Paper on NCBI and Wikipedia published in PLoS Currents: Tree of Life

My paper describing the mapping between NCBI and Wikipedia has been published in PLoS Currents: Tree of Life. You can see the paper here. It's only just gone live, so it's yet to get a PubMed Central number (one of the nice features of PLoS Currents is that the articles get archived in PMC).

Publishing in PLoS Currents: Tree of Life was a pleasant experience. The Google Knol editing environment was easy to use, and the reviewing process quick. It's obviously a new and rather experimental journal, and there are a few things that could be improved. Automatically looking up articles by PubMed identifier is nice, but it would also be great to do this for DOIs as well. Furthermore, the PubMed identifiers aren't displayed as clickable links, which rather defeats the point of having references on the web (I've added DOI links to the articles wherever possible). But, minor grumbles aside, as a way to get an Open Access article published for free, and have it archived in PubMed Central, PLoS Currents is hard to beat. What will be interesting is whether the article receives any comments. This seems to be one area online journals haven't really cracked — providing an environment where people want to engage in discussion.

Linking the NCBI taxonomy to BBC Wildlife Finder

A few weeks ago I spent some time mapping pages from the BBC Wildlife Finder to the equivalent taxa in the NCBI taxonomy. This seemed a useful exercise because the Wildlife Finder pages have some wonderful picture, video, and audio content, as well as other nice features, such as reusing Wikipedia page titles as "slugs" in the BBC page URLs. For example, the Wikipedia page for the Yacare Caiman (Caiman yacare) has the URL http://en.wikipedia.org/wiki/Yacare_Caiman, and the BBC page has the URL http://www.bbc.co.uk/nature/life/Yacare_Caiman. Both share the slug Yacare_Caiman.

After adding these links to iphylo.org/linkout, where you can find them listed on the BBC category page, I've finally uploaded these to the NCBI, so now some 504 NCBI taxon pages have links to high quality multimedia from the BBC.

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Location:Schmiedestraße,Wetter,Germany

Fun things about crustaceans

One side effect of playing with ways to visualise and integrate biology databases is that you stumble across the weird and wonderful stuff that living organisms get up to. My earliest papers were on crustacean taxonomy, so I thought I'd try my latest toy on them.

What lives on crustaceans?

The "symbiome" graph for crustacea shows a range of associations, including marine bacteria (Vibrio), fungi (microsporidians), and other organisms, including other crustacea (crustaceans are at the top of the circle, I'll work on labelling these diagrams a little better).

What do crustaceans live on?

Crustacea (in addition to parasitising other crustacea) parasitise several vertebrates groups, including fish and whales. But they also occur in terrestrial vertebrates. For example, sequence EF583871 is from the pentastomid worm Porocephalus crotali from a dog. When people think of terrestrial crustacea they usually don't think of parasites. There's also a prominent line from crustaceans to what turns out to be corals, representing coral-living barnacles.

It's instructive to compare this with insects, which similarly parasitise vertebrates. The striking difference is the association between insects and flowering plants.



I guess these really need to be made interactive, so we could click on them and discover more about the association represented by each line in the diagram.

Visualising the symbiome: hosts, parasites, and the Tree of Life

Back in 2006 in a short post entitled "Building the encyclopedia of life" I wrote that GenBank is a potentially rich source of information on host-parasite relationships. Often sequences of parasites will include information on the name of the host (the example I used was sequence AF131710 from the platyhelminth Ligophorus mugilinus, which records the host as the Flathead mullet Mugil cephalus).

I've always wanted to explore this idea a bit more, and have finally made a start, in part inspired by the recent VIZBI 2011 meeting. I've grabbed a large chunk of GenBank, mined the sequences for host records, and created some simple visualisations of what I'm terming (with tongue firmly in cheek) the "symbiome". Jonathan Eisen will not be happy, but I need a word that describes the complete set of hosts, mutualists, symbionts with which an organism is associated, and "symbiome" seems appropriate.

Human symbiome
To illustrate the idea, below is the human "symbiome". This diagram shows all the taxa in GenBank arranged in a circle, with lines connecting those organisms that have DNA sequences where humans are recorded as their host.



At a glance, we have a lot of bacteria (the gray bar with E. coli) and fungi (blue bar with Yeast), and a few nematodes and arthropods.

Fig tree symbiome
Next up are organisms collected from fig trees (genus Ficus).


Fig trees have wasp pollinators (the dark line landing near the honey bee Apis), as well as nematodes (dark line landing near Caenorhabditis elegans). There are also some associations with fungi and other arthropods.

Which taxa host insects?
Next up is a plot of all associations involving insects and a host.


The diagram is dominated by insect-flowering plant interactions, followed by insect-vertebrate associations (most likely bird and mammal lice).

