BITEM Biblio

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Journal Article
Vishnyakova D, Pasche E, Lovis C, Ruch P. Utilization of ontology look-up services in information retrieval for biomedical literature. Stud Health Technol Inform. 2013 ;186:155-9.PDF icon efm2013.pdf (274.96 KB)
Pasche E, Gobeill J, Vishnyakova D, Ruch P, Lovis C. Use of controlled vocabularies to improve biomedical information retrieval tasks. Stud Health Technol Inform. 2013 ;192:1068.PDF icon UseOfControlled2013.pdf (122.26 KB)
Teodoro D, Knafou J, Naderi N, Pasche E, Gobeill J, Arighi CN, Ruch P. UPCLASS: a deep learning-based classifier for UniProtKB entry publications. Database [Internet]. 2020 ;2020. Available from: https://doi.org/10.1093/database/baaa026
Mottin L, Pasche E, Gobeill J, de Laval VRech, Gleizes A, Michel P-A?, Bairoch A, Gaudet P, Ruch P. Triage by ranking to support the curation of protein interactions. Database [Internet]. 2017 ;2017(1). Available from: https://academic.oup.com/database/article-lookup/doi/10.1093/database/bax040PDF icon bax040.pdf (830.35 KB)
Mao Y, Van Auken K, Li D, Arighi CN, McQuilton P, G Hayman T, Tweedie S, Schaeffer ML, Laulederkind SJF, Wang S-J, et al. Overview of the gene ontology task at BioCreative IV. Database (Oxford). 2014 ;2014.PDF icon Overview of BioCreative IV.pdf (583.24 KB)
Teodoro D, Sundvall E, Junior MJoão, Ruch P, Freire SMiranda. ORBDA: An openEHR benchmark dataset for performance assessment of electronic health record servers. PloS one. 2018 ;13:e0190028.PDF icon journal.pone_.0190028.pdf (3.18 MB)
Mottin L, Gobeill J, Pasche E, Michel P-A, Cusin I, Gaudet P, Ruch P. neXtA5: accelerating annotation of articles via automated approaches in neXtProt. Database (Oxford) [Internet]. 2016 ;2016. Available from: http://database.oxfordjournals.org/content/2016/baw098.fullPDF icon baw098.pdf (1.04 MB)
Gobeill J, Pasche E, Vishnyakova D, Ruch P. Managing the data deluge: data-driven GO category assignment improves while complexity of functional annotation increases. Database (Oxford). 2013 ;2013:bat041.PDF icon Managing data deluge.pdf (192.78 KB)
Vishnyakova D, Gobeill J, Oezdemir-Zaech F, Kreim O, Vachon T, Clade T, Haenning X, Mikhailov D, Ruch P. Electronic processing of informed consents in a global pharmaceutical company environment. Studies in health technology and informatics. 2013 ;205:995–999.PDF icon SHTI205-0995 (1).pdf (727.63 KB)
Vishnyakova D, Gobeill J, Oezdemir-Zaech F, Kreim O, Vachon T, Clade T, Haenning X, Mikhailov D, Ruch P. Electronic processing of informed consents in a global pharmaceutical company environment. Studies in health technology and informatics [Internet]. 2014 ;205:995–999. Available from: http://doc.rero.ch/record/232970/files/Ruch_Gobeill_Processing_of_informed_consents.pdfPDF icon Ruch_Gobeill_Processing_of_informed_consents.pdf (736.99 KB)
Pasche E, Gobeill J, Kreim O, Oezdemir-Zaech F, Vachon T, Lovis C, Ruch P. Development and tuning of an original search engine for patent libraries in medicinal chemistry. BMC Bioinformatics. 2014 ;15 Suppl 1:S15.PDF icon 1471-2105-15-s1-s15.pdf (1.16 MB)
Pasche E, Chinali M, Gobeill J, Ruch P. Development and Evaluation of a Case-Based Retrieval Service. Studies in health technology and informatics. 2017 ;235:186.PDF icon developmentCBR_preprint.pdf (176.88 KB)
Gobeill J, Gaudinat A, Pasche E, Vishnyakova D, Gaudet P, Bairoch A, Ruch P. Deep Question Answering for protein annotation. Database (Oxford). 2015 ;2015.PDF icon Database-2015-Gobeill-database_bav081.pdf (587.33 KB)
