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

[Don Brutzman]

Attendees: Jakub Flotyński and Don Brutzman.

Using the Web3D Consortium zoom to share desktops is a really effective way to collaborate.

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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.

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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

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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."

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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.

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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?

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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.

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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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