Missing some entries from arXiv or bioRxiv

[Tung Nguyen]

Dear Support Team,

Recently, we have tried to fetch publications of two entries below:

1/ https://doi.org/10.1038/s42256-021-00335-w

2/ https://doi.org/10.1101/2024.03.15.585236

3/ https://doi.org/10.48550/arXiv.2007.02835

However, your service doesn't return anything. 

If I search them using Web Interface, I get both in preprint versions. 

https://europepmc.org/article/PPR/PPR300229 and https://europepmc.org/article/PPR/PPR822903.

API queries

https://www.ebi.ac.uk/europepmc/webservices/rest/search/query=ext_id:10.1101/2024.03.15.585236%20src:med&resulttype=core

and 

https://www.ebi.ac.uk/europepmc/webservices/rest/search/query=ext_id:10.48550/arXiv.2007.02835%20src:med&resulttype=core

Questions

1. Do you know if the syntax is correct? Have you changed anything?
2. The first entry might have been missed or hasn't been updated from preprint to peer-reviewed article. Does that sound right?
3. Regarding preprints (like the second entry or more) from arXiv or bioRxiv, do you support users fetching publication details? If the entry in the request doesn't exist or doesn't support us in getting all the details, we fall back on our error-prone parser. Your answer would be valuable to us.

Best regards,
Tung

[Madhumiethaa Jayaprabha Palanisamy]

Hi Tung,

Thank you for reaching out.

Regarding your questions:

1. Query Formation: It appears that the issue with fetching the publications is due to incorrect query formation. Instead of using ext_id, you should use the doi field in your query. Please try the following format: 

• https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=doi:10.1101/2024.03.15.585236%20src:ppr&resulttype=core

            A comprehensive list of available search fields can be found in Appendix 1 of our reference guide under our Europe PMC Restful Web Service page.

       2. The first entry might have been missed or hasn't been updated from preprint to peer-reviewed article. Does that sound right?  
          Yes, we don't have any entry for the first doi. But we do have the preprint version of it which you can find below:

          [https://europepmc.org/search?query=TITLE%3A%22A%20machine%20learning%20platform%20to%20estimate%20anti-SARS-CoV-  2%20activities%22]  

           https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=doi:10.26434/chemrxiv.12915779.v3

     

    3.  Yes, we do support. You can also find more information on preprints and publication details here:

          https://europepmc.org/Preprints

Hope this clarifies your questions. Please reach out if you have further queries.

Kind regards,

Madhu

 

       

[Tung Nguyen]

Hi Madhu,

Many thanks for your prompt answer!

I made a mistake in the query that I sent you. The parameter should be doi instead of ext_id. However, I am concerned about the parameter src having to be swapped from med to ppr. Could we omit this src parameter? We don't request submitters to give details at such a level. I have tried to remove the src parameter. And I also have the same result. So far so good. 

I am only concerned about the efficiency if the src parameter is missing. With DOI entries, some are from arXiv or bioRxiv as I said in the former email.

if (linkType == PubLP.LinkType.PUBMED) {
  queryString = "${PUBMED_API_URL}ext_id:${id}%20src:med&resulttype=core"
} else if (linkType == PubLP.LinkType.DOI) {
  queryString = "${PUBMED_API_URL}doi:${id}%20src:med&resulttype=core"
}

Your explanation has resolved all my concerns. 

Thanks anyway!

Best regards,
Tung

[Madhumiethaa Jayaprabha Palanisamy]

Hi Tung,

Yes, you can omit the src parameter from the query when you don't have it. This will not impact efficiency as long as the DOI is correctly specified. However, specifying src as med will not retrieve any results if the source is a preprint server like bioRxiv in your case.

Hope this helps.

Kind regards,
Madhu

[Tung Nguyen]

Hi Madhu,

Regarding arXiv, are you considering treating it as bioRxiv and will you accommodate them too? ArXiv's quantitative biology section was launched in 2003. I tried searching some articles, however, it doesn't give anything.

P/S: Here is an interesting question indeed https://academia.stackexchange.com/a/130807. 

Cheers,
Tung

[Madhumiethaa Jayaprabha Palanisamy]

Hi Tung,

We currently only have arXiv preprints relating to COVID between 2020 and 2023. We do have plans to index the quantitative biology section from arXiv but this is pending development.

Kind regards,
Madhu