Linking NCBI taxonomy to GBIF

@rdmpage, given an NCBI taxon ID, how to get GBIF occurrence records via web service?

— Rutger Vos (@rvosa) May 30, 2012

In response to Rutger Vos's question I've started to add GBIF taxon ids to the iPhylo Linkout website. If you've not come across iPhylo Linkout, it's a Semantic Mediawiki-based site were I maintain links between the NCBI taxonomy and other resources, such as Wikipedia and the BBC Nature Wildlife finder. For more background see

Page, R. D. M. (2011). Linking NCBI to Wikipedia: a wiki-based approach. PLoS Currents, 3, RRN1228. doi:10.1371/currents.RRN1228

I'm now starting to add GBIF ids to this site. This is potentially fraught with difficulties. There's no guarantee that the GBIF taxonomy ids are stable, unlike NCBI tax_ids which are fairly persistent (NCBI publish deletion/merge lists when they make changes). Then there are the obvious problems with the GBIF taxonomy itself. But, if you want a way to generate a distribution map for a taxon in the NCBI taxonomy, the quickest way is going to be via GBIF.

The mapping is being made automatically, with some crude checks to try and avoid too many erroneous links (e.g., due to homonyms). It will probably take a few days to complete (the mapping is quick, uploading to the wiki is a bit slower). Using a wiki to manage the mapping makes it easy to correct any spurious matches.

As an example, the page http://iphylo.org/linkout/Ncbi:109175 is for the frog Hyla japonica (NCBI tax_id 109175) and shows links to Wikipedia (http://en.wikipedia.org/wiki/Japanese_Tree_Frog, and to GBIF (http://data.gbif.org/species/2427601/). There's even a link to TreeBASE. I display a GBIF map so you can see what data GBIF currently has for that taxon.



So, we have a wiki page, how do we answer Rutger's original question: how to get GBIF occurrence records via web service?

To do this we can use the RDF output by the Semantic Mediawiki software that underpins the Wiki. You can gte this by clicking on the RDF icon near the bottom of the page, or go to http://iphylo.org/linkout/Special:ExportRDF/Ncbi:109175. The RDF this produces is really, really ugly (and people wonder why the Semantic Web has been slow to take off...). In this RDF you will see the statement:

<rdfs:seeAlso rdf:resource="http://data.gbif.org/species/2427601/"/>

So, arm yourself with XPath, a regular expression, or if you are a serious RDF geek break out the SPARQL, and you can extract the GBIF taxon id for a NCBI taxon. Given that id you can query the GBIF web services. One service that I like is the occurrence density service, which you can use to recreate the 1°×1° density maps shown by GBIF. For example, http://data.gbif.org/ws/rest/density/list?taxonconceptkey=2427601 will get you the squares shown in the screen shot above.

Of course, I have glossed over several issues, such as the errors and redundancy in the GBIF classification, the mismatch between NCBI and GBIF classifications (NCBI has many more ranks than GBIF), and whether the taxon concepts used by the two databases are equivalent (this is likely to be more of an issue for higher taxa). But it's a start.

NCBI to Wikipedia links are now live...

The 52,956 links from NCBI to Wikipedia that I've been busy creating are now "live." If you go to a NCBI taxon such as Sphaerius you'll see something like this:

Clicking the "Wikipedia" link takes you to the Wikipedia page for this taxon. You can see all the links to Wikipedia using the query loproviphylo[filter]. Here are some additional links to try:

NCBI	Wikipedia
8353	Xenopus
83698	Banksia
9766	Balaenoptera

Thanks to Scott Federhen and Kathy Kwan at NCBI for all their assistance in getting this into NCBI Linkout.

Fixing errors
There will be errors and omissions. The best way to fix these is by using the iPhylo Linkout wiki. The page for a NCBI taxon is always http://iphylo.org/linkout/Ncbi:xxxx where xxxx is the NCBI taxonomy id. You can edit/annotate the link there (click on the "edit with form" for a simple web form). I plan to regularly update the links based on this the wiki.

Future
NCBI Linkout provide access statistics so it will be interesting to see how much traffic goes from NCBI to Wikipedia. It will also be interesting to see if this is correlated with increased editing of those Wikipedia pages.

Linking NCBI to Wikipedia

In an earlier post I discussed linking NCBI taxonomy to Wikipedia. One way to tackle this is to add NCBI Taxonomy ID to Wikipedia pages. I reopened the case for adding the Taxonomy IDs to the Taxobox on each taxon page, but this met with substantial resistance. A modified proposal to add them elsewhere to the Wikipedia page seems to be gaining more support (or, at least, less vigorous resistance).

Meanwhile, there are other things that need to be done to linking NCBI and Wikipedia. One is to add Wikipedia page names to NCBI Linkout so that when viewing a NCBI taxon page you will see a link to Wikipedia if a page for the corresponding taxon exists. To create this linkout we need a mapping from NCBI to Wikipedia, and that's what I've been working on for the last few days.

The mapping is still in progress, but essentially I've taken a dump of the NCBI taxonomy for June 3, 2010, and matched the names with those in a the June 18, 2009 dump of Wikipedia that I've analysed elsewhere on this blog. I'll detail the various steps in the mapping elsewhere (there are issues such as synonyms, homonyms, Wikipedia redirects, etc.), but for now things seem to be working reasonably well.

The mapping is being created in a Semantic Mediawiki at http://iphylo.org/linkout/. When complete you will be able to up a NCBI taxon by either it's name (including synonyms and common names) or it's NCBI Taxonomy ID. Where possible I'm mapping the NCBI taxon to Wikipedia, and providing a snippet of text and an image.

I've also extracted bibliographic information from the citations.dmp file that comes with the NCBI dump. This contains the comments that you sometimes see on a taxon page. In a few cases I've added some information manually. For example, the beetle genus Sphaerius has a rather complicated nomenclatural history, which the NCBI page summarises as:

Due to a recent ruling (ICZN 2000), the family and generic names Sphaeriusidae Erichson, 1845, and Sphaerius Waltl, 1838, are both available names and have priority over Microsporidae Crotch, 1873 for the family name and Microsporus Kolenati, 1846 for the single included genus, respectively.

By looking through BioStor I've found some of the papers relating to this ICZN ruling, and added them to the wiki page http://iphylo.org/linkout/Ncbi:174920 (aficionados of zoological nomenclature may enjoy the complexity of the case, due to homonymy between the corresponding family name, Sphaeriidae, and a mollusc family of the same name).

Once thus mapping is complete, it will be time to think of how to get this into NCBI's Linkout, and also how to automatically update the mapping to reflect the growth of both the NCBI taxonomy and Wikipedia. If you visit http://iphylo.org/linkout/ please be aware that the mapping is still being written to the wiki (this is being done via API calls, and adding some 900,000 pages is going to take a while).