Query based on PMIDS
alexmaina opened this issue · comments
I would like to bring your attention about the inability of getpapers to mine content using PMID.
For example, when i run a query using pmid
alex@alex-HP-ProDesk-600-G2-SFF:~$ getpapers -q PMID:27355041 -n -o maina
info: Searching using eupmc API
info: Running in no-execute mode, so nothing will be downloaded
error: Malformed or empty response from EuropePMC. Try running again. Perhaps your query is wrong.
When i run a query using PMCID, i get the following results
alex@alex-HP-ProDesk-600-G2-SFF:~$ getpapers -q PMCID:PMC5026053 -n -o maina
info: Searching using eupmc API
info: Running in no-execute mode, so nothing will be downloaded
info: Found 1 open access results
This document has listed PMID as a possible search field. Can getpapers search using PMIDS?
Thanks for this report
It seems at first glance that this is a problem with EuropePMC (which getpapers depends upon)
You'll see that if you search for PMID:27355041 at europepmc.org it comes up blank. Let me investigate further though.
It seems that at some point they stopped indexing by PMID and instead used the field EXT_ID (but this can also correspond to, for example, Agricola records)
This seems to work for me:
getpapers -q EXT_ID:27355041 -o test
Let me know if you have other problems
Thanks @tarrow it works very well but only where the PMID is for a paper that is Open access. Does this mean getpapers cannot mine titles and abstracts that are not open access in Pubmed/medline?
Sure; you just need to use the -a flag to also get non-open access content. Often there isn't a fulltext available for these though.
Thanks again.....Last question and by no means least. I have a dataset of 10 PMIDS
+------------------+
| accession_number |
+------------------+
| 27747646 |
| 27649863 |
| 27621978 |
| 27478298 |
| 27441216 |
| 27397933 |
| 27386033 |
| 27382606 |
| 27379288 |
| 27355041 |
+------------------+
How can i query 10 PMIDS in a single script?
We don't currently have a way to do this; but we probably should.
The easiest thing would be to simply write a bash script to call getpapers several times. Are you on a unix machine?
I made a new issue for this: #148
Yes I am on a unix machine...is this the same for PMCIDs?