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BIDS-Xu-Lab / bike-datasets

BIKE Datasets
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Kei - water contaminants of emerging concern [WCEC] #1

Closed huanhe4096 closed 1 month ago

huanhe4096 commented 2 months ago

PubMed query:

((("emerging") OR ("emergent")) AND ("water")) AND ("contaminant")
huanhe4096 commented 2 months ago

run the following command in bike-tools/script

python eutil_tools.py run -query '((("emerging") OR ("emergent")) AND ("water")) AND ("contaminant")' \
-task_name WCEC-1k \
-path_folder /data/eutil/ \
-embd_method opentsne
huanhe4096 commented 2 months ago

It won't take too long to finish:

esearch -db pubmed -query '((("emerging") OR ("emergent")) AND ("water")) AND ("contaminant")'
<ENTREZ_DIRECT>
  <Db>pubmed</Db>
  <Count>1476</Count>
  <Query>((("emerging") OR ("emergent")) AND ("water")) AND ("contaminant")</Query>
  <Step>1</Step>
  <Elapsed>1</Elapsed>
</ENTREZ_DIRECT>
* downloading XML
huanhe4096 commented 2 months ago

Go to bike-tools/script and run:

python run_annotator.py /data/eutil/WCEC-1k.tsv --topic-configs "0,2,2;5,3,3;50,4,4;100,10,10"
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