Wednesday, February 29, 2012

Making biodiversity data sticky: it's all about links

Who invented velcro?

Sometimes I need to remind myself just why I'm spending so much time trying to make sense of other people's data, and why I go on (and on) about identifiers. One reason for my obsession is I want data to be "sticky", like the burrs shown in the photo above (Who invented velcro? by A-dep). Shared identifiers are like the hooks on the burrs, if two pieces of data have the same identifier they will stick together. Given enough identifiers and enough data, then we could rapidly assemble a "ball" of interconnected data. A published the diagram below as part of my Elsevier Challenge entry (preprint, published version) summarises some of the links between diverse kinds of biological data:
While in principle many of these links should be trivial to create, in practice they aren't. One major obstacle is the lack of globally unique identifiers, or if such identifiers exist they aren't being used. As a result, our data is anything but sticky. In the absence of identifiers, creating links between different data sets can a significant undertaking. One way to tackle this is focus on just one kind of link at a time and create a database of those links. The diagram below shows some of the links I've been working on:
For example, the iPhylo Linkout project creates links between taxon concepts in NCBI and Wikipedia. The iTaxon project is a mapping between taxonomic names and publications. I've briefly explored mapping host-parasite relationships using GenBank, and I'm currently exploring the links between publications and specimens. This list certainly doesn't exhaust the set of possible links, but it's a start. The challenge is to create sufficient links for biodiversity data to finally coalesce and for us to be able to ask questions that span multiple sources and types of data.

Tuesday, February 28, 2012

GBIF specimens in BioStor: who are the top ten museums with citable specimens?

GbifBrief update on yesterday's post about finding specimens in BioStor. BioStor has some 66,000 articles from BHL, from which I've extracted 143,000 cases of a specimen code being cited in the text. Of these 143,000 occurrences, 81,000 have been matched to an occurrence in GBIF.

The top ten collections with specimens in BioStor are:

DatasetNumber of specimens
NMNH Vertebrate Zoology Herpetology Collections (National Museum of Natural History)11194
Herpetology Collection (University of Kansas Biodiversity Research Center)9619
Herpetology Collection (University of Kansas Biodiversity Research Center)9328
NMNH Invertebrate Zoology Collections (National Museum of Natural History)9061
CAS Herpetology Collection Catalog (California Academy of Sciences)6720
MCZ Herpetology Collection (Museum of Comparative Zoology, Harvard University)5818
NMNH Vertebrate Zoology Fishes Collections (National Museum of Natural History)4642
MCZ Herpetology Collection - Reptile Database (Museum of Comparative Zoology, Harvard University)4380
FMNH Herpetology Collections (Field Museum)2110
FMNH Fishes Collections (Field Museum)2061

This is pretty much what I expected. Virtually complete runs of publications from The Field Museum at Chicago, the University of Kansas, and the Biological Society of Washington are available in BHL, and many of these have been added to BioStor. These journals have extensive taxonomic treatments of vertebrate taxa, particularly frogs, hence herpetology collections dominate the rankings.

There will inevitably be errors in the mapping between specimen codes and GBIF occurrences. I've tried to minimise these by mapping codes within taxonomic groups, but it's clear that there are duplicate codes even within some collections. There is also all manner of variation in the way people cite museum specimens, and these are often different from the codes that appear in GBIF. There will also be issues with extracting specimen codes, and I'm also discovering a few *cough* duplicates of articles in BioStor, so the numbers I present above are liable to change as I clean things up.

But one could imagine a "league table" of museum collections, where we can measure both the extent to which those collections have been digitised, and the extent to which material from those collections have been cited. We could use this to compute measures of the impact of a collection.

But for now I'm browsing the results trying to get a sense of how successful the mapping has been. There are some interesting examples. The specimen codes extracted from the article Review Of The Chewing Louse Genus Abrocomophaga (Phthiraptera : Amblycera), With Description Of Two New Species are those for the mammalian hosts of the lice. Hence someone viewing the records for these specimens and following the link to this paper would discover that these mammals had parasitic lice. If we add other sorts of links to the mix, such as between specimens and DNA sequences, then we can start to build a rich network of connections between the basic data of biodiversity.

