[tdwg-content] status of uBio

Fri Oct 16 17:29:47 CEST 2015

Hi Steve,

if it’s animals you are after and the following characteristics (shared with IPNI):

1) comprehensive
2) names not taxa
3) LSIDs that deference to RDF using consistent vocabulary (TDWG LSID)
4) closed, or at least non-open

then ION (http://www.organismnames.com ) is for you. Each name has an LSID that actually works and returns a name plus (often) a bibliographic citation as a string.

My frustration with Ion being closed, and only serving bibliographic strings instead of DOIs, Handles, BHL BioStor etc. was what led me to *cough* copy ION and augment it to create BioNames http://bionames.org

For example, ION has urn:lsid:organismnames.com:name:5109777 and BioNames has http://bionames.org/names/cluster/5109777 (plus the original description with DOI http://dx.doi.org/10.11646/zootaxa.3616.4.3, see http://bionames.org/references/384cdd42133009235d59af9b41c55290

I’m working on a  similar mapping of references to DOIs, etc. for IPNI...

ION exposes RDF, BioNames doesn’t (which won’t surprise you I guess, it has a JSON API). If it was of use I could add RDF to BioNames, probably JSON-LD.

Regards

Rod

---------------------------------------------------------
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:  Roderic.Page at glasgow.ac.uk<mailto:Roderic.Page at glasgow.ac.uk>
Tel:  +44 141 330 4778
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
ORCID:  http://orcid.org/0000-0002-7101-9767
Citations:  http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ
ResearchGate https://www.researchgate.net/profile/Roderic_Page

On 16 Oct 2015, at 15:51, Steve Baskauf <steve.baskauf at vanderbilt.edu<mailto:steve.baskauf at vanderbilt.edu>> wrote:

Nicky,
Thanks, I'm looking forward to checking it out!  But no animals. :-(
Steve

Nicky Nicolson wrote:
Hello Steve,
Thanks for triggering an interesting thread.
Just waving the IPNI flag for a minute:

1. They have managed to stick around for a long time and are stable in their format (as LSIDs and HTTP proxied LSIDs).
At ipni.org<http://ipni.org/> we support our own HTTP proxy for LSIDs:
http://ipni.org/urn:lsid:ipni.org:names:12345-1
… and it’s been an age since I tried to resolve an LSID using the formal LSID spec but a quick run-through today shows that all the steps appear to be in working order.

2. The coverage of names is really good for plants, animals, different geographic locations, etc.  I also use ITIS identifiers but it's fairly common for me to not be able to find one for the name I need, which almost never happens with uBio.

IPNI is comprehensive for vascular plants (at species level). We’ll be addressing the data gaps at infra-specific level – but it’s very useful for us to be armed with reasons (from users like yourself) as to why we should spend time doing this.

3. It's somewhat clear what uBio identifiers refer to: names vs. something more nebulous involving taxa or ... something.  (Not trying to push your button, Rich Pyle).
IPNI only serves data about names, no taxa here.
We are pushing IPNI IDs into our taxonomic resources so that a user can flexibly match a name and get an IPNI identifier (the nomenclatural part), and then as a later step query a taxonomic resource for their current view as to the taxonomic status of that name. We are aiming for a clean separation of names matching from the (multiple, potentially different) uses of those names to form taxonomies.

4. You can actually get RDF associated with the LSID version of the uBio identifiers.  I was wanting to download some to play with in our new triplestore (http://rdf.library.vanderbilt.edu<http://rdf.library.vanderbilt.edu/>) when I discovered that the server was down.  The RDF is somewhat ad hoc, but hey, it's there.

The HTTP proxy above returns RDF metadata for the specified record.

