| Year |
Citation |
Score |
| 2019 |
Garcia L, Giraldo O, Garcia A, Rebholz-Schuhmann D. Biotea-2-Bioschemas, facilitating structured markup for semantically annotated scholarly publications. Genomics & Informatics. 17: e14. PMID 31307129 DOI: 10.5808/GI.2019.17.2.e14 |
0.31 |
|
| 2018 |
Barros JM, Duggan J, Rebholz-Schuhmann D. Disease mentions in airport and hospital geolocations expose dominance of news events for disease concerns. Journal of Biomedical Semantics. 9: 18. PMID 29895320 DOI: 10.1186/S13326-018-0186-9 |
0.336 |
|
| 2018 |
Oliveira D, Butt AS, Haller A, Rebholz-Schuhmann D, Sahay R. Where to search top-K biomedical ontologies? Briefings in Bioinformatics. PMID 29579141 DOI: 10.1093/Bib/Bby015 |
0.382 |
|
| 2017 |
Jha A, Khan Y, Mehdi M, Karim MR, Mehmood Q, Zappa A, Rebholz-Schuhmann D, Sahay R. Towards precision medicine: discovering novel gynecological cancer biomarkers and pathways using linked data. Journal of Biomedical Semantics. 8: 40. PMID 28927463 DOI: 10.1186/S13326-017-0146-9 |
0.337 |
|
| 2017 |
Karim MR, Michel A, Zappa A, Baranov P, Sahay R, Rebholz-Schuhmann D. Improving data workflow systems with cloud services and use of open data for bioinformatics research. Briefings in Bioinformatics. PMID 28419324 DOI: 10.1093/Bib/Bbx039 |
0.418 |
|
| 2017 |
Hasnain A, Mehmood Q, Sana E Zainab S, Saleem M, Warren C, Zehra D, Decker S, Rebholz-Schuhmann D. BioFed: federated query processing over life sciences linked open data. Journal of Biomedical Semantics. 8: 13. PMID 28298238 DOI: 10.1186/s13326-017-0118-0 |
0.309 |
|
| 2017 |
Khan Y, Saleem M, Mehdi M, Hogan A, Mehmood Q, Rebholz-Schuhmann D, Sahay R. SAFE: SPARQL Federation over RDF Data Cubes with Access Control. Journal of Biomedical Semantics. 8: 5. PMID 28148277 DOI: 10.1186/S13326-017-0112-6 |
0.398 |
|
| 2015 |
Collier N, Groza T, Smedley D, Robinson PN, Oellrich A, Rebholz-Schuhmann D. PhenoMiner: from text to a database of phenotypes associated with OMIM diseases. Database : the Journal of Biological Databases and Curation. 2015. PMID 26507285 DOI: 10.1093/Database/Bav104 |
0.379 |
|
| 2015 |
Oellrich A, Collier N, Groza T, Rebholz-Schuhmann D, Shah N, Bodenreider O, Boland MR, Georgiev I, Liu H, Livingston K, Luna A, Mallon AM, Manda P, Robinson PN, Rustici G, et al. The digital revolution in phenotyping. Briefings in Bioinformatics. PMID 26420780 DOI: 10.1093/Bib/Bbv083 |
0.398 |
|
| 2015 |
Kors JA, Clematide S, Akhondi SA, van Mulligen EM, Rebholz-Schuhmann D. A multilingual gold-standard corpus for biomedical concept recognition: the Mantra GSC. Journal of the American Medical Informatics Association : Jamia. PMID 25948699 DOI: 10.1093/Jamia/Ocv037 |
0.415 |
|
| 2015 |
Machado CM, Rebholz-Schuhmann D, Freitas AT, Couto FM. The semantic web in translational medicine: current applications and future directions. Briefings in Bioinformatics. 16: 89-103. PMID 24197933 DOI: 10.1093/Bib/Bbt079 |
0.443 |
|
| 2014 |
Hoehndorf R, Haendel M, Stevens R, Rebholz-Schuhmann D. Thematic series on biomedical ontologies in JBMS: challenges and new directions. Journal of Biomedical Semantics. 5: 15. PMID 24602198 DOI: 10.1186/2041-1480-5-15 |
