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1

PhenoMiner: from text to a database of phenotypes associated with OMIM diseases

Collier, Nigel, Groza, Tudor, Smedley, Damian, Robinson, Peter N., Oellrich, Anika, Rebholz-Schuhmann, Dietrich

Journal:

Year:

2015

Language:

english

File:

PDF, 1.36 MB

english, 2015

2

Text-mining solutions for biomedical research: enabling integrative biology

Rebholz-Schuhmann, Dietrich, Oellrich, Anika, Hoehndorf, Robert

Journal:

Nature Reviews Genetics

Year:

2012

Language:

english

File:

PDF, 599 KB

english, 2012

3

Assessment of disease named entity recognition on a corpus of annotated sentences

Antonio Jimeno, Ernesto Jimenez-Ruiz, Vivian Lee, Sylvain Gaudan, Rafael Berlanga, Dietrich Rebholz-Schuhmann

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 343 KB

english, 2008

4

Automatic recognition of conceptualization zones in scientific articles and two life science applications

Liakata, M., Saha, S., Dobnik, S., Batchelor, C., Rebholz-Schuhmann, D.

Journal:

Year:

2012

Language:

english

File:

PDF, 715 KB

english, 2012

5

A multilingual gold-standard corpus for biomedical concept recognition: the Mantra GSC

Kors, Jan A, Clematide, Simon, Akhondi, Saber A, van Mulligen, Erik M, Rebholz-Schuhmann, Dietrich

Journal:

Journal of the American Medical Informatics Association

Year:

2015

Language:

english

File:

PDF, 745 KB

english, 2015

6

[IEEE 2017 IEEE International Conference on Big Data (Big Data) - Boston, MA (2017.12.11-2017.12.14)] 2017 IEEE International Conference on Big Data (Big Data) - Querying web polystores

Khan, Yasar, Zimmermann, Antoine, Jha, AlokKumar, Rebholz-Schuhmann, Dietrich, Sahay, Ratnesh

Year:

2017

Language:

english

File:

PDF, 362 KB

english, 2017

7

Disease mentions in airport and hospital geolocations expose dominance of news events for disease concerns

Barros, Joana M., Duggan, Jim, Rebholz-Schuhmann, Dietrich

Journal:

Journal of Biomedical Semantics

Year:

2018

Language:

english

File:

PDF, 1.74 MB

english, 2018

8

Dealing with repetitions in sequencing by hybridization

Jacek Blazewicz, Fred Glover, Marta Kasprzak, Wojciech T. Markiewicz, Ceyda OĞuz, Dietrich Rebholz-Schuhmann, Aleksandra Swiercz

Journal:

Computational Biology and Chemistry

Year:

2006

Language:

english

File:

PDF, 189 KB

english, 2006

9

Protein annotation by EBIMed

Rebholz-Schuhmann, Dietrich, Kirsch, Harald, Arregui, Miguel, Gaudan, Sylvain, Rynbeek, Mark, Stoehr, Peter

Journal:

Nature Biotechnology

Year:

2006

Language:

english

File:

PDF, 610 KB

english, 2006

10

Harmonization of gene/protein annotations: towards a gold standard MEDLINE

Campos, D., Matos, S., Lewin, I., Oliveira, J. L., Rebholz-Schuhmann, D.

Journal:

Year:

2012

Language:

english

File:

PDF, 875 KB

english, 2012

11

Distributed modules for text annotation and IE applied to the biomedical domain

Harald Kirsch, Sylvain Gaudan, Dietrich Rebholz-Schuhmann

Journal:

International Journal of Medical Informatics

Year:

2006

Language:

english

File:

PDF, 135 KB

english, 2006

12

Using argumentation to extract key sentences from biomedical abstracts

Patrick Ruch, Celia Boyer, Christine Chichester, Imad Tbahriti, Antoine Geissbühler, Paul Fabry, Julien Gobeill, Violaine Pillet, Dietrich Rebholz-Schuhmann, Christian Lovis, Anne-Lise Veuthey

Journal:

International Journal of Medical Informatics

Year:

2007

Language:

english

File:

PDF, 684 KB

english, 2007

13

Ontology refinement for improved information retrieval

Antonio Jimeno-Yepes, Rafael Berlanga-Llavori, Dietrich Rebholz-Schuhmann

Journal:

Information Processing & Management

Year:

2010

Language:

english

File:

PDF, 200 KB

english, 2010

14

Measuring prediction capacity of individual verbs for the identification of protein interactions

Dietrich Rebholz-Schuhmann, Antonio Jimeno-Yepes, Miguel Arregui, Harald Kirsch

Journal:

Journal of Biomedical Informatics

Year:

2010

Language:

english

File:

PDF, 216 KB

english, 2010

15

Medical Informatics and Bioinformatics: A Bibliometric Study

Bansard, J.Y., Rebholz-Schuhmann, D., Cameron, G., Clark, D., van Mulligen, E., Beltrame, F., Barbolla, E.D.H., Martin-Sanchez, F., Milanesi, L., Tollis, I., van der Lei, J., Coatrieux, J.L.

