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Replace original_knowledge_source with primary_knowledge_source and aggregator_knowledge_source #628

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gaurav opened this issue Mar 2, 2023 · 1 comment

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@gaurav
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gaurav commented Mar 2, 2023

Biolink recommends that:

Our recommendation would be for data creators to minimally distinguish primary (most upstream) from aggregator / intermediate sources - as this distinction should be knowable in all cases. If the data creator is confident that the primary source was the original source, they can use the original_knowledge_source property. In practice, for a linear chain of retrieval, one source should be declared primary or original, and the rest aggregators. Knowledge Providers will add source provenance related to upstream sources, as well as the provenance related to themselves in their data/messages.

I take this to mean that we should only use original_knowledge_source when we're sure that the knowledge source is the original one (i.e. the publication in which the knowledge was first published), which we don't usually have. Instead, we should replace this with either primary_knowledge_source (e.g. for Noctua, since Noctua really is the primary source of a particular digital representation of a pathway) or aggregator_knowledge_source (e.g. for CTD and Wikipaths, which aggregate pathway information from publications and other sources).

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gaurav commented Mar 10, 2023

We need to do this to meet the requirements in NCATSTranslator/TranslatorArchitecture#86

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