text_mining_targeted_association data and parser update

[edgargaticaCU]

API URL: https://biothings.ncats.io/text_mining_targeted_association
Parser GitHub URL: https://github.com/UCDenver-ccp/text_mining_targeted_association
Git branch/commit: Master 74b3f26
No. Documents: 1,762,002
Structure of documents: Added sources property and fixed publications property

[edgargaticaCU]

I can't assign anyone so I'll just tag @erikyao

[erikyao]

@edgargaticaCU thank you for the information! Will keep you updated

[erikyao]

Hi @edgargaticaCU, I found that we have a new field "source" on https://github.com/UCDenver-ccp/text_mining_targeted_association/blob/master/parser.py#L120, and I think we should add it to the targeted_mapping as well.

[colleenXu]

@edgargaticaCU doing my usual reminder that your SmartAPI yaml will most likely need updating.

Some things I can think of:

• version
• add response-mapping for TRAPI edge.sources data
• do the operations need updating? I noticed that the number of documents have been changing when comparing this update to earlier ones...

[edgargaticaCU]

@erikyao this has been added in commit e1c0d2d

[edgargaticaCU]

@edgargaticaCU doing my usual reminder that your SmartAPI yaml will most likely need updating.

Some things I can think of:

• version
• add response-mapping for TRAPI edge.sources data
• do the operations need updating? I noticed that the number of documents have been changing when comparing this update to earlier ones...

I have updated the YAML locally but am waiting to push the changes until the data have been updated (in case an issue prevents that from happening before the end of the day, I wouldn't want the SmartAPI yaml to reference a property that doesn't exist).
The operations have not changed because the underlying data hasn't changed; this is just an update to the representation. The change in number of documents from the last update is (most likely) because the response from Node Normalizer has changed, causing some nodes and their associated edges to be excluded.

[erikyao]

@colleenXu @edgargaticaCU API updated!

[edgargaticaCU]

I'm commenting here, but let me know if it is better to create a new Issue for this.
Colleen pointed out that the resource_id was set incorrectly in the parser. I have fixed this in revision f4e73cd
Nothing else should have changed, since a new export was not necessary for this fix.

[erikyao]

I'm commenting here, but let me know if it is better to create a new Issue for this.

Colleen pointed out that the resource_id was set incorrectly in the parser. I have fixed this in revision f4e73cd

Nothing else should have changed, since a new export was not necessary for this fix.

No worries. I'll re-deploy it tomorrow.

[erikyao]

Hi @edgargaticaCU, we are experiencing some problem accessing our internal server. Will keep you updated when it's fixed.

[colleenXu]

@erikyao Have things been addressed so this can be re-deployed? Once it is, we'll be ready for the final part of setting up BTE to ingest this API with TRAPI 1.4 source data formatting. Which is discussed here and here

[erikyao]

@colleenXu updated!