The Unified Medical Language System (http://umlsks.nlm.nih.gov) is a repository of biomedical vocabularies developed by the US National Library of Medicine. The UMLS integrates over 2 million names for some 900 000 concepts from more than 60 families of biomedical vocabularies, as well as 12 million relations among these concepts. Vocabularies integrated in the UMLS Metathesaurus include the NCBI taxonomy, Gene Ontology, the Medical Subject Headings (MeSH), OMIM and the Digital Anatomist Symbolic Knowledge Base. UMLS concepts are not only inter-related, but may also be linked to external resources such as GenBank. In addition to data, the UMLS includes tools for customizing the Metathesaurus (MetamorphoSys), for generating lexical variants of concept names (lvg) and for extracting UMLS concepts from text (MetaMap). The UMLS knowledge sources are updated quarterly. All vocabularies are available at no fee for research purposes within an institution, but UMLS users are required to sign a license agreement. The UMLS knowledge sources are distributed on CD-ROM and by FTP.

The combination of recent developments in question-answering research and the availability of unparalleled resources developed specifically for automatic semantic processing of text in the medical domain provides a unique opportunity to explore complex question answering in the domain of clinical medicine. This article presents a system designed to satisfy the information needs of physicians practicing evidence-based medicine. We have developed a series of knowledge extractors, which employ a combination of knowledge-based and statistical techniques, for automatically identifying clinically relevant aspects of MEDLINE abstracts. These extracted elements serve as the input to an algorithm that scores the relevance of citations with respect to structured representations of information needs, in accordance with the principles of evidencebased medicine. Starting with an initial list of citations retrieved by PubMed, our system can bring relevant abstracts into higher ranking positions, and from these abstracts generate responses that directly answer physicians ’ questions. We describe three separate evaluations: one focused on the accuracy of the knowledge extractors, one conceptualized as a document reranking task, and finally, an evaluation of answers by two physicians. Experiments on a collection of real-world clinical questions show that our approach significantly outperforms the already competitive PubMed baseline. 1.

To answer questions from clinical-evidence texts, we identify occurrences of the semantic classes --- disease, medication, patient outcome --- that are candidate elements of the answer, and the relations among them. Additionally, we determine whether an outcome is positive or negative.

This paper presents a hybrid approach to question answering in the clinical domain that combines techniques from summarization and information retrieval.

In retrieving medical free text, users are often interested in answers pertinent to certain scenarios that correspond to common tasks performed in medical practice, e.g., treatment ordiagnosis of a disease. A major challenge in handling such queries is that scenario terms in the query (e.g. treatment) are often too general to match specialized terms in relevant documents (e.g. chemotherapy). In this paper, we propose a knowledge-based query expansion method that exploits the UMLS knowledge source to append the original query with additional terms that are specifically relevant to the query’s scenario(s). We compared the proposed method with traditional statistical expansion that expands terms which are statistically correlated but not necessarily scenario specific. Our study on two standard testbeds shows that the knowledge-based method, by providing scenario-specific expansion, yields notable improvements over the statistical method in terms of average precision-recall. On the OHSUMED testbed, for example, the improvement is more than 5 % averaging over all scenario-specific queries studied and about 10 % for queries that mention certain scenarios, such astreatment of a disease anddifferential diagnosis of a symptom/disease. 1

The ability to accurately model the content structure of text is important for many natural language processing applications. This paper describes experiments with generative models for analyzing the discourse structure of medical abstracts, which generally follow the pattern of “introduction”, “methods”, “results”, and “conclusions”. We demonstrate that Hidden Markov Models are capable of accurately capturing the structure of such texts, and can achieve classification accuracy comparable to that of discriminative techniques. In addition, generative approaches provide advantages that may make them preferable to discriminative techniques such as Support Vector Machines under certain conditions. Our work makes two contributions: at the application level, we report good performance on an interesting task in an important domain; more generally, our results contribute to an ongoing discussion regarding the tradeoffs between generative and discriminative techniques.

Abstract not found

An experiment was performed at the National Library of Medicine ® (NLM ® ) in word sense disambiguation (WSD) using the Journal Descriptor Indexing (JDI) methodology. The motivation is the need to solve the ambiguity problem confronting NLM’s MetaMap system, which maps free text to terms corresponding to concepts in NLM’s Unified Medical Language System ® (UMLS ® ) Metathesaurus ®. If the text maps to more than one Metathesaurus concept at the same high confidence score, MetaMap has no way of knowing which concept is the correct mapping. We describe the JDI methodology, which is ultimately based on statistical associations between words in a training set of MEDLINE ® citations and a small set of journal descriptors (assigned by humans to journals per se) assumed to be inherited by the citations. JDI is the

this paper we present a natural language processing method for extracting causal relations between genetic phenomena and diseases. After presenting the results of a preliminary evaluation, we suggest the use of a graphical display application for viewing the semantic predications produced by the system

The range of publicly available biomedical data is enormous and is expanding fast. This expansion means that researchers now face a hurdle to extracting the data they need from the large numbers of data that are available. Biomedical researchers have turned to ontologies and terminologies to structure and annotate their data with ontology concepts for better search and retrieval. However, this annotation process cannot be easily automated and often requires expert curators. Plus, there is a lack of easy-to-use systems that facilitate the use of ontologies for annotation. This paper presents the Open Biomedical Annotator (OBA), an ontologybased Web service that annotates public datasets