cran: SPARQL | Projects | Ecosyste.ms: Papers

10.1016/j.patter.2021.100322

The role of metadata in reproducible computational research
Cited by: 38
Author(s): Jeremy Leipzig, Daniel Nüst, Charles Tapley Hoyt, Karthik Ram, Jane Greenberg
Software Mentions: 21
Published: over 2 years ago

10.1186/s13742-016-0147-0

2015 Brainhack Proceedings
Cited by: 6
Author(s): R. Cameron Craddock, Pierre Bellec, Daniel S. Margules, B. Nolan Nichols, Jörg P. Pfannmöller, AmanPreet Badhwar, David Kennedy, Jean‐Baptiste Poline, Roberto Toro, Ben Cipollini, Ariel Rokem, Daniel J. Clark, Krzysztof J. Gorgolewski, Daniel J. Clark, Samir Das, Cécile Madjar, Ayan Sengupta, Zia Mohades, Sébastien Déry, Weiran Deng, Eric Earl, Damion V. Demeter, Kate Mills, Glad Mihai, Luka Ružić, Nick Ketz, Andrew E. Reineberg, Marianne C. Reddan, Anne-Lise Goddings, Javier Gonzalez‐Castillo, Caroline Froehlich, Gil Dekel, Daniel S. Margulies, Ben D. Fulcher, Tristan Glatard, Reza Adalat, Natacha Beck, R. Bernard, Najmeh Khalili-Mahani, Pierre Rioux, Marc-Étienne Rousseau, Alan C. Evans, Yaroslav Halchenko, Matteo Visconti di Oleggio Castello, Raúl Hernández-Pérez, Edgar Abarca Morales, Laura V. Cuaya, Kaori Ito, Sook‐Lei Liew, Hans J. Johnson, Erik Kan, Julia Anglin, Michael R. Borich, Neda Jahanshad, Paul Thompson, Marcel Falkiewicz, Julia M. Huntenburg, David O’Connor, Michael P. Milham, Ramon Fraga Pereira, Anibal Sólon Heinsfeld, Alexandre R. Franco, Augusto Buchweitz, Felipe Meneguzzi, Rickson C. Mesquita, Luis C. T. Herrera, Daniela Dentico, Vanessa Sochat, Julio E. Villalon‐Reina, Eleftherios Garyfallidis
Software Mentions: 14
Published: over 7 years ago

10.12688/f1000research.17548.2

Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python
Cited by: 8
Author(s): Klara Kaleb, Alex Warwick Vesztrocy, Adrian M. Altenhoff, Christophe Dessimoz
Software Mentions: 13
Published: about 5 years ago

10.1093/gigascience/giaa102

A single-cell RNA-sequencing training and analysis suite using the Galaxy framework
Cited by: 15
Author(s): Mehmet Tekman, Bérénice Batut, Alexander Ostrovsky, Christophe Antoniewski, D. L. Clements, Fidel Ramírez, Graham Etherington, Hans-Rudolf Hotz, Jelle Scholtalbers, Jonathan Manning, Léa Bellenger, Maria A. Doyle, Mohammad Heydarian, Ni Huang, Nicola Soranzo, Pablo Moreno, Stefan Mautner, Irene Papatheodorou, Anton Nekrutenko, James Taylor, Daniel Blankenberg, Rolf Backofen, Björn Grüning
Software Mentions: 12
Published: over 3 years ago

10.1093/bib/bbaa390

The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling
Cited by: 13
Author(s): Vasundra Touré, Åsmund Flobak, Anna Niarakis, Steven Vercruysse, Martin Kuiper
Software Mentions: 9
Published: over 3 years ago

10.12688/f1000research.18236.1

BioHackathon 2015: Semantics of data for life sciences and reproducible research
Cited by: 5
Author(s): Rutger A. Vos, Toshiaki Katayama, Hiroyuki Mishima, Shin Kawano, Seiichiro Kawashima, Jin-Dong Kim, Yuki Moriya, Toshiaki Tokimatsu, Atsuko Yamaguchi, Yasunori Yamamoto, Hongyan Wu, Peter Amstutz, Erick Antezana, Nobuyuki P. Aoki, Kazuharu Arakawa, Jerven Bolleman, Evan Bolton, Raoul J. P. Bonnal, Hidemasa Bono, Kees Burger, Hirokazu Chiba, K. Bretonnel Cohen, Eric W. Deutsch, Jesualdo Tomás Fernández‐Breis, Gang Fu, Takatomo Fujisawa, Atsushi Fukushima, Alexander García, Naohisa Goto, Tudor Groza, Colin Hercus, Robert Hoehndorf, Kotone Itaya, Nick Juty, Takeshi Kawashima, Jee-Hyub Kim, Akira R. Kinjo, Masaaki Kotera, Kouji Kozaki, Sadahiro Kumagai, Tatsuya Kushida, Thomas Lütteke, Masaaki Matsubara, Joe Miyamoto, Attayeb Mohsen, Hiroshi Mori, Yukiko Naito, Takeru Nakazato, Jeremy Nguyen-Xuan, Kozo Nishida, Naoki Nishida, Hiroyo Nishide, Soichi Ogishima, Toshio Ohta, Shujiro Okuda, Benedict Paten, Jean-Luc Perret, Philip Prathipati, Pjotr Prins, Núria Queralt-Rosiñach, Daisuke Shinmachi, Shinya Suzuki, Tsuyosi Tabata, Terue Takatsuki, Kieron Taylor, Mark Thompson, Ikuo Uchiyama, Bruno Miguel Vieira, Chih-Hsuan Wei, Mark D. Wilkinson, Issaku Yamada, Ryota Yamanaka, Kazutoshi Yoshitake, Akiyasu C. Yoshizawa, Michel Dumontier, Kenjiro Kosaki, Toshihisa Takagi
Software Mentions: 9
Published: about 4 years ago

