BITEM Biblio

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Conference Paper
Teodoro D, Gobeill J, Pasche E, Ruch P, Vishnyakova D, Lovis C. Automatic IPC encoding and novelty tracking for effective patent mining. In: The 8th NTCIR Workshop Meeting on Evaluation of Information Access Technologies: Information Retrieval, Question Answering, and Cross-Lingual Information Access. The 8th NTCIR Workshop Meeting on Evaluation of Information Access Technologies: Information Retrieval, Question Answering, and Cross-Lingual Information Access. Tokyo, Japan; 2010. pp. 309-317. Available from: http://research.nii.ac.jp/ntcir/workshop/OnlineProceedings8/NTCIR/03-NTCIR8-PATMN-TeodoroD.pdfPDF icon BiTeM-PATMN-NTCIR8.pdf (313.05 KB)
Teodoro D, Gobeill J, Pasche E, Vishnyakova D, Ruch P, Lovis C. Automatic Prior Art Searching and Patent Encoding at CLEF-IP '10. In: CLEF (Notebook Papers/LABs/Workshops). CLEF (Notebook Papers/LABs/Workshops). ; 2010. Available from: http://clef2010.org/resources/proceedings/clef2010labs_submission_119.pdfPDF icon Automatic prior art searching and patent encoding at CLEF-IP '10.pdf (293.03 KB)
Bagliesi G, Bauerdick L, Belforte S, Bloom K, Bockelman B, Bonacorsi D, Brew C, D'Hondt J, Egeland R, Elgammal S, et al. The CMS data transfer test environment in preparation for LHC data taking. In: Nuclear Science Symposium Conference Record, 2008. NSS'08. IEEE. Nuclear Science Symposium Conference Record, 2008. NSS'08. IEEE. IEEE; 2008. pp. 3475–3482.PDF icon GBNSSMIC2008.pdf (626.57 KB)
Van Rijen P, Teodoro D, Naderi N, Mottin L, Knafou J, Jeffryes M, Ruch P. A Data-Driven Approach for Measuring the Severity of the Signs of Depression using Reddit Posts. In: Working Notes of CLEF 2019 - Conference and Labs of the Evaluation Forum, Lugano, Switzerland, September 9-12, 2019. Working Notes of CLEF 2019 - Conference and Labs of the Evaluation Forum, Lugano, Switzerland, September 9-12, 2019. ; 2019. Available from: http://ceur-ws.org/Vol-2380/paper_79.pdf
Vishnyakova D, Pasche E, Douglas T, Lovis C, Ruch P. Pathogens and Gene Product Normalization in the Biomedical Literature. In: Large Scale Projects in Ehealth: Partnership in Modernization. Large Scale Projects in Ehealth: Partnership in Modernization. Ios PressInc; 2012. pp. 89–93.PDF icon STC2012_Vishnyakova.pdf (294.94 KB)
Gobeill J, Patsche E, Theodoro D, Veuthey A-L, Lovis C, Ruch P. Question answering for biology and medicine. In: Information Technology and Applications in Biomedicine, 2009. ITAB 2009. 9th International Conference on. Information Technology and Applications in Biomedicine, 2009. ITAB 2009. 9th International Conference on. IEEE; 2009. pp. 1–5.PDF icon ITAB2009 - Gobeill.pdf (1 MB)
Vishnyakova D, Pasche E, Lovis C, Ruch P. System zur Unterstützung der Kuration der Toxikogenomik in der medizinischen Literatur. In: Swiss Medical Informatics. Vol. 28. Swiss Medical Informatics. ; 2012. Available from: http://www.medical-informatics.ch/index.php/smiojs/article/view/6
Conference Proceedings
He J, Nguyen DQuoc, Akhondi SA, Druckenbrodt C, Thorne C, Hoessel R, Afzal Z, Zhai Z, Fang B, Yoshikawa H, et al. An extended overview of the CLEF 2020 ChEMU Lab : information extraction of chemical reactions from patents. Proceedings of the CLEF 2020 conference [Internet]. 2020 :31 p. Available from: http://hesso.tind.io/record/6175
