Reuse of terminological resources for efficient ontological engineering in Life Sciences (2009)
Jimeno-Yepes, Antonio, Jiménez-Ruiz, Ernesto, Berlanga-Llavori, Rafael, Rebholz-Schuhmann, Dietrich
Abstract This paper is intended to explore how to use terminological resources for ontology engineering. Nowadays there are several biomedical ontologies describing overlapping domains, but there is...
Nagel, Kevin, Jimeno-Yepes, Antonio, Rebholz-Schuhmann, Dietrich
Abstract Background A protein annotation database, such as the Universal Protein Resource knowledge base (UniProtKb), is a valuable resource for the validation and interpretation of predicted 3D...
MeSH Up: effective MeSH text classification for improved document retrieval (2009)
Trieschnigg, Dolf, Pezik, Piotr, Lee, Vivian, Jong De, Franciska, Kraaij, Wessel, Rebholz-Schuhmann, Dietrich
Motivation: Controlled vocabularies such as the Medical Subject Headings (MeSH) thesaurus and the Gene Ontology (GO) provide an efficient way of accessing and organizing biomedical information by...
MeSH Up: effective MeSH text classification for improved document retrieval (2009)
Trieschnigg, Dolf, Pezik, Piotr, Lee, Vivian, De Jong, Franciska, Kraaij, Wessel, Rebholz-Schuhmann, Dietrich
Motivation: Controlled vocabularies such as the Medical Subject Headings (MeSH) thesaurus and the Gene Ontology (GO) provide an efficient way of accessing and organizing biomedical information by...
Trieschnigg, Dolf, Pezik, Piotr, Lee, Vivian, Jong De, Franciska, Kraaij, Wessel, Rebholz-Schuhmann, Dietrich
Text mining for biology - the way forward: opinions from leading scientists (2008)
Altman, Russ B, Bergman, Casey M, Blake, Judith, Blaschke, Christian, Cohen, Aaron, Gannon, Frank, ...
Abstract This article collects opinions from leading scientists about how text mining can provide better access to the biological literature, how the scientific community can help with this process,...
Towards Knowledge in the Cloud (2008)
Cerri, Davide, Della Valle, Emanuele, De Francisco Marcos, David, Giunchiglia, Fausto, Naor, Dalit, Nixon, Lyndon, ...
Knowledge in the form of semantic data is becoming more and more ubiquitous, and the need for scalable, dynamic systems to support collaborative work with such distributed, heterogeneous knowledge...
Integrating protein-protein interactions and text mining for protein function prediction (2008)
Jaeger, Samira, Gaudan, Sylvain, Leser, Ulf, Rebholz-Schuhmann, Dietrich
Abstract Background Functional annotation of proteins remains a challenging task. Currently the scientific literature serves as the main source for yet uncurated functional annotations, but curation...
Spasić, Irena, Schober, Daniel, Sansone, Susanna-Assunta, Rebholz-Schuhmann, Dietrich, Kell, Douglas B, Paton, Norman W
Abstract Background Many bioinformatics applications rely on controlled vocabularies or ontologies to consistently interpret and seamlessly integrate information scattered across public resources....
Assessment of disease named entity recognition on a corpus of annotated sentences (2008)
Jimeno, Antonio, Jimenez-Ruiz, Ernesto, Lee, Vivian, Gaudan, Sylvain, Berlanga, Rafael, Rebholz-Schuhmann, Dietrich
Abstract Background In recent years, the recognition of semantic types from the biomedical scientific literature has been focused on named entities like protein and gene names (PGNs) and gene...
Text Mining (Applications Note) Text processing through Web services: Calling Whatizit (2008)
Dietrich Rebholz-schuhmann, Miguel Arregui, Sylvain Gaudan, Harald Kirsch
Motivation: Text-mining (TM) solutions are developing into efficient services to researchers in the biomedical research community. Such solutions have to scale with the growing number and size of...
Essay Facts from Text—Is Text Mining Ready to Deliver? (2008)
Dietrich Rebholz-schuhmann, Harald Kirsch, Francisco Couto
Biological databases offer access to formalized facts about many aspects of biology—genes and gene products, protein structure, metabolic pathways, diseases, organisms, and so on. These databases...