10.3390/biom11081245

Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review
Cited by: 16
Author(s): Fotis A. Baltoumas, Sofia Zafeiropoulou, Evangelos Karatzas, Mikaela Koutrouli, Foteini Thanati, Kleanthi Voutsadaki, Maria Gkonta, Joana Hotova, Ioannis Kasionis, Pantelis Hatzis, Georgios A. Pavlopoulos
Software Mentions: 7
Published: over 2 years ago

10.3762/bjnano.6.165

The eNanoMapper database for nanomaterial safety information
Cited by: 82
Author(s): Nina Jeliazkova, Charalampos Chomenidis, Philip Doganis, Bengt Fadeel, Roland C. Grafström, Barry Hardy, Janna Hastings, Markus Hegi, Vedrin Jeliazkov, Nikolay Kochev, Pekka Kohonen, Cristian R. Munteanu, Haralambos Sarimveis, Bart Smeets, Pantelis Sopasakis, Georgia Tsiliki, David Vorgrimmler, Egon Willighagen
Software Mentions: 7
Published: almost 9 years ago

10.1093/gigascience/giaa157

biotoolsSchema: a formalized schema for bioinformatics software description
Cited by: 7
Author(s): Jon C. Ison, Hans Ienasescu, Emil Karol Rydza, Piotr Jaroslaw Chmura, Kristoffer Rapacki, Alban Gaignard, Veit Schwämmle, Jacques van Helden, Matúš Kalaš, Hervé Ménager
Software Mentions: 7
Published: over 3 years ago

10.1186/1471-2105-12-452

eXframe: reusable framework for storage, analysis and visualization of genomics experiments
Cited by: 5
Author(s): Amit Sinha, Emily Merrill, Scott A. Armstrong, Tim W. Clark, Sudeshna Das
Software Mentions: 7
Published: over 12 years ago

10.15252/msb.20209442

High‐throughput, microscope‐based sorting to dissect cellular heterogeneity
Cited by: 40
Author(s): Nicholas Hasle, Anthony Cooke, Sanjay Srivatsan, Heather Z Huang, Jason J. Stephany, Zachary Krieger, Dana L. Jackson, Weiliang Tang, Sriram Pendyala, Raymond J. Monnat, Cole Trapnell, Emily M. Hatch, Douglas M. Fowler
Software Mentions: 7
Published: almost 4 years ago

10.1371/journal.pcbi.1009382

Biomedical Data Commons (BMDC) prioritizes B-lymphocyte non-coding genetic variants in Type 1 Diabetes
Cited by: 3
Author(s): Samantha N. Piekos, Sadhana Gaddam, Pranav Bhardwaj, Prashanth Radhakrishnan, Ramanathan V. Guha, Anthony E. Oro
Software Mentions: 7
Published: over 2 years ago

10.7717/peerj-cs.387

Semantic micro-contributions with decentralized nanopublication services
Cited by: 11
Author(s): Tobias Kuhn, Ruben Taelman, Vincent Emonet, Haris Antonatos, Stian Soiland‐Reyes, Michel Dumontier
Software Mentions: 6
Published: about 3 years ago

10.1016/j.dib.2020.105757

The molecular entities in linked data dataset
Cited by: 1
Author(s): Dominik Tomaszuk, Łukasz Szeremeta
Software Mentions: 6
Published: almost 4 years ago

10.3389/frobt.2018.00123

A Multimodal Analytics Platform for Journalists Analyzing Large-Scale, Heterogeneous Multilingual, and Multimedia Content
Cited by: 1
Author(s): Stefanos Vrochidis, Anastasia Moumtzidou, Ilias Gialampoukidis, Dimitris Liparas, Gerard Casamayor, Leo Wanner, Nicolaus Heise, Tilman Wagner, Andriy Bilous, Emmanuel Jamin, Boyan Simeonov, Vladimir Alexiev, Reinhard Busch, Ioannis Arapakis, Ioannis Kompatsiaris
Software Mentions: 6
Published: over 5 years ago

10.3389/fninf.2015.00009

Ontology-based approach for in vivo human connectomics: the medial Brodmann area 6 case study
Cited by: 3
Author(s): T. Moreau, Bernard Gibaud
Software Mentions: 6
Published: about 9 years ago

10.1186/1471-2105-14-158

Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient
Cited by: 33
Author(s): Arlin Stoltzfus, Hilmar Lapp, Naim Matasci, Helena F. Deus, Brian L. Sidlauskas, Christian M. Zmasek, Gaurav Vaidya, Enrico Pontelli, Karen Cranston, Rutger A. Vos, Campbell O. Webb, Luke J. Harmon, Megan Pirrung, Brian C. O’Meara, Matthew W. Pennell, Siavash Mirarab, Michael S. Rosenberg, James P. Balhoff, Holly M. Bik, Tracy A. Heath, Peter E. Midford, Joseph W. Brown, Emily Jane McTavish, Jeet Sukumaran, Mark W. Westneat, Michael E. Alfaro, Aaron Steele, G. Gulli Jordan
Software Mentions: 6
Published: about 11 years ago

10.1371/journal.pone.0134011

A Methodology for the Development of RESTful Semantic Web Services for Gene Expression Analysis.
Cited by: 7
Author(s): Gabriela D. A. Guardia, Luís Ferreira Pires, Ricardo Zorzetto Nicoliello Vêncio, Kelen Cristina Ribeiro Malmegrim, Cléver Ricardo Guareis de Farias
Software Mentions: 6
Published: over 9 years ago

10.1038/s41598-020-57716-1

Ontology-driven integrative analysis of omics data through Onassis
Cited by: 9
Author(s): Eugenia Galeota, Kamal Kishore, Mattia Pelizzola
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pone.0071090

Glocal Clinical Registries: Pacemaker Registry Design and Implementation for Global and Local Integration – Methodology and Case Study
Cited by: 29
Author(s): Kátia Regina da Silva, Roberto Costa, Elizabeth Sartori Crevelari, Marianna Sobral Lacerda, Caio Marcos de Moraes Albertini, Martino Martinelli Filho, José Eduardo Santana, João Ricardo Nickenig Vissoci, Ricardo Pietrobon, Jacson Venâncio de Barros
Software Mentions: 6
Published: almost 11 years ago

10.1186/s13326-019-0212-6

Exploring semantic deep learning for building reliable and reusable one health knowledge from PubMed systematic reviews and veterinary clinical notes
Cited by: 6
Author(s): Mercedes Arguello-Casteleiro, Robert Stevens, Julio Des-Diz, Chris Wroe, M.J. Fernandez-Prieto, Nava Maroto, Diego Maseda-Fernandez, George Demetriou, Simon Peters, P. J. W. Noble, Phil Jones, Joanna Dukes‐McEwan, Alan Radford, John Keane, Goran Nenadić
Software Mentions: 6
Published: over 4 years ago

10.1093/bioinformatics/bty181

Reactome Pengine: a web-logic API to the Homo sapiens reactome
Cited by: 6
Author(s): Samuel R Neaves, Sophia Tsoka, Louise A C Millard
Software Mentions: 5
Published: about 6 years ago

10.1186/1471-2105-10-S10-S5

KA-SB: from data integration to large scale reasoning
Cited by: 3
Author(s): María del Mar Roldán‐García, Ismael Navas‐Delgado, Amine Kerzazi, Othmane Chniber, Joaquin J. Molina-Castro, José F. Aldana‐Montes
Software Mentions: 5
Published: over 14 years ago

10.1186/1471-2105-11-387

S3DB core: a framework for RDF generation and management in bioinformatics infrastructures
Cited by: 14
Author(s): Jonas S. Almeida, Helena F. Deus, Wolfgang Maaß
Software Mentions: 5
Published: almost 14 years ago

10.1186/s12918-015-0174-y

SEEK: a systems biology data and model management platform
Cited by: 79
Author(s): Katy Wolstencroft, Stuart Owen, Olga Krebs, Quyen Le Hoang Thuy To Nguyen, Natalie J. Stanford, Martin Golebiewski, Andreas Weidemann, Meik Bittkowski, Lin An, David Shockley, Jacky L. Snoep, Wolfgang Mueller, Carole Goble
Software Mentions: 5
Published: almost 9 years ago

10.1186/s13059-014-0560-6

Gateways to the FANTOM5 promoter level mammalian expression atlas
Cited by: 634
Author(s): Marina Lizio, Jayson Harshbarger, Hisashi Shimoji, Jessica Severin, Takeya Kasukawa, Serkan Sahin, Imad Abugessaisa, Shiro Fukuda, Fumi Hori, Sachi Ishikawa-Kato, Christopher J. Mungall, Peter Arner, J Kenneth Baillie, Nicolas Bertin, Hidemasa Bono, Michiel de Hoon, Alexander D. Diehl, Emmanuel Dimont, Tom C. Freeman, Kaori Fujieda, Winston Hide, Rajaram Kaliyaperumal, Toshiaki Katayama, Timo Lassmann, Terrence F. Meehan, Koro Nishikata, Ono Hiromasa, Michael Rehli, Albin Sandelin, Erik Schultes, Peter A.C. ’t Hoen, Zuotian Tatum, Mark Thompson, Tetsuro Toyoda, Derek W. Wright, Carsten O. Daub, Masayoshi Itoh, Piero Carninci, Yoshihide Hayashizaki, Hideya Kawaji
Software Mentions: 5
Published: over 9 years ago

10.1186/s12859-016-1154-y

Proceedings of the 15th Annual UT-KBRIN Bioinformatics Summit 2016
Cited by: 0
Author(s): Eric C. Rouchka, Julia H. Chariker, Benjamin J. Harrison, Juw Won Park, Xueyuan Cao, Stanley Pounds, Susana C. Raimondi, James R. Downing, Raul C. Ribeiro, Jeffery Rubnitz, Jatinder K. Lamba, Bernie J. Daigle, Deborah C. Hay Burgess, Stephanie Gehrlich, John C. Carmen, Nicholas Johnson, Chandrakanth Emani, Kalpani De Silva, Michael P. Heaton, Theodore S. Kalbfleisch, Teeradache Viangteeravat, Rahul Mudunuri, Oluwaseun T. Ajayi, Fatih Şen, Eunice Y. Huang, Mohammad Mohebbi, Luaire Florian, Douglas Jackson, John Naber, Akm Sabbir, Sally R. Ellingson, Yuping Lu, Charles Phillips, Michael A. Langston, Rahul Kumar Sevakula, Raghuveer Thirukovalluru, Nishchal K. Verma, Yan Cui, Mohammed Sayed, Jing Wang, Qi Liu, Yu Shyr, Xiaofei Zhang, Naresh Prodduturi, Gavin R. Oliver, Diane E. Grill, Jie Na, Jeanette E. Eckel‐Passow, Eric W. Klee, Michael M. Goodin, Mark L. Farman, Harrison A Inocencio, Chanyong Jang, Jerzy W. Jaromczyk, Neil Moore, Kelly L Sovacool, Leon Dent, Mike Izban, Sammed N. Mandape, Shruti S. Sakhare, Siddharth Pratap, Dana Marshall, M Scotty DePriest, James N. MacLeod, H. Marblestone Adam, Ethan Blandford, Joel Campbell, Joshua Castlen, Brittany Dixon, Ginger Gilbert, Aaron Smalter Hall, Philip Kreisle, Jessica Lasher, B.K. Oakes, Allison Speer, Maximilian Valentine, Naga Satya V Rao Nagisetty, Rony Jose, Robert J. Rooney, David S. Hains
Software Mentions: 5
Published: almost 8 years ago

