Monday, 23 September 2013

Taxon of the Day: Escherichia coli

E. coli magnified 10,000 times

Taxon of the Day ventures into the kingdom of bacteria with today's well-known subject. Escherichia coli is a bacteria that inhabits the gut of both animals and people and these days seems to be everywhere and in everything, from your handbag to your watercress. Although only one species, it includes hundreds of strains and serotypes - some good, some bad and some potentially life-threatening. E. coli found in human intestines are mostly harmless and help us to digest food, but others, like the strain officially known as VTEC O157 Phage type 2 VT2, is not so pleasant. VTEC is the abbreviation used for verocytotoxin, the cause of gastrointestinal disease producing  E. coli, of which O157 is the most common strain in the UK. Just recently a leading supermarket chain (in the UK) came to nationwide attention for recalling all of its own brand of watercress due to an outbreak thought to trace back to its produce. As of yet no proof of contamination has been found, but as a precautionary measure due to the many numbers of people who fell ill and were treated in hospital, it was felt necessary to act. It is reported that approximately 1000 cases of E. coli per year are treated in the UK. Transmission can occur in direct and indirect ways, most likely in the above case (if in fact true), it came through eating the watercress that had been contaminated by the faeces of infected animals through the soil.

The etymology of Escherichia coli, relates to the German physician Theodor Escherich (1857-1911) who discovered it in 1885. He did not originally name it after himself, which we all know is a no-no in taxonomy etiquette, but by a subsequent taxonomist who reclassified his original taxon.  coli is the Latin genitive of colon, referring to the intestine that this bacteria inhabits.

While E. coli may be considered the bane of consumers, supermarkets and health workers alike, it is frequently a friend to researchers because of its genetic simplicity and/or fast growth rates. It has been used as an aid in completing the Human Genome Project and as a potential new biofuel among many other positive uses.  It has also been the inspiration, along with other pathogens, for artist Luke Jerram to produce some dramatic art, proving that the agents of our pain can have the most striking and beautiful form when blown in glass!

CoL Annual Checklist: Escherichia coli
CoL contributor: Bacteriology Insight Orienting System
Image copyright: Public Domain

Friday, 20 September 2013

i4Life Part 3: The Catalogue of Life

Catalogue of Life in i4Life data flow

Previous posts in this series:
Part 1: Improving the world's taxonomic data indexing
Part 2: Global Species Databases

The Catalogue of Life provides a unified taxonomic index of living species on Earth. The first Annual Checklist was produced in 2001 on CD and had 204, 216 species. Today it is on DVD and also online and contains over 1.4 million species from over 135 contributing taxonomic databases. The Annual Checklist, as the name suggests, is a once per year fixed edition and so is a referenceable version of the entire Catalogue. Additionally, the Catalogue of Life today produces a second edition - the now monthly updated Dynamic Checklist, this differs in not being a fixed edition, but reflects updates to the supplier databases or inclusion of new databases as and when the Catalogue of Life receive them. Accessing the Catalogue of Life is easy, you can do it through the easy to use browse and search interface online (shown by the 'End User' in the diagram above) or for larger data consumers who want all or part of the Catalogue, it can be done programmatically. Which ever way you choose to do it, the Catalogue of Life tries to make data sharing as easy as possible while ensuring that our contributors are fully credited for their work.

The Catalogue of Life has many users from different fields, including students, nature enthusiasts, ecologists, museum collection managers, publishers, commercial natural product manufacturers and policy makers to name but a few. It is unlikely that a taxonomist would use the Catalogue of Life for the taxa they have expertise in, but taxonomists do use it to investigate related taxa outside of their own area. The Catalogue of Life also provides a taxonomic backbone for large biodiversity data suppliers (i4Life Global Biodiversity Programme partners) where the 1.4 million species names act as an indexing mechanism within their databases, from which all other biodiversity data can radiate. It is this important user group that is central to the goals of i4Life and the tools and processes that it has created to achieve them. Using the Download, Piping and Cross-mapping tools (which will be covered in later posts in this series) developed during i4Life, the Catalogue of Life and its global partners have been able to identify the differences and similarities in their taxonomic catalogues. What follows this, is a process of harmonisation between all catalogues. Once this process is fully completed, it will also give a clearer indication of the remaining gaps in the world's understanding of biodiversity that need to be filled.

Today, we look at what the Catalogue of Life team do (referred to as workflows) to create the monthly Dynamic Checklist before making it available online and to Global Biodiversity Partners for use in their own data portals.

