NICU and algae

[Jim Croft]

> From: federhen at ncbi.nlm.nih.gov (Scott Federhen)
> To: jrc at anbg.gov.au
> Subject: NICU
>
> Jim:
>
> Great! Thanks for putting up the NICU files under gopher.
>
I hope people find it useful and more importantly check it for accuracy
and ommissions.  Or perhaps most importantly, think about what such a
list can or should be used for.

> My name is Scott Federhen, and I'm in charge of the taxonomy project
> here at NCBI/NIH. We are producing a merged sequence database from
> all of the large protein & nucleic acid sequence databases.

?National somethingorother of the National Insitute of Health?

> Each of the existing sequence databases comes with it's own taxonomy;
> unfortunately, they are all very different from each other, and none
> of them is perfect. I have been working on a tree-structured database
> managment tool, and have used it to implement a taxonomy/phylogeny manager.
> With this tool, we have merged the database taxonomies into a single tree,
> and we are working to set up mechanisms by which the taxonomic community
> can maintain this tree for us.
>
I would like to here more about this taxonomic integration project.  Can
you post a summary/background/discussion to taxacom at huh.harvard.edu as
others would be sure to interested as well.

Systematists, taxonomists and museum/herbarium curators of the world see
one of their roles in life roles to provide reliable classifications and
identifications for biological science to use.  And you are absolutely
right - all of them are different and non of them are perfect (except
one's own, of course!).  There have been many international meetings and
many words spoken on this topic but I am not convinced that we are any
closer to an integrated or unified arrangement of life.

As taxonomists and systematists, we would love to maintain such a tree
for you ( it is after all, another justification for our existence and
subsidy from the public purse beyond mere self indulgence and academic
curiosity :-) ).

The modelling of a information/database engine that will handle multiple
and alternative classifications (it seems as though we are stuck with
those) and changing identifications (we are stuck with those too) that
satisfies the arcane practices of taxonomists and the needs of users for
a simple, stable view of the world, is proving very difficult.  There are
a handful of people around the globe working more or less seriously on
this problem and for every solution they come up with, these is some
aspect of the way we do business that can not be accommodated without a
kluge of some form or other.

Perhaps the differing needs and aspirations here are unreconcilable and
maybe we are wasting our time seeking a single solution?  Or is the
problem that there are too many 'single solutions' and individually we
have too much intellectual and emotional investment in one to agree on
using another?

The ASC information model, recently announced on this group is an
attempt to describe a framework that might have a general application to
biological collections (and thus went further than names and
classifications).  The International Organization for Plant Information
(IOPI) has produced a model to handle its plant checklist project and
link into wider botanical information, the SMASCH project at the
herbarium in Berkeleyhas a model to handle herbarum information and the
Missouri Botanical Gardens has developed a detailed model for its own
purposes.  All these are available via FTP, and I urge people to have a
look at them, try and understand them, perhaps implement them and see how
(not if) they can be improved.

We should never lose sight of the fact that taxonomic, nomenclatural and
systematic databases only contain words, words reflecting the opinion of
a taxonomist at one time or another.  Just a type specimen nails down
the biological name (although not its application), a properly curated
voucher specimen is required to nail down the organism(s) under study.
Although a database can describe a change to a taxonomic concept, it can
not always tell where a specimen or sample would end up based only on the
name information.  Taxa are always being combined and divided and
ultimately is not a taxon only the heap of specimens you chose to place
under that name?

> I am very interested in exchanging data with existing taxonomic databases,
> namelists & authority files, culture collections & etc., so I was very happy
> to see the gopher indexed retrieval for the plant NICU files.
>
Yes, the NICU lists could form the basis of a useful authority file of
generic plant names and it has a major advantage advantage of being
freely available over the network.  But there are others that could do a
similar and maybe better job (given that NICU is still being compiled
and corrected).  Index Nominum Genericorum is possibly the most
definitve list of known plant generic names and I understand plans are
underway to make this information available on the network.  Both the
USDA and Kew have prepared printed publications of vascular plant genera
and there is Mabberly's Plant Book.  The USDA list is available from the
taxacom FTP server and gopher as a issue of Flora on Line, and the raw
data files are available on the ANBG gopher (The USDA list is easier to
import into a database than the NICU and we will be doing that as soon
as time and disk space can be found - the good thing about gopher is
that once the folks in Beltsville set up a gopher server for this
database we can all link to it).  Does the botanical community need so
many authoritative lists of generic names, or is it possible to harness
all this effort into a single integrated enterprise?

However, the issue of authority and standards often has little to do
with fitness for the job or with accessibility.  People and files have
authority because the community gives it to them or lets them take it.

> A couple of quick questions: the files at your site are just a concatenation
> of the separate files at the Harvard site, right? And the merged files that
> you've put up don't seem to include the algae, is that correct? At least
> I was not able to find anything for 'Volvox' (one of my personal favorites).
>
Mea culpa - I forgot to include the 'slimes and seaweads'.  _Volvox_ is
now in, along with _Hormosira_ (my personal favourite) and the others.

> Anyway, thanks again!
>
> Scott federhen at ncbi.nlm.nih.gov
>

Now, where are the fungi and lichens?

jim
______________________________________________________________________________
Jim Croft                  [Herbarium CBG]           internet: jrc at anbg.gov.au
Australian National Botanic Gardens                     voice:  +61-6-2509 490
GPO Box 1777, Canberra, ACT 2601, AUSTRALIA               fax:  +61-6-2509 599
____Biodiversity Directorate, Australian National Parks & Wildlife Service____