10.2196/24656

An Automatic Ontology-Based Approach to Support Logical Representation of Observable and Measurable Data for Healthy Lifestyle Management: Proof-of-Concept Study
Cited by: 25
Author(s): Ayan Chatterjee, Andreas Prinz, Martin Gerdes, Santiago Martínez
Software Mentions: 5
Published: about 3 years ago

10.1101/2020.12.21.423860

Analyzing the vast coronavirus literature with CoronaCentral
Cited by: 3
Author(s): Jake Lever, Russ B. Altman
Software Mentions: 5
Published: over 3 years ago

10.1186/s12915-020-00940-y

A protocol for adding knowledge to Wikidata: aligning resources on human coronaviruses
Cited by: 14
Author(s): Andra Waagmeester, Egon Willighagen, Andrew I. Su, Martina Kutmon, José Emilio Labra Gayo, Daniel Fernández-Álvarez, Quentin Groom, Peter J. Schaap, Lisa M. Verhagen, Jasper J. Koehorst
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0252862

Approaches to measure class importance in Knowledge Graphs
Cited by: 2
Author(s): Daniel Fernández-Álvarez, Johannes Frey, José Emilio Labra Gayo, Daniel Gayo-Avello, Sebastian Hellmann
Software Mentions: 5
Published: almost 3 years ago

10.1093/bioinformatics/btv593

Automatic generation of bioinformatics tools for predicting protein–ligand binding sites
Cited by: 12
Author(s): Yusuke Komiyama, Masaki Banno, Kokoro Ueki, Gul Saad, Kentaro Shimizu
Software Mentions: 5
Published: over 8 years ago

10.3389/fgene.2014.00152

Bioinformatics for precision medicine in oncology: principles and application to the SHIVA clinical trial
Cited by: 73
Author(s): Nicolas Servant, Julien Roméjon, Pierre Gestraud, Philippe La Rosa, Georges Lucotte, Séverine Lair, Virginie Bernard, Bruno Zeitouni, Fanny Coffin, Gérôme Jules-Clément, Florent Yvon, Alban Lermine, Patrick Poullet, Stéphane Liva, Stuart Pook, Tatiana Popova, Camille Barette, François D. Prud’homme, Jean Gabriel Dick, Maud Kamal, Christophe Le Tourneau, Emmanuel Barillot, Philippe Hupé
Software Mentions: 5
Published: almost 10 years ago

10.3390/s21113587

A Secure and Scalable Smart Home Gateway to Bridge Technology Fragmentation
Cited by: 3
Author(s): Ezequiel Simeoni, Eugenio Gaeta, Rebeca I. García-Betances, Dave Raggett, Alejandro Martín Medrano Gil, Diego F. Carvajal-Flores, Giuseppe Fico, María Fernanda Cabrera-Umpiérrez, María Teresa Arredondo
Software Mentions: 5
Published: almost 3 years ago

10.1038/s41597-021-00905-y

A resource to explore the discovery of rare diseases and their causative genes
Cited by: 5
Author(s): Friederike Ehrhart, Egon Willighagen, Martina Kutmon, Max van Hoften, Leopold Curfs, Chris T. Evelo
Software Mentions: 4
Published: about 3 years ago

10.3390/s130708060

Context Management Platform for Tourism Applications
Cited by: 14
Author(s): David Buján, David L. Martin, Ortzi Torices, Diego López-de-Ipiña, Carlos Lamsfus, Joseba Abaitua, Aurkene Alzua-Sorzabal
Software Mentions: 4
Published: almost 11 years ago

10.1093/bioinformatics/btw417

SSBD: a database of quantitative data of spatiotemporal dynamics of biological phenomena
Cited by: 35
Author(s): Yukako Tohsato, Kenneth H. L. Ho, Koji Kyoda, Shuichi Onami
Software Mentions: 4
Published: almost 8 years ago

10.1186/s13326-020-00222-0

Structuring, reuse and analysis of electronic dental data using the Oral Health and Disease Ontology
Cited by: 4
Author(s): William D. Duncan, Thankam P. Thyvalikakath, Melissa Haendel, Carlo Torniai, Pedro J. Hernández, Mei Song, Amit Acharya, Daniel J. Caplan, Titus Schleyer, Alan Ruttenberg
Software Mentions: 4
Published: over 3 years ago

10.3389/fninf.2015.00003

Semantic framework for mapping object-oriented model to semantic web languages
Cited by: 10
Author(s): Petr Ježek, Roman Mouček
Software Mentions: 4
Published: about 9 years ago

10.3389/fninf.2017.00018

Neuroimaging, Genetics, and Clinical Data Sharing in Python Using the CubicWeb Framework
Cited by: 1
Author(s): Antoine Grigis, David Goyard, Robin Cherbonnier, Thomas Gareau, Dimitri Papadopoulos Orfanos, Nicolas Chauvat, Adrien Di Mascio, Gunter Schümann, Will Spooren, Declan Murphy, Vincent Frouin
Software Mentions: 4
Published: about 7 years ago

10.1155/2013/983805

NCBI2RDF: Enabling Full RDF-Based Access to NCBI Databases
Cited by: 10
Author(s): Alberto Anguita, Miguel García-Remesal, Diana de la Iglesia, Víctor Maojo
Software Mentions: 4
Published: over 11 years ago

10.1186/2041-1480-4-9

Semantic querying of relational data for clinical intelligence: a semantic web services-based approach
Cited by: 21
Author(s): Alexandre Riazanov, Artjom Klein, Arash Shaban-Nejad, Greg Rose, Alan J. Forster, David L. Buckeridge, Christopher J. O. Baker
Software Mentions: 4
Published: over 11 years ago