As outlined in the previous post in this series, the Catalogue does not produce data itself, instead it acts like a publisher, assembling side-by-side expert taxonomist's global species checklists into a unified and simplified whole. Keeping this huge global taxonomic checklist well organised and up-to-date is a complex task. To achieve this the Catalogue of Life team carries out a process of taxonomic data integrity checks, editorial and aggregation once a month known internally as 'data assembly'. Some of this assembly is automated, some semi-automated and some manual, which ever method is used, the system in place (called the Workbench) allows for a flexibility to move between the three as and when is required.  The editor has overall content control, the data assembly team carry out the updates, and the whole process of production and roll-out is overseen by the CoL Systems Manager. 

Each month a number of steps or workflows occur: Firstly, files are collected or received from GSDs. These are then extracted and transformed into the Catalogue of Life Standard Dataset in text delimited files. Some come this way already, whereas others need more work to get them into a usable format. This data is then transferred into MySQL, the database software that houses the Catalogue of Life. The next step is running checks for data integrity and consistency. Some are carried out and resolved automatically, whereas others, for example ones that deal with nomenclatural and taxonomic issues, may need manual input. After all editorial decisions have been made and updates completed, checklists are merged to form the complete Catalogue and this is then converted to a production schema and deployed on the University of Reading servers.

The following team members have particular responsibility for different stages of this process:

Executive Editor (Dr Yuri Roskov) and Editorial Assistant (Dr Thomas Kunze)
The usability of the Catalogue of Life is dependent on the underlying management classification for unification and simplification. The biological classification systems of different kingdoms follow different Codes and nomenclatural practices, in addition some have alternative classifications within kingdoms.  As noted above, the end user of the Catalogue of Life is generally not an expert in taxonomy so to present multiple taxonomies from which to choose one, would decrease the usability of the Catalogue for one very large user group (although it may improve it for another!). So the management classification, by using a single taxonomy brings all taxa across all kingdoms into a coherent master view, and where possible enforces consistent nomenclature. To place a global species checklist within the Catalogue of Life a specific set of adjustments may need to be decided upon by the editors on where and how to insert it, to make it as consistent as possible, while not losing the essential taxonomic information it has been created to provide.

The Catalogue of Life retains the GSD's own classification
below entry point and uses the management classification above.
When a simplification occurs - for example using the management classification above a GSD insertion point (see picture above) or removal of ranks not recognised by the Catalogue of Life - it is done with the knowledge that the Catalogue of Life links every species to its source database, where a full classification and often extra, associated data can be found by the user.

The Executive Editor is also responsible for continually searching for and identifying new taxonomic data sources. If one is found, the Editor then also facilitates the necessary independent Peer Review process that is required to occur before being accepted into the Catalogue of Life.

Data Assembly (Luvie Paglinawan until July 2013 and Luisa Abucay)
Some data integrity checking does not need taxonomic input, so for example, running a query to check that all synonyms in a checklist have an associated accepted species name or making sure that abbreviations of taxonomic ranks are consistent within a checklist can be carried out automatically, results of which are passed back to the database supplier for consideration of inclusion with the next update. The data assembly do not just run automated checks, they also carry out data transformations as instructed by the editors and do most of the initial data gathering and combining phase of the process.

Systems Manager (Viktor Didziulis)
The informatics processes are overseen by the Systems Manager and once all the updates and assembly have been completed by the data assembly team and editors the Systems Manager will oversee the deployment of the new version of the Dynamic Checklist to the servers. There is more than one server, both for security (ie if one server goes down there is another one running) and for updates, where one can be updated, whilst the other is still running and then vice-versa, so there is no interruption of service to the online Catalogue of Life users.

Global Biodiversity Programmes receive an updated Catalogue of Life database via webservices and the i4Life Download tool. The topic of our next post in this series.

Next up: i4Life Part 4: Download and Web Services

Wednesday, 18 September 2013

i4Life at the Catalogue of Life Global Team meeting

The Catalogue of Life Global Team

This week Alastair Culham and Yuri Roskov from the Reading i4Life team travelled to Leiden, Holland for the annual Catalogue of Life Global Team meeting. The Catalogue of Life Global Team are a group of taxonomic experts from around the world who advise and decide upon scientific policy for the Catalogue of Life. They are made up of Global Species Database custodians, ITIS representatives and Species2000 (the body which governs the Catalogue of Life in financial and legal matters) directors.

On the agenda this time were: 
  • a report on the move of the Species2000 secretariat from Reading University to Naturalis in November this year; 
  • a proposal for updating the Catalogue of Life Management Classification
  • a presentation from Alastair Culham, the i4Life Coordinator, on the soon to be completed project's progress; and 
  • a discussion on how to include fossil taxa in the Catalogue of Life, something that has been presented as a priority by certain members of the Global Team. 
Global Team meetings are always a good chance to connect with parts of the confederation that is the Catalogue of Life.

