add docstrings

src/ontology.jl

@@ -1,4 +1,6 @@
-
+"""
+The collection of all ontology terms and their relations.
+"""
 struct Ontology
     header::Dict{String, Vector{String}}
     prefix::String

src/parser.jl

@@ -1,5 +1,16 @@
 # The OBO Flat File parser
-
+"""
+Represents one entry in the OBO file, e.g.
+```
+[Term]
+id: GO:0000002
+namespace: biological_process
+def: BBB
+name: two
+```
+is stored as `Stanza` with `Typ` = "Term", `id` = "GO:0000002" and
+`tagvalues = Dict("id" => "GO:0000002", "namespace" => ["biological_process"], "def" => ["BBB"], "name" => "two")`.
+"""
 struct Stanza
     Typ::String # Official ones are: "Term", "Typedef" and "Instance"
     id::String
@@ -51,6 +62,7 @@ parseOBO(filepath::AbstractString) = open(parseOBO, filepath, "r")
 
 const r_stanza = r"^\[(.*)\]$"
 
+# returns tagvalues of the current Stanza and the type of the next one
 function parsetagvalues(s)
     vals = TagDict()
 

src/term.jl

@@ -3,6 +3,21 @@ const TagDict = Dict{String, Vector{String}}
 const RefDict = Dict{String, String}
 const RelDict = Dict{Symbol, Set{TermId}}
 
+"""
+Ontology term.
+
+The `Term` object is a node in the direct acyclic ontology graph.
+Its outgoing and incoming edges represent the relations with the other nodes and
+could be retrieved by
+```julia
+relationship(term, sym)
+```
+and
+```julia
+rev_relationship(term, sym)
+```
+respectively, where `sym` is the relationship annotation (e.g. `:part_of`, `:is_a`, `:regulates`).
+"""
 struct Term
     id::TermId
     name::String

src/typedef.jl

@@ -1,3 +1,6 @@
+# FIXME add description
+"""
+"""
 struct Typedef
     id::String
     name::String