Which taxa are hosted by insects?
We can reverse the question and ask what organisms are hosted by insects:


Lots of associations between insects and fungi, as well as bacteria, and a few other organisms, such as nematodes, and Plasmodium (the organism which causes malaria).

Frog symbiome
Lastly, below is the symbiome of frogs. "Worms" feature prominently, as well as the fungus that causes chytridiomycosis.

How the visualisation was made

The symbiome visualisations were made as follows. Firstly DNA sequences were downloaded from EMBL and run through a script that extracted as much metadata as possible, including the contents of the host field (where present). I then took the NCBI taxonomy and generated an ordered list of taxa by walking the tree in postorder, which determines where on the circumference of the circle the taxon lies. Pairs of taxa in an association are connected by a quadratic Bezier curve. The illustration was created using SVG.


Next steps
There are several ways this visualisation could be improved. It's based only only a subset of data (I haven't run all of the sequence databases though the parser yet), and the matching of host taxa is based on exact string matching. All manner of weird and wonderful things get entered in the host field, so we'll need some more sophisticated parsing (see "LINNAEUS: A species name identification system for biomedical literature" doi:10.1186/1471-2105-11-85 for a more general discussion of this issue).

The visualisation is fairly crude at this stage. Circle plots like this are fairly simple to create, and pop up in all sorts of situations (e.g., RNA secondary structure methods, which I did some work on years ago). Of course, Circos would be an obvious tool to use to create the visualisations, but the overhead of installing it and learning how to use it meant I took a shortcut and wrote some SVG from scratch.

Although I've focussed on GenBank as a source of data, this visualisation could also be applied to other data. I briefly touched on this in Tag trees: displaying the taxonomy of names in BHL where a page in the Biodiversity Heritage Library contains the names of a flea and it's mammalian hosts. I think these circle plots would be a great way to highlight possible ecological associations mentioned in a text.

TreeBASE meets NCBI, again

Déjà vu is a scary thing. Four years ago I released a mapping between names in TreeBASE and other databases called TBMap (described here: doi:10.1186/1471-2105-8-158). Today I find myself releasing yet another mapping, as part of my NCBI to Wikipedia project. By embedding the mapping in a wiki, it can be edited, so the kinds of problems I encountered with TbMap, recounted here, here, and here. The mapping in and of itself isn't terribly exciting, but it's the starting point for some things I want to do regarding how to visualise the data in TreeBASE.

Because TreeBASE 2 has issued new identifiers for its taxa (see TreeBASE II makes me pull my hair out), and now contains its own mapping to the NCBI taxonomy, as a first pass I've taken their mapping and added it to http://iphylo.org/linkout. I've also added some obvious mappings that TreeBASE has missed. There are a lot more taxa which could be added, but this is a start.

The TreeBASE taxa that have a mapping each get their own page with a URL of the form http://iphylo.org/linkout/<TreeBase taxon identifier>, e.g. http://iphylo.org/linkout/TB2:Tl257333. This page simply gives the name of the taxon in TreeBASE and the corresponding NCBI taxon id. It uses a Semantic Mediawiki template to generate a statement that the TreeBASE and and NCBI taxa are a "close match". If you go to the corresponding page in the wiki for the NCBI taxon (e.g., http://iphylo.org/linkout/Ncbi:448631) you will see any corresponding TreeBASE taxa listed there. If a mapping is erroneous, we simply need to edit the TreeBASE taxon page in the wiki to fix it. Nice and simple.

At the time of writing the initial mapping is still being loaded (this can take a while). I'll update this post when the uploading has finished.

Some VIZBI 2011 links

Given that the Twitter stream tagged #vizbi will fade away soon, I've grabbed most of the links I tweeted during VIZBI 2011 and have put them here. This isn't intended as a comprehensive list, merely the things which caught my eye, and didn't flash by faster than I could tweet.

Books

• Visual Complexity: Mapping Patterns of Information
• Visual Thinking for Design

Movies

• DNA
• Malaria lifecycle Part 1
• Malaria lifecycle Part 2
• WEHI.TV

People

• Drew Berry
• Manuel Lima
• Tamara Munzner
• Fernada Viégas
• Martin Wattenberg

Software and websites

• Arena 3D
• BioBlender
• BLAST Atlas
• Cerebral v.2.0
• Chromograms
• CloVR
• Cytoscape
• EMAGE
• embedded Python Molecular Viewer (ePMV)
• Fleshmap
• GenomeView
• History Flow
• HivePlots
• ImageVis3D
• JProfileGrid
• Many Eyes
• Molecular Maya
• Molecular Movies
• PathBLAST
• Phyloviewer
• Powerwall
• Quartz Composition of DNA
• Scribl
• Sequence Surveyor
• Shape of Song
• Sybil
• Topiary Explorer
• Vrtual Worm
• Web Seer
• Whole Brain Catalog

