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koudyk / cleanBibImpact

Do papers using cleanBib have more gender-balanced reference lists? Assessing the impact of the cleanBib tool
MIT License
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Automatically list citing papers #11

Open koudyk opened 3 years ago

koudyk commented 3 years ago

Automatically list papers that cite the code/paper/preprint associated with cleanBib.

adswa commented 3 years ago

Hey, I have a script that could be helpful to extend the functionality that you already have! It queries PubMed for citing research based on PMID, and returns the metadata for citing references as a JSON database. I originally wrote it as part of a different hackathon, to update a website's citing research section (so it by default also creates an HTML table). The script is here: https://github.com/psychoinformatics-de/studyforrest-www/blob/master/tools/pubs.py

Shall/Can I adjust it to this project and submit a PR? :)

koudyk commented 3 years ago

Thanks so much! I'll defer to @complexbrains and @SamGuay because they're going to look at this today to see whether Crossref or Pubmed are better

adswa commented 3 years ago

Sounds good! I will be online again in 12ish hours (morning of June 17th in Europe), and I'm @adina on mattermost (but I'm faster in responding on GitHub) :)

SamGuay commented 3 years ago

@adswa, I was looking at the wrong paper earlier :upside_down_face:. We do have a pmid to work with (32561883)!

koudyk commented 3 years ago

Just noting what our plan is here.

I believe @SamGuay is going to integrate both ways of getting citations (correct me if I'm wrong).

Both ways being 1) with our existing code using opencitations.net, and 2) with Adina's code using the pubmed e-utilities.

complexbrains commented 3 years ago

Just to add to that we will also modify Adina's code to collect the data into a data frame as in the existing code.

SamGuay commented 3 years ago

So, after having played with Adina's code, I am not sure it would be worth it to implement the pubmed way as we get way fewer hits than with the current opencitation code.

I'll review #22 in the meantime.

adswa commented 3 years ago

Ah damn, I'm sorry if that has held you up. :/

SamGuay commented 3 years ago

Ahah, no worries, I learned much! Also, this reminds me of the great API by semantic scholar!

FrancoisPgm commented 3 years ago

Hey @koudyk I have a suggestion, since there is already a mecanism to automatically get the citing papers and their refs from open-citations, this issue is technically solved, and the two first milestones from the README can technically be checked. So I would close this issue, and create new ones specific to other APIs we want to add, like a "automatically get citations from Pubmed" or "automatically get citations from googlescholar". I think it could be helpful to have smaller actionable items.