Journal:

IEEE Transactions on Information Technology in Biomedicine

Year:

2007

Language:

english

File:

PDF, 271 KB

english, 2007

16

Reuse of terminological resources for efficient ontological engineering in Life Sciences

Antonio Jimeno-Yepes, Ernesto Jiménez-Ruiz, Rafael Berlanga-Llavori, Dietrich Rebholz-Schuhmann

Journal:

BMC Bioinformatics

Year:

2009

Language:

english

File:

PDF, 548 KB

english, 2009

17

Annotation of protein residues based on a literature analysis: cross-validation against UniProtKb

Kevin Nagel, Antonio Jimeno-Yepes, Dietrich Rebholz-Schuhmann

Journal:

BMC Bioinformatics

Year:

2009

Language:

english

File:

PDF, 2.70 MB

english, 2009

18

Between proteins and phenotypes: annotation and interpretation of mutations

Christopher JO Baker, Dietrich Rebholz-Schuhmann

Journal:

BMC Bioinformatics

Year:

2009

Language:

english

File:

PDF, 308 KB

english, 2009

19

Relations as patterns: bridging the gap between OBO and OWL

Robert Hoehndorf, Anika Oellrich, Michel Dumontier, Janet Kelso, Dietrich Rebholz-Schuhmann, Heinrich Herre

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 244 KB

english, 2010

20

Functional variation of alternative splice forms in their protein interaction networks: a literature mining approach

Şenay Kafkas, Ekrem Varoğlu, Dietrich Rebholz-Schuhmann, Bahar Taneri

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 153 KB

english, 2010

21

Integrating protein-protein interactions and text mining for protein function prediction

Samira Jaeger, Sylvain Gaudan, Ulf Leser, Dietrich Rebholz-Schuhmann

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 534 KB

english, 2008

22

Biomedical Semantics: the Hub for Biomedical Research 2.0

Dietrich Rebholz-Schuhmann, Goran Nenadic

Journal:

Journal of Biomedical Semantics

Year:

2010

Language:

english

File:

PDF, 327 KB

english, 2010

23

Improving the extraction of complex regulatory events from scientific text by using ontology-based inference

Jung-jae Kim, Dietrich Rebholz-Schuhmann

Journal:

Journal of Biomedical Semantics

Year:

2011

Language:

english

File:

PDF, 270 KB

english, 2011

24

Assessment of NER solutions against the first and second CALBC Silver Standard Corpus

Dietrich Rebholz-Schuhmann, Antonio Jimeno Yepes, Chen Li, Senay Kafkas, Ian Lewin, Ning Kang, Peter Corbett, David Milward, Ekaterina Buyko, Elena Beisswanger, Kerstin Hornbostel, Alexandre Kouznetso

Journal:

Journal of Biomedical Semantics

Year:

2011

Language:

english

File:

PDF, 423 KB

english, 2011

25

Towards mature use of semantic resources for biomedical analyses

D Rebholz-Schuhmann, F Rinaldi, S Pyysalo, N Collier, U Hahn

Journal:

Journal of Biomedical Semantics

Year:

2011

Language:

english

File:

PDF, 103 KB

english, 2011

26

Ontology design patterns to disambiguate relations between genes and gene products in GENIA

Robert Hoehndorf, Axel-Cyrille Ngonga Ngomo, Sampo Pyysalo, Tomoko Ohta, Anika Oellrich, Dietrich Rebholz-Schuhmann

Journal:

Journal of Biomedical Semantics

Year:

2011

Language:

english

File:

PDF, 460 KB

english, 2011

27

Poseidon: An information retrieval and extraction system for metagenomic marine science

Marcin Radom, Agnieszka Rybarczyk, Renzo Kottmann, Piotr Formanowicz, Marta Szachniuk, Frank Oliver Glöckner, Dietrich Rebholz-Schuhmann, Jacek Błażewicz