VIZBI 2011

I've spent the last three days at VIZBI, a Workshop on Visualizing Biological Data, held at the Broad Institute in Boston (note that "Broad" rhymes with "Code"). A great conference in a special venue that includes the DNAtrium. Videos of the talks will be online "real soon now", look for the keynotes, which were full of great ideas and visualisations. To get a flavour of the meeting search for the hashtag #vizbi on Twitter (you can also see the tweet stream on the VIZBI home page). All the keynotes were great, but I personally found Tamara Munzer's the most enlightening. She drew on lots of research in visual perception to outline what works and what doesn't when presenting information visually. You can grab a PDF of her presentation here.

One aspect of the meeting which worked really well was the poster presentations. Poster sessions were held during coffee breaks, and after the last talk of the session but before the audience broke for coffee, each author of a poster got 90 seconds to introduce their poster (there were typically around 10 posters per break). This meant the poster authors got a chance to introduce themselves and their work to the workshop audience, and the audience could discover what posters were being displayed. Neat idea.

I gave a presentation on phylogenies, which I've put on slideshare. After explaining that I thought phylogeny visualisation was mostly a solved problem (as evidenced by the large number of tree viewers available), I continued the theme of why I don't think 3D works for phylogeny (except for geophylogenies), made the pitch for building a phylogeny viewer on the iPad, and finished with my recent work on Google Maps-style viewing very large trees.

Phylogeny VIZBI 2011

View more presentations from Roderic Page

Geography and genes: zoomable view of frog NCBI classification with linked map

More zoom viewer experiments (see previous post), this time with a linked map that updates as you browse the tree (SVG-capable browser required). As you browse the frog classification the map updates to show the location of georeferenced sequences in GenBank from the taxa in the part of the tree you are looking at. The map is limited to not more than 200 localities, and many frog sequences aren't georeferenced, but it's a fun way to combine classification and geography. You can try it at:

http://iphylo.org/~rpage/deeptree/7.html

or watch the video:

Zoomable tree with linked map from Roderic Page on Vimeo.

The Mendeley API Binary Battle - win $US 10,001

Now we'll bring the awesome. Mendeley have announced The Mendeley API Binary Battle, with a first prize of $US 10,0001, and some very high-profile judges (Juan Enriquez, Tim O'Reilly, James Powell, Werner Vogels, and John Wilbanks). Deadline for submission is August 31st 2011, with the results announced in October.

The criterion for judging are:

1. How active is your application? We’ll look at your API key usage.


2. How viral is the app? We’ll look at the number of sign ups on Mendeley and/or your application, and we’ll also have an eye on Twitter.


3. Does the application increase collaboration and/or transparency? We’ll look at how much your application contributes to making science more open.


4. How cool is your app? Does it make our jaws drop? Is it the most fun that you can have with your pants on? Is it making use of Facebook, Twitter, etc.?


5. The Binary Battle is open to apps built previous to this announcement.

Start your engines...

Nomenclator Zoologicus meets Biodiversity Heritage Library: linking names directly to literature

Following on from my previous post on microcitations I've blasted all the citations in Nomenclator Zoologicus through my microcitation service and created a simple web site where these results can be browsed.

The web site is here: http://iphylo.org/~rpage/nz/.

To create it I've taken a file dump of Nomenclator Zoologicus provided by Dave Remsen and run all the citations through the microcitation service, storing the results in a simple database. You can search by genus name, author and year, or publication. The search is pretty crude, and in the case of publications can be a bit hit and miss. Citations in Nomenclator Zoologicus are stored as strings, so I've used some crude rules to try and extract the publication name from the rest of the details (such as page numbering).

To get started, you can look at names published by published by Distant in 1910, which you can see below:



If the citation has been found you can click on the icon to view the page in a popup, like this:



You can also click on the page number to be taken to that page in BHL.


I've also added some other links, such as to the name in the Index to Organism Names, as well as bibliographic identifiers such as DOIs, Handles, and links to JSTOR and CiNii.

So far only 10% of Nomenclator Zoologicus records have a match in BHL, which is slightly depressing. Browsing through there are some obvious gaps where my parser clearly failed, typically where multiple pages are included in the citation, or the citation has some additional comments. These could be fixed. There are also cases where the OCR text is so mangled that a match has been rejected because the genus name and text were too different.

This has been hastily assembled, but it's one vision of a simple service where we can go from genus name to being able to see the original publication of that name. There are other things we could do with this mapping, such as enabling BHL to tell users that the reference they are looking at is the original source of a particular name, and enabling services that use BHL content (such as EOL and Atlas of Living Australia to flag which reference in BHL is the one that matters in terms of nomenclature.

