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Rebholz Group Publications

The following is a list of publications for the Rebholz group.




2011

Croset, S., C. Grabmueller, C. Li, S. Kavaliauskas, and D. Rebholz-Schuhmann (2011)
The CALBC RDF Triple store: retrieval over large literature content.
BMC Bioinformatics (To appear)

Hoehndorf, R., M. Dumontier, A. Oellrich, S. Wimalaratne, D. Rebholz-Schuhmann, P. Schofield, and G.V. Gkoutos. (2011)
A common layer of interoperability for biomedical ontologies based on OWL EL. Bioinformatics.
2011 Feb 21. [Epub ahead of print]

Hoehndorf, R., A.-C. Ngonga Ngomo , S. Pyysalo , T. Ohta , A. Oellrich and D. Rebholz-Schuhmann. (2011)
Ontology design patterns to disambiguate relations between genes and gene products in GENIA.
J Biomedical Semantics (To appear).

Kim, J.J., and D. Rebholz-Schuhmann. (2011)
Improving the extraction of complex regulatory events from scientific text by using ontology-based inference.
J Biomedical Semantics (To appear).

McEntyre, J.R., S. Ananiadou, S. Andrews, W.J. Black, R. Boulderstone, P. Buttery, D. Chaplin, S. Chevuru, N. Cobley, L.A. Coleman, P. Davey, B. Gupta, L. Haji-Gholam, C. Hawkins, A. Horne, S.J. Hubbard, J.H. Kim, I. Lewin, V. Lyte, R. MacIntyre, S. Mansoor, L. Mason, J. McNaught, E. Newbold, C. Nobata, E. Ong, W. Pillai, D. Rebholz-Schuhmann, H. Rosie, R. Rowbotham, C.J. Rupp, P. Stoehr, P. Vaughan. (2011)
UKPMC: a full text article resource for the life sciences.
Nucleic Acids Res. 39 (Database issue):D58-65. Epub 2010 Nov 9.

Rebholz-Schuhmann, D., A. Jimeno-Yepes, C. Li, S. Kafkas, I. Lewin, N. Kang, P. Corbett, D. Milward, E. Buyko, E. Beisswanger, K. Hornbostel, A. Kouznetsov, R. Witte, J.B. Laurila, C.J.O. Baker, C.-J. Kuo, S. Clematide, F. Rinaldi, R. Farkas, G. Mora, K. Hara, L. Furlong, M. Rautschka, M. Lara Neves, A. Pascual-Montano, Q. Wei, N. Collier, Md. F. Mahbub Chowdhury, A. Lavelli, R. Berlanga, R. Morante, V. Van Asch, W. Daelemans, J.L. Marina, E. van Mulligen, J. Kors, U. Hahn. (2011)
Assessment of NER solutions against the first and second CALBC Silver Standard Corpus.
J Biomedical Semantics (To appear).


2010

Hoehndorf,R., A. Oellrich, and D. Rebholz-Schuhmann. (2010)
"Interoperability between phenotype and anatomy ontologies." 
Bioinformatics. 2010 Oct 22.

Hoehndorf,R., A. Oellrich, M. Dumontier, J. Kelso, and D. Rebholz-Schuhmann, and H. Herre. (2010)
"Relations as patterns: bridging the gap between OBO and OWL." 
BMC Bioinformatics. 2010 Aug 31;11:441.

Rebholz-Schuhmann,D., N. Collier, J.C. Park, L.S. Wong. (2010)
"Wrestling with biomedical research results: Language resources and literature analysis."
J Bioinform Comput Biol. 2010 Feb;8(1):129-130.

Rebholz-Schuhmann,D., S. Kavaliauskas and P. Pezik. (2010)
"PaperMaker: validation of biomedical scientific publications." 
Bioinformatics 26(7):982-4

Rebholz-Schuhmann,D., A. Jimeno Yepes, E. Van Mulligen, N. Kang, J. Kors, D. Milward, P. Corbett, E. Buyko, E. Beisswanger, and U. Hahn. (2010)
"CALBC Silver Standard Corpus." 
J Bioinform Comput Biol. 2010 Feb;8(1):163-79.

Rebholz-Schuhmann,D., A.J. Jimeno Yepes, E.M. van Mulligen, N. Kang, J. Kors, D. Milward, P. Corbett, E. Buyko, K. Tomanek, E. Beisswanger, and U. Hahn. (2010)
The CALBC Silver Standard Corpus for Biomedical Named Entities: A Study in Harmonizing the Contributions from Four Independent Named Entity Taggers. 
Proc. LREC 2010.

