[BEXIS2-Dev] [bexis] Minor Corrections Needed on Our Data Publisher Page
bexis2-dev at listserv.uni-jena.de
bexis2-dev at listserv.uni-jena.de
Fr Jul 15 16:20:41 CEST 2016
Dear Andreas,
The 103 datasets you have made available are now registered and indexed: http://www.gbif.org/publisher/541c2668-9391-4479-b90f-fe90b365f33b
I have done some random checking on these and I find them to be in good shape. One thing that I would like to see added; is the temporal data. Either a full timestamp or a year-month value would be really nice. My impression is that the data generally does not contain any date information.
Regarding scripting updates and new datasets – I have a prototype script that needs some tweaking, and it will be made available after I am back in the office (summer vacation). I expect to have something ready around mid August.
If you have questions or comments to the indexed data, please let us know ( helpdesk at gbif.org<mailto:helpdesk at gbif.org> ).
With kind regards,
Jan
From: Andreas Ostrowski [mailto:andreas.ostrowski at uni-jena.de]
Sent: 6. juli 2016 16:41
To: Jan Legind
Cc: helpdesk; BExIS List; bexis2-dev at listserv.uni-jena.de
Subject: Re: [bexis] Minor Corrections Needed on Our Data Publisher Page
Hi Jan,
adding new datasets is planned on a yearly basis. Modifying is not planned but could occur due to curating processes.
I can deploy a script. Do I understand it correctly, that this script is used to push our data to your server? It would be really helpful if you could assist me by creating such a script. Do you have any examples from already running instances?
Regarding your question with the module, I Cc this message with the Bexis2 project developers. The software is in re-developing process and such a module could be part of it.
Best Andreas
On 06.07.2016 12:02, helpdesk wrote:
Hi Andreas,
I see the archives behind the URL now. The issue is that there are quite a number of datasets and this makes it impractical to register them one at the time. Each dataset must be registered separately and doing this manually is not very sensible. This is why I am suggesting the option of using some kind of script to register and crawl each of these 103 resources.
May I ask if you are planning to add new datasets on a regular basis, or if you are planning on curating, modifying, or adding to the 103 datasets already existing behind the endpoint you sent me?
If the resources are ‘dynamic’ or there are going to be more datasets added, I recommend having a script in place to register and index those datasets. All this can be done using the GBIF RESTful JSON based API.
I can assist in creating a script that registers these resources in one batch.
Please let me know what you think of this.
On a related note – do you plan on adding a module to the BExIS software that can share biodiversity data with GBIF?
Best,
Jan
From: Andreas Ostrowski [mailto:andreas.ostrowski at uni-jena.de]
Sent: 5. juli 2016 14:24
To: Jan Legind
Cc: helpdesk; BExIS List
Subject: Re: [bexis] Minor Corrections Needed on Our Data Publisher Page
Hi Jan,
the ready compiled zip files are available via the URL I send.
https://www.bexis.uni-jena.de/PublicData/Files/GBIF/
Now I enabled directory browsing for this specific directory and you should see the files. There is no need to supply or confirm anything. I thought if we provide the files via the url you will crawl them from here. Is this right?
I send you an example file a while ago and you meant that it should pass the validation process.
Best Andreas
On 05.07.2016 12:53, Jan Legind wrote:
Dear Andreas,
Let me explains the requirements for getting biodiversity datasets into the GBIF Portal:
- First off, the datasets must be directly available through an open connection without the need to supply credentials
- The dataset must be downloadable in one step (no ‘I understand the license/user-agreement’ tick box or any other intermediary actions)
- There is a validation process when the dataset is downloaded and if the formal requirements are not met the indexing process will be terminated for that dataset.
Since you have an impressive number of datasets ready for publication, I suggest that you get set up with some kind of script or platform to register the datasets programmatically. We have the GBIF API for this kind of work:
http://www.gbif.org/developer/summary
The GBIF IPT installation can do this for you and since you have Darwin Core archives; these could be uploaded straight to the IPT and get validated prior to indexing.
If you wish to run a custom publishing setup, please get back to me.
Best wishes for the summer,
Jan
From: Andreas Ostrowski [mailto:andreas.ostrowski at uni-jena.de]
Sent: 5. juli 2016 11:22
To: Jan Legind
Cc: helpdesk; BExIS List
Subject: Re: [bexis] Minor Corrections Needed on Our Data Publisher Page
Dear Jan,
thanks for your reply. We have our own implementation for generating DwC archives. The (103) zip files are deposited here:
https://www.bexis.uni-jena.de/PublicData/Files/GBIF/
Directory browsing is disabled. Please come back to me if you have any problems (e.g. in crawling the data) or other questions.
Best Andreas
On 01.07.2016 11:35, helpdesk wrote:
Dear Michael,
I have changed the publisher description accordingly and the contact has been updated as well.
Regarding the new DwC archives: If you are using a BioCASE installation or have custom DwC archives, please get back to me with the URL for the zip files.
