Bioinformatics topics from EDAM (http://voxel.dl.sourceforge.net/project/edamontology/EDAM_beta12.obo)

EDAM_topics.tree

* Topic
|---+ Biological data resources
|    |---+ Laboratory resources
|        |---> Microarrays
|        |---> Cell culture resources
|        +---> Medical informatics resources
|    +---+ Biological science resources
        |---> Cell biology resources
        |---+ Developmental biology resources
|            +---> Embryology resources
        +---> Anatomy resources
|---+ Nucleic acid analysis
|    +---> Nucleic acid design
|---+ Protein analysis
|    +---+ Protein function analysis
        +---> Protein function prediction
|---+ Sequence analysis
|    |---> Sequence composition analysis
|    |---+ Sequence comparison
|        +---> Sequence clustering
|    |---> Sequence feature detection
|    |---+ Sequence classification
|        |---> Sequence motifs
|        +---> Sequence profiles and HMMs
|    +---> Primer or probe design
|---+ Structure analysis
|    |---+ Structure prediction
|        +---> Ab initio structure prediction
|    |---+ Structure comparison
|        |---> Structural (3D) profiles
|        +---> Structural clustering
|    +---> Structure determination
|---+ Phylogenetics
|    +---> Phylogeny reconstruction
|---> Proteomics
|---+ Data handling
|    |---> Data search and retrieval
|    |---> Data visualisation
|    |---> Biostatistics
|    |---> Data acquisition and deposition
|    |---> Workflows
|    |---> Data processing and validation
|    +---> Data types and objects
|---+ Chemoinformatics
|    |---+ Pharmacoinformatics
|        +---> Drug design
|    +---> Toxicoinformatics
|---> Transcriptomics
|---+ Literature and reference
|    |---> Documentation and help
|    +---+ Literature analysis
        +---> Text mining
|---+ Ontologies, nomenclature and classification
|    |---> Ontologies
|    |---> Annotation
|    |---> Nomenclature
|    +---> Taxonomy
|---+ Genetics
|    |---> Quantitative genetics
|    +---> Population genetics
|---+ Systems biology
|    |---> Biological system modelling
|    +---> Network or pathway analysis
|---+ Ecoinformatics
|    +---> Biodiversity
|---+ Genomics
|    |---> Functional genomics
|    +---> Comparative genomics
+---> Immunoinformatics

EDAM_topics.yaml

--- 
Biological data resources: 
- Laboratory resources
- Biological science resources
Nucleic acid analysis: 
- Nucleic acid design
Protein analysis: 
- Protein function analysis
Sequence analysis: 
- Sequence composition analysis
- Sequence comparison
- Sequence feature detection
- Sequence classification
- Primer or probe design
Structure analysis: 
- Structure prediction
- Structure comparison
- Structure determination
Phylogenetics: 
- Phylogeny reconstruction
Proteomics: []

Data handling: 
- Data search and retrieval
- Data visualisation
- Biostatistics
- Data acquisition and deposition
- Workflows
- Data processing and validation
- Data types and objects
Chemoinformatics: 
- Pharmacoinformatics
- Toxicoinformatics
Transcriptomics: []

Literature and reference: 
- Documentation and help
- Literature analysis
Ontologies, nomenclature and classification: 
- Ontologies
- Annotation
- Nomenclature
- Taxonomy
Genetics: 
- Quantitative genetics
- Population genetics
Systems biology: 
- Biological system modelling
- Network or pathway analysis
Ecoinformatics: 
- Biodiversity
Genomics: 
- Functional genomics
- Comparative genomics
Immunoinformatics: []

OBO parsing.rb

require './obo'
require 'open-uri'
require 'tree'

# Please excuse this terrible, terrible code. The obo parser was just a quick project to fulfil a quick need.
#  You'll need the obo.rb in the same directory. Get it from https://github.com/robsyme/obo/blob/master/lib/obo.rb 

include Tree

def find_children(parent_node, obo_elements)
  obo_elements.find_all do |element|
    element['is_a'] == parent_node.content
  end
end

def add_children(parent_node, elements)
  children = find_children(parent_node, elements)
  if children
    children.each do |child|
      child_node = TreeNode.new(child['name'], child['id'])
      parent_node << child_node
      add_children(child_node, elements)
    end
  else
    return
  end
end

elements = open("http://downloads.sourceforge.net/project/edamontology/EDAM_beta13.obo") {|ontology_file| Obo::Parser.new(ontology_file).elements.to_a}

root_node = TreeNode.new("Topic", "EDAM:0000003")
add_children(root_node, elements)
root_node.print_tree