Rebholz-Schuhmann,D., and J.J. Kim. (2010)
"Automatic Text Analysis for Bioinformatics Knowledge Discovery".
In: "Knowledge-based Bioinformatics". Editors: A. Bajpai. (To appear)

Rebholz-SchuhmannD., and Nenadic G. (2010)
"Biomedical Semantics: the Hub for Biomedical Research 2.0."
J Biomed Semantics. 2010 Mar 31;1(1):1.

Rebholz-Schuhmann,D., A. Jimeno-Yepes, M. Arregui, and H. Kirsch. (2010)
"Measuring prediction capacity of individual verbs for the identification of protein interactions". 
Journal of biomedical informatics, 43, 200-207.

Rebholz-Schuhmann,D., A. Jimeno-Yepes, C. Li, S. Kafkas, I. Lewin, N. Kang, P. Corbett, D. Milward, E. Buyko, E. Beisswanger, K. Hornbostel, A. Kouznetsov, R. Witte, J.B. Laurila, C.J. Baker, C.J. Kuo, S. Clematide, F. Rinaldi, R. Farkas, G. Mora, K. Hara, L. Furlong, M. Rautschka, M.L. Neves, A. Pascual-Montano, Q. Wei, N. Collier, F.M. Chowdhury, A. Lavelli, R. Berlanga, R. Morante, V. van Asch, W. Daelemans, J.L. Marina, E. van Mulligen, J. Kors, and U. Hahn. (2010)
"Assessment of NER solutions against the first and second CALBC Silver Standard Corpus." 
Proc. of SMBM 2010, Cambridge, U.K.


2009

Baker, C. and D. Rebholz-Schuhmann. (2009)
""Between proteins and phenotypes: annotation and interpretation of mutations".
BMC Bioinformatics, 10 (Suppl 8):I1.

Couto F., Silva, M., Lee, V., Dimmer, E., Camon, E., Apweiler, R., Kirsch, H., Rebholz-Schuhmann, D. (2009)
Verification of Uncurated Protein Annotations.
In Information Retrieval in Biomedicine: Natural Language Processing for Knowledge Integration. IGI Global Publishing.

Hahn, U., Tomanek, K., Buyko, E., Kim, J.J., Rebholz-Schuhmann, D. (2009)
How Feasible and Robust is the Automatic Extraction of Gene Regulation Events? A Cross-Method Evaluation under Lab and Real-Life Conditions.
BioNLP 2009, Bolder, Colorado.

Jimeno Yepes, A., Berlanga-Llavori, R., Rebholz-Schuhmann, D. (2009)
Terminological cleansing for improved retrieval based on ontological terms, Exploiting Semantic Annotations in Information Retrieval
ESAIR 2009, Barcelona, Es.

Jimeno-Yepes, A., Jimenez-Ruiz, E., Berlanga, R., Rebholz-Schuhmann, D. (2009)
Use of shared lexical resources for efficient ontological engineering.
BMC Bioinformatics (accepted for publication)

Jimeno-Yepes, A., Berlanga-Llavori, R., Rebholz-Schuhmann, D. (2009)
Exploitation of ontological resources for scientific literature analysis: searching genes and related diseases.
Journal IEEE Engineering in Medicine and Biology Society (EMBC, accepted for publication).

Jimeno-Yepes, A., Berlanga-Llavori, R., Rebholz-Schuhmann, D. (2009)
Ontology refinement for improved information retrieval.
Journal of Information Processing and Management (accepted for publication)

Jimeno-Yepes, A., Berlanga-Llavori, R., Rebholz-Schuhmann, D. (2009)
Terminological cleansing for improved information retrieval based on ontological terms.
Proc. WSDM 2009, Barcelona, Spain, (2009): p 6-14.

Nagel, K., Jimeno-Yepes, A., Rebholz-Schuhmann, D. (2009)
Annotation of protein residues based on a literature analysis: cross-validation against UniProtKB.
BMC Bioinformatics, Special issue (accepted for publication).

