rdmenezes / ontowiz

Automatically exported from code.google.com/p/ontowiz
0 stars 0 forks source link

OntoPerl discards words before delimitor; causes mismatch between ontology-input and internal data structure #3

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago
What steps will reproduce the problem?
1. Load file "sample_data/IDOMAL.obo".
2. Read the {term}->def() record for "IDOMAL:0000209".
3. Observe that "Dorland'" is missing in the "db" field.

The problem causes loss of information during parsing. The complete stanza for 
the given term is:
----------- from file "sample_data/IDOMAL.obo"----------------------------------
[Term]
id: IDOMAL:0000209
name: tetracycline antibiotic
def: "Any of a group of related broad-spectrum antibiotics, isolated from 
species of Streptomyces or produced semisynthetically." 
[Dorland'sMedicalDictionaryforHealthConsumers:0]
comment: A group of broad-spectrum antibiotics, derivatives of poly cyclic 
naphthacene carboxamide. They have a marked action on blood stages acting as 
inhibitors of ribosomal prot\
ein synthesis.
is_a: IDOMAL:0000672 ! chemical compound
relationship: OBO_REL:has_role IDOMAL:0000643 ! antibiotic
created_by: louis
creation_date: 2008-01-24T03:18:00Z
--------------------------------------------------------------------------------
-

Original issue reported on code.google.com by oeks...@gmail.com on 28 Feb 2013 at 12:53

GoogleCodeExporter commented 9 years ago
Thanks, once again, I hope this will help to minimize the number of errors
generated by onto-perl while parsing external ontologies.
vlmir

Original comment by vladimir.n.mironov@gmail.com on 1 Mar 2013 at 6:44