RDF (or SHACL) Graph Editors?

[Michael DeBellis]

I've been doing some work with SHACL lately. A SHACL shape is just an RDF graph and I've been creating my shapes using Notepad++ which at least does things like balance brackets and parentheses. I was wondering are there any tools out there just for editing RDF graphs that are similar to Protege? Of course RDF isn't as powerful as OWL so I would expect the tool to be simpler but it would be nice to have something other than a text editor. 

Michael

[Ravi Sharma]

Michael 

I do not know if Gruff has anything

https://franz.com/agraph/support/documentation/current/gruff.html#TheGraphicalQueryView

Thanks.
Ravi
(Dr. Ravi Sharma)

MagicJack US 3133935264

India mobile 011 91 96366 58888

 

On Thu, Apr 29, 2021 at 9:55 AM Michael DeBellis <mdebe...@gmail.com> wrote:

I've been doing some work with SHACL lately. A SHACL shape is just an RDF graph and I've been creating my shapes using Notepad++ which at least does things like balance brackets and parentheses. I was wondering are there any tools out there just for editing RDF graphs that are similar to Protege? Of course RDF isn't as powerful as OWL so I would expect the tool to be simpler but it would be nice to have something other than a text editor. 

Michael

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[Steve Ray]

I sometimes use Visual Studio with the SHACL Language Server extension installed. It does syntax checking, autocompletion, various things...

The rest of the time I use TopBraid Composer (there's still a free version available...)

Steve

On Thu, Apr 29, 2021 at 9:55 AM Michael DeBellis <mdebe...@gmail.com> wrote:

I've been doing some work with SHACL lately. A SHACL shape is just an RDF graph and I've been creating my shapes using Notepad++ which at least does things like balance brackets and parentheses. I was wondering are there any tools out there just for editing RDF graphs that are similar to Protege? Of course RDF isn't as powerful as OWL so I would expect the tool to be simpler but it would be nice to have something other than a text editor. 

Michael

--

[Damion Dooley]

This isn't an RDF graph editor directly, but when it comes to RDF shapes as specifications, we've been looking at implementing the under-development LinkML as our platform for describing data specifications.  

https://docs.google.com/presentation/d/1jtV2vQhCwsGv_9fPplkG8ww1ru4V_JYyRGLAm2dxvdE/edit#slide=id.p

Developed for NCATS Translator and a number of other US projects, it promises to have staying power. It can hold/import specs in JSON, YAML, and RDF, and output to various schemas like OWL, Json schema, ShEx, GraphQL, and python, java code objects etc. is promised.  Its specs can be displayed in MKDocs documentation platform as is shown here: https://linkml.github.io/linkml-model/docs/ .

Damion

[Michael DeBellis]

Ravi, actually I've been using Gruff and it is pretty decent for editing these kinds of models. What I've been experimenting with is to start with a very basic model (e.g., instances of the sh:Shape class loaded with the data model I want to define constraints on) and then use the editing capabilities in Gruff to add property values to the basic RDF graphs I start with and then save those graphs and it works pretty well. The reasons I would like something different are:

1) Gruff really wasn't designed for this so it's not the ideal tool. Also, it has so many features it takes a while to get used to it and get really productive. 

2) I'm thinking of putting together some more tutorials on SHACL and I want something new users can use that is easier than just using Notepad++  which is what I mostly use now. Running AllegroGraph (which is required for Gruff) takes a fair amount of work to install. I mean given what you are getting: a very fast graph database with full support for transactions and many other useful features it is well worth the effort but my point is that for people who just want to create SHACL graphs it is more work than they probably want. I would like to find a lightweight tool that can do it. I've been experimenting with some JSON-LD tools. That's the kind of thing I would ideally like. A lightweight tool that doesn't require you have a Linux server (or a virtual one using Docker as I do) the way AllegroGraph does and that still gives you something like a hierarchical editing tool rather than just one based on text. 

Michael

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[Michael DeBellis]

" I sometimes use Visual Studio with the SHACL Language Server extension installed"

Steve, thanks for that pointer. I didn't realize there was anything like that in Visual Studio. That sounds like it might be what I need. Thanks,

Michael

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[Michael DeBellis]

Damion, that also looks very interesting, I will check it out, thanks.

Michael

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[Michael DeBellis]

Steve, I'm starting to download Visual Studio. There are a lot of components. Do you by chance know which specific ones are needed for the SHACL Language Server extension? I'm guessing I should load the following: ASP.net and web development, .NET desktop development, Universal Windows platform development, and from "Other Toolsets": Data storage and processing, data science and analytical applications. Also, I thought I would try their Python development component although I think I'll probably stick with IDLE but it's worth a look. Those are the ones I'm downloading now, there were several others that looked like they might possibly be relevant, if there are specific components I'm missing or components from this list that I should focus on please let me know. I haven't used Visual Studio in a really long time so I'm not familiar with it. thanks again for the pointer.