Pezik, P., Jimeno Yepes, A., Rebholz-Schuhmann, D. (2009)
Using Biomedical Terminological Resources for Information Retrieval.
In Information Retrieval in Biomedicine: Natural Language Processing for Knowledge Integration. IGI Global Publishing. (In press)

Trieschnigg, D., Pezik, P., V. Lee, F. de Jong, W. Kraaij, D. Rebholz-Schuhmann.
MeSH Up: effective MeSH text classification for improved document retrieval.
Bioinformatics. (2009):1412-8. Epub 2009 Apr 17.
PMID: 19376821

2008

Altman, R.B., Bergman, C.M., Blake, J., Blaschke, C., Cohen, A., Gannon, F., Grivell, L., Hahn, U., Hersh, W., Hirschman, L., Jensen, L.J., Krallinger, M., Mons, B., O'Donoghue, S.I., Peitsch,M.C., Rebholz-Schuhmann, D., Shatkay, H., and Valencia, V. (2008)
Text Mining for Biology - the Way Forward: Opinions from Leading Scientists.
Genome Biology 9, no. SUPPL.
PMID: 18834498

Beisswanger, E., Lee, V., Kim, J.J., Rebholz-Schuhmann, D., Splendiani, A., Dameron, O., Schulz, S., and Hahn, Udo. (2008)
Gene Regulation Ontology (GRO): Design Principles and Use Cases.
MIE, Stockholm, 26-29 May 2008

Cerri, D., Della Valle, E., De Francisco Marcos, D., Giunchiglia,F., Naor, D., Nixon, L., Rebholz-Schuhmann, D., Krummenacher, R., and Simperl, E. (2008)
Towards Knowledge in the Cloud.
OTM 2008 Workshops including SEMELS, Monterrey, Mexico, Nov. 9-14, 2008, Proceedings Series: Lecture Notes in Computer Science, Subseries: Information Systems and Applications, incl. Internet/Web, and HCI , Vol. 5333, Meersman, Robert; Tari, Zahir; Herrero, Pilar (Eds.) 2008, XXXV, 1090 p., ISBN: 978-3-540-88874-1

Gaudan, S., Jimeno Yepes, A., Lee, V., and Rebholz-Schuhmann, D. (2008)
Combining Evidence, Specificity, and Proximity towards the Normalization of Gene Ontology Terms in Text.
EURASIP Journal on Bioinformatics and Systems Biology, vol. 2008, Article ID 342746. doi:10.1155/2008/342746.
abstract

Jaeger S., Gaudan S., Leser U., Rebholz-Schuhmann D. (2008)
Integrating Protein-Protein Interactions and Text Mining for Protein Function Prediction.
BMC Bioinformatics 9(8): S2; [Epub ahead of print]
PMID: 18673526

Jimeno Yepes, A., Jimenez-Ruiz, E., Berlanga-Llavori, R., and Rebholz-Schuhmann, D. (2008)
Use of shared lexical resources for efficient ontological engineering.
Semantic Web Applications and Tools for Life Sciences, 2008

Jimeno Yepes, A., Jimenez-Ruiz, E., Lee,V., Gaudan, S., Berlanga, R., and Rebholz-Schuhmann, D. (2008)
Assessment of Disease Named Entity Recognition on a Corpus of Annotated Sentences.
BMC Bioinformatics 9, no. SUPPL. 3 (2008): Article S3.
PMID: 18426548

Kim, J.J., Pezik, P., and Rebholz-Schuhmann, D. (2008)
MedEvi: Retrieving textual evidence of relations between biomedical concepts from Medline.
Bioinformatics 2008 Apr 9; [Epub ahead of print]
PMID: 18400773

Kim J.J., Rebholz-Schuhmann D. (2008)
Categorization of services for seeking information in biomedical literature: a typology for improvement of practice.
Brief Bioinform. 2008 Jul 26; [Epub ahead of print]
PMID: 18660511

Nagel, K., Jimeno Yepes,A., Oldfield,T., and Rebholz-Schuhmann,D. (2008)
Annotation of protein residues based on a literature analysis: cross-validation against UniProtKB Proc.
ECCB 2008 Workshop: Annotation, Interpretation and Management of Mutations (AIMM), Cagliari, Sardinia, Italy, September, June 22, 2008. (Published on CEUR-WS: 17-Dec-2008)

Pezik, P. Jimeno, A., Lee, V., and Rebholz-Schuhmann, D. (2008)
Static Dictionary Features for Term Polysemy Identification.
Proc Lang Res Eval, Conf (LREC-2008), workshop on "Building and evaluating resources for biomedical text mining", Marrakech (Morocco), 28-30 May 2008 (accepted).

Pezik, P., Kim, J.J., and Rebholz-Schuhmann, D. (2008)
MedEvi - A permuted concordancer for the biomedical domain.
Corpus Linguistics, Computer Tools, and Applications - State of the Art (PALC 2007), edited by B. Lewandowska-Tomaszczyk, Peter Lang, pp. 85-96, 2008.

