[Taxacom] Fwd: What can Global Biodiversity Information Facility (GBIF) do for you?

Fri Oct 18 16:21:40 CDT 2013

I believe the Darwin Core term that would carry this information is Occurrence, establishmentMeans.  And, that Occurrence discussion has gone on for months.  Is there another term that should be used?

The "ratified" Darwin Core terms(http://rs.tdwg.org/dwc/terms/#establishmentMeans) says:
Comment: Examples: "cultivated", "invasive", "escaped from captivity", "wild", "native". For discussion see http://code.google.com/p/darwincore/wiki/Occurrence.
But, there is no "ratified" vocabulary yet for establishmentMeans, and so it is used variably to provide cultivated/wild, or native/introduced or invasive/noninvasive in one term.  

The GBIF Darwin Core terms (http://terms.gbif.org/wiki/dwc:establishmentMeans) is more definitive: 
"Notes: The recommended controlled vocabulary includes: 
native 
introduced 
naturalised 
invasive 
managed 
uncertain 
Example(s): "cultivated", "invasive", "escaped from captivity", "wild", "native"

It's not surprising that there is inconsistent availability of cultivated/native/introduced attributes in GBIF data for the use that Rafael describes.  Data providers lack clear direction on what to provide and thus have used it differently with what they provide via this DwC term, or just left it empty. 

Chuck

-----Original Message-----
From: Rafaël Govaerts [mailto:R.Govaerts at kew.org] 
Sent: Thursday, October 17, 2013 5:31 PM
To: r.page at bio.gla.ac.uk
Cc: taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] Fwd: What can Global Biodiversity Information Facility (GBIF) do for you?

Dear Rod, What is a recurring issue is that no distinction is made in GBIF between native, introduced and cultivated specimens. See e.g. Magnolia grandiflora
http://www.gbif.org/species/3153283
This means that I need to check carefully each record, which takes a lot of time. It also means I get regular emails saying GBIF says this species is also in Jawa and when checking it, turns out to be from Bogor botanic garden. So displaying those in a different way would make my work easier and users less confused.
Best, Rafael

________________________________________
From: taxacom-bounces at mailman.nhm.ku.edu [taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Chuck Miller [Chuck.Miller at mobot.org]
Sent: 17 October 2013 22:41
To: Stephen Thorpe
Cc: taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] Fwd: What can Global Biodiversity Information Facility (GBIF) do for you?

So Steve, is your answer to Rod's question "GBIF can do more to get more data for me from outside North America, Europe and Australia"? Or a different answer?

Chuck

On Oct 16, 2013, at 3:15 PM, Stephen Thorpe <stephen_thorpe at yahoo.co.nz> wrote:

> Yes, Michael highlights nicely one of the problems that I see, namely 
> a bad extrapolation from a few well-documented taxa to the bigger picture (all organisms). Sure, for a few selected taxa, we have good data. But for most taxa, we have poor data or even no data (many names on CoL are just names, with no meaningful connection to any actual species, for example). My experiences in "museums" is that they are largely chaotic places with only a small fraction of collections in any suitable state to make public the data. For example, after several years of "coming soon", NZAC database has finally gone live (see http://scd.landcareresearch.co.nz/Search/Search/NZAC). The collection has an estimated 8 million specimens. The database currently (after several years work) has just (1) most holotypes and some paratypes; (2) a significant proportion of carabid beetles, and a significant proportion of Hemiptera, but probably not as high as 50%. That's it! At current rates, it is unlikely to become comprehensive in the foreseeable future. Most of the reliable data on the database is reliable simply because it has already been worked up and published elsewhere (i.e. in taxonomic revisions). So, there are not only big geographic biases, but taxonomic biases, and reliability biases favouring data already published elsewhere...
>
> Stephen
>
>
> ________________________________
> From: Michael Heads <m.j.heads at gmail.com>
> To: taxacom at mailman.nhm.ku.edu
> Sent: Wednesday, 16 October 2013 10:08 PM
> Subject: [Taxacom] Fwd: What can Global Biodiversity Information Facility (GBIF) do for you?
>
>
> GBIF is very good for higher groups in North America, Europe and 
> Australia, but these are well known anyway. For global information 
> it's weak. Look at the map of Magnoliophyta or Aves - huge areas with 
> no information at all in Russia and western China. You're much better 
> off with the standard literature. Outside of the higher groups GBIF is dire, e.g. Coleoptera:
> nothing at all in most of Asia and Africa and large parts of Brazil.
>
> Knapp (Science 341: 1183. 13 Sep. 2013) wrote: 'a look at the [GBIF] 
> data reveals huge bias, with diversity highest in the north temperate 
> zones and most data points as birds.' (On a slightly different topic she also wrote:
> many outside the field of molecular phylogenetics fail to appreciate 
> that these dates, calculated with a "molecular clock" and calibrated 
> with fossils, are minimum dates and come with big error bars. 
> Vicariance is fighting back, too, with the advent of molecular 
> panbiogeography (Heads, 2012))'.
>
>
> ---------- Forwarded message ----------
> From: Michael Heads <m.j.heads at gmail.com>
> Date: Wed, Oct 16, 2013 at 7:39 AM
> Subject: Re: [Taxacom] What can Global Biodiversity Information 
> Facility
> (GBIF) do for you?
> To: Roderic Page <r.page at bio.gla.ac.uk>
>
>
> On Wed, Oct 16, 2013 at 1:21 AM, Roderic Page <r.page at bio.gla.ac.uk> wrote:
>
>> I've recently been appointed Chair of the Science Committee of the 
>> Global Biodiversity Information Facility (GBIF) 
>> http://www.gbif.org/[1]. The committee is a small group of people 
>> with a range of backgrounds, and one of our roles is to advise GBIF 
>> on matters scientific (e.g., what kinds of data GBIF should collect?, 
>> what kinds of scientific questions should GBIF help answer?, etc.).
>>
>> There have been formal surveys (see the papers in the journal 
>> "Biodiversity Informatics"
>> https://journals.ku.edu/index.php/jbi/issue/view/370/showToc), 
>> meetings, and a "vision" statement (the "Global Biodiversity 
>> Informatics Outlook, http://www.biodiversityinformatics.org/). But 
>> there's always the chance that these fora may miss some points of 
>> view, so I'm keen to get feedback on what sort of things GBIF could 
>> do to improve the way it can help people tackle the scientific questions they are interested in.
>>
>> For example, is there some fundamental limitation that GBIF has that 
>> prevents it being useful to you? Is there some feature/data 
>> type/geographic coverage/etc. that could be addressed that would make 
>> it more useful? Is there a role that GBIF should take on that it 
>> hasn't done so? A useful analogy might be to think of the central 
>> role GenBank plays in genomics, both as a place to archive your data 
>> (sequences), a repository of other people's data that you can access, 
>> and a research tool (e.g., BLAST searches to locate similar 
>> sequences). Is that the sort of thing you'd want from GBIF, or is it something entirely different?
>>
>> I'd welcome any comments, suggestions, views, etc. You can reply to 
>> me directly, or to this email list (if it allows discussions). I've 
>> also posted this request on my blog, so you can comment there if you like.
>>
>> I should stress that this is simply me trying to calibrate my 
>> perception of GBIF's role with what others think. Also, note if you 
>> have specific comments on things such as the GBIF web site please use 
>> the feedback tab on the site (that way it will reach the people who can do something about it).
>>
>> [1] For those unfamiliar with GBIF, its mission "is to make the 
>> world's biodiversity data freely and openly available via the 
>> Internet". At present the bulk of the data are observations of 
>> organisms (mostly multicellular eukaryotes, i.e., animals, plants and 
>> fungi) based on either museum collections or observations of living 
>> organisms. You can get an idea of the kind of science that uses 
>> GBIF-hosted data from this list of papers on Mendeley 
>> http://www.mendeley.com/groups/1068301/gbif-public-library/
>>
>> ---------------------------------------------------------
>> 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
>>
>> Email:          r.page at bio.gla.ac.uk
>> Tel:                    +44 141 330 4778
>> Fax:            +44 141 330 2792
>> Skype:          rdmpage
>> Facebook:      http://www.facebook.com/rdmpage
>> LinkedIn:      http://uk.linkedin.com/in/rdmpage
>> Twitter:                http://twitter.com/rdmpage
>> Blog:          http://iphylo.blogspot.com/
>> Home page:      http://taxonomy.zoology.gla.ac.uk/rod/rod.html
>> Wikipedia:      http://en.wikipedia.org/wiki/Roderic_D._M._Page
>> Citations:
>> http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ
>> ORCID:          http://orcid.org/0000-0002-7101-9767
>>
>> _______________________________________________
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>> Celebrating 26 years of Taxacom in 2013.
>>
>
>
>
> --
> Dunedin, New Zealand.
>
> My recent books:
>
> *Molecular panbiogeography of the tropics.* 2012.* *University of 
> California Press, Berkeley.
>
> *Biogeography of Australasia:  A molecular analysis*. Available 
> January 2014. Cambridge University Press, Cambridge.
>
>
>
> --
> Dunedin, New Zealand.
>
> My recent books:
>
> *Molecular panbiogeography of the tropics.* 2012.* *University of 
> California Press, Berkeley.
>
> *Biogeography of Australasia:  A molecular analysis*. Available 
> January 2014. Cambridge University Press, Cambridge.
> _______________________________________________
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> The Taxacom Archive back to 1992 may be searched with either of these methods:
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>
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> Celebrating 26 years of Taxacom in 2013.
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Celebrating 26 years of Taxacom in 2013.