How to Download a MicroBIGG-E Table with >100,000 Rows from NCBI Pathogen Detection

Learn how to download a MicroBIGG-E table containing all CARBAPENEM genes found in Pathogen Detection isolate assemblies on NCBI. Follow a step-by-step guide to select, filter, and download subsets of data in batches to get the complete dataset.

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• MicroBIGG-E
• NCBI
• Pathogen Detection
• Genes

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Uploaded on Sep 09, 2024 | 0 Views

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1. How To: Download a MicroBIGG-E table > 100,000 rows (all CARBAPENEM genes found in Pathogen Detection isolate assemblies) NCBI Pathogen Detection https://www.ncbi.nlm.nih.gov/pathogens

2. At a glance Use MicroBIGG-E https://www.ncbi.nlm.nih.gov/pathogens/microbigge Use filters or search to select rows of interest, in this case subclass:CARBAPENEM Subdivide the search into sets with < 100,000 rows to download in batches Use filters to get results under 100,000 rows Download one file Change filters to get different results under 100,000 rows Download second file Repeat above steps as needed to get the entire set pd-help@ncbi.nlm.nih.gov

3. https://www.ncbi.nlm.nih.gov/pathogens https://www.ncbi.nlm.nih.gov/pathogens 1. Click MicroBIGG-E

4. https://www.ncbi.nlm.nih.gov/pathogens/microbigge https://www.ncbi.nlm.nih.gov/pathogens/microbigge 2. Click Filters bar to show filters 4. Start typing CARBAPENEM to reveal the value 6. Note > 100,000 results 5. Select CARBAPENEM filter 3. Click subclass to show subclass filter

5. https://www.ncbi.nlm.nih.gov/pathogens/microbigge https://www.ncbi.nlm.nih.gov/pathogens/microbigge 7. Select another filter to subset the results

6. https://www.ncbi.nlm.nih.gov/pathogens/microbigge https://www.ncbi.nlm.nih.gov/pathogens/microbigge 8. Select one or more of the options 9. Note that total selected is less than 100,000 10. Click Download button to open download options

7. https://www.ncbi.nlm.nih.gov/pathogens/microbigge https://www.ncbi.nlm.nih.gov/pathogens/microbigge 11. Click Download button to download table

8. https://www.ncbi.nlm.nih.gov/pathogens/microbigge https://www.ncbi.nlm.nih.gov/pathogens/microbigge 12. Deselect the previous filter value 13. Select an alternate to get a different subset of the total rows 14. Note that total selected is less than 100,000 15. Click Download to open download options

9. https://www.ncbi.nlm.nih.gov/pathogens/microbigge https://www.ncbi.nlm.nih.gov/pathogens/microbigge 16. Click Download button to download table

10. More information For full help documentation of the Reference Gene Catalog see: https://www.ncbi.nlm.nih.gov/pathogens/pathogens_help/#microbigge For details about filters see: https://www.ncbi.nlm.nih.gov/pathogens/pathogens_help/#microbigge-filters For details about the table downloads see: https://www.ncbi.nlm.nih.gov/pathogens/pathogens_help/#microbigge-access-download Questions and further help: email pd-help@ncbi.nlm.nih.gov pd-help@ncbi.nlm.nih.gov