Rebholz-Schuhmann, D., Jimeno Yepes, A., Arregui, M., and Kirsch, H. (2008)
Measuring performance of verbs denoting modifying and non-modifying protein interactions.
In Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), Turku, Finland. Ed. Salakoski T., Rebholz-Schuhmann D., Pyysalo S. pp. 109--116. Turku Centre for Computer Science (TUCS).

Rebholz-Schuhmann, D., Arregui, M., Gaudan, S., Kirsch, H., and Jimeno, A. (2008)
Text Processing through Web Services: Calling Whatizit.
Bioinformatics 24, no. 2 (2008): 296-98.
PMID: 18006544

Sasaki, Y., Montemagni, S., Pezik, P., Rebholz-Schuhmann, D., McNaught, J., and Ananiadou, S. (2008)
BioLexicon: A Lexical Resource for the Biology Domain.
In Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), Turku, Finland. Ed. Salakoski T., Rebholz-Schuhmann D., Pyysalo S. pp. 109--116. Turku Centre for Computer Science (TUCS).

Spasić, I., Schober, D., Sansone, S.A., Rebholz-Schuhmann, D., Kell, D.B., and Paton, N.W. (2008)
Facilitating the Development of Controlled Vocabularies for Metabolomics Technologies with Text Mining.
BMC Bioinformatics 9, no. SUPPL. 5 (2008): Article S5.
PMID: 18460187

2007

Bansard, J.Y., Rebholz-Schuhmann, D., Cameron, G., Clark, D., van Mulligen, E., Beltrame, E., Barbolla, E., Martin-Sanchez, F.H., Milanesi, L., Tollis, I., van der Lei, J., and Coatrieux, J.L. (2007)
Medical informatics and bioinformatics: a bibliometric study.
IEEE Trans Inf Technol Biomed. 11(3): 237-43.
PMID: 17521073

Jimeno, A., Jimenez-Ruiz, E., Lee, L., Gaudan, S., Berlanga-Llavori, R., and Rebholz-Schuhmann, D. (2007)
Assessment of diseases named entity recognition on a corpus of annotated sentences.
Proc of LBM 2007, Singpore, Dec 2007 (accepted for publication in BMC Bioinformatics)

Jimeno, A., Pezik, P., and Rebholz-Schuhmann, D. (2007)
Information Retrieval and Information Extraction in TREC Genomics 2007.
TREC Genomics competition, Washington, U.S.A. (Nov 2007)

Rebholz-Schuhmann, D., Arregui, M., Gaudan, M., Kirsch, H., and Jimeno, A. (2007)
Text processing through Web services: Calling Whatizit.
Bioinformatics 2007 24(2): 296-298.
abstract

Rebholz-Schuhmann, D., Kirsch, H., Arregui, M., Gaudan, S., Riethoven, M., and Stoehr, P. (2007)
EBIMed – Text crunching to gather facts for proteins from Medline.
Bioinformatics 23(2): e237-e244.
abstract

Spasic', I., Schober, D., Assunta-Sansone, S., Rebholz-Schuhmann, D., Kell, D., Paton,D., and the Ontology Working Group Members (2007)
Facilitating the development of controlled vocabularies for metabolomics with text mining, in ISMB/ECCB
Special Interest Group (SIG) Meeting Program Materials, Bio-Ontologies SIG Workshop, Vienna, Austria, pp. 103-106 (accepted for publication in BMC Bioinformatics)


2006

Blazewicz, J., Glover, F., Kasprzak,M., Markiewicz, W.T., Oguz,C., Rebholz-Schuhmann, D., Swiercz, A. (2006)
Dealing with repetitions in sequencing by hybridization.
J Comp Biol Chem. 2006 Oct;30(5):313-20. Epub 2006 Aug 30
PMID: 16945587

Couto, F.M., Silva, M.J., Lee, V., Dimmer, E., Camon, E., Apweiler, R., Kirsch, H., and Rebholz-Schuhmann, D. (2006)
GOAnnotator: linking protein GO annotations to evidence text.
J Biomed Discov Collab. Dec 20;1(1):19
PMID: 17181854

Kirsch, H., Gaudan S, Rebholz-Schuhmann D.  (2006) 
Distributed modules for text annotation and IE applied to the biomedical domain. 
Int J Med Inform. 75(6), 496-500.
PMID: 16085453

Rebholz-Schuhmann, D., Cameron,G., Clark, D., Beltrame, F., Coatrieux, J.L., Del Hoyo Barbolla, E., Martin-Sanchez, F., Milanesi, L., Tollis, I., Van der Lei, J. (2006)
SYMBiomatics: Synergies in Medical Informatics and Bioinformatics – exploring current scientific literature for emerging topics.
BITS 2006, Bologna.

