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tools and resources
Honghan Wu edited this page Aug 23, 2016
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- BRAT - http://brat.nlplab.org/ online environment for collaborative text annotation. Syntax: here
- Annotation / Summary Tools
- bioyodie - UMLS/linked life data, available on node1 of slam cluster
- ncbo annotator - [https://bioportal.bioontology.org/help#Annotator_Tab] (https://bioportal.bioontology.org/help#Annotator_Tab)
- SAPIENTA - available at https://bitbucket.org/partridge/sapienta/overview and is for generating summary for scientific articles
- neji - http://bioinformatics.ua.pt/software/neji/ customisable for terms/ontologies
- Ontologies / Vocabularies
- FMA - http://si.washington.edu/content/accessing-fma-ontology
- complementary brain regions - here
- ontologies selected manually for NCBO Annotator
- "acronym": "ICD10", "name": "International Classification of Diseases, Version 10"
- "acronym": "PDON", "name": "Parkinson's Disease Ontology"
- "acronym": "DOID", "name": "Human Disease Ontology"
- "acronym": "ADO", "name": "Alzheimer's disease ontology"
- "acronym": "FMA", "name": "Foundational Model of Anatomy"
- "acronym": "PATO", "name": "Phenotypic Quality Ontology"
- "acronym": "NIFSTD",
"name": "Neuroscience Information Framework (NIF) Standard Ontology". Note:
using NIFSTD will bring in too many annotations from a large number of other ontologies. the result can be easily overwhelmed.
install python-poppler-qt4 on ubuntu as follows
sudo apt-get update
sudo apt-get install python-poppler-qt4