[semantics-public] [x3d-public] X3D Semantic Web Working Group: chapter, talk, Tika and ROBOT tools, COVID/Coronavirus models

Mon Mar 23 13:21:59 PDT 2020

Don, the microscope images of covid are on the cdc site, search site:cdc.gov.
  Also the popular renderings as images are there too.

I can probably duplicate the research if that’s required.

I would first search for the real images, then I assume the rendered ones
are based on that.   Believe it or not, there are only 2 microscopic
images!   There are additional images for corona.

John

On Mon, Mar 23, 2020 at 12:51 PM Don Brutzman <brutzman at nps.edu> wrote:

> Attendees: Jakub Flotyński and Don Brutzman.
>
> Using the Web3D Consortium zoom to share desktops is a really effective
> way to collaborate.
>
> ---
>
> 1. /Publication/.  Jakub is working on book chapter for IGI, 28 pages,
> finishing the references section - 122 so far!
>
> [1] Recent Advances in Web3D Semantic Modeling,
>      Jakub Flotyński,Athanasios Malamos,Don Brutzman,Felix G.
> Hamza-Lup,Nicholas Polys,Leslie F. Sikos,Krzysztof Walczak.
>
> ---
>
> 2. /Presentation/.  Don gave a presentation 12 days ago:
>
> [2] X3D Ontology for Semantic Web was presented as a "Lightning Talk"
>      at US Semantic Technologies Symposium (US2TS).
>      Raleigh North Carolina, 9-11 March 2020.
>      https://us2ts.org
>      https://us2ts.org/lightning-talks#x3dontology
>      https://www.web3d.org/x3d/content/semantics/semantics.html
>
> ---
>
> 3. /Metadata tool./  As described on mailing list, Apache Tika looks
> interesting.  Once we have our X3D metadata -> triple patterns established,
> this is a good opportunity for mainstreaming such conversions.
>
> [3.1] Apache Tika - a content analysis toolkit
>        https://tika.apache.org/
>
> "The Apache Tika™ toolkit detects and extracts metadata and text from over
> a thousand different file types (such as PPT, XLS, and PDF). All of these
> file types can be parsed through a single interface, making Tika useful for
> search engine indexing, content analysis, translation, and much more."
>
> [3.2] [semantics-public] Fwd: [ANNOUNCE] Apache Tika 1.24 released
>
> https://web3d.org/pipermail/semantics-public_web3d.org/2020-March/000089.html
>
> In comparison to Data Format Description Language (DFDL), which is a
> general-purpose approach to regularizing the parsing of semi-structured
> text, Tika appears instead to be focused on structured metadata within
> structured document formats.  Experimentation in the coming months should
> reveal these relationships more precisely.
>
> [3.3] Apache Daffodil (incubating)
>        https://daffodil.apache.org
>
> "Open-source implementation of the Data Format Description Language to
> convert between fixed format data and XML/JSON."
>
> ---
>
> 4. There were a lot of references to Semantic Web Working Group efforts in
> last week's X3D Working Group meeting.  Recommended reading.
>
> [4.1] [x3d-public] X3D minutes 20 MAR 2020: COVID, X3D Ontology, PBR, Xj3D,
>        Blender and MeshLab, CollisionCollection, IFS in CADInterchange,
> CORS
>
> https://web3d.org/pipermail/x3d-public_web3d.org/2020-March/011913.html
>
> It is interesting to think that as we establish metadata patterns for X3D,
> we might integrate their use and production in other 3D and XML authoring
> tool chains that include Blender, MeshLab, XMLSpy and other products.
>
> ---
>
> 5. /COVID model for conversion using X3D Ontology?/
>
> > NIH COVID models: Nicholas notes that multiple assets are now available
> in X3D and VRML.
> >
> > [2.2] COVID
> >>
> https://3dprint.nih.gov/discover?terms=covid&field_model_category_tag_tid%5B%5D=94
> >
> > [2.3] Corona
> >>
> https://3dprint.nih.gov/discover?terms=corona&field_model_category_tag_tid%5B%5D=94
>
> We decided to try and convert such a model to Turtle .ttl during this