New developments (most of the functionality outlined above is 8-10 years old), I’ve been working on exposing IPNI data through standard match services – namely the Open Refine reconciliation API, which permits much more flexible names look-ups using a lot of heuristics gathered from matching data port exercises carried out at Kew over the past few years. Currently the main hitch with this service is that it includes duplicate records. This is something we’re working on resolving right now.
The service is outlined here: http://data1.kew.org/reconciliation/ and details of the IPNI service in particular are here: http://data1.kew.org/reconciliation/about/IpniName

If you’re interested in using IPNI, I’d be happy to hear any comments on the functionality above and / or any requests as to how we can make it more useful for you.

cheers,
Nicky

From: tdwg-content-bounces at lists.tdwg.org<mailto:tdwg-content-bounces at lists.tdwg.org> [mailto:tdwg-content-bounces at lists.tdwg.org] On Behalf Of Steve Baskauf
Sent: 16 October 2015 14:09
To: Dmitry Mozzherin <dmozzherin at gmail.com><mailto:dmozzherin at gmail.com>
Cc: Chuck Miller (Contact) <chuck.miller at mobot.org><mailto:chuck.miller at mobot.org>; tdwg-content at lists.tdwg.org<mailto:tdwg-content at lists.tdwg.org>; Jonathan A Rees <rees at mumble.net><mailto:rees at mumble.net>; Shorthouse, David <david.shorthouse at umontreal.ca><mailto:david.shorthouse at umontreal.ca>
Subject: Re: [tdwg-content] status of uBio

Thanks all for the information and comments about the status of uBio.  I'm glad to hear that the server will probably come back up.  If not, then I hope the data will be made available to those who said they would be willing to host it.

I have been interested in using the uBio identifiers for several reasons:
1. They have managed to stick around for a long time and are stable in their format (as LSIDs and HTTP proxied LSIDs).
2. The coverage of names is really good for plants, animals, different geographic locations, etc.  I also use ITIS identifiers but it's fairly common for me to not be able to find one for the name I need, which almost never happens with uBio.
3. It's somewhat clear what uBio identifiers refer to: names vs. something more nebulous involving taxa or ... something.  (Not trying to push your button, Rich Pyle).
4. You can actually get RDF associated with the LSID version of the uBio identifiers.  I was wanting to download some to play with in our new triplestore (http://rdf.library.vanderbilt.edu<http://rdf.library.vanderbilt.edu/>) when I discovered that the server was down.  The RDF is somewhat ad hoc, but hey, it's there.

There isn't really any other source that has all of these characteristics.  So please keep uBio going indefinitely, if at all possible.
Steve

Dmitry Mozzherin wrote:
I had been administering uBio for the last year, but now I am moving from MBL. uBio machine is in a bad shape, and it crashes after a few hours of work. My plan is to create Docker containers for database, code and data, which should make whole system much more stable, and much more manageable. Good news I will definitely try my best to do it, the bad news I am spread thinner than usual with move, transferring hardware and grant, GN things, EOL things, and figuring out what to do with the house etc. uBio 'code' part is about 35 Gb, which makes the task more complicated, but I am quite optimistic that I will be able to make containers and put them either on an  MBL machine, run it from University of Illinois, or give it to Naturalis -- depending on what will make more sense for Dave Remsen, MBL and all interested in the project.

--

Steven J. Baskauf, Ph.D., Senior Lecturer

Vanderbilt University Dept. of Biological Sciences

postal mail address:

PMB 351634

Nashville, TN  37235-1634,  U.S.A.

delivery address:

2125 Stevenson Center

1161 21st Ave., S.

Nashville, TN 37235

office: 2128 Stevenson Center

phone: (615) 343-4582,  fax: (615) 322-4942

If you fax, please phone or email so that I will know to look for it.

http://bioimages.vanderbilt.edu<http://bioimages.vanderbilt.edu/>

http://vanderbilt.edu/trees

--
Steven J. Baskauf, Ph.D., Senior Lecturer
Vanderbilt University Dept. of Biological Sciences

postal mail address:
PMB 351634
Nashville, TN  37235-1634,  U.S.A.

delivery address:
2125 Stevenson Center
1161 21st Ave., S.
Nashville, TN 37235

office: 2128 Stevenson Center
phone: (615) 343-4582,  fax: (615) 322-4942
If you fax, please phone or email so that I will know to look for it.
http://bioimages.vanderbilt.edu<http://bioimages.vanderbilt.edu/>
http://vanderbilt.edu/trees

_______________________________________________
tdwg-content mailing list
tdwg-content at lists.tdwg.org<mailto:tdwg-content at lists.tdwg.org>
http://lists.tdwg.org/mailman/listinfo/tdwg-content

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://lists.tdwg.org/pipermail/tdwg-content/attachments/20151016/974e80f3/attachment.html 