See also
PubMed
text-mining
Open references
MET network in PubMed: a text-mined network visualization and curation system.
Dai HJ, Su CH, Lai PT, Huang MS, Jonnagaddala J, Rose Jue T, Rao S, Chou HJ, Milacic M, Singh O, Syed-Abdul S, Hsu WL.
Database (Oxford). 2016 May 30;2016. pii: baw090. doi:10.1093/database/baw090 . Print 2016.
PMID: #27242035# Free
Home > Resources in pathology > Databases in pathology
Databases in pathology
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PubMed text-mining
10 October 2016 -
biomedical event
10 October 2016See also
biological processes
biological functions
Open references
TrigNER: automatically optimized biomedical event trigger recognition on scientific documents. Campos D, Bui QC, Matos S, Oliveira JL.
Source Code Biol Med. 2014 Jan 8;9(1):1. doi:10.1186/1751-0473-9-1.
PMID: #24401704# Free -
named entity recognition
10 October 2016recognition of named entities (NER)
The recognition of named entities (NER) is an elementary task in biomedical text mining.
A number of NER solutions have been proposed in recent years, taking advantage of available annotated corpora, terminological resources and machine-learning techniques.
Currently, the best performing solutions combine the outputs from selected annotation solutions measured against a single corpus. However, little effort has been spent on a systematic analysis of (...) -
PubMed text-mining
8 October 2016Examples
Building a glaucoma interaction network using a text mining approach.
Soliman M, Nasraoui O, Cooper NG.
BioData Min. 2016 May 5;9:17.
doi:10.1186/s13040-016-0096-2.
PMID: #27152122# / Free -
named-entity recognition
12 October 2015Named-entity recognition (NER) plays an important role in the development of biomedical databases. However, the existing NER tools produce multifarious named-entities which may result in both curatable and non-curatable markers. To facilitate biocuration with a straightforward approach, classifying curatable named-entities is helpful with regard to accelerating the biocuration workflow.
Links
http://ikmbio.csie.ncku.edu.tw/coinner/ introduction.htm
References
Curatable Named-Entity (...) -
semantic ontology
12 October 2015Open references
A User-Centric Knowledge Creation Model in a Web of Object-Enabled Internet of Things Environment. Kibria MG, Fattah SM, Jeong K, Chong I, Jeong YK. Sensors (Basel). 2015 Sep 18;15(9):24054-86. doi:10.3390/s150924054 . PMID: #26393609# (Free) -
FusionCancer
18 September 2015FusionCancer: a database of cancer fusion genes derived from RNA-seq data
http://donglab.ecnu.edu.cn/databases/FusionCancer/
Open references
FusionCancer: a database of cancer fusion genes derived from RNA-seq data. Wang Y, Wu N, Liu J, Wu Z, Dong D. Diagn Pathol. 2015 Jul 28;10:131. doi:10.1186/s13000-015-0310-4 . PMID: #26215638# (Free) -
semantic annotation
13 October 2014Open References
Automated semantic annotation of rare disease cases: a case study. Taboada M, RodrÃguez H, MartÃnez D, Pardo M, Sobrido MJ. Database (Oxford). 2014 Jun 4;2014. pii: bau045. doi:10.1093/database/bau045 . PMID: #24903515# [Free] -
annotations
3 October 2014WP
Types
genome annotation
gene annotation
protein annotation
DNA variant annotation
Annotations in pathology
phenotype annotation
semantic annotation
Open references
Harmonization of gene/protein annotations: towards a gold standard MEDLINE.
Campos D, Matos S, Lewin I, Oliveira JL, Rebholz-Schuhmann D.
Bioinformatics. 2012 May 1;28(9):1253-61. doi:10.1093/bioinformatics/bts125.
PMID: #22419783# (Free)
The CHEMDNER corpus of chemicals and drugs and its (...) -
EHR data mining
22 September 2014electronic health records EHR
Open references
Mining Electronic Health Records using Linked Data. Odgers DJ, Dumontier M. AMIA Jt Summits Transl Sci Proc. 2015 Mar 23;2015:217-21. eCollection 2015. PMID: #26306276# (Free)
References
Building the graph of medicine from millions of clinical narratives, 2014 - http://dx.doi.org/10.5061/dryad.jp917
Pathak, J., Kho, A. N. & Denny, J. C. Electronic health records-driven phenotyping: challenges, recent advances, and perspectives. J. (...)