0.374 |
|
| 2014 |
Rebholz-Schuhmann D, Grabmüller C, Kavaliauskas S, Croset S, Woollard P, Backofen R, Filsell W, Clark D. A case study: semantic integration of gene-disease associations for type 2 diabetes mellitus from literature and biomedical data resources. Drug Discovery Today. 19: 882-9. PMID 24201223 DOI: 10.1016/J.Drudis.2013.10.024 |
0.441 |
|
| 2014 |
Croset S, Overington JP, Rebholz-Schuhmann D. The functional therapeutic chemical classification system. Bioinformatics (Oxford, England). 30: 876-83. PMID 24177719 DOI: 10.1093/Bioinformatics/Btt628 |
0.4 |
|
| 2014 |
Li C, Liakata M, Rebholz-Schuhmann D. Biological network extraction from scientific literature: state of the art and challenges. Briefings in Bioinformatics. 15: 856-77. PMID 23434632 DOI: 10.1093/Bib/Bbt006 |
0.405 |
|
| 2013 |
Collier N, Tran MV, Le HQ, Ha QT, Oellrich A, Rebholz-Schuhmann D. Learning to recognize phenotype candidates in the auto-immune literature using SVM re-ranking. Plos One. 8: e72965. PMID 24155869 DOI: 10.1371/Journal.Pone.0072965 |
0.413 |
|
| 2013 |
Oellrich A, Grabmüller C, Rebholz-Schuhmann D. Automatically transforming pre- to post-composed phenotypes: EQ-lising HPO and MP. Journal of Biomedical Semantics. 4: 29. PMID 24131519 DOI: 10.1186/2041-1480-4-29 |
0.336 |
|
| 2013 |
Rebholz-Schuhmann D, Kim JH, Yan Y, Dixit A, Friteyre C, Hoehndorf R, Backofen R, Lewin I. Evaluation and cross-comparison of lexical entities of biological interest (LexEBI). Plos One. 8: e75185. PMID 24124474 DOI: 10.1371/Journal.Pone.0075185 |
0.417 |
|
| 2013 |
Rebholz-Schuhmann D, Kafkas S, Kim JH, Li C, Jimeno Yepes A, Hoehndorf R, Backofen R, Lewin I. Evaluating gold standard corpora against gene/protein tagging solutions and lexical resources. Journal of Biomedical Semantics. 4: 28. PMID 24112383 DOI: 10.1186/2041-1480-4-28 |
0.374 |
|
| 2013 |
Rebholz-Schuhmann D, Kafkas S, Kim JH, Jimeno Yepes A, Lewin I. Monitoring named entity recognition: the League Table. Journal of Biomedical Semantics. 4: 19. PMID 24034148 DOI: 10.1186/2041-1480-4-19 |
0.387 |
|
| 2013 |
Li C, Jimeno-Yepes A, Arregui M, Kirsch H, Rebholz-Schuhmann D. PCorral--interactive mining of protein interactions from MEDLINE. Database : the Journal of Biological Databases and Curation. 2013: bat030. PMID 23640984 DOI: 10.1093/Database/Bat030 |
0.456 |
|
| 2013 |
Hakenberg J, Nenadic G, Rebholz-Schuhmann D, Kim JD. Literature mining solutions for life science research. Advances in Bioinformatics. 2013: 320436. PMID 23365570 DOI: 10.1155/2013/320436 |
0.479 |
|
| 2013 |
Harrow I, Filsell W, Woollard P, Dix I, Braxenthaler M, Gedye R, Hoole D, Kidd R, Wilson J, Rebholz-Schuhmann D. Towards virtual knowledge broker services for semantic integration of life science literature and data sources. Drug Discovery Today. 18: 428-34. PMID 23247259 DOI: 10.1016/J.Drudis.2012.11.012 |
0.432 |
|
| 2012 |
