Dietrich Rebholz-Schuhman

Summary

Affiliation: Wellcome Trust Genome Campus
Country: UK

Publications

  1. pmc Quantitative comparison of mapping methods between Human and Mammalian Phenotype Ontology
    Anika Oellrich
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
    J Biomed Semantics 3:S1. 2012
  2. doi request reprint Text-mining solutions for biomedical research: enabling integrative biology
    Dietrich Rebholz-Schuhmann
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nat Rev Genet 13:829-39. 2012
  3. pmc Ontology design patterns to disambiguate relations between genes and gene products in GENIA
    Robert Hoehndorf
    European Bioinformatics Institute, Hinxton, Cambridge, UK
    J Biomed Semantics 2:S1. 2011
  4. pmc Improving the extraction of complex regulatory events from scientific text by using ontology-based inference
    Jung Jae Kim
    School of Computer Engineering, Nanyang Technological University, Singapore
    J Biomed Semantics 2:S3. 2011
  5. pmc The BioLexicon: a large-scale terminological resource for biomedical text mining
    Paul Thompson
    School of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
    BMC Bioinformatics 12:397. 2011
  6. pmc Annotation of protein residues based on a literature analysis: cross-validation against UniProtKb
    Kevin Nagel
    European Bioinformatics Institute, Hinxton, Cambridge, UK
    BMC Bioinformatics 10:S4. 2009
  7. pmc Assessment of disease named entity recognition on a corpus of annotated sentences
    Antonio Jimeno
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    BMC Bioinformatics 9:S3. 2008
  8. pmc Reuse of terminological resources for efficient ontological engineering in Life Sciences
    Antonio Jimeno-Yepes
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    BMC Bioinformatics 10:S4. 2009
  9. pmc Integrating protein-protein interactions and text mining for protein function prediction
    Samira Jaeger
    Knowledge Management in Bioinformatics, Humboldt University Berlin, Unter den Linden 6, 10099 Berlin, Germany
    BMC Bioinformatics 9:S2. 2008
  10. pmc Facilitating the development of controlled vocabularies for metabolomics technologies with text mining
    Irena Spasic
    Manchester Centre for Integrative Systems Biology, The University of Manchester, 131 Princess Street, Manchester, M1 7ND, UK
    BMC Bioinformatics 9:S5. 2008