10.1093/database/baw145

Text mining resources for the life sciences
Cited by: 34
Author(s): Piotr Przybyła, Matthew Shardlow, Sophie Aubin, Robert Bossy, Richard Eckart de Castilho, Stelios Piperidis, John McNaught, Sophia Ananiadou
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0255562

An adaptive spark-based framework for querying large-scale NoSQL and relational databases
Cited by: 0
Author(s): Eman A. Khashan, Ali I. El-Desouky, Sally M. Elghamrawy
Software Mentions: 4
Published: almost 3 years ago

10.7717/peerj.5551

BioWorkbench: a high-performance framework for managing and analyzing bioinformatics experiments
Cited by: 11
Author(s): Maria Luiza Mondelli, Thiago Tavares Magalhães, Guilherme Loss, Michael Wilde, Ian Foster, Marta Mattoso, Daniel S. Katz, Hélio J. C. Barbosa, Ana Tereza Ribeiro de Vasconcelos, Kary Ocaña, Luiz M. R. Gadelha
Software Mentions: 4
Published: over 5 years ago

10.12688/f1000research.21027.2

A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL
Cited by: 0
Author(s): Ana Claudia Sima, Christophe Dessimoz, Kurt Stockinger, Monique Zahn-Zabal, Tarcisio Mendes de Farias
Software Mentions: 4
Published: almost 4 years ago

10.3389/fcimb.2017.00031

Persistence of Functional Protein Domains in Mycoplasma Species and their Role in Host Specificity and Synthetic Minimal Life
Cited by: 10
Author(s): Tjerko Kamminga, Jasper J. Koehorst, Paul Vermeij, Simen-Jan Slagman, Vítor A. P. Martins dos Santos, Jetta J. E. Bijlsma, Peter J. Schaap
Software Mentions: 4
Published: over 7 years ago

10.3390/ijerph10116106

IAServ: An Intelligent Home Care Web Services Platform in a Cloud for Aging-in-Place
Cited by: 27
Author(s): Chuan‐Jun Su, Chang-Yu Chiang
Software Mentions: 4
Published: over 10 years ago

10.1101/2020.08.17.254839

KG-COVID-19: a framework to produce customized knowledge graphs for COVID-19 response
Cited by: 5
Author(s): Justin Reese, Deepak Unni, Tiffany J. Callahan, Luca Cappelletti, Vida Ravanmehr, Seth Carbon, Tommaso Fontana, Hannah Blau, Nicolas Matentzoglu, Nomi L. Harris, Monica Munoz‐Torres, Peter N. Robinson, Marcin P. Joachimiak, Christopher J. Mungall
Software Mentions: 4
Published: almost 4 years ago

10.1186/1471-2105-15-176

QMachine: commodity supercomputing in web browsers
Cited by: 17
Author(s): Sean R. Wilkinson, Jonas S. Almeida
Software Mentions: 4
Published: almost 10 years ago

10.7554/eLife.52614

Wikidata as a knowledge graph for the life sciences
Cited by: 64
Author(s): Andra Waagmeester, Gregory S. Stupp, Sebastian Burgstaller-Muehlbacher, Benjamin M. Good, Malachi Griffith, Obi L. Griffith, Kristina Hanspers, Henning Hermjakob, Toby Hudson, Kevin Hybiske, Sarah M. Keating, Magnus Manske, Michael Mayers, Daniel Mietchen, Elvira Mitraka, Alexander Pico, Tim Putman, Anders Riutta, Núria Queralt-Rosiñach, Lynn M. Schriml, Thomas Shafee, Denise Slenter, Ralf Stephan, Katherine Thornton, Ginger Tsueng, Roger Tu, Sabah Ul-Hasan, Egon Willighagen, Chunlei Wu, Andrew I. Su
Software Mentions: 4
Published: about 4 years ago

10.3390/s21134322

Semantic Data Mining in Ubiquitous Sensing: A Survey
Cited by: 2
Author(s): Grzegorz J. Nalepa, Szymon Bobek, Krzysztof Kutt, Martin Atzmueller
Software Mentions: 4
Published: almost 3 years ago

10.1155/2014/134023

Managing, Analysing, and Integrating Big Data in Medical Bioinformatics: Open Problems and Future Perspectives
Cited by: 105
Author(s): Ivan Merelli, Horacio Pérez‐Sánchez, Sandra Gesing, Daniele D’Agostino
Software Mentions: 4
Published: over 10 years ago

10.3389/fphar.2019.00415

Computational Advances in Drug Safety: Systematic and Mapping Review of Knowledge Engineering Based Approaches
Cited by: 7
Author(s): Pantelis Natsiavas, Andigoni Malousi, Cédric Bousquet, Marie-Christine Jaulent, Vassilis Koutkias
Software Mentions: 4
Published: about 5 years ago

10.3390/s17020403

Towards a Semantic Web of Things: A Hybrid Semantic Annotation, Extraction, and Reasoning Framework for Cyber-Physical System
Cited by: 27
Author(s): Zhenyu Wu, Yuan Xu, Yunong Yang, Chunhong Zhang, Xinning Zhu, Yang Ji
Software Mentions: 4
Published: about 7 years ago

10.3390/s20113166

A Distributed Stream Processing Middleware Framework for Real-Time Analysis of Heterogeneous Data on Big Data Platform: Case of Environmental Monitoring
Cited by: 15
Author(s): Adeyinka K. Akanbi, Muthoni Masinde
Software Mentions: 4
Published: almost 4 years ago

10.1186/1471-2105-9-295

Systems biology driven software design for the research enterprise
Cited by: 18
Author(s): John P. Boyle, Christopher C. Cavnor, Sarah Killcoyne, Ilya Shmulevich
Software Mentions: 4
Published: almost 16 years ago