Rebholz-Schuhmann D, Oellrich A, Hoehndorf R. Text-mining solutions for biomedical research: enabling integrative biology. Nature Reviews. Genetics. 13: 829-39. PMID 23150036 DOI: 10.1038/Nrg3337 |
0.411 |
|
| 2012 |
Oellrich A, Gkoutos GV, Hoehndorf R, Rebholz-Schuhmann D. Quantitative comparison of mapping methods between Human and Mammalian Phenotype Ontology. Journal of Biomedical Semantics. 3: S1. PMID 23046555 DOI: 10.1186/2041-1480-3-S2-S1 |
0.346 |
|
| 2012 |
Oellrich A, Hoehndorf R, Gkoutos GV, Rebholz-Schuhmann D. Improving disease gene prioritization by comparing the semantic similarity of phenotypes in mice with those of human diseases. Plos One. 7: e38937. PMID 22719993 DOI: 10.1371/Journal.Pone.0038937 |
0.339 |
|
| 2012 |
Campos D, Matos S, Lewin I, Oliveira JL, Rebholz-Schuhmann D. Harmonization of gene/protein annotations: towards a gold standard MEDLINE. Bioinformatics (Oxford, England). 28: 1253-61. PMID 22419783 DOI: 10.1093/Bioinformatics/Bts125 |
0.378 |
|
| 2012 |
Liakata M, Saha S, Dobnik S, Batchelor C, Rebholz-Schuhmann D. Automatic recognition of conceptualization zones in scientific articles and two life science applications. Bioinformatics (Oxford, England). 28: 991-1000. PMID 22321698 DOI: 10.1093/Bioinformatics/Bts071 |
0.448 |
|
| 2012 |
Radom M, Rybarczyk A, Kottmann R, Formanowicz P, Szachniuk M, Glöckner FO, Rebholz-Schuhmann D, Błazewicz J. Poseidon: An information retrieval and extraction system for metagenomic marine science Ecological Informatics. 12: 10-15. DOI: 10.1016/J.Ecoinf.2012.07.003 |
0.374 |
|
| 2011 |
Kim JJ, Rebholz-Schuhmann D. Improving the extraction of complex regulatory events from scientific text by using ontology-based inference. Journal of Biomedical Semantics. 2: S3. PMID 22166672 DOI: 10.1186/2041-1480-2-S5-S3 |
0.404 |
|
| 2011 |
Rebholz-Schuhmann D, Jimeno Yepes A, Li C, Kafkas S, Lewin I, Kang N, Corbett P, Milward D, Buyko E, Beisswanger E, Hornbostel K, Kouznetsov A, Witte R, Laurila JB, Baker CJ, et al. Assessment of NER solutions against the first and second CALBC Silver Standard Corpus. Journal of Biomedical Semantics. 2: S11. PMID 22166494 DOI: 10.1186/2041-1480-2-S5-S11 |
0.394 |
|
| 2011 |
Hoehndorf R, Ngonga Ngomo AC, Pyysalo S, Ohta T, Oellrich A, Rebholz-Schuhmann D. Ontology design patterns to disambiguate relations between genes and gene products in GENIA. Journal of Biomedical Semantics. 2: S1. PMID 22166341 DOI: 10.1186/2041-1480-2-S5-S1 |
0.442 |
|
| 2011 |
Rebholz-Schuhmann D, Rinaldi F, Pyysalo S, Collier N, Hahn U. Towards mature use of semantic resources for biomedical analyses. Journal of Biomedical Semantics. 2: I1. PMID 22166304 DOI: 10.1186/2041-1480-2-S5-I1 |
0.438 |
|
| 2011 |
Thompson P, McNaught J, Montemagni S, Calzolari N, del Gratta R, Lee V, Marchi S, Monachini M, Pezik P, Quochi V, Rupp CJ, Sasaki Y, Venturi G, Rebholz-Schuhmann D, Ananiadou S. The BioLexicon: a large-scale terminological resource for biomedical text mining. Bmc Bioinformatics. 12: 397. PMID 21992002 DOI: 10.1186/1471-2105-12-397 |
0.47 |
|
| 2011 |