Monday, February 27, 2012

Linking GBIF and the Biodiversity Heritage Library

Following on from exploring links between GBIF and GenBank here I'm going to look at links between GBIF and the primary literature, in this case articles scanned by the Biodiversity Heritage Library (BHL). The OCR text in BHL can be mined for a variety of entities. BHL itself has used uBio's tools to identity taxonomic names in the OCR text, and in my BioStor project I've extracted article-level metadata and geographic co-ordinates. Given that many articles in BioStor list museum specimens I wrote some code to extract these (see Extracting museum specimen codes from text) and applied this to the OCR text for those articles.

Having a list of specimens is nice, but in this digital age I want to be able to find out more about these specimens. An obvious solution is try and match these specimen codes to the specimen records held by GBIF. Linking to GBIF is complicated by the fact that museum codes are not unique. For example, "FMNH 147942" could refer to a bird, an amphibian, or a mammal. To tackle the non uniqueness I use the taxonomic names extracted from each page by BHL to work out what taxon an article is mainly "about". To do this I use the Catalogue of Life classification to get "paths" for each name (i.e., the lineage of each taxon down to the root of the classification) and then find the majority-rule path. You can see these paths in the "Taxonomic classification" displayed on a page for a BioStor article. If there are multiple GBIF specimens for the same code I test whether the taxon or rank "class" in the GBIF record is in the majority-rule path for the article. If so, I accept that specimen as the match to the code.

There are also issues where the specimen codes in GBIF have been modified during input (e.g., USNM 730715 has become USNM 730715.457409). There are also the inevitable OCR errors that may cause museum codes to be missed or otherwise corrupted. Bearing all this in mind, BioStor now has specimen pages (these are still being generated as I write this). For example, the page for FMNH 147942 lists the three articles in BioStor that cite this specimen code:


All three specimens have been mapped on to GBIF occurrence When BioStor displays the articles it now lists the specimen codes that have been extracted from the article, together with the GBIF logo if the specimen has been matched to a GBIF record. For example, here is a screenshot from Deep-water octopods (Mollusca: Cephalopoda) of the northeastern Pacific:

The map has been extracted from the OCR text (an obvious next step would be to add localities associated with the specimen records). Below the map are the specimen codes. The lack of some USNM specimens is probably due to misinterpreted specimen codes, whereas the CAS specimens don't seem to be online (the California Academy of Sciences has some of its collections in GBIF, but not its molluscs).

Where next?
Once these links between BioStor (and hence, BHL) and GBIF are created then we can do some interesting things. If you visit BioStor and want to learn more about a specimen you can click on the link an view the record in GBIF. We could also envisage doing the reverse. GBIF could augment the information it displays about a specimen by displaying a link to the content in BioStor (e.g., "this specimen is cited by these articles"). Those articles may contain further information about that specimen (for example, the habitat it was collected from, how secure is its identification, and so on).

We could also start to compute the "impact" of different museum collections based on the number of citations of specimens from their collections (this idea is explored further in this paper:, free preprint available here: hdl:10101/npre.2008.1760.1).

All of this works because we are linking objects (in this case articles and specimens) via their identifiers. Consequently, the links are as stable as their identifiers, which is why I've been pursuing the issue of specimen identifiers recently (see here, here, and here). If GBIF maintains the URLs for the specimens I've linked to, then links I've created could persist. If these URLs are likely to change (e.g., because the metadata from the host institution has changed) then the links (and any associated value we get from them) disappear. This is why I want globally unique, resolvable, persistent identifiers for specimens.

Thursday, February 23, 2012

How many specimens does GBIF really have?

GbifDuplicate 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:

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 and (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.

Wednesday, February 22, 2012

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 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
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.

Tuesday, February 21, 2012

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 America 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 ( 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 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, 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.

Thursday, February 16, 2012

EOL Phylogenetic Tree Challenge

34106 130 130The Encyclopedia of Life have announced the EOL Phylogenetic Tree Challenge. The contest has two purposes:

It provides a testbed for the Evolutionary Informatics community to develop robust methods for producing, serving, and evaluating large, biologically meaningful trees that will be useful both to the research community and to broader audiences.

