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ORCIDBenjamin M. Good
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- affiliation: Scripps Research Institute, San Diego, CA, USA
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Journal Articles
- 2021
[j24]Benjamin M. Good, Kimberly Van Auken, David P. Hill, Huaiyu Mi, Seth Carbon, James P. Balhoff, Laurent-Philippe Albou
, Paul D. Thomas, Christopher J. Mungall, Judith A. Blake, Peter D'Eustachio:
Reactome and the Gene Ontology: digital convergence of data resources. Bioinform. 37(19): 3343-3348 (2021)- [j23]Seth Carbon, Eric Douglass, Benjamin M. Good, Deepak R. Unni, Nomi L. Harris, Christopher J. Mungall, Siddartha Basu, Rex L. Chisholm, Robert J. Dodson, Eric Hartline, Petra Fey, Paul D. Thomas, Laurent-Philippe Albou, Dustin Ebert, Michael J. Kesling, Huaiyu Mi, Anushya Muruganujan, Xiaosong Huang, Tremayne Mushayahama, Sandra A. LaBonte, Deborah A. Siegele, Giulia Antonazzo, Helen Attrill, Nick H. Brown, Phani V. Garapati, Steven J. Marygold, Vitor Trovisco, Gilberto dos Santos, Kathleen Falls, Christopher J. Tabone, Pinglei Zhou, Joshua L. Goodman, Victor B. Strelets, Jim Thurmond, Penelope Garmiri, Rizwan Ishtiaq, Milagros Rodríguez-López, Marcio Luis Acencio, Martin Kuiper, Astrid Lægreid, Colin Logie, Ruth C. Lovering, Barbara Kramarz, Shirin C. C. Saverimuttu, Sandra M. Pinheiro, Heather Gunn, Renzhi Su, Katherine E. Thurlow, Marcus C. Chibucos, Michelle G. Giglio, Suvarna Nadendla, James B. Munro, Rebecca C. Jackson, Margaret J. Duesbury, Noemi del-Toro, Birgit H. M. Meldal, Kalpana Paneerselvam, Livia Perfetto, Pablo Porras, Sandra E. Orchard, Anjali Shrivastava, Hsin-Yu Chang, Robert D. Finn, Alex L. Mitchell, Neil D. Rawlings, Lorna J. Richardson, Amaia Sangrador-Vegas, Judith A. Blake, Karen R. Christie, Mary E. Dolan, Harold J. Drabkin, David P. Hill, Li Ni, Dmitry M. Sitnikov, Midori A. Harris, Stephen G. Oliver, Kim Rutherford, Valerie Wood, Jaqueline Hayles, Jürg Bähler, Elizabeth R. Bolton, Jeffrey DePons, Melinda R. Dwinell, G. Thomas Hayman, Mary L. Kaldunski, Anne E. Kwitek, Stanley J. F. Laulederkind, Cody Plasterer, Marek Tutaj, Mahima Vedi, Shur-Jen Wang, Peter D'Eustachio, Lisa Matthews, James P. Balhoff, Suzi A. Aleksander, Michael J. Alexander, J. Michael Cherry, Stacia R. Engel, Felix Gondwe, Kalpana Karra, Stuart R. Miyasato, Robert S. Nash, Matt Simison, Marek S. Skrzypek, Shuai Weng, Edith D. Wong, Marc Feuermann, Pascale Gaudet, Anne Morgat, Erica Bakker, Tanya Z. Berardini, Leonore Reiser, Shabari Subramaniam, Eva Huala, Cecilia N. Arighi, Andrea H. Auchincloss, Kristian B. Axelsen, Ghislaine Argoud-Puy, Alex Bateman, Marie-Claude Blatter, Emmanuel Boutet, Emily Bowler, Lionel Breuza, Alan J. Bridge, Ramona Britto, Hema Bye-A-Jee, Cristina Casals-Casas, Elisabeth Coudert, Paul Denny, Anne Estreicher, Maria Livia Famiglietti, George E. Georghiou, Arnaud Gos, Nadine Gruaz-Gumowski, Emma Hatton-Ellis, Chantal Hulo, Alexandr Ignatchenko, Florence Jungo, Kati Laiho, Philippe Le Mercier, Damien Lieberherr, Antonia Lock, Yvonne Lussi, Alistair MacDougall, Michele Magrane, Maria Jesus Martin, Patrick Masson, Darren A. Natale, Nevila Hyka-Nouspikel, Ivo Pedruzzi, Lucille Pourcel, Sylvain Poux, Sangya Pundir, Catherine Rivoire, Elena Speretta, Shyamala Sundaram, Nidhi Tyagi, Kate Warner, Rossana Zaru, Cathy H. Wu, Alexander D. Diehl, Juancarlos Chan, Christian A. Grove, Raymond Y. N. Lee, Hans-Michael Müller, Daniela Raciti, Kimberly Van Auken, Paul W. Sternberg, Matthew Berriman, Michael Paulini, Kevin L. Howe, Sibyl Gao, Adam Wright, Lincoln Stein, Douglas G. Howe, Sabrina Toro, Monte Westerfield, Pankaj Jaiswal, Laurel Cooper, Justin Elser:
The Gene Ontology resource: enriching a GOld mine. Nucleic Acids Res. 49(Database-Issue): D325-D334 (2021) - [j22]Justin T. Reese, Deepak R. Unni, Tiffany J. Callahan, Luca Cappelletti, Vida Ravanmehr, Seth Carbon, Kent A. Shefchek, Benjamin M. Good, James P. Balhoff, Tommaso Fontana, Hannah Blau, Nicolas Matentzoglu, Nomi L. Harris, Monica C. Munoz-Torres, Melissa A. Haendel, Peter N. Robinson, Marcin P. Joachimiak, Christopher J. Mungall:
KG-COVID-19: A Framework to Produce Customized Knowledge Graphs for COVID-19 Response. Patterns 2(1): 100155 (2021) - 2020
- [j21]Núria Queralt-Rosinach, Gregory S. Stupp, Tong Shu Li, Michael Mayers, Maureen E. Hoatlin, Matthew Might, Benjamin M. Good, Andrew I. Su:
Structured reviews for data and knowledge-driven research. Database J. Biol. Databases Curation 2020 (2020) - [j20]Ginger Tsueng, Max Nanis, Jennifer T. Fouquier, Michael Mayers, Benjamin M. Good, Andrew I. Su:
Applying citizen science to gene, drug and disease relationship extraction from biomedical abstracts. Bioinform. 36(4): 1226-1233 (2020) - 2019
- [j19]Tim E. Putman, Kevin Hybiske, Derek Jow, Cyrus Afrasiabi, Sebastien Lelong, Marco Alvarado Cano, Gregory S. Stupp, Andra Waagmeester, Benjamin M. Good, Chunlei Wu, Andrew I. Su:
ChlamBase: a curated model organism database for the Chlamydia research community. Database J. Biol. Databases Curation 2019: baz091 (2019) - 2017
- [j18]Tim E. Putman, Sebastien Lelong, Sebastian Burgstaller-Muehlbacher, Andra Waagmeester, Colin M. Diesh, Nathan A. Dunn, Monica C. Munoz-Torres, Gregory S. Stupp, Chunlei Wu, Andrew I. Su, Benjamin M. Good:
WikiGenomes: an open web application for community consumption and curation of gene annotation data in Wikidata. Database J. Biol. Databases Curation 2017: bax025 (2017) - 2016
- [j17]Ritu Khare, Benjamin M. Good, Robert Leaman, Andrew I. Su, Zhiyong Lu:
Crowdsourcing in biomedicine: challenges and opportunities. Briefings Bioinform. 17(1): 23-32 (2016) - [j16]Àlex Bravo, Tong Shu Li, Andrew I. Su, Benjamin M. Good, Laura I. Furlong:
Combining machine learning, crowdsourcing and expert knowledge to detect chemical-induced diseases in text. Database J. Biol. Databases Curation 2016 (2016) - [j15]Sebastian Burgstaller-Muehlbacher, Andra Waagmeester, Elvira Mitraka, Julia Turner, Tim E. Putman, Justin Leong, Chinmay Naik, Paul Pavlidis, Lynn M. Schriml, Benjamin M. Good, Andrew I. Su:
Wikidata as a semantic framework for the Gene Wiki initiative. Database J. Biol. Databases Curation 2016 (2016) - [j14]Tong Shu Li, Àlex Bravo, Laura I. Furlong, Benjamin M. Good, Andrew I. Su:
A crowdsourcing workflow for extracting chemical-induced disease relations from free text. Database J. Biol. Databases Curation 2016 (2016) - [j13]Tim E. Putman, Sebastian Burgstaller-Muehlbacher, Andra Waagmeester, Chunlei Wu, Andrew I. Su, Benjamin M. Good:
Centralizing content and distributing labor: a community model for curating the very long tail of microbial genomes. Database J. Biol. Databases Curation 2016 (2016) - [j12]Karthik Gangavarapu, Vyshakh Babji, Tobias Meißner, Andrew I. Su, Benjamin M. Good:
Branch: an interactive, web-based tool for testing hypotheses and developing predictive models. Bioinform. 32(13): 2072-2074 (2016) - 2013
- [j11]Benjamin M. Good, Andrew I. Su:
Crowdsourcing for bioinformatics. Bioinform. 29(16): 1925-1933 (2013) - [j10]Erik L. Clarke, Salvatore Loguercio, Benjamin M. Good, Andrew I. Su:
A task-based approach for Gene Ontology evaluation. J. Biomed. Semant. 4(S-1): S4 (2013) - [j9]Hassan Masum, Aarthi Rao, Benjamin M. Good, Matthew H. Todd, Aled M. Edwards, Leslie Chan, Barry A. Bunin, Andrew I. Su, Zakir Thomas, Philip E. Bourne:
Ten Simple Rules for Cultivating Open Science and Collaborative R&D. PLoS Comput. Biol. 9(9) (2013) - 2012
- [j8]Benjamin M. Good, Erik L. Clarke, Salvatore Loguercio, Andrew I. Su:
Building a biomedical semantic network in Wikipedia with Semantic Wiki Links. Database J. Biol. Databases Curation 2012 (2012) - [j7]Benjamin M. Good, Erik L. Clarke, Salvatore Loguercio, Andrew I. Su:
Linking genes to diseases with a SNPedia-Gene Wiki mashup. J. Biomed. Semant. 3(S-1): S6 (2012) - [j6]Benjamin M. Good, Erik L. Clarke, Luca de Alfaro, Andrew I. Su:
The Gene Wiki in 2011: community intelligence applied to human gene annotation. Nucleic Acids Res. 40(Database-Issue): 1255-1261 (2012) - 2009
- [j5]Benjamin M. Good, Joseph T. Tennis, Mark D. Wilkinson:
Social tagging in the life sciences: characterizing a new metadata resource for bioinformatics. BMC Bioinform. 10: 313 (2009) - [j4]Benjamin M. Good, Joseph T. Tennis:
Term based comparison metrics for controlled and uncontrolled indexing languages. Inf. Res. 14(1) (2009) - 2007
- [j3]Young C. Song, Edward A. Kawas, Benjamin M. Good, Mark D. Wilkinson, Scott J. Tebbutt:
DataBiNS: a BioMoby-based data-mining workflow for biological pathways and non-synonymous SNPs. Bioinform. 23(6): 780-782 (2007) - 2006
- [j2]Benjamin M. Good, Mark D. Wilkinson:
The Life Sciences Semantic Web is Full of Creeps! Briefings Bioinform. 7(3): 275-286 (2006) - [j1]Benjamin M. Good, Edward A. Kawas, Byron Yu-Lin Kuo, Mark D. Wilkinson:
iHOPerator: user-scripting a personalized bioinformatics Web, starting with the iHOP website. BMC Bioinform. 7: 534 (2006)
Conference and Workshop Papers
- 2019
- [c17]Ginger Tsueng, Max Nanis, Jennifer T. Fouquier, Michael Mayers, Benjamin M. Good, Andrew I. Su:
Applying Citizen Science to Gene, Drug, Disease Relationship Extraction from Biomedical Abstracts. AKBC 2019 - 2018
- [c16]James P. Balhoff, Benjamin M. Good, Seth Carbon, Chris Mungall:
Arachne: an OWL RL Reasoner Applied to Gene Ontology Causal Activity Models (and Beyond). ISWC (P&D/Industry/BlueSky) 2018 - 2016
- [c15]Benjamin M. Good, Sebastian Burgstaller-Muehlbacher, Elvira Mitraka, Timothy Putman, Andrew I. Su, Andra Waagmeester:
Opportunities and Challenges Presented by Wikidata in the Context of Biocuration. ICBO/BioCreative 2016 - [c14]Benjamin M. Good, Timothy Putman, Andrew I. Su, Andra Waagmeester, Sebastian Burgstaller-Muehlbacher, Elvira Mitraka:
Opportunities and Challenges Presented by Wikidata in the Context of Biocuration. ICBO/BioCreative 2016 - [c13]Andra Waagmeester, Egon L. Willighagen, Núria Queralt Rosinach, Elvira Mitraka, Sebastian Burgstaller-Muehlbacher, Tim E. Putman, Julia Turner, Lynn M. Schriml, Paul Pavlidis, Andrew I. Su, Benjamin M. Good:
Linking Wikidata to the Rest of the Semantic Web. SWAT4LS 2016 - 2015
