How many specimens does GBIF really have?

Duplicate records are the bane of any project that aggregates data from multiple sources. Mendeley, for example, has numerous copies of the same article, as documented by Duncan Hull (How many unique papers are there in Mendeley?). In their defence, Mendeley is aggregating data from lots of personal reference libraries and hence they will often encounter the same article with slightly differing metadata (we all have our own quirks when we store bibliographic details of papers). It's a challenging problem to identify and merge records which are not identical, but which are clearly the same thing.

What I'm finding rather more alarming is that GBIF has duplicate records for the same specimen from the same data provider. For example, the specimen USNM 547844 is present twice:

• http://data.gbif.org/occurrences/157337271/
• http://data.gbif.org/occurrences/244120356/

As far as I can tell this is the same specimen, but the catalogue numbers differ (547844 versus 547844.6544573). Apart from this the only difference is when the two records were indexed. The source for 547844 was last indexed August 9, 2009, the source for 547844.6544573 was first indexed August 22, 2010. So it would appear that some time between these two dates the US National Museum of Natural History (NMNH) changed the catalogue codes (by appending another number), so GBIF has treated them as two distinct specimens. Browsing other GBIF records from the NMNH shows the same pattern. I've not quantified the extent of this problem, but it's probably a safe bet that every NMNH herp specimen occurs twice in GBIF.

Then there are the records from Harvard's Museum of Comparative Zoology that are duplicates, such as http://data.gbif.org/occurrences/33400333/ and http://data.gbif.org/occurrences/328478233/ (both for specimen MCZ A-4092, in this case the collectionCode is either "Herp" or "HERPAMPH"). These are records that have been loaded at different times, and because the metadata has changed GBIF hasn't recognised that these are the same thing.

At the root of this problem is the lack of globally unique identifiers for specimens, or even identifiers that are unique and stable within a dataset. The Darwin Core wiki lists a field for occurrenceID for which it states:

The occurrenceID is supposed to (globally) uniquely identify an occurrence record, whether it is a specimen-based occurrence, a one-time observation of a species at a location, or one of many occurrences of an individual who is being tracked, monitored, or recaptured. Making it globally unique is quite a trick, one for which we don't really have good solutions in place yet, but one which ontologists insist is essential.

Well, now we see the side effect of not tackling this problem - our flagship aggregator of biodiversity data has duplicate records. Note that this has nothing to do with "ontologists" (whatever they are), it's simple data management. Assign a unique id (a primary key in a database will do fine) that can be used to track the identity of an object even as its metadata changes. Otherwise you are reduced to matching based on metadata, and if that is changeable then you have a problem.

Now, just imagine the potential chaos if we start changing institution and collection codes to conform to the Darwin Core triplet. In the absence of unique identifiers (again, these can be local to the data set) GBIF is going to be faced with a massive data reconciliation task to try and match old and new specimen records.

The other problem, of course, is that my plan to use GBIF occurrence URLs as globally unique identifiers for specimens is looking pretty shaky because they are unique (the same specimen can have more than one) and if GBIF cleans up the duplicates a number of these URLs will disappear. Bugger.

Clustering strings

Revisiting an old idea (Clustering taxonomic names) I've added code to cluster strings into sets of similar strings to the phyloinformatics course site.

This service (available at http://iphylo.org/~rpage/phyloinformatics/services/clusterstrings.php) takes a list of strings, one per line, and returns a list of clusters. For example, given the names

Ferrusac 1821
Bonavita 1965
Ferussa 1821
Fer.
Lamarck 1812
Ferussac 1821

the service finds three clusters, displayed here using Google images:



(Note to self, investigate canviz as an alternative for displaying graphviz graphs.)

If you are curious, these strings are taxonomic authorities associated with the name Helicella, and based on this clustering there are three taxonomic names, one of which has three different variations of the author's name.

Why LSIDs suck

I'll keep this short: LSIDs suck because they are so hard to set up that many LSIDs don't actually work. Because of this there seems to be no shame in publishing "fake" LSIDs (LSIDs that look like LSIDs but which don't resolve using the LSID protocol). Hey, it's hard work, so let's just stick them on a web page but not actually make them resolvable. Hence we have an identifier that people don't recognise (most people have no idea what an LSID is) and which we have no expectations that it will actually work. This devalues the identifier to the point where it becomes effectively worthless.

Now consider URLs. If you publish a URL I expect it to work (i.e., I paste it into a web browser and I get something). If it doesn't work then I can conclude that the URL is wrong, or that you are a numpty and can't run a web site (or don't care enough about your content to keep the URL working). At no point am I going to say "gee, it's OK that this URL doesn't resolve because these things are hard work."