Collaborators

Detail Information

Publications32

  1. pmc Quantitative comparison of mapping methods between Human and Mammalian Phenotype Ontology
    Anika Oellrich
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
    J Biomed Semantics 3:S1. 2012
    ..Our results suggest that combining both approaches will yield a better mappings in terms of completeness, specificity and application purposes...
  2. doi request reprint Text-mining solutions for biomedical research: enabling integrative biology
    Dietrich Rebholz-Schuhmann
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nat Rev Genet 13:829-39. 2012
    ..Here we explore the latest advancements in automated literature analysis and its contribution to innovative research approaches...
  3. pmc Ontology design patterns to disambiguate relations between genes and gene products in GENIA
    Robert Hoehndorf
    European Bioinformatics Institute, Hinxton, Cambridge, UK
    J Biomed Semantics 2:S1. 2011
    ..Consistent semantic annotations facilitate the automatic discovery of new information through deductive inferences...
  4. pmc Improving the extraction of complex regulatory events from scientific text by using ontology-based inference
    Jung Jae Kim
    School of Computer Engineering, Nanyang Technological University, Singapore
    J Biomed Semantics 2:S3. 2011
    ..Previous approaches associate lexical and syntactic resources with ontologies for the semantic analysis, but fall short in testing the benefits from the use of domain knowledge...
  5. pmc The BioLexicon: a large-scale terminological resource for biomedical text mining
    Paul Thompson
    School of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
    BMC Bioinformatics 12:397. 2011
    ..Additionally, such resources typically do not provide information about how terms relate to each other in texts to describe events...
  6. pmc Annotation of protein residues based on a literature analysis: cross-validation against UniProtKb
    Kevin Nagel
    European Bioinformatics Institute, Hinxton, Cambridge, UK
    BMC Bioinformatics 10:S4. 2009
    ..However, these methods were limited to point mutation extraction and do not extract features for the annotation of proteins at the residue level...
  7. pmc Assessment of disease named entity recognition on a corpus of annotated sentences
    Antonio Jimeno
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    BMC Bioinformatics 9:S3. 2008
    ....
  8. pmc Reuse of terminological resources for efficient ontological engineering in Life Sciences
    Antonio Jimeno-Yepes
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    BMC Bioinformatics 10:S4. 2009
    ..As a result, we have created a reference thesaurus for this project, named HeCTh...
  9. pmc Integrating protein-protein interactions and text mining for protein function prediction
    Samira Jaeger
    Knowledge Management in Bioinformatics, Humboldt University Berlin, Unter den Linden 6, 10099 Berlin, Germany
    BMC Bioinformatics 9:S2. 2008
    ..To enhance the precision of the results, we furthermore implemented a procedure that validates all predictions based on findings reported in the literature...
  10. pmc Facilitating the development of controlled vocabularies for metabolomics technologies with text mining
    Irena Spasic
    Manchester Centre for Integrative Systems Biology, The University of Manchester, 131 Princess Street, Manchester, M1 7ND, UK
    BMC Bioinformatics 9:S5. 2008
    ..However, it is time-consuming and non trivial to construct these resources manually...
  11. pmc Relations as patterns: bridging the gap between OBO and OWL
    Robert Hoehndorf
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    BMC Bioinformatics 11:441. 2010
    ..Since the Web Ontology Language (OWL) is an expressive language with a formal semantics, it is suitable to de ne the meaning of relations accurately...
  12. pmc SYMBIOmatics: synergies in Medical Informatics and Bioinformatics--exploring current scientific literature for emerging topics
    Dietrich Rebholz-Schuhman
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    BMC Bioinformatics 8:S18. 2007
    ..To provide input to the survey, the scientific literature was analysed to extract topics relevant to both medical informatics and bioinformatics...
  13. ncbi request reprint CALBC silver standard corpus
    Dietrich Rebholz-Schuhmann
    EMBL Outstation Hinxton, European Bioinformatics Institute, Hinxton, Cambridge CB101SD, UK
    J Bioinform Comput Biol 8:163-79. 2010
    ..We expect that we can improve corpus building activities both in terms of the numbers of named entity classes being covered, as well as the size of the corpus in terms of annotated documents...
  14. pmc Facts from text--is text mining ready to deliver?
    Dietrich Rebholz-Schuhmann
    European Bioinformatics Institute, Cambridge, United Kingdom
    PLoS Biol 3:e65. 2005
  15. pmc PaperMaker: validation of biomedical scientific publications
    D Rebholz-Schuhmann
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Bioinformatics 26:982-4. 2010
    ..The automatic analysis of scientific literature can support authors in writing their manuscripts...
  16. pmc Automatic extraction of mutations from Medline and cross-validation with OMIM
    Dietrich Rebholz-Schuhmann
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
    Nucleic Acids Res 32:135-42. 2004
    ..Access to the database of extracted mutation-gene pairs is available through the web pages of the EBI (refer to http://www.ebi. ac.uk/rebholz/index.html)...
  17. ncbi request reprint EBIMed--text crunching to gather facts for proteins from Medline
    Dietrich Rebholz-Schuhmann
    European Bioinformatics Institute, Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD, UK
