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monarch-initiative / pyphetools

Python Phenopacket Tools
https://monarch-initiative.github.io/pyphetools/
MIT License
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biocurator #107

Closed pnrobinson closed 2 months ago

pnrobinson commented 2 months ago

The biocurator string needs to have the date, e.g. ORCID:0000-0000-0000-0000[2024-04-01] currently, the date is not being added to the string. We can add today's date on the HPOA creation script

matentzn commented 2 months ago

As a suggestion for future annotation file formats it would be beneficial to split these into two fields, as we now have to have specific etl code to integrate the annotations into a knowledge graph. We have a lot of annotations to orcids, and if we want to aggregate across these, like in "counting how many contributions", we cant have the date in that string as well.

pnrobinson commented 2 months ago

Well, it would be difficult with shell commands but trivial for a python script to separate the ORCIDs from the dates... I do not think we want to have separate columns, because now at least we are recording updates by adding a second CURIE[date] to the annotation entry. I think the main use case is to count contributions, and this will become more important moving forward because phenopackets will allow us to democratize the process to some extent. I would be fine with removing the dates and the amendations, it is not mission critical and maybe we should not overcomplicate things. I do not know if external software is depending on the current format thougb

pnrobinson commented 2 months ago

fixed