Hoehndorf R, Dumontier M, Oellrich A, Rebholz-Schuhmann D, Schofield PN, Gkoutos GV. Interoperability between biomedical ontologies through relation expansion, upper-level ontologies and automatic reasoning. Plos One. 6: e22006. PMID 21789201 DOI: 10.1371/Journal.Pone.0022006 |
0.449 |
|
| 2011 |
Hoehndorf R, Dumontier M, Oellrich A, Wimalaratne S, Rebholz-Schuhmann D, Schofield P, Gkoutos GV. A common layer of interoperability for biomedical ontologies based on OWL EL. Bioinformatics (Oxford, England). 27: 1001-8. PMID 21343142 DOI: 10.1093/Bioinformatics/Btr058 |
0.383 |
|
| 2011 |
McEntyre JR, Ananiadou S, Andrews S, Black WJ, Boulderstone R, Buttery P, Chaplin D, Chevuru S, Cobley N, Coleman LA, Davey P, Gupta B, Haji-Gholam L, Hawkins C, Horne A, ... ... Rebholz-Schuhmann D, et al. UKPMC: a full text article resource for the life sciences. Nucleic Acids Research. 39: D58-65. PMID 21062818 DOI: 10.1093/Nar/Gkq1063 |
0.367 |
|
| 2011 |
Kafkas S, VaroÄlu E, Rebholz-Schuhmann D, Taneri B. Diversity in the Interactions of Isoforms Linked to Clustered Transcripts: A Systematic Literature Analysis Journal of Proteomics & Bioinformatics. 4: 1-10. DOI: 10.4172/Jpb.1000198 |
0.34 |
|
| 2011 |
Croset S, Grabmüller C, Rebholz-Schuhmann D. A Semantic Model for Federated Queries Over a Normalized Corpus Nature Precedings. DOI: 10.1038/Npre.2011.5823.2 |
0.333 |
|
| 2011 |
Croset S, Grabmüller C, Li C, Kavaliauskas S, Rebholz-Schuhmann D. The CALBC RDF Triple store: retrieval over large literature content Nature Precedings. DOI: 10.1038/Npre.2011.5383.2 |
0.47 |
|
| 2010 |
Hoehndorf R, Oellrich A, Rebholz-Schuhmann D. Interoperability between phenotype and anatomy ontologies. Bioinformatics (Oxford, England). 26: 3112-8. PMID 20971987 DOI: 10.1093/Bioinformatics/Btq578 |
0.43 |
|
| 2010 |
Hoehndorf R, Oellrich A, Dumontier M, Kelso J, Rebholz-Schuhmann D, Herre H. Relations as patterns: bridging the gap between OBO and OWL. Bmc Bioinformatics. 11: 441. PMID 20807438 DOI: 10.1186/1471-2105-11-441 |
0.428 |
|
| 2010 |
Rebholz-Schuhmann D, Nenadic G. Biomedical semantics: the hub for biomedical research 2.0. Journal of Biomedical Semantics. 1: 1. PMID 20618983 DOI: 10.1186/2041-1480-1-1 |
0.409 |
|
| 2010 |
Rebholz-Schuhmann D, Kavaliauskas S, Pezik P. PaperMaker: validation of biomedical scientific publications. Bioinformatics (Oxford, England). 26: 982-4. PMID 20200010 DOI: 10.1093/Bioinformatics/Btq060 |
0.398 |
|
| 2010 |
Rebholz-Schuhmann D, Jimeno Yepes AJ, Van Mulligen EM, Kang N, Kors J, Milward D, Corbett P, Buyko E, Beisswanger E, Hahn U. CALBC silver standard corpus. Journal of Bioinformatics and Computational Biology. 8: 163-79. PMID 20183881 DOI: 10.1142/S0219720010004562 |
0.44 |
|
| 2010 |
Rebholz-Schuhmann D, Collier N, Park JC, Wong L. Wrestling with biomedical research results: language resources and literature analysis. Introduction. Journal of Bioinformatics and Computational Biology. 8: 129-30. PMID 20183878 DOI: 10.1142/S0219720010004598 |
0.36 |
|
| 2010 |