Monday, 16 September 2013

The 106th Annual Meeting of the German Zoological Association, Munich, Germany, 13-16/09/2013

Thomas Kunze and Yuri Roskov attended the 106th Annual Meeting of the German Zoological Association, Munich, Germany, 13-16/09/2013

Taxon of the Day: Ursinia calenduliflora

Ursinia calenduliflora

Taxon of the Day moves to South Africa for an annual, endemic herb found throughout the region known as Namaqualand. Ursinia calenduliflora (DC.) N.E.Br. is just one of hundreds of flowering species found in this unique floral region. In peak springtime (usually mid-august to mid-september) the most spectacular flower displays can be found, where multi-coloured carpets span as far as the eye can see. Duration, timing and intensity of displays are all determined by weather,  mostly notably, amount and arrival time of rain. A good year can never be accurately predicted, although many try, as it can help with marketing the region as an annual tourist destination. Most of the year, this area of north west southern Africa is a barren desert, with very little green let alone other colours, which makes the short period of flowering, seemingly unimaginable beforehand, even more incredible.

Different floras and online resources, unsurprisingly considering its wide distribution over a region inhabited by indigenous and settler communities, cite different common names. Le Roux (2005) uses the Afrikaans name Berggousblom which translates to mountain daisy, others use english names including Namaqua Parachute Daisy (Manning, 2009) and Springbok rock ursinia. TotD would like to know what the The Nama people, native inhabitants of this region for thousands of years, whose language contain distinctive click click sounds, have named this plant. Something different to the above for sure.

A small dancing part of a big carpet
The genus Ursinia in the family Asteraceae, is named after the botanists Johan Ursinu (1608-1666) and contains 43 species in the Catalogue of Life supplied by the Global Compositae Checklist. All species collectively referred to as parachute daisies, are native to southern Africa, with the highest concentration in the Western Cape. One species is the exception, U.nana is reportedly found in Ethiopia.

CoL Annual Checklist: Ursinia calenduliflora
CoL contributor: Global Compositae Checklist
Image copyright: RLF Matthias

Wednesday, 11 September 2013

Catalogue of Life in Galway

Thomas Kunze and Viktoras Didziulis with their posters

The Catalogue of Life was represented at the 48th Annual European Marine Biology Symposium in Galway, Ireland on 19-23 August 2013, by Thomas Kunze (CoL Editorial Assistant), Viktoras Didziulis (CoL Systems Manager) and Yuri Roskov (CoL Executive Editor). Below is their account of the event:

The conference brought together over 200 academic practitioners in marine biology (biologists, oceanaologist, geologists, ecologists, taxonomists and project managers) from over 20 countries for networking and dissemination of their research. The conference highlighted the need for sustainable management of the oceanic resources against a backdrop of climate change and ocean acidification.

The Catalogue of Life presented the following three posters, which summarised i4Life activity in Workpackage 3 (2012-2013):

  • Overview of marine taxa suppliers in the Catalogue of Life by Yuri Roskov
  • Proto-GSD in the Catalogue of Life – a case study on Mollusca and Platyhelmintes by Thomas Kunze
  • Master data management and user services of the Catalogue of Life by Viktoras Didziulis 

With these three posters different aspects of the Catalogue were highlighted - the technical side, editorial work and the general composition of marine data. 

By visiting the conference, we were able to present the product - the Catalogue of Life, and gain access to both users and partners. The Editorial team is always on the look out for new contributors in gap areas to improve species coverage. In Galway, one of the outcomes of attending this meeting was that we were able to meet, among others, marine protistologists (people working with Protista and Chromista) and discuss the possibilities for additional Global Species Checklists in these groups.  From the partner side of things, we were happy to meet several members of WoRMS, a major contributor to the Catalogue of Life. The Catalogue Life has a wide user base across many different fields, ecologists being one such group; this conference with many in attendance, also gave us the opportunity to target new users in this area.


Monday, 9 September 2013

Global Species Database Spotlight: BdelloideaBase

Jacob 'trying out' an Armascirus mite t-shirt

The interview below is with Professor Jacob den Heyer who this year retires from his taxonomic work. He first contributed to the Catalogue of Life in 2010 with CunaxidBase. This was substituted with the extended BdelloideaBase in the 2011 Annual Checklist. The Bdelloidea are free-living, predatory mites with a cosmopolitan distribution, inhabiting practically all temperate zones. The Catalogue of Life wishes to thank Jacob for this unique database which contributes to the quality and taxonomic coverage of the Catalogue. Future updates will be provided by Michael Skvarla of the Dept. of Entomology, University of Arkansas.

Database name:


Your name: 

Prof. Jacob den Heyer (D.Sc.)

Your position: 

Compiler and custodian of the database until July 2013.

Where is database located?
South Africa

What taxon/taxa does your database cover?
Mite Superfamily Bdelloidea which includes the families Cunaxidae and Bdellidae.

