Dataset Information

Using contextual and lexical features to restructure and validate the classification of biomedical concepts.

ABSTRACT:

Background

Biomedical ontologies are critical for integration of data from diverse sources and for use by knowledge-based biomedical applications, especially natural language processing as well as associated mining and reasoning systems. The effectiveness of these systems is heavily dependent on the quality of the ontological terms and their classifications. To assist in developing and maintaining the ontologies objectively, we propose automatic approaches to classify and/or validate their semantic categories. In previous work, we developed an approach using contextual syntactic features obtained from a large domain corpus to reclassify and validate concepts of the Unified Medical Language System (UMLS), a comprehensive resource of biomedical terminology. In this paper, we introduce another classification approach based on words of the concept strings and compare it to the contextual syntactic approach.

Results

The string-based approach achieved an error rate of 0.143, with a mean reciprocal rank of 0.907. The context-based and string-based approaches were found to be complementary, and the error rate was reduced further by applying a linear combination of the two classifiers. The advantage of combining the two approaches was especially manifested on test data with sufficient contextual features, achieving the lowest error rate of 0.055 and a mean reciprocal rank of 0.969.

Conclusion

The lexical features provide another semantic dimension in addition to syntactic contextual features that support the classification of ontological concepts. The classification errors of each dimension can be further reduced through appropriate combination of the complementary classifiers.

SUBMITTER: Fan JW

PROVIDER: S-EPMC2014782 | biostudies-literature | 2007 Jul

REPOSITORIES: biostudies-literature

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Publications

Using contextual and lexical features to restructure and validate the classification of biomedical concepts.

Fan Jung-Wei JW Xu Hua H Friedman Carol C

BMC bioinformatics 20070724

<h4>Background</h4>Biomedical ontologies are critical for integration of data from diverse sources and for use by knowledge-based biomedical applications, especially natural language processing as well as associated mining and reasoning systems. The effectiveness of these systems is heavily dependent on the quality of the ontological terms and their classifications. To assist in developing and maintaining the ontologies objectively, we propose automatic approaches to classify and/or validate the ...[more]

PMID: 17650333

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Project description:BackgroundAs biomedical knowledge is rapidly evolving, concept enrichment of biomedical terminologies is an active research area involving automatic identification of missing or new concepts. Previously, we prototyped a lexical-based formal concept analysis (FCA) approach in which concepts were derived by intersecting bags of words, to identify potentially missing concepts in the National Cancer Institute (NCI) Thesaurus. However, this prototype did not handle concept naming and positioning. In this paper, we introduce a sequenced-based FCA approach to identify potentially missing concepts, supporting concept naming and positioning.MethodsWe consider the concept name sequences as FCA attributes to construct the formal context. The concept-forming process is performed by computing the longest common substrings of concept name sequences. After new concepts are formalized, we further predict their potential positions in the original hierarchy by identifying their supertypes and subtypes from original concepts. Automated validation via external terminologies in the Unified Medical Language System (UMLS) and biomedical literature in PubMed is performed to evaluate the effectiveness of our approach.ResultsWe applied our sequenced-based FCA approach to all the sub-hierarchies under Disease or Disorder in the NCI Thesaurus (19.08d version) and five sub-hierarchies under Clinical Finding and Procedure in the SNOMED CT (US Edition, March 2020 release). In total, 1397 potentially missing concepts were identified in the NCI Thesaurus and 7223 in the SNOMED CT. For NCI Thesaurus, 85 potentially missing concepts were found in external terminologies and 315 of the remaining 1312 appeared in biomedical literature. For SNOMED CT, 576 were found in external terminologies and 1159 out of the remaining 6647 were found in biomedical literature.ConclusionOur sequence-based FCA approach has shown the promise for identifying potentially missing concepts in biomedical terminologies.

Project description:In this paper, we discuss the results of two experiments, one off-line (acceptability judgment) and the other on-line (eye-tracking), targeting Object Cleft (OC) constructions. In both experiments, we used the same materials presenting a manipulation on person features: second person plural pronouns and plural definite determiners alternate in introducing a full NP ("it was [DP1 the/you [NP bankers]]i that [DP2 the/you [NP lawyers]] have avoided _i at the party") in a language, Italian, with overt person (and number) subject-verb agreement. As results, we first observed that the advantage of the bare pronominal forms reported in previous experiments (Gordon et al., 2001; Warren and Gibson, 2005, a.o.) is lost when the full NP (the "lexical restriction" in Belletti and Rizzi, 2013) is present. Second, an advantage for the mismatch condition, Art 1 -Pro 2, in which the focalized subject is introduced by the determiner and the OC subject by the pronoun, as opposed to the matching Pro 1 -Pro 2 condition, is observed, both off-line (higher acceptability and accuracy in answering comprehension questions after eyetracking) and on-line (e.g., smaller number of regressions from the subject region); third, we found a relevant difference between acceptability and accuracy in comprehension questions: despite similar numerical patterns in both off-line measures, the difference across conditions in accuracy is mostly not significant, while it is significant in acceptability. Moreover, while the matching condition Pro 1 -Pro 2 is perceived as nearly ungrammatical (far below the mean acceptability across-conditions), the accuracy in comprehension is still high (close to 80%). To account for these facts, we compare different formal competence and processing models that predict difficulties in OC constructions: similarity-based (Gordon et al., 2001, a.o.), memory load (Gibson, 1998), and intervention-based (Friedmann et al., 2009) accounts are compared to processing oriented ACT-R-based predictions (Lewis and Vasishth, 2005) and to top-down Minimalist derivations (Chesi, 2015). We conclude that most of these approaches fail in making predictions able to reconcile the competence and the performance perspective in a coherent way to the exception of the top-down model that is able to predict correctly both the on-line and the off-line main effects obtained.

Dataset Information

Using contextual and lexical features to restructure and validate the classification of biomedical concepts.

Background

Results

Conclusion

Publications

Using contextual and lexical features to restructure and validate the classification of biomedical concepts.

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