If you are publishing with the IPT you should be able to directly associate new datasets with BE using this passw0rd:
Best regards,
Jan
From: michael.owonibi at googlemail.com<mailto:michael.owonibi at googlemail.com> [mailto:michael.owonibi at googlemail.com] On Behalf Of Michael Owonibi
Sent: 27. juni 2016 10:59
To: helpdesk
Cc: BExIS List
Subject: Re: [bexis] Minor Corrections Needed on Our Data Publisher Page
Dear Jan,
I sent you this mail below sometimes ago and I have not gotten any response from you with respect to how we can go ahead.
I will really appreciate a response from you.
Thanks a lot.
Best regards.
On 15 June 2016 at 09:31, Michael Owonibi <michael.owonibi at uni-jena.de<mailto:michael.owonibi at uni-jena.de>> wrote:
Dear Jan,
We would like to
1)Change the text under the description of data publisher to this below
"The Biodiversity Exploratories (BE) are a German Science Foundation
funded research project (DFG Priority Programme 1374). It has three
research Exploratories (areas) which serve as open research platform
for biodiversity and ecosystem research groups of Germany. The study
objective of the BE include the understanding of the relationship
between biodiversity of different taxa and levels, the role of land use
and management for biodiversity, and the role of biodiversity for
ecosystem processes. As such, many of the researchers collect
biodiversity-related datasets from three main areas in Germany, and
these data often contain species occurrence information"
2) Change the name of the Administrative Contact to Christiane Fischer
On a different topic - We have created link for each of our Darwin Core
Archive for each of our datasets, and we are not sure about how to
submit these links to GBIF. Can you please give us more information on
how to proceed?
Thanks a lot for your assistance.
On 6/14/2016 11:39 AM, helpdesk wrote:
> Dear Michael,
>
> Please send me the changes you wish to see on the publisher page and I will update it. There is no easy way for publishers to implement changes to the organization page in GBIF themselves.
>
> Best regards,
>
> Jan K. Legind
> Data manager, GBIF Secretariat
>
>
> -----Original Message-----
> From: Michael Owonibi [mailto:michael.owonibi at uni-jena.de<mailto:michael.owonibi at uni-jena.de>]
> Sent: 14. juni 2016 10:48
> To: helpdesk
> Cc: BExIS List
> Subject: Minor Corrections Needed on Our Data Publisher Page
>
> Dear Helpdesk,
>
>
> We are registered as data provider on GBIF, and our page can be found on http://www.gbif.org/publisher/541c2668-9391-4479-b90f-fe90b365f33b .
>
> There are a few typos on this page that we would like to correct, and we would like to know how we can go about this.
>
> Thanks
>
>
> --
> Michael Owonibi, PhD
> BExIS Data Manager
> Friedrich-Schiller-University
> Institut für Informatik
> Leutragraben 1, Jentower
> 07743 Jena
> Germany
> Phone.: +49(0)3641-946440<tel:%2B49%280%293641-946440>
> Web: http://fusion.cs.uni-jena.de/professur/about-us/team/michael-owonibi
>
--
Michael Owonibi, PhD
BExIS Data Manager
Friedrich-Schiller-University
Institut für Informatik
Leutragraben 1, Jentower
07743 Jena
Germany
Phone.: +49(0)3641-946440<tel:%2B49%280%293641-946440>
Web: http://fusion.cs.uni-jena.de/professur/about-us/team/michael-owonibi
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--
Michael Owonibi, PhD
BExIS Data Manager
Friedrich-Schiller-University
Institut für Informatik
Leutragraben 1, Jentower
07743 Jena
Germany
Phone.: +49(0)3641-946440
Web: http://fusion.cs.uni-jena.de/professur/about-us/team/michael-owonibi
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--
Andreas Ostrowski
Datenmanagement Biodiversitaets-Exploratorien
Friedrich-Schiller-Universität Jena
Institut für Informatik
Leutragraben 1, Jentower
07743 Jena
Tel.: ++ 49 3641 9 46431
E-Mail: andreas.ostrowski at uni-jena.de<mailto:andreas.ostrowski at uni-jena.de>
WWW: http://www.biodiversity-exploratories.de
--
--
Andreas Ostrowski
Datenmanagement Biodiversitaets-Exploratorien
Friedrich-Schiller-Universität Jena
Institut für Informatik
Leutragraben 1, Jentower
07743 Jena
Tel.: ++ 49 3641 9 46431
E-Mail: andreas.ostrowski at uni-jena.de<mailto:andreas.ostrowski at uni-jena.de>
WWW: http://www.biodiversity-exploratories.de
--
--
Andreas Ostrowski
Datenmanagement Biodiversitaets-Exploratorien
Friedrich-Schiller-Universität Jena
Institut für Informatik
Leutragraben 1, Jentower
07743 Jena
Tel.: ++ 49 3641 9 46431
E-Mail: andreas.ostrowski at uni-jena.de<mailto:andreas.ostrowski at uni-jena.de>
WWW: http://www.biodiversity-exploratories.de
--
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