Microcitations: linking nomenclators to BHL

One of the challenges of linking databases of taxonomic names to the primary literature is the minimal citation style used by nomenclators (see my earlier post Nomenclators + digitised literature = fail).

For example, consider Nomenclator Zoologicus. Volumes 1-10 of this list of generic names in zoology were digitised in 2004 and put online by uBio (for more details of this project see Taxonomic informatics tools for the electronic Nomenclator Zoologicus, pmid:16501061). In Nomenclator Zoologicus the citation for the genus Abana is:

Ann. Mag. nat. Hist., (8) 2, 72.

The challenge is to link this short citation to the digital version of the corresponding article. I've been sitting on a copy of the digitised Nomenclator Zoologicus kindly provided by Dave Remsen, and I've finally started to look at the problem of mining it for links to databases such as BHL.

You can see the first attempt at http://biostor.org/microcitation.php. This form takes a genus name and the short citation and attempts to locate the corresponding page in BHL. It then checks whether the name is present on that page. Locating a page in a journal can be a challenge given the often rather ropey metadata in BHL, but BioStor uses a combination of fuzzy string matching and crude kludges to find the best match. But a further complication is that OCR errors may mean the taxonomic name we are looking for might not be detected on the page.

For example, if we search for the citation for the genus Aethriscus, Ann. Mag. nat. Hist., (7) 10, 329. we find two candidate pages in the journal Ann. Mag. nat. Hist, but neither contains the string "Aethriscus". However, if we use approximate string matching we find the OCR text for one page has the string "thriscus". This differs by only two characters from "Aethriscus", and so is a possible match (shown in orange).

Looking at the scanned page we can see the likely source of the problem:

In the original publication the name Aethriscus was written as Æthriscus. The ligature Æ has been corrupted by the OCR engine, and in Nomenclator Zoologicus the name is written without the ligature, hence the failure to exactly match the name with the text. These are some of the challenges faced when trying to close the circle and link names to literature.

The microcitation parser is still pretty crude, but usable. You can get results in either HTML or JSON, so the task of mapping microcitations to BHL pages can be automated. At present the name matching assumes you are looking at a single word (e.g., a genus), I need to extend it to handle binomials.

BioStor updates on Twitter

BioStor has had a Twitter account @biostor_org for a while, but it's not been active. I finally got around to hooking it up to BioStor, so that now every time an article is added to BioStor, the title of that article and it's URL appears in the @biostor_org Twitter feed.

Activity on this feed will be variable, depending on whether articles are being added manually, or in bulk. But it's a handy way to keep tabs on the growing number of articles being harvested from the Biodiversity Heritage Library.

Zooming a large tree, now with thumbnails

Continuing experiments with a zoom viewer for large trees (see previous post), I've now made a demo where the labels are clickable. If the NCBI taxon has an equivalent page in Wikipedia the demo displays and link to that page (and, if present, a thumbnail image). Give it a try at

http://iphylo.org/~rpage/deeptree/3.html

or watch the short video clip below:

Zoomable viewer with Wikipedia thumbnails from Roderic Page on Vimeo.

Mendeley, OpenURL, BioStor, and BHL

Mendeley has added a feature which makes it easier to use Mendeley with repositories such as BioStor and BHL. As announced in Get Full Text: Mendeley now works with your local library via OpenURL, you can now add OpenURL resolvers to your Mendeley account:

We’ve added a button to the catalog pages that will allow you to get the article from your library right in Mendeley. This feature will link you directly to the full text copy according to your institutional access rights.

Ironically, in the UK access to electronic articles from a University is pretty seamless via the UK Access Management Federation, so I don't need to add an OpenURL resolver to get full text for an article. But this new feature does enable another way to access to articles in my BioStor repository. By adding the BioStor OpenURL to your Mendeley account, you can search for articles from your Mendeley library in BioStor.

The Mendeley blog post explains how to set up an OpenURL resolver. Go to your Mendeley account and click on the My Account button in the upper right corner of then page, then select Account Details, then the Sharing/Importing tab, or just click here.

Click on Add library manually, then enter the name of the resolver (e.g., "BioStor") and the URL http://biostor.org/openurl:

If you view a reference in Mendeley, you will now see something like this:

In addition to the DOI and the URL, this reference now displays a Find this paper at menu. Clicking on it shows the default services, together with any OpenURL resolvers you've added (in this case, BioStor):

You can add multiple resolvers, so we could add the BHL OpenURL resolver http://www.biodiversitylibrary.org/openurl, although finding articles isn't BHL OpenURL resolver's strong point.

Now, what would be very handy is if Mendeley were to complete the circle by providing their own OpenURL resolver, so that people could find articles in Mendeley from metadata such as article title, journal, volume, and starting page. The Mendeley API might be a way to implement this, although its search features lack the granularity needed.