It enables the Encyclopedia of Life to organise the information it aggregates according to phylogenetic relationships; in other words, it provides a direct pipeline from research results to practical use.

First prize is a trip to iEvoBio 2012, this year in Ottawa, Canada. For more details visit the challenge website. There is also an EOL community devoted to this challenge.

Challenges are great things, especially ones with worthwhile tasks and decent prizes. EOL badly needs a phylogenetic perspective, so this is a welcome development.

But (there's always a but), I can't help feeling that we need something a little more radical. The tree of life isn't a tree. At deep levels it's a forest, and even at shallow levels things are a complicated tangle of gene trees. Sometimes the tree is clear, sometimes not, and some of this is real and some reflects our ignorance.

If you want a simple tree to navigate, then I'd argue that the NCBI tree is a pretty good start, and EOL already has this. What would be really cool is to have a way to navigate that makes it clear that phylogenetic knowledge has a degree of uncertainty, and that the "tree of life" might be better depicted as a set of overlapping trees. The mental image I have is of a collage of trees from different data sets, superimposed over each other, with perhaps an underlying consensus to help navigate. This visualisation could be zoomable, because in some ways the tree of life is fractal. Trees don't stop at species, as the wealth of barcoding and phylogeographic studies show. Given computational constraints (not to mention visualisation issues), I wonder whether there is an effective limit to the size of any one tree in terms of number of taxa. What varies is the taxonomic scope. So we could imagine a backbone tree based on slowly evolving genes, we zoom in and more trees appear, but at lower levels, and finally we hit populations and individuals, trees that may have 100's of samples, but a very narrow scope.

This is all rather poorly articulated, but I can't help wondering whether a phylogenetic classification will end up distorting the very thing we're trying to depict. It also looses connection with the underlying data (and trees), which for me is a huge drawback of existing classifications. There's no sense of why they are the way they are. There's a chance here to bring together ideas that have been kicking around in the phylogenetic community for a couple of decades and rethink how we navigate the "tree of life".

Friday, February 10, 2012

BLAST a sequence and get a tree and a map

I've updated the BLAST a sequence and get a tree tool described in a previous post to output additional details, such as a list of the sequences used to build the tree and some basic metadata (such as the taxon name, name of any associated host, publication, and geographic coordinates). If the sequences are geotagged, then you will also see a little map showing the localities. As ever, all this relies on SVG, so if you're browser doesn't support that out won't see much.

The example below is for the sequence EU399074, which falls in a cluster of "dark taxa"; in this case, DNA barcode sequences that haven't been properly labelled.


Wednesday, February 08, 2012

Automating the creation of geophylogenies: NEXUS + delimited text = KML

One thing which has always frustrated me about geophylogenies is how tedious they are to create. In theory, they should be pretty straightforward to generate. We take a tree, get point localities for each leaf in the tree, and generate the KML to display on Google Earth. The tedious part is getting the latitude and longitude data in the right format, and linking the leaves in the tree to the locality data.

To help reduce the tedium I've create a tool that tries to automate this as much as possible. The goal is to be able to paste in a NEXUS tree, and a table of localities, and get back a KML tree. Some publishers are making it easier to extract data from articles. For example, if you go to a paper such as you will see a widget on the right labelled Table download.


If you click on the Find tables button you can download the tables in CSV format. In this case, Table 1 has latitude and longitude data for all the taxa in the tree in TreeBASE study S10103. With some regular expressions we can figure out which column has the latitude and longitude data, and parse values like (10°12′N, 84°09′W) to extract the numerical values for latitude and longitude.

It is also pretty straightforward to be able to read a tree in NEXUS format and extract the taxon names. At this point we have two sets of names (those from the tree and those from the table) which might not be the same (in this case they aren't, we have "Craugastor cf. podiciferus FMNH 257672" and "FMNH 257672"). Matching these names up by hand would be tedious, but as described in Matching names in phylogeny data files we can use maximum weighted bipartite matching to compute an optimal matching between the two sets of labels.

