Made exo.obo OBO format compliant #14
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When checking out CTDbase#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](https://github.com/INCATools/ontology-development-kit/blob/master/docs/License.md) 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 [] ``` To be compatible with standard ontology tools!
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When checking out #11 I also noticed a significant amount of other formatting errors; I have now, hopefully fixed them all. In summary:
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!