> call, but the hard part was choosing one!  For example:
>
> [5.1] PanDDA analysis group deposition --
>        Crystal Structure of COVID-19 main protease in complex with
> Z1220452176
>        Submitted by: Nicholas Polys
>        https://3dprint.nih.gov/discover/3dpx-013158
>
> [5.2] 6Y84 COVID-19 main protease with unliganded active site
>        (2019-nCoV, coronavirus disease 2019, SARS-CoV-2)
>        Submitted by: Nicholas Polys
>        https://3dprint.nih.gov/discover/3DPX-013157
>
> [5.3] Twitter by @Web3DConsortium
>        Structure SARS coronavirus @SciMeg @NIH #X3D #VRML main protease
>        by Dr. Meghan McCarthy
>        https://twitter.com/Web3DConsortium/status/1230166552235790336
>
> [5.4] Structure of SARS coronavirus main protease in complex with the
> alpha-ketoamide
>        Submitted by: Meghan McCarthy
>        https://3dprint.nih.gov/discover/3dpx-012875
>
> [5.5] TurboSquid: Coronavirus 3D Models
>        https://www.turbosquid.com/3d-model/coronavirus
>        [see attached image... wow]
>
> we kept looking for one that looks like public renditions of the overall
> coronavirus, with little success.
>
> we spent a lot of time search for such models.  other than NIH, most
> models cost money (somewhat surprisingly).  continued searching...
>
> [5.6] What 3D printing a coronavirus taught me about DFAM and rapid
> prototyping
>        by Shuvom Ghose, 19 Feb 2020
>
> https://grabcad.com/tutorials/what-3d-printing-a-coronavirus-taught-me-about-dfam-and-rapid-prototyping
>
> Outstanding tutorial!  Highly recommended.  Couldn't find the model
> though... does anyone else see it there?
>
> So still need to "pick" a model or two for inclusion.
>
> Request to x3d-public: what is the "best" free model to convert into X3D
> for the archives?
>
> ---
>
> 6. /ROBOT is an OBO Tool/
>
> Problem:  ARQ is an excellent command-line tool for queries but it does
> not have a reasoner capability built in.
>
> ROBOT allows performing SPARQL queries with a reasoner included that makes
> inferences on the ontology.  We need that for deeper X3D Ontology queries.
>
> [6.1] X3D Ontology for Semantic Web: Queries
>        https://www.web3d.org/x3d/content/semantics/semantics.html#Queries
>
> At US2TS saw a very impressive presentation and capability as follows.
>
> [6.2] ROBOT is an OBO Tool
>        https://robot.obolibrary.org
>
> [6.3] ROBOT Tutorial
>        https://github.com/ontodev/robot-tutorial
>        https://ontodev.github.io/robot-tutorial/#/title-slide
>
> [6.4] ROBOT query
>        https://robot.obolibrary.org/query
>
> [6.5] "ROBOT: A Tool for Automating Ontology Workflows"
>        by Rebecca C. Jackson1, James P. Balhoff, Eric Douglass, Nomi L.
> Harris, Christopher J. Mungall and James A. Overton
>        BMC Bioinformatics (2019) 20:407,
> https://doi.org/10.1186/s12859-019-3002-3
>        https://rdcu.be/bMnHT
>
> Don will continue working to integrate this capability into our X3D
> Ontology build.
>
> ---
>
> 7. X3D Ontology and all examples are now building under Java OpenJDK 14.
> Implementation details match yesterday's X3DJSAIL announcement.
>
> [7.1] [x3d-public] X3DJSAIL updated to Java OpenJDK 14
>
> https://web3d.org/pipermail/x3d-public_web3d.org/2020-March/011918.html
>
> Assuming continued progress on these topics, next week we will likely dive
> into metadata mappings.
>
> Thanks for your time today Jakub, see you next next week at regular time
> (0800 pacific).  Other participants welcome.
>
> Having fun with X3D Semantic Web!  8)
>
> all the best, Don
> --
> Don Brutzman  Naval Postgraduate School, Code USW/Br
> brutzman at nps.edu
> Watkins 270,  MOVES Institute, Monterey CA 93943-5000 USA   +1.831.656.2149
> X3D graphics, virtual worlds, navy robotics
> http://faculty.nps.edu/brutzman
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