Create KML tree

You can try the Create KML tree tool at

To get started, try it with the data below. In step 1 paste in the NEXUS tree, in step 2 paste in the table from the original paper. If all goes as it should, you will see a table displaying the matching, and the KML which you can save and open in Google Earth. If you have the Google Earth Plug-in installed, then you should see the KML displayed on Google Earth in your web browser.

I've tested the tool on only a few examples, so there will be cases where it fails. It also assumes that every taxon in the tree has latitude and longitude values, and that the first column in the table is the taxon name (you'll need to edit the file if this is not the case).

Here is the tree used in the example...

Tl254954 'Craugastor cf. podiciferus FMNH 257672',
Tl254956 'Craugastor cf. podiciferus FMNH 257653',
Tl254965 'Craugastor cf. podiciferus UCR 16356',
Tl254960 'Craugastor sp. A USNM 563039',
Tl254938 'Craugastor sp. A USNM 563040',
Tl254945 'Craugastor cf. podiciferus UCR 16360',
Tl254928 'Craugastor cf. podiciferus UCR 17439',
Tl254959 'Craugastor cf. podiciferus UCR 17462',
Tl254951 'Craugastor cf. podiciferus FMNH 257596',
Tl254967 'Craugastor sp. A FMNH 257689',
Tl254934 'Craugastor cf. podiciferus UCR 16355',
Tl254964 'Craugastor cf. podiciferus FMNH 257671',
Tl254963 'Craugastor cf. podiciferus UCR 16358',
Tl254952 'Craugastor cf. podiciferus UCR 18062',
Tl254926 'Craugastor cf. podiciferus UCR 17442',
Tl254968 'Craugastor sp. A FMNH 257562',
Tl254939 'Craugastor cf. podiciferus UCR 17441',
Tl254946 'Craugastor cf. podiciferus FMNH 257757',
Tl254942 'Craugastor cf. podiciferus MVZ 149813',
Tl254961 'Craugastor cf. podiciferus FMNH 257595',
Tl254969 'Craugastor cf. podiciferus UCR 17469',
Tl254932 'Craugastor cf. podiciferus MVZ 164825',
Tl254970 'Craugastor sp. A AJC 0891',
Tl254943 'Craugastor cf. podiciferus UCR 16357',
Tl254929 'Craugastor cf. podiciferus FMNH 257673',
Tl254950 'Craugastor cf. podiciferus FMNH 257756',
Tl254944 'Craugastor cf. podiciferus FMNH 257652',
Tl254953 'Craugastor cf. podiciferus UCR 16359',
Tl254931 'Craugastor cf. podiciferus UCR 17443',
Tl254940 'Craugastor stejnegerianus UCR 16332',
Tl254935 'Craugastor underwoodi UCR 16315',
Tl254958 'Craugastor cf. podiciferus UCR 16354',
Tl254966 'Craugastor sp. A AJC 0890',
Tl254949 'Craugastor cf. podiciferus FMNH 257758',
Tl254933 'Craugastor cf. podiciferus UCR 16361',
Tl254962 'Craugastor cf. podiciferus FMNH 257651',
Tl254948 'Craugastor cf. podiciferus FMNH 257670',
Tl254971 'Craugastor cf. podiciferus FMNH 257669',
Tl254936 'Craugastor cf. podiciferus FMNH 257550',
Tl254957 'Craugastor underwoodi USNM 561403',
Tl254947 'Craugastor cf. podiciferus FMNH 257755',
Tl254927 'Craugastor cf. podiciferus UCR 16353',
Tl254925 'Craugastor bransfordii MVUP 1875',
Tl254930 'Craugastor cf. podiciferus UTA A 52449',
Tl254955 'Craugastor tabasarae MVUP 1720',
Tl254941 'Craugastor cf. longirostris FMNH 257678',
Tl254937 'Craugastor cf. longirostris FMNH 257561' ;
TREE 'Fig. 2' = ((Tl254955,(Tl254941,Tl254937)),(((((Tl254954,Tl254942,Tl254933,Tl254948,Tl254971),((Tl254934,Tl254958,Tl254927),((Tl254964,Tl254929),Tl254930))),(((Tl254965,(Tl254963,Tl254943)),(Tl254959,Tl254969),(Tl254951,Tl254961)),((Tl254928,Tl254926,Tl254939,Tl254931),(Tl254952,Tl254932)))),((((Tl254956,Tl254936),Tl254946,Tl254950,(Tl254944,Tl254962),Tl254947),Tl254949),(Tl254945,Tl254953))),((((Tl254960,Tl254938),(Tl254970,Tl254966)),(Tl254967,Tl254968)),((Tl254940,Tl254925),(Tl254935,Tl254957)))));