Pasche E, Gobeill J, Mottin L, Mottaz A, Teodoro D, Van Rijen P, Ruch P. Customizing a Variant Annotation-Support Tool: an Inquiry into Probability Ranking Principles for TREC Precision Medicine. TREC 2017 Proceedings [Internet]. 2018 . Available from: https://trec.nist.gov/pubs/trec26/papers/BiTeM-PM.pdfPDF icon BiTeM-PM-2017.pdf (318.65 KB)
Anton BP, Chang Y-C, Brown P, Choi H-P, Faller LL, Guleria J, Hu Z, Klitgord N, Levy-Moonshine A, Maksad A, et al. The COMBREX project: design, methodology, and initial results. PLoS Biol. 2013 ;11(8):e1001638.PDF icon Combrex.pdf (508.12 KB)
Gobeill J, Pasche E, Vishnyakova D, Ruch P. Closing the loop: from paper to protein annotation using supervised Gene Ontology classification. Database (Oxford). 2014 ;2014.PDF icon Closing the loop.pdf (362.62 KB)
Pasche E, Ruch P, Teodoro D, Huttner A, Harbarth S, Gobeill J, Wipfli R, Lovis C. Assisted Knowledge Discovery for the Maintenance of Clinical Guidelines. PLoS ONE [Internet]. 2013 ;8:e62874. Available from: http://dx.doi.org/10.1371%2Fjournal.pone.0062874
Veuthey A-L, Bridge A, Gobeill J, Ruch P, McEntyre JR, Bougueleret L, Xenarios I. Application of text-mining for updating protein post-translational modification annotation in UniProtKB. BMC Bioinformatics. 2013 ;14(1):104.
Britan A, Cusin I, Hinard V, Mottin L, Pasche E, Gobeill J, de Laval VRech, Gleizes A, Teixeira D, Michel P-A, et al. Accelerating annotation of articles via automated approaches: evaluation of the neXtA5 curation-support tool by neXtProt. Database [Internet]. 2018 ;2018. Available from: https://academic.oup.com/database/article/doi/10.1093/database/bay129/5255187http://academic.oup.com/database/article-pdf/doi/10.1093/database/bay129/27329435/bay129.pdfPDF icon bay129.pdf (18.93 MB)
Conference Paper
Copara J, Knafou J, Naderi N, Moro C, Ruch P, Teodoro D. Contextualized French Language Models for Biomedical Named Entity Recognition. In: Actes de la 6e conférence conjointe Journées d'Études sur la Parole (JEP, 31e édition), Traitement Automatique des Langues Naturelles (TALN, 27e édition), Rencontre des Étudiants Chercheurs en Informatique pour le Traitement Automatique des Langues. Actes de la 6e conférence conjointe Journées d'Études sur la Parole (JEP, 31e édition), Traitement Automatique des Langues Naturelles (TALN, 27e édition), Rencontre des Étudiants Chercheurs en Informatique pour le Traitement Automatique des Langues. ATALA; 2020.
Knafou J, Naderi N, Copara J, Teodoro D, Ruch P. BiTeM at WNUT 2020 Shared Task-1: Named Entity Recognition over Wet Lab Protocols using an Ensemble of Contextual Language Models. In: Proceedings of the Sixth Workshop on Noisy User-generated Text (W-NUT 2020). Proceedings of the Sixth Workshop on Noisy User-generated Text (W-NUT 2020). Online: Association for Computational Linguistics; 2020. Available from: https://www.aclweb.org/anthology/2020.wnut-1.40PDF icon 2020.wnut-1.40.pdf (842.21 KB)
Mottin L, Gobeill J, Mottaz A, Pasche E, Gaudinat A, Ruch P. BiTeM at CLEF eHealth Evaluation Lab 2016 Task 2: Multilingual Information Extraction. In: CLEF 2016. CLEF 2016. Evora, Portugal: CEUR-WS.org - CEUR Workshop Proceedings; 2016. Available from: http://ceur-ws.org/Vol-1609/16090094.pdfPDF icon BiTeM at CLEF eHealth Evaluation Lab 2016.pdf (307.61 KB)

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