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Protocols

MedPost specifications

Information


Unique identifier OMICS_19801
Name MedPost
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline L. Smith

Publication for MedPost

MedPost citations

 (41)
call_split

Clinical Natural Language Processing in languages other than English: opportunities and challenges

2018
J Biomed Semantics
PMCID: 5877394
PMID: 29602312
DOI: 10.1186/s13326-018-0179-8
call_split See protocol

[…] ic to the biomedical or clinical domain.In this respect, English is by far the most resource-rich language, with advanced tools dedicated to the biomedical domain such as part-of-speech taggers (e.g. MedPOST []), parsers (e.g. GATE [], Charniak-McClosky [], enju []), biomedical concept extractors (e.g. MetaMap [], cTAKES [, ], NCBO []). For other languages, data and resources are sometimes scarce. […]

library_books

Assigning factuality values to semantic relations extracted from biomedical research literature

2017
PLoS One
PMCID: 5497973
PMID: 28678823
DOI: 10.1371/journal.pone.0179926

[…] bserved reduction in microalbuminuria, deserves further investigation.(b) C0078056:Vascular Cell Adhesion Molecule-1-DISRUPTS-C0730345:MicroalbuminuriaSemRep relies on the UMLS SPECIALIST Lexicon [], MedPost part-of-speech tagger [], and noun phrase chunking, and it is supported by MetaMap [] for normalizing noun phrases to UMLS Metathesaurus concepts. Entrez Gene [] serves as a supplementary sour […]

library_books

Rotiferan Hox genes give new insights into the evolution of metazoan bodyplans

2017
Nat Commun
PMCID: 5431905
PMID: 28377584
DOI: 10.1038/s41467-017-00020-w

[…] Hox genes isolated from Brachionus manjavacas have been deposited with GenBank under accession numbers KT989538 (Bm-Hox2), KT989539 (Bm-Hox3), KT989540 (Bm-Hox4), KT989541 (Bm-Hox6), and KT989542 (Bm-MedPost). The amino-acid sequence of Bm-Hox5 is available in the Figshare Repository under the identifier 10.6084/m9.figshare.4616125. […]

library_books

Sortal anaphora resolution to enhance relation extraction from biomedical literature

2016
BMC Bioinformatics
PMCID: 4832532
PMID: 27080229
DOI: 10.1186/s12859-016-1009-6

[…] nesias for nearly 5 decades.Amantadine-ISA-Antiviral AgentsAmantadine-TREATS-Parkinson DiseaseAmantadine-TREATS-Levodopa-induced dyskinesiasSemRep processing relies on the UMLS SPECIALIST Lexicon [], MedPost part-of-speech tagger [], and underspecified syntactic analysis, and it is supported by MetaMap [] for normalizing noun phrases to UMLS Metathesaurus concepts. Entrez Gene [] serves as a suppl […]

call_split

Automatically Detecting Failures in Natural Language Processing Tools for Online Community Text

2015
J Med Internet Res
PMCID: 4642409
PMID: 26323337
DOI: 10.2196/jmir.4612
call_split See protocol

[…] phrase, sentence, or paragraph. POS taggers are commonly used in NLP and have many different applications, such as phrase parsers. In our analysis, we discovered that MetaMap uses a POS tagger called MedPost SKR (Semantic Knowledge Representation) [] to split text into phrases. However, it did not use the resulting POS information when mapping to the UMLS. Such POS failures could have been overloo […]

library_books

Recognition and Evaluation of Clinical Section Headings in Clinical Documents Using Token Based Formulation with Conditional Random Fields

2015
Biomed Res Int
PMCID: 4563061
PMID: 26380302
DOI: 10.1155/2015/873012

[…] owing preprocessing was applied. First, the raw text was extracted from the clinical data while retaining the original line breaks. The text distinguished by the line breaks was then processed by the MedPost tagger [] to further split it into lines of texts that consist of tokens. Each line was then aligned with the annotations of domain experts to generate training instances for the machine learn […]


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MedPost institution(s)
Computational Biology Branch, National Center for Biotechnology Information, Bethesda, MD, USA; Cognitive Science Branch, Lister Hill National Center for Biomedical Communications, Bethesda, MD, USA

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