...and here is the table:

Taxon and institutional vouchera,Locality ID,Collection localityb,Geographic coordinates/approximate location,Elevation (m),GenBank accession number12S,16S,COI,c-myc
1. UTA A-52449,1,"Puntarenas, CR","(10°18′N, 84°48′W)",1520,EF562312,EF562365,None,EF562417
2. MVZ 149813,2,"Puntarenas, CR","(10°18′N, 84°42′W)",1500,EF562319,EF562373,EF562386,EF562430
3. FMNH 257669,1,"Puntarenas, CR","(10°18′N, 84°47′W)",1500,EF562320,EF562372,EF562380,EF562432
4. FMNH 257670,1,"Puntarenas, CR","(10°18′N, 84°47′W)",1500,EF562317,EF562336,EF562376,EF562421
5. FMNH 257671,1,"Puntarenas, CR","(10°18′N, 84°47′W)",1500,EF562314,EF562374,EF562409,None
6. FMNH 257672,1,"Puntarenas, CR","(10°18′N, 84°47′W)",1500,EF562318,None,EF562382,None
7. FMNH 257673,1,"Puntarenas, CR","(10°18′N, 84°47′W)",1500,EF562311,EF562343,EF562392,None
8. UCR 16361,3,"Alejuela, CR","(10°13′ N, 84°22′W)",1930,EF562321,EF562371,EF562375,EF562431
9. UCR 16353,4,"Heredia, CR","(10°12′N, 84°09′W)",1500,EF562313,EF562349,None,EF562420
10. UCR 16354,4,"Heredia, CR","(10°12′N, 84°09′W)",1500,EF562315,EF562363,None,EF562418
11. UCR 16355,4,"Heredia, CR","(10°12′N, 84°09′W)",1500,EF562316,EF562366,None,EF562419
12. UCR 18062,6,"Heredia, CR","(10°10′N, 84°06′W)",1900,EF562302,EF562342,EF562395,None
13. UCR 17439,5,"Heredia, CR","(10°09′N, 84°09′W)",2000,EF562298,EF562341,EF562387,EF562427
14. UCR 17441,5,"Heredia, CR","(10°09′N, 84°09′W)",2000,EF562299,EF562345,EF562388,EF562429
15. UCR 17442,5,"Heredia, CR","(10°09′N, 84°09′W)",2000,EF562300,EF562337,EF562385,EF562422
16. UCR 17443,5,"Heredia, CR","(10°09′N, 84°09′W)",2000,EF562301,EF562340,EF562384,EF562428
17. UCR 17462,5,"Heredia, CR","(10°09′N, 84°09′W)",2000,EF562309,EF562355,EF562406,EF562440
18. UCR 17469,5,"Heredia, CR","(10°09′N, 84°09′W)",2000,EF562310,EF562334,EF562405,EF562414
19. MVZ 164825,7,"Heredia, CR","(10° 05′N, 84° 04′W)",2100,EF562303,EF562346,EF562381,EF562423
20. UCR 16357,8,"San José, CR","(10°02′N, 83°57′W)",1600,EF562306,EF562339,EF562400,EF562433
21. UCR 16358,8,"San José, CR","(10°02′N, 83°57′W)",1600,EF562307,EF562370,EF562412,EF562415
22. UCR 16356,8,"San José, CR","(10°01′N, 83°56′W)",1940,EF562308,EF562329,None,None
23. UCR 16359,10,"San José, CR","(9°26′N, 83°41′W)",1313,EF562297,EF562369,EF562396,None