Rebholz-Schuhmann D, Jimeno-Yepes A, Arregui M, Kirsch H. Measuring prediction capacity of individual verbs for the identification of protein interactions. Journal of Biomedical Informatics. 43: 200-7. PMID 19818874 DOI: 10.1016/J.Jbi.2009.09.007 |
0.431 |
|
| 2010 |
Kafkas Ş, Varoğlu E, Rebholz-Schuhmann D, Taneri B. Functional variation of alternative splice forms in their protein interaction networks: a literature mining approach Bmc Bioinformatics. 11: 1-2. DOI: 10.1186/1471-2105-11-S5-P1 |
0.385 |
|
| 2010 |
Jimeno-Yepes A, Berlanga-Llavori R, Rebholz-Schuhmann D. Ontology refinement for improved information retrieval Information Processing and Management. 46: 426-435. DOI: 10.1016/J.Ipm.2009.05.008 |
0.407 |
|
| 2009 |
Jimeno-Yepes A, Jiménez-Ruiz E, Berlanga-Llavori R, Rebholz-Schuhmann D. Reuse of terminological resources for efficient ontological engineering in Life Sciences. Bmc Bioinformatics. 10: S4. PMID 19796401 DOI: 10.1186/1471-2105-10-S10-S4 |
0.379 |
|
| 2009 |
Nagel K, Jimeno-Yepes A, Rebholz-Schuhmann D. Annotation of protein residues based on a literature analysis: cross-validation against UniProtKb. Bmc Bioinformatics. 10: S4. PMID 19758468 DOI: 10.1186/1471-2105-10-S8-S4 |
0.409 |
|
| 2009 |
Baker CJ, Rebholz-Schuhmann D. Between proteins and phenotypes: annotation and interpretation of mutations. Bmc Bioinformatics. 10: I1. PMID 19758463 DOI: 10.1186/1471-2105-10-S8-I1 |
0.415 |
|
| 2009 |
Waagmeester A, Pezik P, Coort S, Tourniaire F, Evelo C, Rebholz-Schuhmann D. Pathway enrichment based on text mining and its validation on carotenoid and vitamin A metabolism. Omics : a Journal of Integrative Biology. 13: 367-79. PMID 19715393 DOI: 10.1089/Omi.2009.0029 |
0.302 |
|
| 2009 |
Trieschnigg D, Pezik P, Lee V, de Jong F, Kraaij W, Rebholz-Schuhmann D. MeSH Up: effective MeSH text classification for improved document retrieval. Bioinformatics (Oxford, England). 25: 1412-8. PMID 19376821 DOI: 10.1093/Bioinformatics/Btp249 |
0.47 |
|
| 2009 |
Trieschnigg D, Pezik P, Lee V, de Jong F, Kraaij W, Rebholz-Schuhmann D. Response to comment on 'MeSH-up: Effective MeSH text classification for improved document retrieval' Bioinformatics. 25: 2772. DOI: 10.1093/Bioinformatics/Btp484 |
0.312 |
|
| 2008 |
Altman RB, Bergman CM, Blake J, Blaschke C, Cohen A, Gannon F, Grivell L, Hahn U, Hersh W, Hirschman L, Jensen LJ, Krallinger M, Mons B, O'Donoghue SI, Peitsch MC, ... Rebholz-Schuhmann D, et al. Text mining for biology--the way forward: opinions from leading scientists. Genome Biology. 9: S7. PMID 18834498 DOI: 10.1186/Gb-2008-9-S2-S7 |
0.419 |
|
| 2008 |
Jaeger S, Gaudan S, Leser U, Rebholz-Schuhmann D. Integrating protein-protein interactions and text mining for protein function prediction. Bmc Bioinformatics. 9: S2. PMID 18673526 DOI: 10.1186/1471-2105-9-S8-S2 |
0.355 |
|
| 2008 |
Kim JJ, Rebholz-Schuhmann D. Categorization of services for seeking information in biomedical literature: a typology for improvement of practice. Briefings in Bioinformatics. 9: 452-65. PMID 18660511 DOI: 10.1093/Bib/Bbn032 |
0.388 |
|
| 2008 |