Pasche E, Teodoro D, Gobeill J, Vishnyakova D, Ruch P, Lovis C. KART, a knowledge authoring and refinement tool for clinical guidelines development. BMC Proceedings [Internet]. 2011 ;5:O49. Available from: http://www.biomedcentral.com/1753-6561/5/S6/O49PDF icon KART_2011.pdf (170.85 KB)
Vishnyakova D, Pasche E, Teodoro D, Ruch P, Lovis C. Pathogens and Genome Normalization for Literature-based Knowledge Discovery. 23 rd International Conference of the European Federation for Medical Informatics [Internet]. 2011 . Available from: http://person.hst.aau.dk/ska/mie2011/CD/MIE_2011_Content/Posters/031_or_submission_228_2_am_sm_ok.pdfPDF icon MIE2001_DVISHNYAKOVA_fv.pdf (114.87 KB)
Vishnyakova D, Pasche E, Ruch P. Selection of relevant articles for curation for the Comparative Toxicogenomic Database. 2012 BioCreative Workshop [Internet]. 2012 :31-38. Available from: http://www.biocreative.org/media/store/files/2012/Proceedings_BC2012_.pdf
Vishnyakova D, Gobeil J, Ruch P. Using a Question-Answering Approach In Machine Reading Task Of Biomedical Texts About The Alzheimer Disease. CLEF 2013 Conference. 2013 ;Vol-1179.PDF icon CLEF2013wn-QA4MRE-VishnyakovaEt2013.pdf (472.09 KB)
Journal Article
Pasche E, Gobeill J, Teodoro D, Gaudinat A, Vishnykova D, Lovis C, Ruch P. An advanced search engine for patent analytics in medicinal chemistry. Studies in health technology and informatics. 2012 ;180:204-9.PDF icon advancedsearchengine_2012.pdf (632.5 KB)
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.
Pasche E, Gobeill J, Teodoro D, Vishnyakova D, Huttner A, Ruch P, Lovis C. Assister la création de guides de bonnes pratiques par des techniques de recherche d’information. Swiss Medical Informatics [Internet]. 2012 ;28. Available from: http://157.161.181.107/smi/index.php/smiojs/article/view/15PDF icon assistercreation_2012.pdf (356.21 KB)
Gobeill J, Gaudinat A, Pasche E, Teodoro D, Vishnyakova D, Ruch P. BiTeM group report for TREC Medical Records Track 2011. 2011 .PDF icon RUCH_BitemGroupeTRECmedical2011.pdf (285.04 KB)
Gobeill J, Gaudinat A, Pasche E, Teodoro D, Vishnyakova D, Ruch P. BiTeM site report for TREC Chemistry 2010: Impact of Citations Feedback for Patent Prior Art Search and Chemical Compounds Expansion for Ad Hoc Retrieval. 2010 .
Vishnyakova D, Pasche E, Gobeill J, Gaudinat A, Lovis C, Ruch P. Classification and prioritization of biomedical literature for the comparative toxicogenomics database. Studies in health technology and informatics. 2012 ;180:210-4.PDF icon pmid22874182.pdf (177.05 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)
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)
Teodoro D, Pasche E, Vishnyakova D, De Vloed B, Depraetere K, Ruch P, Lovis C. A cross-site antimicrobial resistance surveillance system using semantic web technologies. BMC Proceedings [Internet]. 2011 ;5:O35. Available from: http://www.biomedcentral.com/1753-6561/5/S6/O35
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)
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, 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, Gobeill J, Oezdemir-Zaech F, Vachon T, Lovis C, Ruch P. Development of a text search engine for medicinal chemistry patents. EMBnet.journal [Internet]. 2012 ;18(Suppl B). Available from: http://journal.embnet.org/index.php/embnetjournal/article/view/545PDF icon Developmenttext_2012.pdf (82.57 KB)

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