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biotoolsregistry : discovery portal for bioinformatics
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Automatically fetch DOI from PMID or PMCID #199

Open khillion opened 7 years ago

joncison commented 7 years ago

I'm not sure on the specifics, but I think DOIs are required for the AltMetric widgets, so we'll want to do this. @ekry can confirm. I expect it's something to add to the list for this Summer.

khillion commented 7 years ago

Thank you, it would be pretty convenient, especially since <citation> tag in XML for galaxy only supports doi or bibtex (source: https://docs.galaxyproject.org/en/master/dev/schema.html#tool-citations-citation).

joncison commented 7 years ago

Good to know, but technically @khillion or @hmenager do you know the easiest way to do this? There surely must be some service ...

hansioan commented 7 years ago

I found this: https://www.ncbi.nlm.nih.gov/pmc/pmctopmid/ (for GUI) and its corresponding API https://www.ncbi.nlm.nih.gov/pmc/tools/id-converter-api/

When the publication annotation students worked on annotating tools with DOIs there were some cases in which a publication has a PMID / PMCID, but doesn't have a DOI. Just an FYI

redmitry commented 7 years ago

Hello,

Here are the URLs I use to verify whether the IDs are OK:

 private final static URI doiResolverURI =

URI.create("https://doi.org/"); private final static URI pmidResolverURI = URI.create("https://www.ncbi.nlm.nih.gov/pubmed/"); private final static URI pmcidResolverURI = URI.create("https://www.ncbi.nlm.nih.gov/pmc/articles/");

Cheers,

Dmitry

On 7/5/2017 9:56 AM, Hans Ienasescu wrote:

I found this: https://www.ncbi.nlm.nih.gov/pmc/pmctopmid/ (for GUI) and its corresponding API https://www.ncbi.nlm.nih.gov/pmc/tools/id-converter-api/

When the publication annotation students worked on annotating tools with DOIs there were some cases in which a publication has a PMID / PMCID, but doesn't have a DOI. Just an FYI

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khillion commented 7 years ago

@hansioan I have been using the API to retrieve DOI from PMID and PMCID and I observed two different scenarios when it could not find it:

magnuspalmblad commented 2 months ago

The reverse would also be useful - ideally the GUI would automatically look up the other two identifiers when the user enters one.