Notes on how many georeferenced DNA sequences there are in GenBank, and how many could potentially be georeferenced.
BCT Bacterial sequences PRI Primate sequences ROD Rodent sequences MAM Other mammalian sequences VRT Other vertebrate sequences INV Invertebrate sequences PLN Plant and Fungal sequences VRL Viral sequences PHG Phage sequences RNA Structural RNA sequences SYN Synthetic and chimeric sequ UNA Unannotated sequences
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi
?db=nucleotide nucleotides
&term=ddbj embl genbank with limits[filt]
NOT transcriptome[All Fields] ignore transcriptome data
NOT mRNA[filt] ignore mRNA data
NOT TSA[All Fields] ignore TSA
NOT scaffold[All Fields] ignore scaffold
AND src lat lon[prop] include records that have source feature "lat_lon"
AND 2010/01/01:2010/12/31[pdat] from this date range
AND gbdiv_pri[PROP] restrict search to PRI division (primates)
AND srcdb_genbank[PROP] Need this if we query by division, see NBK49540
Numbers of nucleotide sequences that have latitude and longitudes in GenBank for each year.
| Date | PRI | ROD | MAM | VRT | INV | PLN |
|---|---|---|---|---|---|---|
| 2010/01/01 | 4 | 127 | 2552 | 9551 | 92692 | 7174 |
| 2011/01/01 | 371 | 1204 | 8160 | 17657 | 78494 | 7968 |
| 2012/01/01 | 6 | 5803 | 4214 | 21696 | 84060 | 27314 |
| 2013/01/01 | 297 | 349 | 761 | 10764 | 70411 | 23435 |
| 2014/01/01 | 15 | 2904 | 4761 | 14598 | 68076 | 14018 |
| 2015/01/01 | 174 | 527 | 1983 | 17843 | 363538 | 35501 |
| 2016/01/01 | 58 | 2615 | 1263 | 14898 | 757893 | 22813 |
| 2017/01/01 | 938 | 1758 | 1017 | 10712 | 75066 | 28180 |
Numbers of nucleotide sequences that don't have latitude and longitudes in GenBank for each year but do have the country field and hence could be georeferenced.
| Date | PRI | ROD | MAM | VRT | INV | PLN |
|---|---|---|---|---|---|---|
| 2010/01/01 | 6660 | 2654 | 5534 | 32666 | 62577 | 56692 |
| 2011/01/01 | 3998 | 3266 | 6210 | 33717 | 74015 | 98664 |
| 2012/01/01 | 5377 | 5590 | 7283 | 55332 | 86945 | 103379 |
| 2013/01/01 | 10928 | 4805 | 8013 | 66373 | 69719 | 95817 |
| 2014/01/01 | 9727 | 3492 | 6751 | 59913 | 77816 | 135372 |
| 2015/01/01 | 8922 | 6774 | 13964 | 60578 | 85867 | 167337 |
| 2016/01/01 | 6430 | 3384 | 10860 | 62238 | 95711 | 145111 |
| 2017/01/01 | 11474 | 3520 | 4912 | 41159 | 91219 | 109747 |