How many species names do you hold? 
Cunaxidae 405
Bdellidae 267

Friday, 6 September 2013

Taxon of the Day: Monotropa uniflora

A gang of Monotropa uniflora

Monotropa uniflora L. from the plant family Ericaceae is commonly known as Indian Pipe, Ghost plant, Ice plant or Corpse plant. It is an established but hard to find inhabitant of coniferous forest understory found in parts of North America as listed by ITIS regional through the Catalogue of Life. It is also reported to be found in parts of Asia, northern South America and northern Europe. 

The plant is quite a sight and is often found in a bunch with others starkly shooting up from the dark ground. The plant's lack of green is a result of the absence of chlorophyll as it doesn't need sunlight to grow, allowing it to inhabit the shadiest of places. Instead it has a beneficial, symbiotic relationship with the fungi that lives in the soil around it; where the fungi absorbs nutrients of decaying vegetation whilst Monotropa uniflora, through its roots, in turn feeds off of the fungi. Unlike the mycorrhizal mutualistic relationship of the fungi with its surrounding vegetation, this plant gives nothing back so is considered parasitic. 

The etymology of this plant describes different aspects of its appearance and growth habit. Where uniflora refers to the fact that a stem usually ends in one flower (ie uni -one, flora-flower) and monotropa means 'one turn' 
(down to up) which the flowerhead will do when matures to fruit. When in flower the head hangs down and 'Pipe' refers to the stem and head looking like the stem and bowl of a pipe. The Indian bit possibly relates to its visual similarity to a calumet, the ceremonial smoking pipe of indigenous american peoples, or the many medicinal uses they found for this plant. Ghost flower alludes to its pure whiteness and general elusiveness to anyone that would like to see it.

The plants emerge above ground in summer and once fertilised the head bends up and the whole plant turns black giving rise to another of its common names 'Corpse plant'. It produces fruits before autumn and disperses them until the following spring. If you pick one it will also turn black and dissolve in your hand. Wild plants that can not be transported or grown in our gardens have a special mystique and allure and Monotropa uniflora is one such plant.

CoL Annual Checklist: Monotropa uniflora
CoL contributor: ITIS Regional
Image copyright: Sage Ross [CC-BY-SA-3.0-2.5-2.0-1.0 or GFDL], via Wikimedia Commons

Thursday, 5 September 2013

Taxon of the Day: Cygnus

Taxon of the Day reviews the etymology, appearance, distribution and calls (care of xeno-canto) of the 6 species of Cygnus or Swan found in the world and the Catalogue of Life.  

C.atratus - Black Swan

C. atratus or Black Swan is native to Australia but has been introduced to many gardens and places of human interest in the temperate world like the one recorded in Tawain below. atratus is Latin for 'blackened or dark' which makes sense as the Black Swan is black although has a striking red bill with lateral white stripe. 

Wednesday, 4 September 2013

Taxon of the Day: Vandenboschia speciosa

Vandenboschia speciosa - a fertile frond

Today's Taxon of the Day has been produced by Michael Hassler the owner of the Catalogue of Life's new Global Species Database for Ferns. He writes:

Vandenboschia speciosa (Willd.) Kunkel (= Trichomanes speciosum Willd.) is a member of the Hymenophyllaceae, the Filmy Ferns. This is a family of ca. 500 species of small - often minute – ferns which resemble mosses more than typical ferns. They have thin, translucent tissue which requires wet habitats to live in, and reside mostly on bark, tree trunks or, more rarely, on wet earth or rocks, and can form large mats. Their mats can be intricately twined into “true” moss patches with whom they share not only the looks but also the habitat. Most species readily develop fertile fronds (sporophytes), but a few relict populations of northern and temperate climates have restricted themselves into existing as gametophytes only.

Monday, 2 September 2013

Taxon of the Day: Drosera sect. Ergaleium

A Rainbow sundew - Drosera menziesii 

Today's Taxon of the Day entry has been written by Alastair Culham and his MSc Plant Diversity student Thomas Cooper.

In 1978 Rica Erikson coined the name ‘Rainbow sundews’ to describe a fascinating and unique group of climbing sundews from Western Australia that can grow up to 3 metres in length. These sundews, known botanically as Drosera subgenus Ergaleium DC. section Ergaleium, often climb over and through the sparse shrubs of Western Australia and can produce rainbow like effects as their sticky tentacles intercept sunlight. Unlike northern hemisphere sundews, which tend to occupy wet and boggy areas and are dormant in the cold winters, the Rainbow sundews have the ability to form an underground tuber for summer dormancy when their habitats dry out. There are currently 27 recognised species of Rainbow sundews, most of which occur in south-west Australia however a few spread out as far as the Himalayas (and possibly Africa). Drosera subgenus Ergaleium DC. section Ergaleium species are easily identified by their elongated and wiry stems (see picture below).