Works by Ruttenberg, Alan

Results: 24

flowCL: ontology-based cell population labelling in flow cytometry.

Published in:

Bioinformatics, 2015, v. 31, n. 8, p. 1337, doi. 10.1093/bioinformatics/btu807

By:

Courtot, Mélanie;
Meskas, Justin;
Diehl, Alexander D.;
Droumeva, Radina;
Gottardo, Raphael;
Jalali, Adrin;
Taghiyar, Mohammad Jafar;
Maecker, Holden T.;
McCoy, J. Philip;
Ruttenberg, Alan;
Scheuermann, Richard H.;
Brinkman, Ryan R.

Publication type:

Article

flowCL: ontology-based cell population labelling in flow cytometry.

Published in:

2015

By:

Courtot, Mélanie;
Meskas, Justin;
Diehl, Alexander D.;
Droumeva, Radina;
Gottardo, Raphael;
Jalali, Adrin;
Taghiyar, Mohammad Jafar;
Maecker, Holden T.;
McCoy, J. Philip;
Ruttenberg, Alan;
Scheuermann, Richard H.;
Brinkman, Ryan R.

Publication type:

Product Review

A strategy for building neuroanatomy ontologies.

Published in:

2012

By:

Osumi-Sutherland, David;
Reeve, Simon;
Mungall, Christopher J.;
Neuhaus, Fabian;
Ruttenberg, Alan;
Jefferis, Gregory S. X. E.;
Armstrong, J. Douglas

Publication type:

Correction Notice

A strategy for building neuroanatomy ontologies.

Published in:

Bioinformatics, 2012, v. 28, n. 9, p. 1262, doi. 10.1093/bioinformatics/bts113

By:

Osumi-Sutherland, David;
Reeve, Simon;
Mungall, Christopher J.;
Neuhaus, Fabian;
Ruttenberg, Alan;
Jefferis, Gregory S. X. E.;
Armstrong, J. Douglas

Publication type:

Article

Detection of Activity Centers in Cellular Pathways Using Transcript Profiling.

Published in:

Journal of Biopharmaceutical Statistics, 2004, v. 14, n. 3, p. 701, doi. 10.1081/BIP-200025678

By:

Pradines, Joel;
Rudolph-Owen, Laura;
Hunter, John;
Leroy, Patrick;
Cary, Michael;
Coopersmith, Robert;
Dancik, Vlado;
Eltsefon, Yelena;
Farutin, Victor;
Leroy, Christophe;
Rees, Jonathan;
Rose, David;
Rowley, Steve;
Ruttenberg, Alan;
Wieghardt, Patrick;
Sander, Chris;
Reich, Christian

Publication type:

Article

Correction: Toll-Like Receptor Signaling in Vertebrates: Testing the Integration of Protein, Complex, and Pathway Data in the Protein Ontology Framework.

Published in:

PLoS ONE, 2015, v. 10, n. 6, p. 1, doi. 10.1371/journal.pone.0131148

By:

Arighi, Cecilia;
Shamovsky, Veronica;
Masci, Anna Maria;
Ruttenberg, Alan;
Smith, Barry;
Natale, Darren A.;
Wu, Cathy;
D’Eustachio, Peter

Publication type:

Article

Toll-Like Receptor Signaling in Vertebrates: Testing the Integration of Protein, Complex, and Pathway Data in the Protein Ontology Framework.

Published in:

PLoS ONE, 2015, v. 10, n. 4, p. 1, doi. 10.1371/journal.pone.0122978

By:

Arighi, Cecilia;
Shamovsky, Veronica;
Masci, Anna Maria;
Ruttenberg, Alan;
Smith, Barry;
Natale, Darren A.;
Wu, Cathy;
D’Eustachio, Peter

Publication type:

Article

The Logic of Surveillance Guidelines: An Analysis of Vaccine Adverse Event Reports from an Ontological Perspective.

Published in:

PLoS ONE, 2014, v. 9, n. 3, p. 1, doi. 10.1371/journal.pone.0092632

By:

Courtot, Mélanie;
Brinkman, Ryan R.;
Ruttenberg, Alan

Publication type:

Article

Structuring, reuse and analysis of electronic dental data using the Oral Health and Disease Ontology.