    Bioinformatics 23:e237-44. 2007
    ..We conclude that EBIMed improves access to information where proteins and drugs are involved in the same biological process, e.g. statements with GO annotations of proteins, protein-protein interactions and effects of drugs on proteins...
  18. ncbi request reprint Text processing through Web services: calling Whatizit
    Dietrich Rebholz-Schuhmann
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
    Bioinformatics 24:296-8. 2008
    ..For large quantities of the user's own text, the server can be operated in a streaming mode (http://www.ebi.ac.uk/webservices/whatizit)...
  19. doi request reprint Measuring prediction capacity of individual verbs for the identification of protein interactions
    Dietrich Rebholz-Schuhmann
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB101SD, UK
    J Biomed Inform 43:200-7. 2010
    ..Programmatic access to the text processing modules is available online (www.ebi.ac.uk/webservices/whatizit/info.jsf) and the full analysis of Medline abstracts will be made through the Web pages of the Rebholz group...
  20. ncbi request reprint Resolving abbreviations to their senses in Medline
    S Gaudan
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Bioinformatics 21:3658-64. 2005
    ..Resolving an abbreviation in a document consists of retrieving its sense in use. Abbreviation resolution improves accuracy of document retrieval engines and of information extraction systems...
  21. doi request reprint Exploitation of ontological resources for scientific literature analysis: searching genes and related diseases
    Antonio Jimeno-Yepes
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, U K
    Conf Proc IEEE Eng Med Biol Soc 2009:7073-8. 2009
    ..For knowledge discovery (KD) solutions the identified concepts in the scientific literature are used to relate entities to each other, e.g. to identify gene-disease relations based on shared molecular functions...
  22. ncbi request reprint Distributed modules for text annotation and IE applied to the biomedical domain
    Harald Kirsch
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Int J Med Inform 75:496-500. 2006
    ..The server and the underlying software are available to the public...
  23. doi request reprint Pathway enrichment based on text mining and its validation on carotenoid and vitamin A metabolism
    Andra Waagmeester
    European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD United Kingdom
    OMICS 13:367-79. 2009
    ..The remaining 10 terms were classified as biomarkers or nutrients. Automatic literature analysis improves the enrichment of pathways with entities already described in the scientific literature...
  24. pmc MeSH Up: effective MeSH text classification for improved document retrieval
    Dolf Trieschnigg
    European Bioinformatics Institute, Hinxton, UK
    Bioinformatics 25:1412-8. 2009
    ..Different methods of automating the assignment of MeSH concepts have been proposed to replace manual annotation, but they are either limited to a small subset of MeSH or have only been compared with a limited number of other systems...
  25. doi request reprint Categorization of services for seeking information in biomedical literature: a typology for improvement of practice
    Jung Jae Kim
    European Bioinformatics Institute, EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Brief Bioinform 9:452-65. 2008
    ..Also, they may inspire future bioinformaticians to further innovative development in this field...
  26. pmc MedEvi: retrieving textual evidence of relations between biomedical concepts from Medline
    Jung Jae Kim
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB101SD, UK
    Bioinformatics 24:1410-2. 2008
    ..AVAILABILITY: http://www.ebi.ac.uk/tc-test/textmining/medevi/..
  27. pmc UKPMC: a full text article resource for the life sciences
    Johanna R McEntyre
    EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 39:D58-65. 2011
    ..Here we describe UKPMC and clarify the relationship between PMC and UKPMC, providing historical context and future directions, 10 years on from when PMC was first launched...
  28. ncbi request reprint Using argumentation to extract key sentences from biomedical abstracts
    Patrick Ruch
    SIM, University Hospitals of Geneva, Geneva, CH, Switzerland
    Int J Med Inform 76:195-200. 2007
    ..We design and assess the performance of an automatic key sentence selector, which classifies sentences into four argumentative moves: PURPOSE, METHODS, RESULTS and..
  29. ncbi request reprint Protein annotation by EBIMed
    Dietrich Rebholz-Schuhmann
    Nat Biotechnol 24:902-3. 2006
  30. ncbi request reprint Gene Regulation Ontology (GRO): design principles and use cases
    Elena Beisswanger
    Jena University Language and Information Engineering JULIE Lab, Jena, Germany
    Stud Health Technol Inform 136:9-14. 2008
    ..The GRO has just been submitted to the OBO library and is currently under review. It is available at http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html...
  31. ncbi request reprint Dealing with repetitions in sequencing by hybridization
    Jacek Blazewicz
    Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60 965 Poznan, Poland
    Comput Biol Chem 30:313-20. 2006
    ..The spectra prepared from the sequences taken from GenBank are available on our website http://bio.cs.put.poznan.pl/...
  32. ncbi request reprint Computer-assisted generation of a protein-interaction database for nuclear receptors
    Sylvie Albert
    LION bioscience AG, 69123 Heidelberg, Germany
    Mol Endocrinol 17:1555-67. 2003
    ..The data set obtained serves as a source for information on NR interactions, as well as a reference data set for the improvement of advanced text-mining methods...