Building a semantically annotated corpus of clinical texts

In this paper, we describe the construction of a semantically annotated corpus of clinical texts for use in the development and evaluation of systems for automatically extracting clinically significant information from the textual component of patient records. The paper details the sampling of textual material from a collection of 20,000 cancer patient records, the development of a semantic annotation scheme, the annotation methodology, the distribution of annotations in the final corpus, and the use of the corpus for development of an adaptive information extraction system. The resulting corpus is the most richly semantically annotated resource for clinical text processing built to date, whose value has been demonstrated through its use in developing an effective information extraction system. The detailed presentation of our corpus construction and annotation methodology will be of value to others seeking to build high-quality semantically annotated corpora in biomedical domains

Implementing a Portable Clinical NLP System with a Common Data Model - a Lisp Perspective

This paper presents a Lisp architecture for a portable NLP system, termed LAPNLP, for processing clinical notes. LAPNLP integrates multiple standard, customized and in-house developed NLP tools. Our system facilitates portability across different institutions and data systems by incorporating an enriched Common Data Model (CDM) to standardize necessary data elements. It utilizes UMLS to perform domain adaptation when integrating generic domain NLP tools. It also features stand-off annotations that are specified by positional reference to the original document. We built an interval tree based search engine to efficiently query and retrieve the stand-off annotations by specifying positional requirements. We also developed a utility to convert an inline annotation format to stand-off annotations to enable the reuse of clinical text datasets with inline annotations. We experimented with our system on several NLP facilitated tasks including computational phenotyping for lymphoma patients and semantic relation extraction for clinical notes. These experiments showcased the broader applicability and utility of LAPNLP.Comment: 6 pages, accepted by IEEE BIBM 2018 as regular pape

Improving approximation of domain-focused, corpus-based, lexical semantic relatedness

Semantic relatedness is a measure that quantifies the strength of a semantic link between two concepts. Often, it can be efficiently approximated with methods that operate on words, which represent these concepts. Approximating semantic relatedness between texts and concepts represented by these texts is an important part of many text and knowledge processing tasks of crucial importance in many domain-specific scenarios. The problem of most state-of-the-art methods for calculating domain-specific semantic relatedness is their dependence on highly specialized, structured knowledge resources, which makes these methods poorly adaptable for many usage scenarios. On the other hand, the domain knowledge in the fields such as Life Sciences has become more and more accessible, but mostly in its unstructured form - as texts in large document collections, which makes its use more challenging for automated processing. In this dissertation, three new corpus-based methods for approximating domain-specific textual semantic relatedness are presented and evaluated with a set of standard benchmarks focused on the field of biomedicine. Nonetheless, the proposed measures are general enough to be adapted to other domain-focused scenarios. The evaluation involves comparisons with other relevant state-of-the-art measures for calculating semantic relatedness and the results suggest that the methods presented here perform comparably or better than other approaches. Additionally, the dissertation also presents an experiment, in which one of the proposed methods is applied within an ontology matching system, DisMatch. The performance of the system was evaluated externally on a biomedically themed ‘Phenotype’ track of the Ontology Alignment Evaluation Initiative 2016 campaign. The results of the track indicate, that the use distributional semantic relatedness for ontology matching is promising, as the system presented in this thesis did stand out in detecting correct mappings that were not detected by any other systems participating in the track. The work presented in the dissertation indicates an improvement achieved w.r.t. the stat-of-the-art through the domain adapted use of the distributional principle (i.e. the presented methods are corpus-based and do not require additional resources). The ontology matching experiment showcases practical implications of the presented theoretical body of work

NCBO Ontology Recommender 2.0: An Enhanced Approach for Biomedical Ontology Recommendation

Biomedical researchers use ontologies to annotate their data with ontology terms, enabling better data integration and interoperability. However, the number, variety and complexity of current biomedical ontologies make it cumbersome for researchers to determine which ones to reuse for their specific needs. To overcome this problem, in 2010 the National Center for Biomedical Ontology (NCBO) released the Ontology Recommender, which is a service that receives a biomedical text corpus or a list of keywords and suggests ontologies appropriate for referencing the indicated terms. We developed a new version of the NCBO Ontology Recommender. Called Ontology Recommender 2.0, it uses a new recommendation approach that evaluates the relevance of an ontology to biomedical text data according to four criteria: (1) the extent to which the ontology covers the input data; (2) the acceptance of the ontology in the biomedical community; (3) the level of detail of the ontology classes that cover the input data; and (4) the specialization of the ontology to the domain of the input data. Our evaluation shows that the enhanced recommender provides higher quality suggestions than the original approach, providing better coverage of the input data, more detailed information about their concepts, increased specialization for the domain of the input data, and greater acceptance and use in the community. In addition, it provides users with more explanatory information, along with suggestions of not only individual ontologies but also groups of ontologies. It also can be customized to fit the needs of different scenarios. Ontology Recommender 2.0 combines the strengths of its predecessor with a range of adjustments and new features that improve its reliability and usefulness. Ontology Recommender 2.0 recommends over 500 biomedical ontologies from the NCBO BioPortal platform, where it is openly available.Comment: 29 pages, 8 figures, 11 table

Using distributional similarity to organise biomedical terminology

We investigate an application of distributional similarity techniques to the problem of structural organisation of biomedical terminology. Our application domain is the relatively small GENIA corpus. Using terms that have been accurately marked-up by hand within the corpus, we consider the problem of automatically determining semantic proximity. Terminological units are dened for our purposes as normalised classes of individual terms. Syntactic analysis of the corpus data is carried out using the Pro3Gres parser and provides the data required to calculate distributional similarity using a variety of dierent measures. Evaluation is performed against a hand-crafted gold standard for this domain in the form of the GENIA ontology. We show that distributional similarity can be used to predict semantic type with a good degree of accuracy

Automatic Identification of Biomedical Concepts in Spanish Language Unstructured Clinical Texts

[Poster]. IHI'10 ACM International Health Informatics Symposium Arlington, VA, USA - November 11-12, 2010The processing of health information from medical records and, especially, clinical notes is a complex task due to the nature of the texts themeselves (i.e., hand-written and containing semi-structured or unstructured data) and the diversity of the terminology used. While certain technologies exist to process these types of texts and data in the English language, only a few such initiatives exist for similar texts and data in the Spanish language. This paper presents a new proposal for the semantic annotation of Spanish-language clinical notes, implementing an automated tool similar to the UMLS MetaMap Transfer (MMTx) for the identification of biomedical concepts in the Spanish-language SNOMED CT ontology. Moreover, an assessment of the tool using 100 Spanish-language clinical notes is presented. Using the clinical notes manually annotated by specialists of a Spanish hospital as the gold standard, it is concluded that precision scores are sufficiently good for the several types of matching achieved by the automated tool proposed. The research presented in this contribution offers a launching point for the establishment of semantic relationships between concepts and the application of mining techniques to Spanish-language clinical notes.This study has been partially supported by the MAVIR Consortium (S2009/TIC-1542) and by the TIN2007-67407-C03-01 project BRAVOPublicad