[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
Mi Jul 6 16:41:16 CEST 2016
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
>
> _______________________________________________
> bexis mailing list
> bexis at listserv.uni-jena.de <mailto:bexis at listserv.uni-jena.de>
> https://lserv.uni-jena.de/mailman/listinfo/bexis
>
>
>
> --
>
> 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
>
>
>
>
>
> _______________________________________________
>
> bexis mailing list
>
> bexis at listserv.uni-jena.de <mailto:bexis at listserv.uni-jena.de>
>
> https://lserv.uni-jena.de/mailman/listinfo/bexis
>
>
>
>
> --
>
> 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
WWW: http://www.biodiversity-exploratories.de
--
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