Identifying Human Phenotype Terms by Combining Machine Learning and Validation Rules.
Named-Entity Recognition is commonly used to identify biological entities such as proteins, genes, and chemical compounds found in scientific articles. The Human Phenotype Ontology (HPO) is an ontology that provides a standardized vocabulary for phenotypic abnormalities found in human diseases. This...
| Publicado en: | BioMed Research International Vol. 2017; pp. 1 - 9 |
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| Autores principales: | , , |
| Formato: | research tables/charts Journal Article |
| Publicado: |
Wiley-Blackwell
11/9/2017
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| Acceso en línea: | Ver este registro en EBSCOhost |
| fields | @attributes: recordID: 1 pdfLink: plink: https://search.ebscohost.com/login.aspx?direct=true&db=ccm&AN=126267288&site=ehost-live header: @attributes: shortDbName: ccm uiTerm: 126267288 longDbName: CINAHL Complete uiTag: AN controlInfo: bkinfo: dissinfo: jinfo: jid: 23146133 FT2T jtl: BioMed Research International issn: 23146133 maglogo: N pubinfo: dt: 11/9/2017 vid: 2017 pid: 480 pub: Wiley-Blackwell place: Malden, Massachusetts artinfo: ui: 126267288 126267288 126267288 10.1155/2017/8565739 126267288 ppf: 1 ppct: 8 formats: fmt: @attributes: type: P tig: atl: Identifying Human Phenotype Terms by Combining Machine Learning and Validation Rules. aug: au: Lobo, Manuel Lamurias, Andre Couto, Francisco M. affil: LaSIGE, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal sug: subj: Phenotype Machine Learning Systems Validation Linguistics Language Processing Ontologies Human ab: Named-Entity Recognition is commonly used to identify biological entities such as proteins, genes, and chemical compounds found in scientific articles. The Human Phenotype Ontology (HPO) is an ontology that provides a standardized vocabulary for phenotypic abnormalities found in human diseases. This article presents the Identifying Human Phenotypes (IHP) system, tuned to recognize HPO entities in unstructured text. IHP uses Stanford CoreNLP for text processing and applies Conditional Random Fields trained with a rich feature set, which includes linguistic, orthographic, morphologic, lexical, and context features created for the machine learning-based classifier. However, the main novelty of IHP is its validation step based on a set of carefully crafted manual rules, such as the negative connotation analysis, that combined with a dictionary can filter incorrectly identified entities, find missed entities, and combine adjacent entities. The performance of IHP was evaluated using the recently published HPO Gold Standardized Corpora (GSC), where the system Bio-LarK CR obtained the best F-measure of 0.56. IHP achieved an F-measure of 0.65 on the GSC. Due to inconsistencies found in the GSC, an extended version of the GSC was created, adding 881 entities and modifying 4 entities. IHP achieved an F-measure of 0.863 on the new GSC. pubtype: Academic Journal doctype: research tables/charts Journal Article ougenre: Article language: English refInfo: holdings: @attributes: islocal: N |
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