Spasi? I, Schober D, Sansone SA, Rebholz-Schuhmann D, Kell DB, Paton NW. Facilitating the development of controlled vocabularies for metabolomics technologies with text mining. Bmc Bioinformatics. 9: S5. PMID 18460187 DOI: 10.1186/1471-2105-9-S5-S5 |
0.406 |
|
| 2008 |
Gaudan S, Jimeno Yepes A, Lee V, Rebholz-Schuhmann D. Combining evidence, specificity, and proximity towards the normalization of Gene Ontology terms in text. Eurasip Journal On Bioinformatics & Systems Biology. 342746. PMID 18437221 DOI: 10.1155/2008/342746 |
0.449 |
|
| 2008 |
Jimeno A, Jimenez-Ruiz E, Lee V, Gaudan S, Berlanga R, Rebholz-Schuhmann D. Assessment of disease named entity recognition on a corpus of annotated sentences. Bmc Bioinformatics. 9: S3. PMID 18426548 DOI: 10.1186/1471-2105-9-S3-S3 |
0.438 |
|
| 2008 |
Kim JJ, Pezik P, Rebholz-Schuhmann D. MedEvi: retrieving textual evidence of relations between biomedical concepts from Medline. Bioinformatics (Oxford, England). 24: 1410-2. PMID 18400773 DOI: 10.1093/Bioinformatics/Btn117 |
0.4 |
|
| 2008 |
Rebholz-Schuhmann D, Arregui M, Gaudan S, Kirsch H, Jimeno A. Text processing through Web services: calling Whatizit. Bioinformatics (Oxford, England). 24: 296-8. PMID 18006544 DOI: 10.1093/Bioinformatics/Btm557 |
0.434 |
|
| 2007 |
Rebholz-Schuhmann D, Kirsch H, Arregui M, Gaudan S, Riethoven M, Stoehr P. EBIMed--text crunching to gather facts for proteins from Medline. Bioinformatics (Oxford, England). 23: e237-44. PMID 17237098 DOI: 10.1093/Bioinformatics/Btl302 |
0.422 |
|
| 2007 |
Ruch P, Boyer C, Chichester C, Tbahriti I, Geissbühler A, Fabry P, Gobeill J, Pillet V, Rebholz-Schuhmann D, Lovis C, Veuthey AL. Using argumentation to extract key sentences from biomedical abstracts. International Journal of Medical Informatics. 76: 195-200. PMID 16815739 DOI: 10.1016/J.Ijmedinf.2006.05.002 |
0.398 |
|
| 2006 |
Couto FM, Silva MJ, Lee V, Dimmer E, Camon E, Apweiler R, Kirsch H, Rebholz-Schuhmann D. GOAnnotator: linking protein GO annotations to evidence text. Journal of Biomedical Discovery and Collaboration. 1: 19. PMID 17181854 DOI: 10.1186/1747-5333-1-19 |
0.469 |
|
| 2006 |
Kirsch H, Gaudan S, Rebholz-Schuhmann D. Distributed modules for text annotation and IE applied to the biomedical domain. International Journal of Medical Informatics. 75: 496-500. PMID 16085453 DOI: 10.1016/J.Ijmedinf.2005.06.011 |
0.434 |
|
| 2005 |
Gaudan S, Kirsch H, Rebholz-Schuhmann D. Resolving abbreviations to their senses in Medline. Bioinformatics (Oxford, England). 21: 3658-64. PMID 16037121 DOI: 10.1093/Bioinformatics/Bti586 |
0.416 |
|
| 2005 |
Rebholz-Schuhmann D, Kirsch H, Couto F. Facts from text--is text mining ready to deliver? Plos Biology. 3: e65. PMID 15719064 DOI: 10.1371/Journal.Pbio.0030065 |
0.515 |
|
| 2003 |
Albert S, Gaudan S, Knigge H, Raetsch A, Delgado A, Huhse B, Kirsch H, Albers M, Rebholz-Schuhmann D, Koegl M. Computer-assisted generation of a protein-interaction database for nuclear receptors. Molecular Endocrinology (Baltimore, Md.). 17: 1555-67. PMID 12738764 DOI: 10.1210/Me.2002-0424 |
0.347 |
|
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