Databases in pathology

• PubMed text-mining
  10 October 2016

  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

• biomedical event
  10 October 2016

  See 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 2016

  recognition 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 2016

  Examples
  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 2015

  Named-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 2015

  Open 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 2015

  FusionCancer: 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 2014

  Open References
  Automated semantic annotation of rare disease cases: a case study. Taboada M, Rodríguez H, Martínez D, Pardo M, Sobrido MJ. Database (Oxford). 2014 Jun 4;2014. pii: bau045. doi:10.1093/database/bau045 . PMID: #24903515# [Free]

• annotations
  3 October 2014

  WP
  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 2014

  electronic 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. (...)

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