24. UCR 16360,10,"San José, CR","(9°26′N, 83°41′W)",1313,EF562296,EF562368,None,EF562434
25. FMNH 257595,9,"Cartago, CR","(9°44′N, 83°46′W)",1600,EF562304,EF562338,EF562408,None
26. FMNH 257596,9,"Cartago, CR","(9°44′N, 83°46′W)",1600,EF562305,EF562335,None,EF562416
27. FMNH 257550,11,"Puntarenas, CR","(8°47′N, 82°59′W)",1350,EF562294,EF562330,EF562393,EF562443
28. FMNH 257651,11,"Puntarenas, CR","(8°47′N, 82°59′W)",1350,EF562291,EF562367,EF562402,EF562435
29. FMNH 257652,11,"Puntarenas, CR","(8°47′N, 82°59′W)",1350,EF562288,EF562364,EF562390,None
30. FMNH 257653,11,"Puntarenas, CR","(8°47′N, 82°59′W)",1350,EF562292,EF562354,EF562392,EF562438
31. FMNH 257755,11,"Puntarenas, CR","(8°46′N, 82°59′W)",1410,EF562289,EF562344,EF562379,None
32. FMNH 257756,11,"Puntarenas, CR","(8°46′N, 82°59′W)",1410,EF562290,EF562347,EF562377,EF562413
33. FMNH 257757,11,"Puntarenas, CR","(8°46′N, 82°59′W)",1410,EF562293,EF562352,EF562383,EF562437
34. FMNH 257758,11,"Puntarenas, CR","(8°46′N, 82°59′W)",1410,EF562295,EF562348,EF562397,EF562436
35. USNM 563039,12,"Chiriquí, PA","(8°48′N, 82°24′W)",1663,EF562284,EF562356,EF562389,EF562445
36. USNM 563040,12,"Chiriquí, PA","(8°48′N, 82°24′W)",1663,EF562285,EF562350,EF562391,EF562439
37. AJC 0890,12,"Chiriquí, PA","(8°48′N, 82°24′W)",1663,EF562282,EF562351,EF562398,EF562444
38. MVUP 1880,12,"Chiriquí, PA","(8°48′N, 82°24′W)",1663,EF562283,EF562358,EF562399,EF562442
39. FMNH 257689,12,"Chiriquí, PA","(8°45′N, 82°13′W)",1100,EF562287,EF562353,EF562407,EF562446
40. FMNH 257562,12,"Chiriquí, PA","(8°45′N, 82°13′W)",1100,EF562286,EF562357,EF562410,EF562441
41. USNM 561403,N/A,"Heredia, CR","(10°24′N, 84°03′W)",800,EF562323,EF562361,EF562378,None
42. UCR 16315,N/A,"Alejuela, CR","(10°13′N, 84°35′W)",960,EF562322,EF562362,EF562394,None
43. UCR 16332,N/A,"San José, CR","(9°18′N, 83°46′W)",900,EF562325,EF562360,EF562411,AY211320
44. MVUP 1875 fitzingeri group,N/A,"BDT, PA","(9°24′N, 82°17′W)",50,EF562324,EF562359,None,AY211304
45. MVUP 1720,N/A,"Coclé, PA","(8°40′N, 80°35′W)",800,EF562326,EF562332,EF562401,EF562424
46. FMNH 257561,N/A,"Chiriquí, PA","(8°45′N, 82°13′W)",1100,EF562327,EF562331,None,EF562426
47. FMNH 257678,N/A,"Chiriquí, PA","(8°45′N, 82°13′W)",1100,EF562328,EF562333,EF562404,EF562425

