Christophe Roeder

ORCID:

0000-0003-3889-2473

Publications

Journal

• Williams, L.A., Fox, L.M., Roeder, C., Hunter, L.E.
  Negotiating a Text Mining License for Faculty Researchers.
  Sep 2014 ·Information Technology and Libraries link This paper won the 2016 Daniel T. Richards prize of the Collection Development Section of the Medical Library Association.
• Funk, C., Baumgartner, W. Jr, Garcia, B., Roeder, C., Bada, M., Cohen, K.B., Hunter, L.E., Verspoor, K.
  Large-scale biomedical concept recognition: An evalutation of current automatic annotators and their parameters.
  BMC Bioinformatics 2014 15:59 DOI: 10.1186/1471-2105-15-59 link
• Verspoor, K., Cohen, K.B., Lanfranchi, A., Warner, C., Johnson, H.L., Roeder, C., Choi, J.D., Funk, C., Malenkiy, Y., Eckert, M., Xue, N., Baumgartner Jr., W.A., Bada, M., Palmer, M., Hunter L.E.
  A corpus of full-text journal articles is a robust evaluation tool for revealing differences in performance of biomedical natural language processing tools.
  BMC Bioinformatics 2012 Aug 17, 13:207. link
• Cohen, K.B., Verspoor, K., Johnson, H., Roeder, C., Ogren, P., Baumgartner, W., White, E. Tipney, H., and Hunter, L.
  High-precision biological event extraction: Effects of system and data.
  Computational Intelligence, 2011, 27(4):681-701 link
• Yoshinobu Kano, Jari Björne, Filip Ginter, Tapio Salakoski, Ekaterina Buyko, Udo Hahn, K Bretonnel Cohen, Karin Verspoor, Christophe Roeder, Lawrence E Hunter, Halil Kilicoglu, Sabine Bergler, Sofie Van Landeghem, Thomas Van Parys , Yves Van de Peer, Makoto Miwa, Sophia Ananiadou, Mariana Neves, Alberto Pascual-Montano, Arzucan Özgür, Dragomir R Radev, Sebastian Riedel, Rune Sætre, Hong-Woo Chun, Jin-Dong Kim, Sampo Pyysalo, Tomoko Ohta and Jun’ichi Tsujii.
  U-Compare bio-event meta-service: compatible BioNLP event extraction services.
  BMC Bioinformatics 2011 12(1).481 link
• Cohen KB, Johnson HL, Verspoor K, Roeder C, Hunter LE.
  The structural content aspects of abstracts versus bodies of full text journal articles are different.
  BMC Bioinformatics. 2010 Sep 29;11:492 link
• Verspoor K, Roeder C, Johnson HL, Cohen KB, Baumgartner WA Jr, Hunter LE.
  Exploring species-based strategies for gene normalization.
  IEEE/ACM Trans Comput Biol Bioinform. 2010 Jul-Sep;7(3):462-71. link
• Roeder C, Jonquet C, Shah NH, Baumgartner WA Jr, Verspoor K, Hunter L.
  A UIMA Wrapper for the NCBO Annotator.
  Bioinformatics. 2010 Jul 15;26(14):1800-1. Epub 2010 May 26 link

Conference

• Kevin Bretonnel Cohen, Jingbo Xia, Christophe Roeder, Lawrence E Hunter
  Reproducibility in Natural Language Processing: A Case Study of Two R Libraries for Mining PubMed/MEDLINE
  LREC Int Conf Lang Resour Eval. 2016 May ; 2016(W23): 6–12.
• The Colorado BioCreative III Gene Normalization task sub-mission
  K Verspoor, KM Livingston, C Roeder, T Christiansen, HL Johnson, KB Cohen, WA Baumgartner Jr, LE Hunter
  Proceedings of BioCreative III Workshop, 140 2010
• K Bretonnel Cohen, Arrick Lanfranchi, William Corvey, William A Baumgartner Jr, Christophe Roeder, Philip V Ogren, Martha Palmer, Lawrence E Hunter.
  Annotation of all coreference in biomedical text: Guideline selection and adaptation.
  2nd Workshop on Building and Evaluating Resources for Biomedical Text Mining Tuesday, 18 th March 2010 link
• K Bretonnel Cohen, Christophe Roeder, William A Baumgartner Jr, Lawrence E Hunter, Karin Verspoor.
  Test suite design for ontology concept recognition systems.
  LREC 2010, 17-23 May 2010 link
• Cartic Ramakrishnan, William Baumgartner, Judith Blake, Gully Burns, Kevin Cohen, Harold Drabkin, Janan Eppig, Eduard Hovy, Chun-nan Hsu, Lawrence Hunter, Tommy Ingulfsen, Hiroaki Onda, Sandeep Pokkunuri, Ellen Rilof, Christophe Roeder and Karin Verspoor.
  Building the Scientific Knowledge Mine (SciKnowMine): a community-driven framework for text mining tools in direct service to biocuration."
  In Workshop "New Challenges for NLP Frameworks" collocated with The seventh international conference on Language Resources and Evaluation (LREC) 2010. link
• K Verspoor, WA Baumgartner Jr., C Roeder, and L Hunter.
  Abstracting the Types away from a UIMA Type System.
  in Chiarcos, C., Eckhart de Castilho, Stede, M. (eds), Von der Form aur Bedeutung: Text automatisch verarbeiten / From Form to Meaning: Processing Texts Automatically. Proceedings of the Biennial GSCL Conference 2009 Tuebingen: Narr 2009, p. 249-256. link
• Christophe Roeder, Philip V. Ogren, William A. Baumgartner Jr., Lawrence Hunter.
  Simplifying UIMA Component Developmnet and Testing with Java Annotations and Dependency Injection,
  in Chiarcos, C., Eckhart de Castilho, Stede, M. (eds), Von der Form aur Bedeutung: Text automatisch verarbeiten / From Form to Meaning: Processing Texts Automatically. Tuebingen: Narr, 2009, link
• KB Cohen, K Verspoor, HL Johnson, C Roeder, PV Ogren, WA Baumgartner Jr., E White, H Tipney, and L Hunter.
  High-precision biological event extraction with a concept recognizer.
  Proceedings of the Workshop on BioNLP: Shared Task 2009, pp 50-58, Association for Computational Linguistics. link