Journal:

Ecological Informatics

Year:

2012

Language:

english

File:

PDF, 783 KB

english, 2012

28

Pathway Enrichment Based on Text Mining and Its Validation on Carotenoid and Vitamin A Metabolism

Waagmeester, Andra, Pezik, Piotr, Coort, Susan, Tourniaire, Franck, Evelo, Chris, Rebholz-Schuhmann, Dietrich

Journal:

Omics A Journal of Integrative Biology

Year:

2009

Language:

english

File:

PDF, 477 KB

english, 2009

29

Systems Biology and Bioinformatics in Aging Research: A Workshop Report

Fuellen, Georg, Dengjel, Jörn, Hoeflich, Andreas, Hoeijemakers, Jan, Kestler, Hans A., Kowald, Axel, Priebe, Steffen, Rebholz-Schuhmann, Dietrich, Schmeck, Bernd, Schmitz, Ulf, Stolzing, Alexandra, Sü

Journal:

Rejuvenation Research

Year:

2012

Language:

english

File:

PDF, 235 KB

english, 2012

30

Facilitating the development of controlled vocabularies for metabolomics technologies with text mining

Irena Spasić, Daniel Schober, Susanna-Assunta Sansone, Dietrich Rebholz-Schuhmann, Douglas B Kell, Norman W Paton

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.03 MB

english, 2008

31

Biological network extraction from scientific literature: state of the art and challenges

Li, C., Liakata, M., Rebholz-Schuhmann, D.

Journal:

Briefings in Bioinformatics

Year:

2014

Language:

english

File:

PDF, 654 KB

english, 2014

32

Evaluating gold standard corpora against gene/protein tagging solutions and lexical resources

Rebholz-Schuhmann, Dietrich, Kafkas, Senay, Kim, Jee-Hyub, Li, Chen, Yepes, Antonio, Hoehndorf, Robert, Backofen, Rolf, Lewin, Ian

Journal:

Journal of Biomedical Semantics

Year:

2013

Language:

english

File:

PDF, 1.40 MB

english, 2013

33

A case study: semantic integration of gene–disease associations for type 2 diabetes mellitus from literature and biomedical data resources

Rebholz-Schuhmann, Dietrich, Grabmüller, Christoph, Kavaliauskas, Silvestras, Croset, Samuel, Woollard, Peter, Backofen, Rolf, Filsell, Wendy, Clark, Dominic

Journal:

Drug Discovery Today

Year:

2014

Language:

english

File:

PDF, 809 KB

english, 2014

34

Towards Virtual Knowledge Broker services for semantic integration of life science literature and data sources

Harrow, Ian, Filsell, Wendy, Woollard, Peter, Dix, Ian, Braxenthaler, Michael, Gedye, Richard, Hoole, David, Kidd, Richard, Wilson, Jabe, Rebholz-Schuhmann, Dietrich

Journal:

Drug Discovery Today

Year:

2013

Language:

english

File:

PDF, 1.01 MB

english, 2013

35

[World Scientific Publishing Co. Pte. Ltd. Biocomputing 2012 - The Pacific Symposium - Kohala Coast, Hawaii, USA (2012.01.03-2012.01.07)] Biocomputing 2012 - Proceedings of the Pacific Symposium - LINKING PHARMGKB TO PHENOTYPE STUDIES AND ANIMAL MODELS OF DISEASE FOR DRUG REPURPOSING

HOEHNDORF, ROBERT, OELLRICH, ANIKA, REBHOLZ-SCHUHMANN, DIETRICH, SCHOFIELD, PAUL N., GKOUTOS, GEORGIOS V.

Year:

2012

Language:

english

File:

PDF, 1.41 MB

english, 2012

36

MeSH Up: effective MeSH text classification for improved document retrieval

Trieschnigg, D., Pezik, P., Lee, V., de Jong, F., Kraaij, W., Rebholz-Schuhmann, D.

Journal:

Year:

2009

Language:

english

File:

PDF, 119 KB

english, 2009

37

[IEEE 2009 Annual International Conference of the IEEE Engineering in Medicine and Biology Society - Minneapolis, MN (2009.09.3-2009.09.6)] 2009 Annual International Conference of the IEEE Engineering in Medicine and Biology Society - Exploitation of ontological resources for scientific literature analysis: Searching genes and related diseases

Jimeno-Yepes, A., Berlanga-Llavori, R., Rebholz-Schuhmann, D.

