Add source column to merged context CSVs #52
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| merged,webbox,http://webbox.ecs.soton.ac.uk/ns#,canonical | ||
| merged,WEBELEMENTS,https://www.webelements.com/,canonical | ||
| merged,webservice,http://www.openlinksw.com/ontology/webservices#,canonical | ||
| merged,webtlab,http://webtlab.it.uc3m.es/,can |
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See here - WIKIDATA comes from the Bioregistry
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The prefix in bioregistry is wikidata, not WIKIDATA right?
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correct, but the processing in this repo uppercases the bioregistry prefixes
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right; so should the source be prefixmaps?
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I don't consider prefixmaps to be its own registry, this is just a transform on a Bioregistry prefix. Given #48 and biopragmatics/bioregistry#969, it should be more obvious how all uppercase prefix synonyms get in.
If we were to change the "source" annotation to be "prefixmaps" from content derived from the Bioregistry, then annotating the source would be sort of self-defeating
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@sierra-moxon so to try and explain again, the point of the source column is to help track down where a given expansion came from. In this case, even though a transformation was done on it, it's still from the Bioregistry.
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how about we call it "expansion_source" ?
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@cthoyt - did you see that this was "approved" and had this question for you? Please merge as you see fit, but consider being more explicit in the naming of this column.
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I did not see this, thank you for the ping. I will update that as you suggested :)
| merged,webbox,http://webbox.ecs.soton.ac.uk/ns#,canonical | ||
| merged,WEBELEMENTS,https://www.webelements.com/,canonical | ||
| merged,webservice,http://www.openlinksw.com/ontology/webservices#,canonical | ||
| merged,webtlab,http://webtlab.it.uc3m.es/,can |
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See here - wd comes from Prefix.cc
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@sierra-moxon please let me know if there's anything you'd like changed here / what the way forward is |
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@sierra-moxon can we please merge this? It will also solve @glass-ships' problem in #55 |
Closes #51
This PR adds an additional field to the
PrefixExpansionclass that can be optionally annotated with the source from which the class was instantiated. This is then used during theContext.combine()function such that when themergedandmerged.oakcontexts are generated, each record gets annotated with the simple context from which it came.This PR also runs the ETL pipeline to regenerate the merged prefix maps, now with the sources annotated in the merged files. The new
sourcecolumn does not affect reading in any way.Interestingly, this sheds some light on #49 - now we know that the
WIKIDATAprefix comes from the Bioregistry andwdfrom Prefix.cc.