[esip-semantictech] Documentation for the Semantic Portal

Fri Mar 10 12:55:04 EST 2017

Thanks for the context John.

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

           [cid:image001.png at 01D29984.64E90010]

 Dare Mighty Things

From: John Graybeal <jbgraybeal at mindspring.com>
Date: Friday, March 10, 2017 at 9:50 AM
To: "HUHNS, MICHAEL" <HUHNS at mailbox.sc.edu>
Cc: "Mcgibbney, Lewis J (398M)" <Lewis.J.Mcgibbney at jpl.nasa.gov>, "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

Thank you Michael for providing the information on the Virtual Appliance, somehow I missed that bit of the thread earlier.  In case it helps, a clarification of our numbering: The "Virtual Appliance Release 2.4" is at version 4.15 of the BioPortal software, which was released March 2015 (but not separately documented in the BioPortal Release Notes [1]. (Sorry, I know the numbering is confusing, to me too.)

While the distribution of the Virtual Appliance does include source code, I imagine the ESIP deployment requires an account on the Linux machine to view that. Of course, anyone can request their own copy of the Virtual Appliance[2], and look at the source code of the distributed version that way, too.

An open question of community interest is the schedule for the next release of the NCBO virtual appliance.

The good news is that we at NCBO[3] see this as one of our highest priorities at this point. (Especially now that the system deployed at Stanford (https://bioportal.bioontology.org) has such a nice interface. Check it out!) We have recently started the preparations that are required, which will take some time in this case.

The bad news is that we rely on our Virtual Appliance creation specialist, who is quite heavily in demand right now: in addition to work-related matters, he is looking forward to a 6-week leave at the end of the month. Good news for him, but it will inevitably delay the VA work.

So we have this update scheduled, but it won’t be released very soon. Happily, the functional lag in the Virtual Appliance is unlikely to affect the fundamental behaviors of the system undergoing ESIP testing. While the new landing page look and feel is different, and there are definitely fixes and improvements, I expect all the core services in the Virtual Appliance to work the same way, with the same reliability, given the relatively low traffic on the ESIP Semantic Repository site. (You can review the BioPortal Release Notes to see the detailed changes for yourself.)

John

[1] BioPortal Virtual Appliance Release Notes: https://www.bioontology.org/wiki/index.php/BioPortal_Release_Notes
[2] To request your own copy, see https://www.bioontology.org/wiki/index.php/Category:NCBO_Virtual_Appliance
[3] NCBO = National Center for Biomedical Ontologies, the NIH funding center that originated BioPortal development at Stanford.

====================
John Graybeal
Technical Program Manager
NCBO BioPortal
Stanford Center for Biomedical Informatics Research

On Feb 6, 2017, at 2:29 PM, HUHNS, MICHAEL via esip-semanticweb <esip-semanticweb at lists.esipfed.org<mailto:esip-semanticweb at lists.esipfed.org>> wrote:

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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 Dare Mighty Things
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John Graybeal
jbgraybeal at mindspring.com<mailto:jbgraybeal at mindspring.com>

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