Ashburner, Michael, Leser, Ulf, Rebholz-Schuhmann, Dietrich
Researchers in Text Mining and researchers active in developing ontological resources provide solutions to preserve semantic information properly, i.e. in ontologies and/or fact databases....
Spasic, Irena, Schober, Daniel, Sansone, Susanna-Assunta, Rebholz-Schuhmann, Dietrich, Kell, Douglas B., Paton, Norman W.
Background. Many bioinformatics applications rely on controlled vocabularies or ontologies to consistently interpret and seamlessly integrate information scattered across public resources....
Text processing through Web services: calling Whatizit (2008)
Rebholz-Schuhmann, Dietrich, Arregui, Miguel, Gaudan, Sylvain, Kirsch, Harald, Jimeno, Antonio
Motivation: Text-mining (TM) solutions are developing into efficient services to researchers in the biomedical research community. Such solutions have to scale with the growing number and size of...
Kim, Jung-jae, Rebholz-Schuhmann, Dietrich
Biomedical researchers have to efficiently explore the scientific literature, keeping the focus on their research. This goal can only be achieved if the available means for accessing the literature...
MedEvi: Retrieving textual evidence of relations between biomedical concepts from Medline (2008)
Kim, Jung-jae, Pezik, Piotr, Rebholz-Schuhmann, Dietrich
Summary: Search engines running on MEDLINE abstracts have been widely used by biologists to find publications that are related to their research. The existing search engines such as PubMed, however,...
EBIMed--text crunching to gather facts for proteins from Medline (2007)
Rebholz-Schuhmann, Dietrich, Kirsch, Harald, Arregui, Miguel, Gaudan, Sylvain, Riethoven, Mark, Stoehr, Peter
Summary: To allow efficient and systematic retrieval of statements from Medline we have developed EBIMed, a service that combines document retrieval with co-occurrence-based analysis of Medline...
EBIMed--text crunching to gather facts for proteins from Medline. Bioinformatics (2007)
Dietrich Rebholz-schuhmann, Harald Kirsch, Miguel Arregui, Sylvain Gaudan, Mark Riethoven, Peter Stoehr
Vol. 23 ECCB 2006, pages e237–e244 doi:10.1093/bioinformatics/btl302
GOAnnotator: linking protein GO annotations to evidence text (2006)
Couto, Francisco M, Silva, Mário J, Lee, Vivian, Dimmer, Emily, Camon, Evelyn, Apweiler, Rolf, ...
Abstract Background Annotation of proteins with gene ontology (GO) terms is ongoing work and a complex task. Manual GO annotation is precise and precious, but it is time-consuming. Therefore, instead...
Distributed modules for text annotation and IE applied to the biomedical domain (2006)
Harald Kirsch, Dietrich Rebholz-schuhmann
Biological databases contain facts from scientific literature, which have been curated by hand to ensure high quality. Curation is timeconsuming and can be supported by information extraction...
Dietrich Rebholz-schuhmann, Harald Kirsch, Sylvain Gaudan, Miguel Arregui
Publishers of biomedical journals increasingly use XML as the underlying document format. We present a modular text-processing pipeline that inserts XML markup into such documents in every processing...
Facts from Text—Is Text Mining Ready to Deliver? (2005)
Dietrich Rebholz-Schuhmann, Harald Kirsch, Francisco Couto
The mining of information from scientific literature using computational tools has tremendous potential for knowledge discovery, but how close are we to realizing this potential?
Francisco M. Couto, Mário J. Silva, Vivian Lee, Evelyn Camon, Rolf Apweiler, Harald Kirsch, ...
Technical reports are available at
Lll’05 challenge: genic interaction extraction with alignments and finite state automata (2005)
Jörg Hakenberg, Conrad Plake, Ulf Leser, Harald Kirsch, Dietrich Rebholz-schuhmann
We present a system for the identification of syntax patterns describing interactions between genes and proteins in scientific text. The system uses sequence alignments applied to sentences annotated...