10.1038/s41597-019-0263-7

The Empusa code generator and its application to GBOL, an extendable ontology for genome annotation
Cited by: 9
Author(s): Jesse C. J. van Dam, Jasper J. Koehorst, Jon Olav Vik, Vítor A. P. Martins dos Santos, Peter J. Schaap, María Suárez-Diez
Software Mentions: 4
Published: over 4 years ago

10.1038/s41597-019-0055-0

BioWordVec, improving biomedical word embeddings with subword information and MeSH
Cited by: 269
Author(s): Yijia Zhang, Qingyu Chen, Zhihao Yang, Hongfei Lin, Zhiyong Lu
Software Mentions: 4
Published: about 5 years ago

10.1155/2014/121782

Towards the Novel Reasoning among Particles in PSO by the Use of RDF and SPARQL
Cited by: 17
Author(s): Iztok Fister, Xin-She Yang, Karin Ljubič, Dušan Fister, Janez Brest
Software Mentions: 4
Published: over 10 years ago

10.3390/s21010010

MUP: Simplifying Secure Over-The-Air Update with MQTT for Constrained IoT Devices
Cited by: 4
Author(s): Kristina Sahlmann, Vera Clemens, Michael A. Nowak, Bettina Schnor
Software Mentions: 4
Published: over 3 years ago

10.1186/s13326-017-0118-0

BioFed: federated query processing over life sciences linked open data
Cited by: 43
Author(s): Ali Hasnain, Qaiser Mehmood, Syeda Sana e Zainab, Muhammad Saleem, Claude N. Warren, Durre Zehra, Stefan Decker, Dietrich Rebholz‐Schuhmann
Software Mentions: 4
Published: about 7 years ago

10.1186/2041-1480-5-42

Executing SADI services in Galaxy
Cited by: 7
Author(s): Mikel Egaña Aranguren, Alejandro Rodríguez Gonzàlez, Mark D. Wilkinson
Software Mentions: 4
Published: over 10 years ago

10.1186/s13326-018-0181-1

Deep learning meets ontologies: experiments to anchor the cardiovascular disease ontology in the biomedical literature
Cited by: 32
Author(s): Mercedes Argüello Casteleiro, George Demetriou, Warren Read, Maria Jesus Fernandez Prieto, Nava Maroto, Diego Maseda Fernandez, Goran Nenadić, Julie Klein, John Keane, Robert Stevens
Software Mentions: 4
Published: about 6 years ago

10.1155/2016/6741418

An Interoperability Platform Enabling Reuse of Electronic Health Records for Signal Verification Studies
Cited by: 10
Author(s): Mustafa Yuksel, Suat Gönül, Gökçe Banu Laleci Ertürkmen, Ali Anıl Sınacı, Paolo Invernizzi, Sara Facchinetti, Andrea Migliavacca, Tomas Bergvall, Kristof Depraetere, Jos De Roo
Software Mentions: 4
Published: over 8 years ago

10.1186/1471-2105-10-S12-S7

XML-based approaches for the integration of heterogeneous bio-molecular data
Cited by: 26
Author(s): Marco Mesiti, Ernesto Jiménez-Ruiz, Ismael Sanz, Rafael Berlanga, Paolo Perlasca, Giorgio Valentini, David Manset
Software Mentions: 4
Published: over 14 years ago

10.12688/wellcomeopenres.10210.2

SciLite: a platform for displaying text-mined annotations as a means to link research articles with biological data
Cited by: 17
Author(s): Aravind Venkatesan, Jee-Hyub Kim, Francesco Talo, Michele Ide-Smith, Julien Gobeill, Jacob Carter, Riza Theresa Batista-Navarro, Sophia Ananiadou, Patrick Ruch, Johanna McEntyre
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pcbi.1009041

Ten simple rules for making a vocabulary FAIR
Cited by: 19
Author(s): Simon J. Cox, Alejandra N. González-Beltrán, Barbara Magagna, Maria-Cristina Marinescu
Software Mentions: 4
Published: almost 3 years ago

10.1186/2041-1480-5-41

Structuring research methods and data with the research object model: genomics workflows as a case study
Cited by: 26
Author(s): Kristina Hettne, Harish Dharuri, Jun Zhao, Katy Wolstencroft, Khalid Belhajjame, Stian Soiland‐Reyes, Eleni Mina, Mark Thompson, Don Cruickshank, L. Verdes–Montenegro, Julián Garrido, David De Roure, Óscar Corcho, Graham Klyne, Reinout van Schouwen, Peter A C ‘t Hoen, Sean Bechhofer, Carole Goble, Marco Roos
Software Mentions: 4
Published: over 9 years ago

10.7717/peerj-cs.297

Data in the time of COVID-19: a general methodology to select and secure a NoSQL DBMS for medical data
Cited by: 9
Author(s): Kamal A. ElDahshan, Abd Allah A. AlHabshy, Gaber E. Abutaleb
Software Mentions: 3
Published: over 3 years ago

10.1186/2041-1480-3-11

COEUS: “semantic web in a box” for biomedical applications
Cited by: 37
Author(s): Pedro Lopes, José Luís Oliveira
Software Mentions: 3
Published: over 12 years ago

10.7717/peerj-cs.164

20 GB in 10 minutes: a case for linking major biodiversity databases using an open socio-technical infrastructure and a pragmatic, cross-institutional collaboration
Cited by: 4
Author(s): Anne E. Thessen, Jorrit Poelen, Matthew Collins, Jen Hammock
Software Mentions: 3
Published: over 5 years ago

10.1186/2041-1480-2-S1-S1

Biomedical semantics in the Semantic Web
Cited by: 12
Author(s): Andrea Splendiani, Albert Burger, Adrian Paschke, Paolo Romano, M. Scott Marshall
Software Mentions: 3
Published: about 13 years ago