Monday, February 06, 2012

Using Google Refine and taxonomic databases (EOL, NCBI, uBio, WORMS) to clean messy data

RefineGoogle Refine is an elegant tool for data cleaning. One of its most powerful features is the ability to call "Reconciliation Services" to help clean data, for example by matching names to external identifiers. Google Refine comes with the ability to use Freebase reconciliation services, but you can also add external services. Inspired by this I've started to implement services to reconcile taxonomic names.

The services I've implemented so far are:
  • EOL
  • NCBI taxonomy
  • uBio FindIT
  • GBIF
  • Global Names Index

To use these you need to add the URLs above to Google Refine (see example below). The EOL, NCBI and WORMS do a basic name lookup. The uBio FindIT service extracts a taxonomic name from a string, and can be viewed as a "taxonomic name cleaner".

How to use reconciliation services

Start a Google Refine session. Save the names below to a text file and open it as a new project.

Achatina fulica (giant African snail)
Acromyrmex octospinosus ST040116-01
Alepocephalus bairdii (Baird's smooth-head)
Alaska Sea otter (Enhydra lutris kenyoni)
Toxoplasma gondii
Leucoagaricus gongylophorus
Themisto gaudichaudii

You should see something like this:

Click on the column header Names and choose ReconcileStart reconciling.


A dialog will popup asking you to select a service.


If you've already added a service it will be in the list on the left. If not, click the Add Standard Services... button at the bottom left and paste in the URL (in this case

Once the service has loaded click on Start Reconciling. Once it has finished you should see most of the names linked to uBio (click on a name to check this):


Sometimes there may be more than one possible match, in which case these will be listed in the cell. Once you have reconciled the data you may want to do something with the reconciliation. For example, if you want to get the ids for the names you've just matched you can create a new column based on the reconciliation. Click on the Names column header and choose Edit columnAdd column based on this column.... A dialog box will be displayed:


In the box labelled Expression enter and give the column a name (e.g., "NamebankID"). You will now have a column of uBio NamebankIDs for the names:


You could also get the names uBio extracted by creating a column based on the values of To compare this with the original values, click on the Names column header and choose ReconcileActionsClear reconciliation data. Now you can see the original input names, and the string uBio extracted from each name:


These are some very simple ideas for using Google Refine with taxonomic name services. Obvious extensions would to use services that provide an "accepted name", or services that support approximate string matching so you could catch spelling mistakes (most of the services I've implemented here have some degree of support for these features).

Development notes
The code for these services is in Github (undocumented as yet, that's on the to do list). I had a few hiccups getting these services to work. There is detailed documentation at, but this seems a little out of step with what actually happens. Based on the documentation I thought Google Refine called a reconciliation service using HTTP GET, but in fact it uses POST. Google Refine always called my reconciliation service using "Multiple Query Mode", which meant supporting this mode wasn't optional. Once these issues were sorted out (turning on the Java console as per David Huynh's tip helped) things work pretty well.

Thursday, February 02, 2012

Browsing TreeBASE using a genome browser-like interface

One of the things I find frustrating about TreeBASE is that there's no easy way to get an overview of what it contains. What is it's taxonomic coverage like? Is it dominated by plants and fungi, or are there lots of animal trees as well? Are the obvious gaps in our phylogenetic knowledge, or do the phylogenies it contains pretty much span the tree of life?

As part of my phyloinformatics course I've put together a simple browser to navigate through TreeBASE. The inspiration comes from genome browsers (e.g., the UCSC Genome Browser) where the genome is treated as a linear set of co-ordinates, and features of the genome are displayed as "tracks".

Hgt genome 596a ac7fe0

For my browser, I've used the order in which nodes appear in the NCBI tree as you go from left to right as the set of co-ordinates (actually, from top to bottom as my browser displays the co-ordinate axis vertically).


I then place each TreeBASE tree within this classification by taking the TreeBASE → NCBI mapping provided by TreeBASE and finding the "majority rule" taxon for each tree (in a sense, the taxa that summarises what the tree is about). Each tree is represented by a vertical line depicting the span of the corresponding NCBI taxon (corresponding to a "track" in a genome browser). Taking the majority-rule taxon rather than say, the span of the tree, makes it possible to pack the vertical lines tightly together so that they take up less space (the ordering from left to right is determined by the NCBI taxonomy).

If you mouse-over a vertical bar you can see the title of the study that published the tree. If you click on the vertical bar you'll see the tree displayed on the right (if your web browser understands SVG, that is). If you click on the background you will drill down a level in the NCBI classification. To go back up the classification, click on the arrow at the top left of the browser.

This is all very preliminary, but you can take it for a spin at

Below is a short video walking you through some examples.