Roderic Page rdmpage

GenBank, BOLD, GBIF (ZSM iBOL)

// GBIF occurrence

Sequence geotagged in Genbank, but not in GBIF

Example from http://iphylo.blogspot.co.uk/2012/02/linking-gbif-and-genbank.html where Genbank sequence EU443164 is geotagged and linked to a voucher specimen which GBIF does not know is geotagged.

Simple case of specimen and sequence both in GBIF

Cluster multiple occurrence records in GBIF

In this example we have the same sequence GQ247641 in two sequence datasets ("European Molecular Biology Laboratory Australian Mirror" and "Geographically tagged INSDC sequences"), and also the voucher specimen ("AM W.35546.001" or "AMS:W.35546") also occurs in GBIF (provided by "Australian Museum provider for OZCAM"). Linking the two sequence occurrences is trivial, we just link by the accession "GQ247641". Linking the sequence to the museum specimen requires matching the slightly different strings "AM W.35546.001" and "AMS:W.35546".

The graph links three records in GBIf that all refer to the same thing.

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	When copying MySQL database files (i.e. the binary files in /usr/local/mysql/data ) to a new machine we need to set permissions.

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	== GBIF geotagged, sequence in Genbank not geotagged


	//hide
	//setup
	//output
	[source,cypher]
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	// GBIF occurrence

	How many articles?

	SELECT COUNT(reference_id) FROM rdmp_reference WHERE PageID <> 0;
	+---------------------+
	\| COUNT(reference_id) \|
	+---------------------+
	\| 106617 \|
	+---------------------+
	1 row in set (0.08 sec)

	"Catalog# (TTU-M)","TK#","Genus","Species","Country","State","County","Collection Date","Tissues Available","Preparator"
	"84773","104001","ARTIBEUS","OBSCURUS","ECUADOR","PASTAZA DISTRICT","---","7/19/2001","Yes","HAYNIE, M L"
	"Subspecies: ---Specific Locality: 5 KM E PUYO, SAFARI HOSTERIA PARKElevation: ---Zone: 18Easting: 166624Northing: 9840350Latitude: ---Longitude: ---Collector: BAKER, R J ET ALPreparation Type: SBSex: FEMALEAssociated Sequences: ---Specimen#: ---Prep#: 157Prep Date: 7/19/2001Total Length (mm): 100Tail Length (mm): 0Foot Length (mm): 11Ear Length (mm): 12Weight (g): 14.9Tail Broken: NoTragus Length (mm): 0Forearm Length (mm): 0Reproductive Notes: ---Age: ADULT"