Published in:

Journal of Biomedical Semantics, 2020, v. 11, n. 1, p. N.PAG, doi. 10.1186/s13326-020-00222-0

By:

Duncan, William D.;
Thyvalikakath, Thankam;
Haendel, Melissa;
Torniai, Carlo;
Hernandez, Pedro;
Song, Mei;
Acharya, Amit;
Caplan, Daniel J.;
Schleyer, Titus;
Ruttenberg, Alan

Publication type:

Article

The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0088-7

By:

Diehl, Alexander D.;
Meehan, Terrence F.;
Bradford, Yvonne M.;
Brush, Matthew H.;
Dahdul, Wasila M.;
Dougall, David S.;
Yongqun He;
Osumi-Sutherland, David;
Ruttenberg, Alan;
Sarntivijai, Sirarat;
Van Slyke, Ceri E.;
Vasilevsky, Nicole A.;
Haendel, Melissa A.;
Blake, Judith A.;
Mungall, Christopher J.

Publication type:

Article

OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0064-2

By:

Jingshan Huang;
Gutierrez, Fernando;
Strachan, Harrison J.;
Dejing Dou;
Weili Huang;
Smith, Barry;
Blake, Judith A.;
Eilbeck, Karen;
Natale, Darren A.;
Yu Lin;
Bin Wu;
de Silva, Nisansa;
Xiaowei Wang;
Zixing Liu;
Borchert, Glen M.;
Ming Tan;
Ruttenberg, Alan

Publication type:

Article

The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology.

Published in:

Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0066-0

By:

Jingshan Huang;
Eilbeck, Karen;
Smith, Barry;
Blake, Judith A.;
Dejing Dou;
Weili Huang;
Natale, Darren A.;
Ruttenberg, Alan;
Jun Huan;
Zimmermann, Michael T.;
Guoqian Jiang;
Yu Lin;
Bin Wu;
Strachan, Harrison J.;
Yongqun He;
Shaojie Zhang;
Xiaowei Wang;
Zixing Liu;
Borchert, Glen M.;
Ming Tan

Publication type:

Article

The neurological disease ontology.

Published in:

Journal of Biomedical Semantics, 2013, v. 4, n. 1, p. 3, doi. 10.1186/2041-1480-4-42

By:

Jensen, Mark;
Cox, Alexander P.;
Chaudhry, Naveed;
Ng, Marcus;
Sule, Donat;
Duncan, William;
Weinstock-Guttman, Bianca;
Smith, Barry;
Ruttenberg, Alan;
Szigeti, Kinga;
Diehl, Alexander D.;
Ray, Patrick

Publication type:

Article

Modeling biomedical experimental processes with OBI.

Published in:

Journal of Biomedical Semantics, 2010, v. 1, n. Suppl 1, p. 1, doi. 10.1186/2041-1480-1-S1-S7

By:

Brinkman, Ryan R.;
Courtot, Mélanie;
Derom, Dirk;
Fostel, Jennifer M.;
Yongqun He;
Lord, Phillip;
Malone, James;
Parkinson, Helen;
Peters, Bjoern;
Rocca-Serra, Philippe;
Ruttenberg, Alan;
Sansone, Susanna-Assunta;
Soldatova, Larisa N.;
Stoeckert, Jr., Christian J.;
Turner, Jessica A.;
Jie Zheng

Publication type:

Article

The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration.

Published in:

Nature Biotechnology, 2007, v. 25, n. 11, p. 1251, doi. 10.1038/nbt1346

By:

Smith, Barry;
Ashburner, Michael;
Rosse, Cornelius;
Bard, Jonathan;
Bug, William;
Ceusters, Werner;
Goldberg, Louis J.;
Eilbeck, Karen;
Ireland, Amelia;
Mungall, Christopher J.;
Leontis, Neocles;
Rocca-Serra, Philippe;
Ruttenberg, Alan;
Sansone, Susanna-Assunta;
Scheuermann, Richard H.;
Nigam Shah;
Whetzel, Patricia L.;
Lewis, Suzanna

Publication type:

Article

Edge-count probabilities for the identification of local protein communities and their organization.

Published in:

Proteins, 2006, v. 62, n. 3, p. 800, doi. 10.1002/prot.20799

By:

Farutin, Victor;
Robison, Keith;
Lightcap, Eric;
Dancik, Vlado;
Ruttenberg, Alan;
Letovsky, Stanley;
Pradines, Joel

Publication type:

Article

Life sciences on the Semantic Web: the Neurocommons and beyond.

Published in:

Briefings in Bioinformatics, 2009, v. 10, n. 2, p. 193, doi. 10.1093/bib/bbp004

By:

Ruttenberg, Alan;
Rees, Jonathan A.;
Samwald, Matthias;
Marshall, M. Scott

Publication type:

Article

Computational knowledge integration in biopharmaceutical research.

