This experiment takes two taxa for the same lizard (Geckonia chazaliae or Tarentola chazaliae) and runs a query to discover that these taxa are duplicates. In other words, GBIF has the same lizard twice in its classification.
Geckonia chazaliae (name) ion:614045
Geckonia chazaliae (taxon) gbif:2445625
Tarentola chazaliae (name) ion:1748852
Tarentola chazaliae (taxon) gbif:5843252
| = Network versioning using relationnodes | |
| Recently there was a nice blog on versioning networks by Ian Robinson (http://iansrobinson.com/2014/05/13/time-based-versioned-graphs/[read it here]) on using identity nodes and separating structure from state. In this gist I'd like to put in my 2 cents by introducing another approach using _relationnodes_. This is more about structure of a network than about states of nodes, but it treats versioning differently. As Ian states in his blog, there's always a trade-off to be made, since versioning causes an extra load on storage and processing. | |
| == Relationnodes? | |
| === What are relationnodes? | |
| Relation nodes are intermediary nodes between two network nodes that represents the relation between the nodes. | |
| So, if A and B are two network nodes, instead of connecting them with a relationship of `[:RELTYPE]`, |
| <html xmlns="http://www.w3.org/1999/xhtml"> | |
| <head> | |
| <title>WKT</title> | |
| <style type="text/css"> | |
| #info { | |
| position: absolute; | |
| top: 70px; | |
| left: 550px; | |
| width: 350px; | |
| } |
| How many articles? | |
| SELECT COUNT(reference_id) FROM rdmp_reference WHERE PageID <> 0; | |
| +---------------------+ | |
| | COUNT(reference_id) | | |
| +---------------------+ | |
| | 106617 | | |
| +---------------------+ | |
| 1 row in set (0.08 sec) |
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.
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.
| == GBIF geotagged, sequence in Genbank not geotagged | |
| //hide | |
| //setup | |
| //output | |
| [source,cypher] | |
| ---- | |
| // GBIF occurrence |
| When copying MySQL database files (i.e. the binary files in /usr/local/mysql/data ) to a new machine we need to set permissions. | |
| For the database "db" we do the following: | |
| sudo chown -R _mysql db | |
| sudo chgrp -R _mysql db | |
| sudo chmod -R 644 db | |
| sudo chmod 755 db |