10.1186/2041-1480-4-6

The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies
Cited by: 27
Author(s): Toshiaki Katayama, Mark D. Wilkinson, Gos Micklem, Seiichiro Kawashima, Atsuko Yamaguchi, Mitsuteru Nakao, Yasunori Yamamoto, Shinobu Okamoto, Kenta Oouchida, Hong Woo Chun, Jan Aerts, Hammad Afzal, Erick Antezana, Kazuharu Arakawa, Bruno Aranda, François Belleau, Jerven Bolleman, Raoul Jean Pierre Bonnal, Brad Chapman, Peter J. A. Cock, Tore Eriksson, Paul M. Gordon, Naohisa Goto, Kazuhiro Hayashi, Heiko Horn, Ryosuke Ishiwata, Eli Kaminuma, Arek Kasprzyk, Hideya Kawaji, Nobuhiro Kido, Young Joo Kim, Akira R. Kinjo, Fumikazu Konishi, Kyung Hoon Kwon, Alberto Labarga, Anna‐Lena Lamprecht, Yuling Lin, Pierre Livet, Luke McCarthy, Hideyuki Morita, Katsuhiko Murakami, Koji Nagao, Kozo Nishida, Kunihiro Nishimura, Tatsuya Nishizawa, Soichi Ogishima, Keiichiro Ono, Kazuki Oshita, Keun Joon Park, Pjotr Prins, Taro Saito, Matthias Samwald, Venkata Satagopam, Yasumasa Shigemoto, Richard N. Smith, Andrea Splendiani, Hideaki Sugawara, James Taylor, Rutger A. Vos, David Withers, Chisato Yamasaki, Christian M. Zmasek, Shoko Kawamoto, Kosaku Okubo, Kiyoshi Asai, Toshihisa Takagi
Software Mentions: 3
Published: over 11 years ago

10.7717/peerj-cs.254

An approach for semantic integration of heterogeneous data sources
Cited by: 6
Author(s): Giuseppe Fusco, Lerina Aversano
Software Mentions: 3
Published: about 4 years ago

10.1093/gigascience/giaa003

HAMAP as SPARQL rules—A portable annotation pipeline for genomes and proteomes
Cited by: 5
Author(s): Jerven Bolleman, Edouard de Castro, Delphine Baratin, Sébastien Géhant, Beatrice A Cuche, Andrea H. Auchincloss, Elisabeth Coudert, Chantal Hulo, Patrick Masson, Ivo Pedruzzi, Catherine Rivoire, Ioannis Xénarios, Nicole Redaschi, Alan Bridge
Software Mentions: 3
Published: over 4 years ago

10.1186/s13059-016-0924-1

JBrowse: a dynamic web platform for genome visualization and analysis
Cited by: 595
Author(s): Robert Buels, Eric Yao, Colin Diesh, Richard D. Hayes, Monica Muñoz-Torres, Gregg Helt, David Goodstein, Christine G. Elsik, Suzanna Lewis, Lincoln Stein, Ian Holmes
Software Mentions: 3
Published: about 8 years ago

10.1186/2041-1480-4-5

Dynamic enhancement of drug product labels to support drug safety, efficacy, and effectiveness
Cited by: 21
Author(s): Richard D. Boyce, John R. Horn, Oktie Hassanzadeh, Anita de Waard, Jodi Schneider, Joanne S. Luciano, Majid Rastegar-Mojarad, Maria Liakata
Software Mentions: 3
Published: over 11 years ago

10.3389/fpls.2018.00352

MorphDB: Prioritizing Genes for Specialized Metabolism Pathways and Gene Ontology Categories in Plants
Cited by: 7
Author(s): Arthur Zwaenepoel, Tim Diels, David Amar, Thomas Van Parys, Ron Shamir, Yves Van de Peer, Oren Tzfadia
Software Mentions: 3
Published: about 6 years ago

10.7717/peerj.6739

Ozymandias: a biodiversity knowledge graph
Cited by: 18
Author(s): Roderic Page
Software Mentions: 3
Published: about 5 years ago

10.1016/j.patter.2020.100155

KG-COVID-19: A Framework to Produce Customized Knowledge Graphs for COVID-19 Response
Cited by: 54
Author(s): Justin Reese, Deepak Unni, Tiffany J. Callahan, Luca Cappelletti, Vida Ravanmehr, Seth Carbon, Kent Shefchek, Benjamin M. Good, James P. Balhoff, Tommaso Fontana, Hannah Blau, Nicolas Matentzoglu, Nomi L. Harris, Monica Munoz‐Torres, Melissa Haendel, Peter N. Robinson, Marcin P. Joachimiak, Christopher J. Mungall
Software Mentions: 3
Published: over 3 years ago

10.3897/zookeys.150.1766

Data issues in the life sciences
Cited by: 93
Author(s): Anne E. Thessen, David J. Patterson
Software Mentions: 3
Published: over 12 years ago

10.1186/1756-0500-4-487

Computational toxicology using the OpenTox application programming interface and Bioclipse
Cited by: 17
Author(s): Egon Willighagen, Nina Jeliazkova, Barry Hardy, Roland C. Grafström, Ola Spjuth
Software Mentions: 3
Published: over 12 years ago

10.1186/1756-0500-3-175

OntoFox: web-based support for ontology reuse
Cited by: 170
Author(s): Zuoshuang Xiang, Mélanie Courtot, Ryan R. Brinkman, Alan Ruttenberg, Yongqun He
Software Mentions: 3
Published: almost 14 years ago

10.1186/1759-4499-1-3

Head in the clouds: Re-imagining the experimental laboratory record for the web-based networked world
Cited by: 6
Author(s): Cameron Neylon
Software Mentions: 3
Published: over 15 years ago

