Background: Most of our biomedical knowledge is only accessible through texts. The biomedical literature grows exponentially and PubMed comprises over 18.000.000 literature abstracts. Recently much effort has been put into the creation of biomedical ontologies which capture biomedical facts. The exploitation of ontologies to explore the scientific literature is a new area of research. Motivation: When people search, they have questions in mind. Answering questions in a domain requires the knowledge of the terminology of that domain. Classical search engines do not provide background knowledge for the presentation of search results. Ontology annotated structured databases allow for data-mining. The hypothesis is that ontology annotated literature databases allow for text-mining. The central problem is to associate scientific publications with ontological concepts. This is a prerequisite for ontology-based literature search. The question then is how to answer biomedical questions using ontologies and a literature corpus. Finally the task is to automate bibliometric analyses on an corpus of scientific publications. Approach: Recent joint efforts on automatically extracting information from free text showed that the applied methods are complementary. The idea is to employ the rich terminological and relational information stored in biomedical ontologies to markup biomedical text documents. Based on established semantic links between documents and ontology concepts the goal is to answer biomedical question on a corpus of documents. The entirely annotated literature corpus allows for the first time to automatically generate bibliometric analyses for ontological concepts, authors and institutions. Results: This work includes a novel annotation framework for free texts with ontological concepts. The framework allows to generate recognition patterns rules from the terminological and relational information in an ontology. Maximum entropy models can be trained to distinguish the meaning of ambiguous concept labels. The framework was used to develop a annotation pipeline for PubMed abstracts with 27,863 Gene Ontology concepts. The evaluation of the recognition performance yielded a precision of 79.9% and a recall of 72.7% improving the previously used algorithm by 25,7% f-measure. The evaluation was done on a manually created (by the original authors) curation corpus of 689 PubMed abstracts with 18,356 curations of concepts. Methods to reason over large amounts of documents with ontologies were developed. The ability to answer questions with the online system was shown on a set of biomedical question of the TREC Genomics Track 2006 benchmark. This work includes the first ontology-based, large scale, online available, up-to-date bibliometric analysis for topics in molecular biology represented by GO concepts. The automatic bibliometric analysis is in line with existing, but often out-dated, manual analyses. Outlook: A number of promising continuations starting from this work have been spun off. A freely available online search engine has a growing user community. A spin-off company was funded by the High-Tech Gründerfonds which commercializes the new ontology-based search paradigm. Several off-springs of GoPubMed including GoWeb (general web search), Go3R (search in replacement, reduction, refinement methods for animal experiments), GoGene (search in gene/protein databases) are developed.

Background: Most of our biomedical knowledge is only accessible through texts. The biomedical literature grows exponentially and PubMed comprises over 18.000.000 literature abstracts. Recently much effort has been put into the creation of biomedical ontologies which capture biomedical facts. The exploitation of ontologies to explore the scientific literature is a new area of research. Motivation: When people search, they have questions in mind. Answering questions in a domain requires the knowledge of the terminology of that domain. Classical search engines do not provide background knowledge for the presentation of search results. Ontology annotated structured databases allow for data-mining. The hypothesis is that ontology annotated literature databases allow for text-mining. The central problem is to associate scientific publications with ontological concepts. This is a prerequisite for ontology-based literature search. The question then is how to answer biomedical questions using ontologies and a literature corpus. Finally the task is to automate bibliometric analyses on an corpus of scientific publications. Approach: Recent joint efforts on automatically extracting information from free text showed that the applied methods are complementary. The idea is to employ the rich terminological and relational information stored in biomedical ontologies to markup biomedical text documents. Based on established semantic links between documents and ontology concepts the goal is to answer biomedical question on a corpus of documents. The entirely annotated literature corpus allows for the first time to automatically generate bibliometric analyses for ontological concepts, authors and institutions. Results: This work includes a novel annotation framework for free texts with ontological concepts. The framework allows to generate recognition patterns rules from the terminological and relational information in an ontology. Maximum entropy models can be trained to distinguish the meaning of ambiguous concept labels. The framework was used to develop a annotation pipeline for PubMed abstracts with 27,863 Gene Ontology concepts. The evaluation of the recognition performance yielded a precision of 79.9% and a recall of 72.7% improving the previously used algorithm by 25,7% f-measure. The evaluation was done on a manually created (by the original authors) curation corpus of 689 PubMed abstracts with 18,356 curations of concepts. Methods to reason over large amounts of documents with ontologies were developed. The ability to answer questions with the online system was shown on a set of biomedical question of the TREC Genomics Track 2006 benchmark. This work includes the first ontology-based, large scale, online available, up-to-date bibliometric analysis for topics in molecular biology represented by GO concepts. The automatic bibliometric analysis is in line with existing, but often out-dated, manual analyses. Outlook: A number of promising continuations starting from this work have been spun off. A freely available online search engine has a growing user community. A spin-off company was funded by the High-Tech Gründerfonds which commercializes the new ontology-based search paradigm. Several off-springs of GoPubMed including GoWeb (general web search), Go3R (search in replacement, reduction, refinement methods for animal experiments), GoGene (search in gene/protein databases) are developed.