Video Tip of the Week: ZooBank and species nomenclature
Nomenclature may not be the hottest topic in biology. But it really is foundational for the organization of data, and crucial to bioinformatics resources. I first came into contact with the importance of standardized naming conventions when I worked at The Jackson Lab, which included part of the mouse gene nomenclature committee. As I began to become immersed in database organization it certainly became more clear how important it was to use official names, and to collect all the synonyms for these items. If I use a name for gene or a mouse strain in database X, and you use a name in database Y, we need to know we are both talking about the same thing.
Nomenclature can get pretty contentious too. I remember hearing about the threat of lawsuits from folks who had a preferred name for their gene and did not want the official group to alter that.
But I had not been immersed at all in species nomenclature. But as we get more and more sequence data from possibly newly described species, clearly that process has to be standardized and stored as well. And synthetic species–what to do about them?
In December I became aware of the new resource for zoological nomenclature, ZooBank. From the ICZN, or International Committeee on Zoological Nomenclature, the new resource for organization and access to their repository.
I was alerted to this by @AgroBioDiverse, and this tweet:
@CorrieMoreau Great short video from @fieldmuseum about taxonomic nomenclature “What’s in a Name?” Includes several women in science http://t.co/zdAx2wQl
This is a nice video of the importance and history of zoological nomenclature, and it’s embedded here. But do check out their whole post for more background and helpful links.
When I began to research the backstory for the new ZooBank resource, I came across a big change to the animal nomenclature world that came about last fall. It seems that it is now possible to publish in an online-only journal to get credit for a species name. Welcome to the new century! As described in a Nature editorial:
Previously, the first official description of anything that crawled, flew, wriggled, walked or swam across Earth needed to be formally written up and recorded in print, where it would remain in perpetuity for future scientists to reference.
It never occurred to me that physical paper was a requirement. Apparently this had been a pretty contentious issue over a few years. It was covered in a number of publications. In this interesting interview about the complexity of the problem this caused, Frank-Thorsten Krell described the dilemma some faced:
Authors who opted out of electronic pre-publication often had to wait over six months until their paper appeared in a printed issue. For authors publishing in open-access, online-only journals the situation was even more acute. Should they go for the widest dissemination of their results, but violate the Code? Some did .
So it’s sorted now. And you can publish in online-only journals and get credit in ZooBank and the ICZN system.
But let’s turn now to looking specifically at the new resource. ZooBank is an attempt to wrangle what’s been called a “biodiversity information crisis”.
…it is for this reason that the ICZN is investing considerable time in making functional and stable resources for nomenclature, and the sciences that it supports…
Certainly this will be important for the basic organization and access of the information. But also for connecting people who might need to know more about the species and specimens. Just recently at BioStar there was a question about accessing museum samples for possibly sequencing them.
So for this tip of the week I present the video about ZooBank. Have a look at this resource, and raise the awareness of the importance of nomenclature for data access and sharing.
[There is another ZooBank video about how to use their site here: http://www.zoobank.org/VideoGuide but it won't run for me. I have written to their web team and hope to paste it in when it's working.]
If you want to go even deeper into nomenclature, you might want to also explore the Global Names Architecture (GNA). There are a number of interesting projects over there.
Field Museum video and post with more details and links: What’s in a Name?
Global Names Architecture: http://globalnames.org/
Editorial (2012). The name game Nature, 489 (7415), 178-178 DOI: 10.1038/489178a
Krell, F. (2012). Electronic publication of new animal names – An interview with Frank-T. Krell, Commissioner of the International Commission on Zoological Nomenclature and Chair of the ICZN ZooBank Committee BMC Evolutionary Biology, 12 (1) DOI: 10.1186/1471-2148-12-184
Baker, E., & Michel, E. (2011). Data standards, sense and stability: Scratchpads, the ICZN and ZooBank ZooKeys, 150 DOI: 10.3897/zookeys.150.2248
Paul Voosen, E&E reporter. ‘I found it cool to try to build a species with my own hands’. Greenwire: