Benjamin M. Good
Lawrence Berkeley National Laboratory
6 Papers
16 Citations
Benjamin M. Good is an academic researcher from Lawrence Berkeley National Laboratory. The author has contributed to research in topics: Web service & Ontology (information science). The author has an hindex of 3, co-authored 6 publications.
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Papers
The Gene Ontology Resource: 20 years and still GOing strong
Seth Carbon,Eric Douglass,Nathan Dunn,Benjamin M. Good,Nomi L. Harris,Suzanna E. Lewis,Christopher J. Mungall,S. Basu,Rex L. Chisholm,Robert J. Dodson,E. Hartline,Petra Fey,Paul Thomas,Laurent-Philippe Albou,Dustin Ebert,M. J. Kesling,Huaiyu Mi,Anushya Muruganujan,Xiaosong Huang,S. Poudel,Tremayne Mushayahama,James C. Hu,Sandra A. LaBonte,Deborah A. Siegele,Giulia Antonazzo,Helen Attrill,Nicholas H. Brown,S. Fexova,Phani V. Garapati,T. E.M. Jones,Steven J Marygold,Gillian Millburn,Alix J. Rey,Vítor Trovisco,G. Dos Santos,David B. Emmert,Kathleen Falls,Pinglei Zhou,Joshua L. Goodman,Victor B. Strelets,Jim Thurmond,Mélanie Courtot,D. S. Osumi,Helen Parkinson,Paola Roncaglia,Marcio Luis Acencio,Martin Kuiper,A. Lreid,Colin Logie,Ruth C. Lovering,Rachael P. Huntley,Paul Denny,Nancy H. Campbell,Barbara Kramarz,Vanessa Acquaah,S. H. Ahmad,H. Chen,J. H. Rawson,Marcus C. Chibucos,Michelle G. Giglio,Suvarna Nadendla,Rebecca Tauber,Margaret Duesbury,N. T. Del,Birgit H M Meldal,Livia Perfetto,Pablo Porras,Sandra Orchard,Anjali Shrivastava,Z. Xie,Hsin-Yu Chang,Robert D. Finn,Alex L. Mitchell,Neil D. Rawlings,Lorna Richardson,Amaia Sangrador-Vegas,Judith A. Blake,Karen R. Christie,Mary E. Dolan,H. Drabkin,David P. Hill,Li Ni,D. Sitnikov,Midori A. Harris,Stephen G. Oliver,Kim Rutherford,Valerie Wood,Jacqueline Hayles,Jürg Bähler,Antonia Lock,Elizabeth R Bolton,J L De Pons,Melinda R. Dwinell,G. T. Hayman,Stan Laulederkind,Mary Shimoyama,Marek Tutaj,Shur-Jen Wang,Peter D'Eustachio,Lisa Matthews,James P. Balhoff,Suzi Aleksander,Gail Binkley,B. L. Dunn,J. M. Cherry,Stacia R. Engel,Felix Gondwe,Kalpana Karra,Kevin A. MacPherson,Stuart R. Miyasato,Robert S. Nash,P. C. Ng,Travis K. Sheppard,A. Shrivatsav Vp,Matt Simison,Marek S. Skrzypek,Shuai Weng,Edith D. Wong,Marc Feuermann,Pascale Gaudet,E. Bakker,Tanya Z. Berardini,Leonore Reiser,Shankar Subramaniam,Eva Huala,C. Arighi,A. Auchincloss,K. Axelsen,G. P. Argoud,Alex Bateman,B. Bely,M. C. Blatter,E. Boutet,L. Breuza,A. Bridge,R. Britto,H. Bye-A-Jee,C. Casals-Casas,E. Coudert,A. Estreicher,L. Famiglietti,P. Garmiri,George Georghiou,A. Gos,N. Gruaz-Gumowski,E. Hatton-Ellis,U. Hinz,C. Hulo,A. Ignatchenko,F. Jungo,G. Keller,K. Laiho,P. Lemercier,D. Lieberherr,Y. Lussi,A. Mac-Dougall,M. Magrane,Maria Jesus Martin,P. Masson,D. A. Natale,N. N. Hyka,I. Pedruzzi,K. Pichler,S. Poux,C. Rivoire,M. Rodriguez-Lopez,T. Sawford,Elena Speretta,A. Shypitsyna,A. Stutz,S. Sundaram,M. Tognolli,N. Tyagi,Kate Warner,Rossana Zaru,C. Wu,Juancarlos Chan,J. Cho,Sibyl Gao,Christian A. Grove,M. C. Harrison,Kevin L. Howe,Raymond Lee,Jane E. Mendel,Hans-Michael Müller,Daniela Raciti,K. Van Auken,Matthew Berriman,Lincoln Stein,Paul W. Sternberg,Doug Howe,Sabrina Toro,Monte Westerfield +192 more
TL;DR: GO-CAM, a new framework for representing gene function that is more expressive than standard GO annotations, has been released, and users can now explore the growing repository of these models.
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Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems.
Paul Thomas,David P. Hill,Huaiyu Mi,David Osumi-Sutherland,Kimberly Van Auken,Seth Carbon,James P. Balhoff,Laurent-Philippe Albou,Benjamin M. Good,Pascale Gaudet,Suzanna E. Lewis,Christopher J. Mungall +11 more
TL;DR: GO-CAM is developed, a structured framework for linking multiple GO annotations into an integrated model of a biological system that will enable new applications in pathway and network analysis, as well as improve standard GO annotations for traditional GO-based applications.
KG-COVID-19: A Framework to Produce Customized Knowledge Graphs for COVID-19 Response
Justin T. 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,Monica Munoz-Torres,Melissa A. Haendel,Peter N. Robinson,Marcin P. Joachimiak,Christopher J. Mungall +18 more
- 08 Jan 2021
TL;DR: KG-COVID-19 is created, a flexible framework that ingests and integrates heterogeneous biomedical data to produce knowledge graphs (KGs) and can be applied to other problems in which siloed biomedical data must be quickly integrated for different research applications, including future pandemics.
Reactome and the Gene Ontology: Digital convergence of data resources.
Benjamin M. Good,Kimberly Van Auken,David P. Hill,Huaiyu Mi,Seth Carbon,James P. Balhoff,Laurent-Philippe Albou,Paul Thomas,Christopher J. Mungall,Judith A. Blake,Peter D'Eustachio +10 more
TL;DR: Pathways2GO as mentioned in this paper is a software tool to convert the entire set of normal human Reactome pathways into GO-CAMs, yielding standard GO annotations from Reactome content and supporting enhanced quality control for both Reactome and GO, yielding a nearly seamless conversion between these two resources.
Knowledge Beacons: Web services for data harvesting of distributed biomedical knowledge.
Lance M. Hannestad,Vlado Dančík,Meera Godden,Imelda W. Suen,Kenneth Casimir Huellas-Bruskiewicz,Benjamin M. Good,Christopher J. Mungall,Richard Bruskiewich +7 more
TL;DR: Hannestad et al. as discussed by the authors developed a Translator-Knowledge-Beacon API and associated software, which is open source and currently available for access at https://github.com/NCATS-Tangerine/translator-knowledge-beacon.