Abstracts

• Sofia Z Dard, Bryan Laraway, Christophe Roeder, Stephanie S Hong, Maya Choudhury, James W Cavallon, Katie R Bradwell, Hyun Woo Kim, Tim Schwab, Emily R Pfaff. N3C Scorecards: A Centralized and Systematic Approach to Data Quality. AMIA 2023
• Complex Heart Failure Phenotypes Differ in Response to Medical Therapy and Exercise Training
  M Merrill, C Roeder, M Butler, B Doran, L Stevens, C Goerg, D Kao
  Circulation 138 (Suppl_1), A16910-A16910
• Latent Cluster Analysis Using Clinical and Functional Characteristics Identifies Novel Phenotypes of Patients With Reduced Ejection Fraction Enrolled in the HF-ACTION Trial …
  B Doran, C Roeder, M Merrill, P Jhund, L Stevens, J McMurray, C Görg, DP Kao
  Circulation 138 (Suppl_1), A12890-A12890 2018

Conference Talks

• Christophe Roeder, William A. Baumgartner Jr., Kevin Livingston, Lawrence Hunter. A Distributed Framework for Computation on the Results of Large Scale NLP, Rocky Mountain Bioinformatics Conference 2011, Snowmass, CO link
• Christophe Roeder, Tom Christiansen, Helen Johnson, Karin Verspoor, Gully Burns, Lawrence Hunter. Full Text Biomedical Literature Processing: More Than a Scaling Challenge, Rocky Mountain Bioinformatics Conference 2010, Snowmass, CO link

Conference Posters

• Stephanie Hong, Thomas Richards, Benjamin Amor, Tim Schwab, Philip Sparks, Maya Choudhury, Saad Ljazouli, Peter Leese, Amin Manna, Christophe Roeder, Tanner Zhang, Lisa Eskenazi, Bryan Laraway, James Cavallon, Eric Kim, Shijia Zhang, Emir Amaro Syailendra, Shawn O’Neil, Davera Gabriel, Sigfried Gold, Tricia Francis, Andrew Girvin, Emily Pfaff, Anita Walden, Harold Lehmann, Melissa Haendel, Ken Gersing, Christopher G Chute. Augmenting the National COVID Cohort Collaborative (N3C) Dataset with Medicare and Medicaid (CMS) Data, Secure and Deidentified Clinical Dataset, OHDSI Symposium, October 2023
• Alaa Radwan, James L Martin, Chris Roeder, David P Kao, Heather D Anderson, Emily C Hearst, Christina L Aquilante. Projected Prevalence of Actionable Exposure to Pharmacogeneti Supportive Care Medications among Patients with Gastrointestinal Cancers, University of Colorado School of Pharmacy Graduate Symposium, April 2023.
• Haibin Liu, William A Baumgartner Jr, Natalie Catlett, Andrea Matthews, Phoebe Roberts, Christophe Roeder, Aaron Van Hooser, Daniel Ziemek, Lawrence E. Hunter, K. Bretonnel Cohen. Automatic Generation of BEL Statements from Text-mined Biological Events, ISMB 2013, Berlin, Germany
• Chris Roeder, Katy Sadowski, Maxim Moinat, Philip Solovyev, Sonia Araujo, et al, Clincial Trial DAta Conventsions for the OMOP CDM, Proposal to OHDSI OMOP CDM, July 2020 presented at OHDSI Symposium 2020, winner 2020 Best Contribution in Observational Data Standards
• Christhope Roeder, Karin Verspoor, Scaling Text Mining to One Million Documents, ISMB 2010, Boston, MA link
• Christophe Roeder, William A. Baumgartner Jr., Lawrence Hunter. Integrating Web Services into Biomedical Text Mining, Rocky Mountain Bioinformatics Conference 2009, Snowmass, CO link

Workshops/Workgroups

• Stephanie Hong, Thomas Richards, Benjamin Amor, Tim Schwab,..., Christophe Roeder,..., Melissa Haendel, Ken Gersing, Christopher Chute, Augmenting the National COVID Cohort Collaborative (N3C) Dataset with Medicare and Medicaid (CMS) Data, Secure and Deidentified Clinical Dataset, OHDSI Symposium November, 2023
• Nicolas Matentzoglu, Yann Le Franc, Tiffany Callahan, Chris Mungall, Chris Roeder, James McLaughlin, Nomi Harris. 1st Mapping Commons Workshop on Simple Standard for Sharing Ontology Mappings, colocated with Biocuration 2023, Concept Set Mappings
• HL7 FHIR Phenopackets WG, September 2022
• FHIR-OMOP Terminologies Subgroup at SSSOM Workshop at OHDSI Symposium October 2022
• HL7 FHIR FHIR-OMOP WG, January 2023

Acknowledgements

• Chapter "Biomedical natural language processing and text mining" in the book "Methods in Biomedical Informatics", chapter by Kevin Bretonnel Cohen, book by I Sarkar. Academic Press, 2013
• Programming Perl, 4th edition, Tom Christiansen, 2012