Year:

2009

Language:

english

File:

PDF, 383 KB

english, 2009

38

[IEEE 2011 22nd International Conference on Database and Expert Systems Applications (DEXA) - Toulouse, France (2011.08.29-2011.09.2)] 2011 22nd International Workshop on Database and Expert Systems Applications - Exploitation of Cross-References between Terminological Resources within the CALBC Context

Jimenez-Ruiz, Ernesto, Rebholz-Schuhmann, Dietrich, Lewin, Ian

Year:

2011

Language:

english

File:

PDF, 509 KB

english, 2011

39

CALBC SILVER STANDARD CORPUS

REBHOLZ-SCHUHMANN, DIETRICH, YEPES, ANTONIO JOSÉ JIMENO, VAN MULLIGEN, ERIK M., KANG, NING, KORS, JAN, MILWARD, DAVID, CORBETT, PETER, BUYKO, EKATERINA, BEISSWANGER, ELENA, HAHN, UDO

Journal:

Journal of Bioinformatics and Computational Biology

Year:

2010

Language:

english

File:

PDF, 1.14 MB

english, 2010

40

WRESTLING WITH BIOMEDICAL RESEARCH RESULTS: LANGUAGE RESOURCES AND LITERATURE ANALYSIS

REBHOLZ-SCHUHMANN, D., COLLIER, NIGEL, PARK, JONG C., WONG, LIMSOON

Journal:

Journal of Bioinformatics and Computational Biology

Year:

2010

Language:

english

File:

PDF, 103 KB

english, 2010

41

Categorization of services for seeking information in biomedical literature: a typology for improvement of practice

Kim, J.-j., Rebholz-Schuhmann, D.

Journal:

Briefings in Bioinformatics

Year:

2008

Language:

english

File:

PDF, 198 KB

english, 2008

42

Text processing through Web services: calling Whatizit

Rebholz-Schuhmann, D., Arregui, M., Gaudan, S., Kirsch, H., Jimeno, A.

Journal:

Year:

2008

Language:

english

File:

PDF, 79 KB

english, 2008

43

MedEvi: Retrieving textual evidence of relations between biomedical concepts from Medline

Kim, J.-j., Pezik, P., Rebholz-Schuhmann, D.

Journal:

Year:

2008

Language:

english

File:

PDF, 167 KB

english, 2008

44

The functional therapeutic chemical classification system

Croset, S., Overington, J. P., Rebholz-Schuhmann, D.

Journal:

Year:

2014

Language:

english

File:

PDF, 739 KB

english, 2014

45

A common layer of interoperability for biomedical ontologies based on OWL EL

Hoehndorf, R., Dumontier, M., Oellrich, A., Wimalaratne, S., Rebholz-Schuhmann, D., Schofield, P., Gkoutos, G. V.

Journal:

Year:

2011

Language:

english

File:

PDF, 127 KB

english, 2011

46

Resolving abbreviations to their senses in Medline

Gaudan, S., Kirsch, H., Rebholz-Schuhmann, D.

Journal:

Year:

2005

Language:

english

File:

PDF, 352 KB

english, 2005

47

Automatic extraction of mutations from Medline and cross-validation with OMIM

Rebholz-Schuhmann, D.

Journal:

Nucleic Acids Research

Year:

2004

Language:

english

File:

PDF, 248 KB

english, 2004

48

Thematic series on biomedical ontologies in JBMS: challenges and new directions

Hoehndorf, Robert, Haendel, Melissa, Stevens, Robert, Rebholz-Schuhmann, Dietrich

Journal:

Journal of Biomedical Semantics

Year:

2014

Language:

english

File:

PDF, 287 KB

english, 2014

49

Combining Evidence, Specificity, and Proximity towards the Normalization of Gene Ontology Terms in Text

Gaudan, S., Jimeno Yepes, A., Lee, V., Rebholz-Schuhmann, D.

Journal:

EURASIP Journal on Bioinformatics and Systems Biology

Year:

2008

Language:

english

File:

PDF, 746 KB

english, 2008

50

GOAnnotator: linking protein GO annotations to evidence text

Couto, Francisco M, Silva, Mário J, Lee, Vivian, Dimmer, Emily, Camon, Evelyn, Apweiler, Rolf, Kirsch, Harald, Rebholz-Schuhmann, Dietrich

Journal:

Journal of Biomedical Discovery and Collaboration

Year:

2006

Language:

english

File:

PDF, 977 KB

english, 2006