[Taxacom] [SPAM?] Re: GenBank (was The economics of biodiversity database initiatives)

[Roderic Page]

Hi Adam,

Locality data in GenBank is variable, but increasingly sequences (specially barcodes) are appearing with GPS-derived coordinates. Some sequences are linked to voucher specimens (admittedly a lot fewer than would be desirable), in other cases you can go to the publication that made the sequences available and get the data there (again, less than desirable, it would be nice to automate this).

I disagree that 

> 
> There is absolutely no way to verify that a sequence belongs to taxon A 
> rather than taxon B, other than the say-so of the researcher submitting the 
> sequence to GenBank.
>  

One of the advantages of sequences is that we can build a tree and discover potentially misidentified sequences, indeed this is one of the quickest ways to discover potential problems. It won't always work, but it is more testable than a simple assertion that a sequence belongs to a given taxon.

Regards

Rod

On 28 Oct 2013, at 11:56, Adam Cotton wrote:

> ----- Original Message ----- 
> From: "Rafaël Govaerts" <R.Govaerts at kew.org>
> To: "'Roderic Page'" <r.page at bio.gla.ac.uk>; "Taxacom" 
> <taxacom at mailman.nhm.ku.edu>
> Sent: Monday, October 28, 2013 6:08 PM
> Subject: Re: [Taxacom] The economics of biodiversity database initiatives
> 
> 
> Dear Rod,
> The difference is that GenBank provides real objects, namely the sequence 
> while GBIF only provides an interpretation of an underlying real object (the 
> specimen or observed organism). If images of the specimen or observed 
> organism were attached to each record the data would become of real use.
> With types there has been a lot of effort towards that as everyone realised 
> that knowing the type is Smith 3672 is of little use, you need an image as 
> now provided by Jstor for many taxa.
> Rafaël
>> 
>> 
>> 
> 
> 
> My major gripe with GenBank is the unverifiability of the taxa that have 
> sequences listed in the website.
> 
> GenBank neither provides accurate locality data (only country - which is a 
> political, not natural entity) nor determination beyond species, or even 
> photographs which could be used to verify the origin of the sequence.
> 
> Here in Thailand (and many other countries) we often find different species 
> and subspecies in the various parts of the country which correspond to 
> different zoogeographical regions. If I access a sequence in GenBank from 
> 'Thailand' it is impossible to verify which part of the country the specimen 
> came from, and thus which actual taxon has been analysed. This is important, 
> since taxa are regularly split or lumped as taxonomic research progresses, 
> and the sequence in GenBank will thus become redundant if the original taxon 
> is not verifiable.
> 
> There is absolutely no way to verify that a sequence belongs to taxon A 
> rather than taxon B, other than the say-so of the researcher submitting the 
> sequence to GenBank. I know of at least one DNA analysis paper in my own 
> field where some taxa were misidentified at species level, and these are 
> relatively easy to identify from photographs compared with many organisms. I 
> spotted one error just by looking at a black and white photocopy of a plate 
> illustrating some of the specimens analysed in that paper, and most papers 
> do not actually illustrate every specimen analysed.
> 
> If GenBank included locality data and photographic evidence of the taxon it 
> would be much more useful long term. In not so many years from now it will 
> no longer be possible to verify the identity of sequences by e-mailing the 
> author to ask them!
> 
> Adam. 
> 
> 
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---------------------------------------------------------
Roderic Page
Professor of Taxonomy
Institute of Biodiversity, Animal Health and Comparative Medicine
College of Medical, Veterinary and Life Sciences
Graham Kerr Building
University of Glasgow
Glasgow G12 8QQ, UK

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