiu; Romana Vavrek; Jeff Sacramento; Michael B. Orr; John C. Gensel; Jeffrey S. Grethe; Maryann E. Martone; Karim Fouad; et al. (Neuroinformatics, 2022)

The Antibody Registry: ten years of registering antibodies. - Anita E. Bandrowski; Mason Pairish; Peter Eckmann; Jeffrey S. Grethe; Maryann E. Martone (Nucleic Acids Res., 2023)

The past, present and future of neuroscience data sharing: a perspective on the state of practices and infrastructure for FAIR. - Maryann E. Martone (Frontiers Neuroinformatics, 2023)

A Maturity Model for Operations in Neuroscience Research. - Erik C. Johnson; Thinh T. Nguyen; Benjamin K. Dichter; Frank Zappulla; Montgomery Kosma; Kabilar Gunalan; Yaroslav O. Halchenko; Shay Q. Neufeld; Michael Schirner; Petra Ritter; Maryann E. Martone; Brock A. Wester; et al. (CoRR, 2024)

Ten simple rules for recognizing data and software contributions in hiring, promotion, and tenure. - Iratxe Puebla; Giorgio A. Ascoli; Jeffrey Blume; John Chodacki; Joshua Finnell; David N. Kennedy; Bernard Mair; Maryann E. Martone; Jamie Wittenberg; Jean-Baptiste Poline (PLoS Comput. Biol., 2024)

Developing a multiscale neural connectivity knowledgebase of the autonomic nervous system. - Fahim T. Imam; Thomas H. Gillespie; Ilias Ziogas; Monique Surles-Zeigler; Susan J. Tappan; Ibrahim Burak Özyurt; Jyl Boline; Bernard de Bono; Jeffrey S. Grethe; Maryann E. Martone (Frontiers Neuroinformatics, 2025)