When checking out #11 I also noticed a significant amount of other formatting errors; I have now, hopefully fixed them all. In summary:
1) I have not changed any content, other than UMLS CUI syntax and a handful of faulty namespace declarations
2) I have made the whole ontology OBO compliant by adding this information in the header:
format-version: 1.2
default-namespace: source
ontology: exo
property_value: http://purl.org/dc/elements/1.1/description "ExO is intended to bridge the gap between exposure science and diverse environmental health disciplines including toxicology, epidemiology, disease surveillance, and epigenetics." xsd:string
property_value: http://purl.org/dc/elements/1.1/title "Exposure ontology (ExO)" xsd:string
property_value: http://purl.org/dc/terms/license https://creativecommons.org/licenses/by/4.0/
3) Changed a faulty xref in ExO:0000116 and ExO:0000120
4) To force the creation dates into OBO format (most of them were already correct) I had to add some random time (hours, minutes) to them.
An example term change:
Previously:
[Term]
id: ExO:0000153
name: Other Race
is_a: ExO:0000109 ! race
disjoint_from: ExO:0000154 ! Pacific Islander
disjoint_from: ExO:0000155 ! Puerto Rican
disjoint_from: ExO:0000156 ! Samoan
disjoint_from: ExO:0000157 ! Vietnamese
disjoint_from: ExO:0000158 ! White
property_value: created:by "cgrondin" xsd:string
property_value: creation:date "2017-04-07" xsd:string
property_value: hasRelatedSynonym "Other" xsd:string
property_value: http://purl.obolibrary.org/obo/def "A person of non-specified racial, cultural, or geographic origins." xsd:string
property_value: http://purl.obolibrary.org/obo/namespace "exposure_receptor" xsd:string
Now:
[Term]
id: ExO:0000153
name: Other Race
namespace: exposure_receptor
def: "A person of non-specified racial, cultural, or geographic origins." []
synonym: "Other" RELATED []
is_a: ExO:0000109 ! race
disjoint_from: ExO:0000154 ! Pacific Islander
disjoint_from: ExO:0000155 ! Puerto Rican
disjoint_from: ExO:0000156 ! Samoan
disjoint_from: ExO:0000157 ! Vietnamese
disjoint_from: ExO:0000158 ! White
created_by: cgrondin
creation_date: 2017-04-07T03:47:29Z
The only thing that I did not fix, which is still broken the way you have it, is the actual synonym syntax:
synonym: "medicine\nmedication\ndrug" RELATED []
Should be changed to:
synonym: "medicine" RELATED []
synonym: "medication" RELATED []
synonym: "drug" RELATED []
When checking out #11 I also noticed a significant amount of other formatting errors; I have now, hopefully fixed them all. In summary:
1) I have not changed any content, other than UMLS CUI syntax and a handful of faulty namespace declarations 2) I have made the whole ontology OBO compliant by adding this information in the header:
3) Changed a faulty xref in ExO:0000116 and ExO:0000120 4) To force the creation dates into OBO format (most of them were already correct) I had to add some random time (hours, minutes) to them.
An example term change:
Previously:
Now:
The only thing that I did not fix, which is still broken the way you have it, is the actual synonym syntax:
Should be changed to:
To be compatible with standard ontology tools!