Published in:

Briefings in Bioinformatics, 2003, v. 4, n. 3, p. 260, doi. 10.1093/bib/4.3.260

By:

Ficenec, David;
Osborne, Mark;
Pradines, Joel;
Richards, Dan;
Felciano, Ramon;
Cho, Raymond J.;
Chen, Richard O.;
Liefeld, Ted;
Owen, James;
Ruttenberg, Alan;
Reich, Christian;
Horvath, Joseph;
Clark, Tim

Publication type:

Article

OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies.

Published in:

Database: The Journal of Biological Databases & Curation, 2021, v. 2021, p. 1, doi. 10.1093/database/baab069

By:

Jackson, Rebecca;
Matentzoglu, Nicolas;
Overton, James A;
Vita, Randi;
Balhoff, James P;
Buttigieg, Pier Luigi;
Carbon, Seth;
Courtot, Melanie;
Diehl, Alexander D;
Dooley, Damion M;
Duncan, William D;
Harris, Nomi L;
Haendel, Melissa A;
Lewis, Suzanna E;
Natale, Darren A;
Osumi-Sutherland, David;
Ruttenberg, Alan;
Schriml, Lynn M;
Smith, Barry;
Stoeckert Jr., Christian J

Publication type:

Article

OntoFox: web-based support for ontology reuse.

Published in:

BMC Research Notes, 2010, v. 3, p. 175, doi. 10.1186/1756-0500-3-175

By:

Zuoshuang Xiang;
Courtot, Mélanie;
Brinkman, Ryan R.;
Ruttenberg, Alan;
Yongqun He

Publication type:

Article

Improving the Quality and Utility of Electronic Health Record Data through Ontologies.

Published in:

Standards (2305-6703), 2023, v. 3, n. 3, p. 316, doi. 10.3390/standards3030023

By:

Lin, Asiyah Yu;
Arabandi, Sivaram;
Beale, Thomas;
Duncan, William D.;
Hicks, Amanda;
Hogan, William R.;
Jensen, Mark;
Koppel, Ross;
Martínez-Costa, Catalina;
Nytrø, Øystein;
Obeid, Jihad S.;
Oliveira, Jose Parente de;
Ruttenberg, Alan;
Seppälä, Selja;
Smith, Barry;
Soergel, Dagobert;
Zheng, Jie;
Schulz, Stefan

Publication type:

Article

Protein Ontology (PRO): enhancing and scaling up the representation of protein entities.

Published in:

Nucleic Acids Research, 2017, v. 45, n. D1, p. D339, doi. 10.1093/nar/gkw1075

By:

Natale, Darren A.;
Arighi, Cecilia N.;
Blake, Judith A.;
Bona, Jonathan;
Chuming Chen;
Sheng-Chih Chen;
Christie, Karen R.;
Cowart, Julie;
D’Eustachio, Peter;
Diehl, Alexander D.;
Drabkin, Harold J.;
Duncan, William D.;
Huang, Hongzhan;
Ren, Jia;
Ross, Karen;
Ruttenberg, Alan;
Shamovsky, Veronica;
Smith, Barry;
Qinghua Wang;
Jian Zhang

Publication type:

Article

Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration.

Published in:

Nucleic Acids Research, 2017, v. 45, n. D1, p. D347, doi. 10.1093/nar/gkw918

By:

Ong, Edison;
Zuoshuang Xiang;
Bin Zhao;
Yue Liu;
Yu Lin;
Jie Zheng;
Mungall, Chris;
Courtot, Mélanie;
Ruttenberg, Alan;
Yongqun He

Publication type:

Article

Protein Ontology: a controlled structured network of protein entities.

Published in:

Nucleic Acids Research, 2014, v. 42, n. D1, p. D415, doi. 10.1093/nar/gkt1173

By:

Natale, Darren A.;
Arighi, Cecilia N.;
Blake, Judith A.;
Bult, Carol J.;
Christie, Karen R.;
Cowart, Julie;
D’Eustachio, Peter;
Diehl, Alexander D.;
Drabkin, Harold J.;
Helfer, Olivia;
Huang, Hongzhan;
Masci, Anna Maria;
Ren, Jia;
Roberts, Natalia V.;
Ross, Karen;
Ruttenberg, Alan;
Shamovsky, Veronica;
Smith, Barry;
Yerramalla, Meher Shruti;
Zhang, Jian

Publication type:

Article