Automatic extraction of mutations from Medline and cross-validation with OMIM (2004)
Rebholz-Schuhmann, Dietrich, Marcel, Stephane, Albert, Sylvie, Tolle, Ralf, Casari, Georg, Kirsch, Harald
Mutations help us to understand the molecular origins of diseases. Researchers, therefore, both publish and seek disease‐relevant mutations in public databases and in scientific literature, e.g....
Automatic extraction of mutations from Medline and cross-validation with OMIM
Rebholz-Schuhmann, Dietrich, Marcel, Stephane, Albert, Sylvie, Tolle, Ralf, Casari, Georg, Kirsch, Harald
Mutations help us to understand the molecular origins of diseases. Researchers, therefore, both publish and seek disease-relevant mutations in public databases and in scientific literature, e.g....
Facts from Text—Is Text Mining Ready to Deliver?
Rebholz-Schuhmann, Dietrich, Kirsch, Harald, Couto, Francisco
The mining of information from scientific literature using computational tools has tremendous potential for knowledge discovery, but how close are we to realizing this potential?
Automatic extraction of mutations from Medline and cross-validation with OMIM
Rebholz-Schuhmann, Dietrich, Marcel, Stephane, Albert, Sylvie, Tolle, Ralf, Casari, Georg, Kirsch, Harald
Mutations help us to understand the molecular origins of diseases. Researchers, therefore, both publish and seek disease-relevant mutations in public databases and in scientific literature, e.g....
Facts from Text—Is Text Mining Ready to Deliver?
Rebholz-Schuhmann, Dietrich, Kirsch, Harald, Couto, Francisco
The mining of information from scientific literature using computational tools has tremendous potential for knowledge discovery, but how close are we to realizing this potential?
GOAnnotator: linking protein GO annotations to evidence text
Couto, Francisco M, Silva, Mário J, Lee, Vivian, Dimmer, Emily, Camon, Evelyn, Apweiler, Rolf, ...
Assessment of disease named entity recognition on a corpus of annotated sentences
Jimeno, Antonio, Jimenez-Ruiz, Ernesto, Lee, Vivian, Gaudan, Sylvain, Berlanga, Rafael, Rebholz-Schuhmann, Dietrich
Spasić, Irena, Schober, Daniel, Sansone, Susanna-Assunta, Rebholz-Schuhmann, Dietrich, Kell, Douglas B, Paton, Norman W
MedEvi: Retrieving textual evidence of relations between biomedical concepts from Medline
Kim, Jung-jae, Pȩzik, Piotr, Rebholz-Schuhmann, Dietrich
Summary: Search engines running on MEDLINE abstracts have been widely used by biologists to find publications that are related to their research. The existing search engines such as PubMed, however,...
Integrating protein-protein interactions and text mining for protein function prediction
Jaeger, Samira, Gaudan, Sylvain, Leser, Ulf, Rebholz-Schuhmann, Dietrich
Text mining for biology - the way forward: opinions from leading scientists
Altman, Russ B, Bergman, Casey M, Blake, Judith, Blaschke, Christian, Cohen, Aaron, Gannon, Frank, ...
This article collects opinions from leading scientists about how text mining can provide better access to the biological literature, how the scientific community can help with this process, what the...
MeSH Up: effective MeSH text classification for improved document retrieval
Trieschnigg, Dolf, Pezik, Piotr, Lee, Vivian, De Jong, Franciska, Kraaij, Wessel, Rebholz-Schuhmann, Dietrich
Motivation: Controlled vocabularies such as the Medical Subject Headings (MeSH) thesaurus and the Gene Ontology (GO) provide an efficient way of accessing and organizing biomedical information by...
Annotation of protein residues based on a literature analysis: cross-validation against UniProtKb
Nagel, Kevin, Jimeno-Yepes, Antonio, Rebholz-Schuhmann, Dietrich
Reuse of terminological resources for efficient ontological engineering in Life Sciences
Jimeno-Yepes, Antonio, Jiménez-Ruiz, Ernesto, Berlanga-Llavori, Rafael, Rebholz-Schuhmann, Dietrich
This paper is intended to explore how to use terminological resources for ontology engineering. Nowadays there are several biomedical ontologies describing overlapping domains, but there is not a...