10.7717/peerj.3997

Indicators for the use of robotic labs in basic biomedical research: a literature analysis
Cited by: 9
Author(s): Paul Groth, Jessica Cox
Software Mentions: 3
Published: over 6 years ago

10.3389/fdata.2020.00012

FoodKG: A Tool to Enrich Knowledge Graphs Using Machine Learning Techniques
Cited by: 8
Author(s): Mohamed Gharibi, Arun Zachariah, Praveen Rao
Software Mentions: 3
Published: about 4 years ago

10.1002/mp.14322

FAIR‐compliant clinical, radiomics and DICOM metadata of RIDER, interobserver, Lung1 and head‐Neck1 TCIA collections
Cited by: 16
Author(s): Petros Kalendralis, Zhenwei Shi, Alberto Traverso, Ananya Choudhury, Matthijs Sloep, Ivan Zhovannik, Martijn P.A. Starmans, Detlef Grittner, Peter Feltens, R. Monshouwer, Stefan Klein, Rianne Fijten, Hugo J.W.L. Aerts, André Dekker, Johan van Soest, Leonard Wee
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12859-014-0386-y

Finding gene regulatory network candidates using the gene expression knowledge base
Cited by: 8
Author(s): Aravind Venkatesan, Sushil Tripathi, Alejandro Sanz de Galdeano, Ward Blondé, Astrid Lægreid, Vladimir Mironov, Martin Kuiper
Software Mentions: 3
Published: over 9 years ago

10.1093/molbev/msz150

Advances and Applications in the Quest for Orthologs
Cited by: 68
Author(s): Natasha Glover, Christophe Dessimoz, Ingo Ebersberger, Kristoffer Forslund, Toni Gabaldón, Jaime Huerta-Cepas, Maria Jesus Martin, Matthieu Muffato, Mateus Patrício, Cécile Pereira, Alan Wilter Sousa da Silva, Yan Wang, Erik L. L. Sonnhammer, Paul D. Thomas
Software Mentions: 3
Published: almost 5 years ago

10.3389/fbioe.2015.00038

Metabolonote: A Wiki-Based Database for Managing Hierarchical Metadata of Metabolome Analyses
Cited by: 33
Author(s): Takeshi Ara, Mitsuo Enomoto, Masanori Arita, Chiaki Ikeda, Kota Kera, Manabu Yamada, Takaaki Nishioka, Tasuku Ikeda, Yoshito Nihei, Daisuke Shibata, Shigehiko Kanaya, Nozomu Sakurai
Software Mentions: 3
Published: about 9 years ago

10.1002/mp.13844

Technical Note: Ontology‐guided radiomics analysis workflow (O‐RAW)
Cited by: 35
Author(s): Zhenwei Shi, Alberto Traverso, Johan van Soest, André Dekker, Leonard Wee
Software Mentions: 3
Published: over 4 years ago

10.12688/f1000research.9416.3

Protein domain architectures provide a fast, efficient and scalable alternative to sequence-based methods for comparative functional genomics
Cited by: 4
Author(s): Jasper J. Koehorst, Edoardo Saccenti, Peter J. Schaap, Vítor A. P. Martins dos Santos, María Suárez-Diez
Software Mentions: 3
Published: almost 7 years ago

10.1186/1471-2105-15-S14-S4

linkedISA: semantic representation of ISA-Tab experimental metadata
Cited by: 55
Author(s): Alejandra N. González-Beltrán, Eamonn Maguire, Susanna-Assunta Sansone, Philippe Rocca-Serra
Software Mentions: 3
Published: over 9 years ago

10.1093/database/baw015

Wikidata as a semantic framework for the Gene Wiki initiative
Cited by: 47
Author(s): Sebastian Burgstaller-Muehlbacher, Andra Waagmeester, Elvira Mitraka, Julia Turner, Tim Putman, Justin Leong, Chinmay Naik, Paul Pavlidis, Lynn M. Schriml, Benjamin M. Good, Andrew I. Su
Software Mentions: 3
Published: over 8 years ago

10.1242/dev.196097

Planarian Anatomy Ontology: a resource to connect data within and across experimental platforms
Cited by: 9
Author(s): Stephanie H. Nowotarski, Erin L Davies, Sofia Robb, E. J. Ross, Nicolas Matentzoglu, Viraj Doddihal, Mol Mir, Melainia McClain, Alejandro Sánchez Alvarado
Software Mentions: 3
Published: almost 3 years ago

10.1186/s12911-019-0806-z

A mobile health monitoring-and-treatment system based on integration of the SSN sensor ontology and the HL7 FHIR standard
Cited by: 49
Author(s): Shaker El–Sappagh, Farman Ali, Abdeltawab Hendawi, Jun‐Hyeog Jang, Kyung Sup Kwak
Software Mentions: 3
Published: about 5 years ago

10.12688/wellcomeopenres.15355.2

GeneDB and Wikidata
Cited by: 2
Author(s): Magnus Manske, Ulrike Böhme, Christoph Püthe, Matthew Berriman
Software Mentions: 3
Published: over 4 years ago

10.1186/1471-2105-10-309

SSWAP: A Simple Semantic Web Architecture and Protocol for semantic web services
Cited by: 58
Author(s): Damian D. G. Gessler, Gary Schiltz, Gregory D. May, Shulamit Avraham, Christopher D. Town, David M. Grant, Rex T. Nelson
Software Mentions: 3
Published: over 14 years ago

10.1155/2020/3041498

SCALEUS-FD: A FAIR Data Tool for Biomedical Applications
Cited by: 5
Author(s): Arnaldo Pereira, Rui Pedro Lopes, José Luís Oliveira
Software Mentions: 3
Published: over 3 years ago

Projects: cran: SPARQL

Papers Mentioning SPARQL 660