[esip-semantictech] Documentation for the Semantic Portal

Tue Mar 7 15:48:54 EST 2017

Thanks John. Clarification always helps, so I appreciate it.
Lewis

Dr. Lewis John McGibbney Ph.D., B.Sc.
Data Scientist II
Computer Science for Data Intensive Applications Group 398M
Jet Propulsion Laboratory
California Institute of Technology
4800 Oak Grove Drive
Pasadena, California 91109-8099
Mail Stop : 158-256C
Tel:  (+1) (818)-393-7402
Cell: (+1) (626)-487-3476
Fax:  (+1) (818)-393-1190
Email: lewis.j.mcgibbney at jpl.nasa.gov

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From: John Graybeal <jbgraybeal at mindspring.com>
Date: Tuesday, March 7, 2017 at 12:14 PM
To: "Mcgibbney, Lewis J (398M)" <Lewis.J.Mcgibbney at jpl.nasa.gov>
Cc: "Michael N. Huhns Ph.D." <HUHNS at mailbox.sc.edu>, "esip-semanticweb at lists.esipfed.org" <esip-semanticweb at lists.esipfed.org>, Line Pouchard <linepouchard at gmail.com>
Subject: Re: [esip-semantictech] Documentation for the Semantic Portal

Hi Lewis,

All API calls to BioPortal require an API key. What may be making you think otherwise is that the same URL entered into a browser may return a submission, because the API key is saved in the browser’s configuration. (I forget the details of that, it just magically works for me. I can find you more information on the details if you want.)

So although many of the examples don’t include the API key, in fact it is required. This page has a basic outline (see the first item under Common Parameters): http://data.bioontology.org/documentation#nav_usage

Feel free to make such requests to the support list for BioPortal, support at bioontology.org<mailto:support at bioontology.org>.

John

---------------------------------------
John Graybeal
jbgraybeal at mindspring.com<mailto:jbgraybeal at mindspring.com>

On Mar 7, 2017, at 12:00, Mcgibbney, Lewis J (398M) via esip-semanticweb <esip-semanticweb at lists.esipfed.org<mailto:esip-semanticweb at lists.esipfed.org>> wrote:

Hi Folks,
Can anyone confirm if the following documentation applies to the Semantic Portal?
http://data.bioontology.org/documentation#OntologySubmission
I’m trying to GET a response from our portal as follows

REQUEST: curl http://semanticportal.esipfed.org/submissions
RESPONSE: The page you are looking for could not be found | NCBO BioPortal

REQUEST: curl http://semanticportal.esipfed.org/ontologies/GCMD-DIF/submissions?display=submissionId,version
RESPONSE: The page you are looking for could not be found | NCBO BioPortal

REQUEST: curl http://semanticportal.esipfed.org/ontologies/:GCMD-DIF/submissions?display=submissionId,version
RESPONSE: The page you are looking for could not be found | NCBO BioPortal

I’m pretty sure I should not require use of my ‘apikey’ simply for making a GET request. If someone could let me know or provide an example it would be appreciated.
Thank you
Lewis

Dr. Lewis John McGibbney Ph.D., B.Sc.
Data Scientist II
Computer Science for Data Intensive Applications Group 398M
Jet Propulsion Laboratory
California Institute of Technology
4800 Oak Grove Drive
Pasadena, California 91109-8099
Mail Stop : 158-256C
Tel:  (+1) (818)-393-7402
Cell: (+1) (626)-487-3476
Fax:  (+1) (818)-393-1190
Email: lewis.j.mcgibbney at jpl.nasa.gov<mailto:lewis.j.mcgibbney at jpl.nasa.gov>

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 Dare Mighty Things

From: "HUHNS, MICHAEL" <HUHNS at mailbox.sc.edu<mailto:HUHNS at mailbox.sc.edu>>
Date: Monday, February 6, 2017 at 2:29 PM
To: "Mcgibbney, Lewis J (398M)" <Lewis.J.Mcgibbney at jpl.nasa.gov<mailto:Lewis.J.Mcgibbney at jpl.nasa.gov>>, "esip-semanticweb at lists.esipfed.org<mailto:esip-semanticweb at lists.esipfed.org>" <esip-semanticweb at lists.esipfed.org<mailto:esip-semanticweb at lists.esipfed.org>>
Cc: Line Pouchard <linepouchard at gmail.com<mailto:linepouchard at gmail.com>>
Subject: RE: Documentation for the Semantic Portal

Hi Lewis,

I can answer some of your questions. The code is developed by the NCBO project, which is being directed now by John Graybeal. The developers occasionally roll up all needed software packages with the latest patched software into an image (a “virtual appliance”) that can be installed on a web server. For a while it ran on one of my servers at the U. of South Carolina, but now we run it as a service on the ECITE server. After installation, we modify it cosmetically to use the ESIP logo and earth science terminology and upload a small number of ontologies.

The last time NCBO created a virtual appliance was ~2 years ago, which is why our version 2.4 is so far behind NCBO 4.29 and has many unpatched errors. John might know when the next virtual appliance will be created.

The Semantic Portal code is basically the NCBO code on the GitHub Repository, which is public.

There is an NCBO-maintained wiki with documentation for working with the Portal and the virtual appliance at
https://www.bioontology.org/wiki/index.php/Main_Page

Cheers,
Mike

From: esip-semanticweb [mailto:esip-semanticweb-bounces at lists.esipfed.org] On Behalf Of Mcgibbney, Lewis J (398M) via esip-semanticweb
Sent: Friday, February 03, 2017 10:09 PM
To: esip-semanticweb at lists.esipfed.org<mailto:esip-semanticweb at lists.esipfed.org>
Subject: [esip-semantictech] Documentation for the Semantic Portal

Hi Line/John,

Can one of you please point me to the documentation for interacting with the ontology server [0]?
I acknowledge that John, you mentioned that most of the documentation is managed over on the NCBO website, but if we has a link here it would be most helpful.
I’ve also found a bunch of code on the NCBO Github repository such as [1] which details how to interact with the NCBO service. I am currently evaluating whether this will work when I attempt to programmatically interact with [0].

Another question I have, where is the Semantic Portal code stored? Is it public?

Finally, the Semantic Portal states version 2.4, and bioportal is ahead at current release 4.29 (October 2016). Is there any relationship between the two? Is the former meant to shadow the latter?

Thanks very much in advance,
Lewis

[0] http://semanticportal.esipfed.org/ontologies
[1] https://github.com/ncbo/ncbo_rest_sample_code

Dr. Lewis John McGibbney Ph.D., B.Sc.
Data Scientist II
Computer Science for Data Intensive Applications Group 398M
Jet Propulsion Laboratory
California Institute of Technology
4800 Oak Grove Drive
Pasadena, California 91109-8099
Mail Stop : 158-256C
Tel:  (+1) (818)-393-7402
Cell: (+1) (626)-487-3476
Fax:  (+1) (818)-393-1190
Email: lewis.j.mcgibbney at jpl.nasa.gov<mailto:lewis.j.mcgibbney at jpl.nasa.gov>

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