Rebholz-Schuhmann, D., Kirsch, H., Gaudan, S., Arregui, M., and Nenadic, G. (2006)
Annotation and Disambiguation of Semantic Types in Biomedical Text: a Cascaded Approach to Named Entity Recognition.
Workshop on multidimensional markup with Xml (XMLNLP), EACL 2006, Trente, Italy.

Rebholz-Schuhmann, D., Kirsch, H., Nenadic, G. (2006)
IeXML: towards a framework for interoperability of text processing modules to improve annotation of semantic types in biomedical text.
BioLINK, ISMB 2006, Fortaleza, Brazil.

Ruch, P., Boyer, C., Chichester, C., Tbahriti, I., Geissbuhler, A., Fabry,P., Gobeill, J., Pillet, V., Rebholz-Schuhmann, D., Lovis, C., and Veuthey, A.L. (2006)
Using argumentation to extract key sentences from biomedical abstracts.
Int J Med Inform. 76(2-3): 195-200.
PMID: 16815739



2005

Gaudan, S., Kirsch, H., and Rebholz-Schuhmann, D. (2005) 
Resolving abbreviations to their senses in Medline. 
Bioinformatics 21(18):3658-64
PMID: 16037121

Hakenberg, J., et al. (2005)
LLL’05 Challenge: Genic Interaction Extraction with Alignments and Finite State Automata.In 4th Learning Language in Logic Workshop (LLL05) at the 22nd Int Conf on Machine Learning (James Cussens, Claire Nédellec), 38-45
Stud Health Technol Inform. 116:835-40.
more info

Rebholz-Schuhmann, D., Kirsch, H. and Couto, F. (2005)
Facts from text-is text mining ready to deliver?
PLos Biol., 3 (2): e65.
PMID: 15719064

Rebholz-Schuhmann, D.,et al. (2005)
Facts from Text – information extraction online. In Dagstuhl Seminar 05441 “Managing and Mining Genome Information:Frontiers in Bioinformatics (Blazewicz, J., et al., eds)
Int J Med Inform. 75(6), 496-500.
more Info

Ruch, P., Baud, R., Chichester, C., Geissbuhler, A., Lisacek, F., Marty, J., Rebholz-Schuhmann, D., Tbahriti, I., and Veuthey, AL. (2005) 
Extracting key sentences with latent argumentative structuring. 
Stud Health Technol Inform. 116:835-40.
PMID: 16160362

Rebholz-Schuhmann,D., Kirsch, H., Arregui, M., Gaudan, S., Rynbeek, M., and Stoehr, P.
Protein annotation by EBIMed
Nature Biotechnology, 24(8), 902-903.
PMID: 16900125



2004

Rebholz-Schuhmann, D. and Kirsch, H. (2004)
Extraction of biomedical facts - a modular Web server at the EBI (Whatizit).
Proceedings HDL 2004, Bath, UK.
PMID: 12738764

Rebholz-Schuhmann, D., Marcel, S., Albert, S.,Tolle, R., Casari, G. and Kirsch, H. (2004)
Automatic extraction of mutations from Medline and cross-validation with OMIM.
Nucleic Acids Res, 32(1):135--142.
Stud Health Technol Inform. 116:835-40.
PMID: 14704350



2003

Albert, S., Gaudan, S., Knigge, H., Raetsch, A., Delgado, A., Huhse, B., Kirsch, H., Albers, M., Rebholz-Schuhmann, D. and Koegl, M. (2003)
Computer-assisted generation of a protein-interaction database for nuclear receptors.
J. Mol. Endocrinol., 17 (8): 1555-67.
PMID: 12738764



Workshop Proceedings

Rebholz-Schuhmann, D. and Kirsch, H. (2004)
Extraction of biomedical facts - a modular Web server at the EBI (Whatizit).
Proceedings HDL 2004, Bath, UK.
PMID: 12738764



Selected Poster Presentations

Kirsch, H., Gaudan, S., and Rebholz-Schuhmann, D. (2004)
Whatizit - A Server Pipeline on a Linux cluster for Text Annotation in the Biomedical Domain.
ISMB 2004, Glasgow, UK.
Link: Poster@ISMB 2004































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