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Hi,
The code only keeps one alt_id for a term since it stores it as a value for alt_id key in annotation. Would it be possible for you to fix this behavior so multiple alt_ids can be available through the api?
Thanks!
Can you be more specific to what Class should be modified in order to adapt the API? I mean the method you are accessing that only returns one alt_id and should return multiple ones. I guess the data structure should be changed to key:List(value), but I want to check the dependencies on the API.
Also, isn't alt_id unique for each term? I have checked some .obo files and I could not see a term with multiple alt_ids. Can you show an example or give a use case for it?
We would also be grateful if you could submit a pull request for this change.
Hi
Made a PR for this as fix seems quite easy and doesn't break any API as it is just altering an Annotation value ( defined as Object) to be a jva.util.List, not a String
Is Annotation too generic a mechanism though for modelling information on a well -defined data structure like obo, would it be better to have specific methods like getAltIds(), getComments() etc? (Not for this issue, just a general comment)
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lafita commentedon Aug 7, 2017
Hi @tulay, thank you for reporting the issue!
Can you be more specific to what Class should be modified in order to adapt the API? I mean the method you are accessing that only returns one
alt_idand should return multiple ones. I guess the data structure should be changed tokey:List(value), but I want to check the dependencies on the API.Also, isn't
alt_idunique for each term? I have checked some.obofiles and I could not see a term with multiplealt_ids. Can you show an example or give a use case for it?We would also be grateful if you could submit a pull request for this change.
lafita commentedon Aug 7, 2017
I checked the specification of the OBO file format and there can be multiple number of
alt_id.ftp://ftp.geneontology.org/go/www/GO.format.obo-1_2.shtml
So this has to be changed. @tulay do you think you can submit a PR for it?
richarda23 commentedon Aug 28, 2021
Hi
Made a PR for this as fix seems quite easy and doesn't break any API as it is just altering an Annotation value ( defined as Object) to be a jva.util.List, not a String
Is Annotation too generic a mechanism though for modelling information on a well -defined data structure like obo, would it be better to have specific methods like getAltIds(), getComments() etc? (Not for this issue, just a general comment)