- [c12]Robert Leaman, Benjamin M. Good, Andrew I. Su, Zhiyong Lu:
Session Introduction. Pacific Symposium on Biocomputing 2015: 267-269 - [c11]Benjamin M. Good, Max Nanis, Chunlei Wu, Andrew I. Su:
Microtask Crowdsourcing for Disease Mention Annotation in PubMed Abstracts. Pacific Symposium on Biocomputing 2015: 282-293 - [c10]Elvira Mitraka, Andra Waagmeester, Sebastian Burgstaller-Muehlbacher, Lynn M. Schriml, Andrew I. Su, Benjamin M. Good:
Wikidata: A Platform for Data Integration and Dissemination for the Life Sciences and Beyond. SWAT4LS 2015: 69-73 - 2012
- [c9]Salvatore Loguercio, Erik L. Clarke, Benjamin M. Good, Andrew I. Su:
A Task-Based Approach for Large-Scale Evaluation of the Gene Ontology. HISB 2012: 144 - [c8]Benjamin M. Good, Salvatore Loguercio, Max Nanis, Andrew I. Su:
genegames.org: High-Throughput Access to Biological Knowledge and Reasoning through Online Games. HISB 2012: 145 - 2008
- [c7]Benjamin M. Good, Joseph T. Tennis:
Evidence of term-structure differences among folksonomies and controlled indexing languages. ASIST 2008: 1-7 - [c6]François Belleau, Nicole Tourigny, Benjamin M. Good, Jean Morissette:
Bio2RDF : A Semantic Web Atlas of Post Genomic Knowledge about Human and Mouse. DILS 2008: 153-160 - 2007
- [c5]Byron Yu-Lin Kuo, Thomas Hentrich, Benjamin M. Good, Mark D. Wilkinson:
Tag clouds for summarizing web search results. WWW 2007: 1203-1204 - [c4]Benjamin M. Good, Mark D. Wilkinson:
Ontology engineering using volunteer labor. WWW 2007: 1243-1244 - 2006
- [c3]Benjamin M. Good, James Hartzell, Rodney S. Tosten:
A Smarter FAQ. IKE 2006: 142-148 - [c2]Benjamin M. Good, Erin M. Tranfield, Poh C. Tan, Marlene Shehata, Gurpreet K. Singhera, John Gosselink, Elena B. Okon, Mark D. Wilkinson:
Fast, Cheap and Out of Control: A Zero Curation Model for Ontology Development. Pacific Symposium on Biocomputing 2006: 128-139 - 1999
- [c1]Barbara Starr, Vinay K. Chaudhri, Boris Katz, Benjamin M. Good, Jérôme Thoméré:
HIKE (HPKB Integrated Knowledge Environment) - A Query Interface and Integrated Knowledge Environment for HPKB. AAAI/IAAI 1999: 927-928
Editorship
- 2012
- [e1]Alexander García Castro, Christoph Lange, Frank van Harmelen, Benjamin M. Good:
Proceedings of the 2nd Workshop on Semantic Publishing, co-located with the 9th Extended Semantic Web Conference, SePublica@ESWC 2012, Hersonissos, Crete, Greece, May 28, 2012. CEUR Workshop Proceedings 903, CEUR-WS.org 2012 [contents]
Informal and Other Publications
- 2015
- [i5]Benjamin M. Good, Gavin Ha, Chi K. Ho, Mark D. Wilkinson:
OntoLoki: an automatic, instance-based method for the evaluation of biological ontologies on the Semantic Web. CoRR abs/1502.06025 (2015) - [i4]Tong Shu Li, Benjamin M. Good, Andrew I. Su:
Exposing ambiguities in a relation-extraction gold standard with crowdsourcing. CoRR abs/1505.06256 (2015) - [i3]Karthik Gangavarapu, Vyshakh Babji, Tobias Meißner, Andrew I. Su, Benjamin M. Good:
Branch: An interactive, web-based tool for testing hypotheses and developing predictive models. CoRR abs/1509.06808 (2015) - 2014
- [i2]Benjamin M. Good, Max Nanis, Andrew I. Su:
Microtask crowdsourcing for disease mention annotation in PubMed abstracts. CoRR abs/1408.1928 (2014) - 2013
- [i1]Benjamin M. Good, Andrew I. Su:
Crowdsourcing for Bioinformatics. CoRR abs/1302.6667 (2013)
Coauthor Index
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