Now you might argue that whether your LSID resolves is an even better way for me to assess your technical ability (because it's hard work to do it right). Fair enough, but the fact that even major resources (such as Catalogue of Life) can't get them to work reliably reduces the value of this test (it's a poor predictor of the quality of the resource). Or, perhaps the LSID is a signal that you get this "globally unique identifier thing" and maybe one day will make the LSIDs work. No, it's a signal you don't care enough about identifiers to make them actually work today.

As soon as people decided it's OK to publish LSIDs that don't work, LSIDs were doomed. The most immediate way for me to determine whether you are providing useful information (resolving the identifier) is gone. And with that goes any sense that I can trust LSIDs.

Linking GBIF and Genbank

As part of my mantra that it's not about the data, it's all about the links between the data, I've started exploring matching GenBank sequences to GBIF occurrences using the specimen_voucher codes recorded in GenBank sequences. It's quickly becoming apparent that this is not going to be easy. Specimen codes are not unique, are written in all sorts of ways, there are multiple codes for the same specimen (GenBank sequences may be associated with museum catalogue entries, or which field or collector numbers).

So why undertake what is fast looking like a hopeless task? There are several reasons:

1. GBIF occurrences have a unique URL which we could potentially use as a unique, resolvable identifier for the corresponding specimen.
2. Linking GenBank to GBIF would make it possible for GBIF to list sequences associated with a specimen, as well as the associated publication, which means we could demonstrate the "impact" of a specimen. In the simplest terms this could be the number of sequences and publications that use data from the specimen, more sophisticated approaches could use PageRank-like measures, see hdl:10101/npre.2008.1760.1.
3. Having a unique identifier that is shared across different databases makes it easier to combine data from different sources. For example, if a sequence in GenBank lacks geographic coordinates but the voucher specimen in GBIF is georeferenced, we can use that information to locate the sequence in geographic space (and hence build geophylogenies or add spatial indexes to databases such as TreeBASE). Conversely, if the GenBank sequence is georeferenced but the GBIF record isn't we can update the GBIF record and possibly expand the range of the corresponding taxon (this was part of the motivation behind hdl:10101/npre.2009.3173.1.

As an example, below is the GBIF 1° density map for the frog Pristimantis ridens from GBIF, with the phylogeny from Wang et al.Phylogeography of the Pygmy Rain Frog (Pristimantis ridens) across the lowland wet forests of isthmian Central Americahttp://dx.doi.org/10.1016/j.ympev.2008.02.021 layered over it. I created the KML tree from the corresponding tree in TreeBASE using the tool I described earlier. You can grab the KML for the tree here.



As we'd expect, there is a lot of overlap in the two sources of data. If we investigate further, there are records that are in fact based on the same specimen. For example, if we download the GBIF KML file with individual placemarks we see that in the northern part of the range their are 15 GBIF occurrences that map onto the same point as one of the terminal taxa in the tree.



One of these 15 GBIF records (http://data.gbif.org/occurrences/244335848) is for specimen USNM 514547, which is the voucher specimen for EU443175. This gives us a link between the record in GBIF and the record in GenBank. It also gives us a URI we can use for the specimen http://data.gbif.org/occurrences/244335848 instead of the unresolvable and potentially ambiguous USNM 514547.

If we view the geophylogeny from a different vantage point we see numerous localities that don't have occurrences in GBIF.



Close inspection reveals that some of the specimens listed in the Wang et al. paper are actually in GBIF, but lack geographic coordinates. For example the OTU "Pristimantis ridens Nusagandi AJC 0211" has the voucher specimen FMNH 257697. This specimen is in GBIF as http://data.gbif.org/occurrences/57919777/, but without coordinates, so it doesn't appear on the GBIF map. However, both the Wang et al. paper and the GenBank record for the sequence from this specimen EU443164 give the latitude and longitude. In this example, GBIF gives us a unique identifier for the specimen, and GenBank provides data on location that GBIF lacks.

Part of GBIFs success is due to the relative ease of integrating data by taxonomic names (despite the problems caused by synonyms, homonyms, misspellings, etc.) or using spatial coordinates (which immediately enables integration with environmental data. But if we want to integrate at deeper levels then specimen records are the glue that connects GBIF (and its contributing data sources) to sequence databases, phylogenies, and the taxonomic literature (via lists of material exampled). This will not be easy, certainly for legacy data that cites ambiguous specimen codes, but I would argue that the potential rewards are great.