Michael

On Fri, Apr 30, 2021 at 5:21 AM Steve Ray <st...@steveray.com> wrote:

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[bruces...@cox.net]

Great slides in this presentation – website very good looking.   https://yosemiteproject.org/

 

I like the breadth of your stated mission: “Semantic interoperability of all structured healthcare information”

 

“Make it all work together”.  Reminds me a bit of the online healthcare system in Santa Barbara called “My Chart” – which links many healthcare facilities and departments together, helps organize interdepartmental coordination, billing and patient scheduling, etc.

 

***

 

My own motivations are essentially humanitarian – which no doubt includes healthcare.

 

I might want to describe the “domain” of my own interest as something like “the optimization of ethical cybernetic democracy” – presuming or anticipating that something like this is feasible and desirable and perhaps essential.  I personally suspect it’s the only thing that will work under our converging collective load, along with its dangerous fragmentation and suspicion.

 

In my project, I’m talking about the left side of this equation: Standardize the Standards.  I’m looking at basic things like the definition of number and dimension and “hierarchical level”.  Is there “one best way” to do these things?  Can we build linkage across these levels, using a consistent framework that connects the continuum with all systems of categories that are grounded in (defined by values in) the continuum?  I am exploring the idea of “synthetic dimensionality” as a way to build that bridge.

 

On the right side of your formula, you cite “Crowdsource Translations”.  Hmm – very interesting.  How would that work?  “Statistical aggregation of common definitions” ?

 

I wonder if some method of crowdsourcing could help overcome the common rigidity of traditional formal semantic ontology definitions – by defining some allowances for context-specific interpretations (??)

 

To fully generalize semantic ontology, that’s really a problem that must be solved.  Otherwise, it seems to me, we are accepting an inevitable fragmentation – an attitude I doubt will have a long life-span in an era of increasing globalization and network interconnections – while seawater levels continue to rise and water tables are sinking….

 

Thanks.

 

Bruce Schuman

Santa Barbara CA USA

bruces...@cox.net / 805-705-9174

www.origin.org / www.integralontology.net

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[Damion Dooley]

I should clarify - I'm not part of the Yosemite project. I am part of a 20 person Public Health Bioinformatics Group at SFU focusing on bioinformatics on the one side, and data harmonization on the other, with an overall One Health and public health mandate.  We've mainly been operating within the OBO Foundry family of ontologies (LinkML is lead by some in that community), and indeed I have turned to that "encyclopedia of domain specific ontologies" model as the only way to maintain my sanity in a sea of classes, instances, and object and data properties!  (I especially advocate for a core of shared generic relations across domain ontologies and their components = the glue that holds data together).

My lab increasingly works with research, government and industry partners, and the pressure is on to deliver that ontology-driven data harmonization future the semantic web community has (er!) been anticipating for a number of years.  Our lab is testing out LinkML, to use in software like our DataHarmonizer browser based spreadsheet tabular data management software which aims to be populated entirely with ontology driven vocabulary.  We are trying these specifications directly in OWL, with an output to JSON and YAML formats, and having DataHarmonizer operate directly off of the JSON one.  The end user experience however must barely show a trace of ontology abstraction and complexity. In another direction we will revamp our GEEM software to work off of the LinkML compatible specification (managed in Protege) to yield data management forms such as this Draft Sequence Repository Contextual Data Standard (takes a few seconds to load).  I acknowledge however that there are a number of other RDF/ schema.org compatible vocabularies (e.g. GS1) for us to integrate with. It seems LinkML is enabling this flexibility of vocabulary reuse.

[Ravi Sharma]

In the past I used to work with Visual Studio and SQLServer RDBMS but separately with SPARQL.

This is for serious developers I realize.

Thanks.
Ravi
(Dr. Ravi Sharma)

MagicJack US 3133935264

India mobile 011 91 96366 58888

 

On Fri, Apr 30, 2021 at 1:22 PM Damion Dooley <damion...@gmail.com> wrote:

I should clarify - I'm not part of the Yosemite project. I am part of a 20 person Public Health Bioinformatics Group at SFU focusing on bioinformatics on the one side, and data harmonization on the other, with an overall One Health and public health mandate.  We've mainly been operating within the OBO Foundry family of ontologies (LinkML is lead by some in that community), and indeed I have turned to that "encyclopedia of domain specific ontologies" model as the only way to maintain my sanity in a sea of classes, instances, and object and data properties!  (I especially advocate for a core of shared generic relations across domain ontologies and their components = the glue that holds data together).

My lab increasingly works with research, government and industry partners, and the pressure is on to deliver that ontology-driven data harmonization future the semantic web community has (er!) been anticipating for a number of years.  Our lab is testing out LinkML, to use in software like our DataHarmonizer browser based spreadsheet tabular data management software which aims to be populated entirely with ontology driven vocabulary.  We are trying these specifications directly in OWL, with an output to JSON and YAML formats, and having DataHarmonizer operate directly off of the JSON one.  The end user experience however must barely show a trace of ontology abstraction and complexity. In another direction we will revamp our GEEM software to work off of the LinkML compatible specification (managed in Protege) to yield data management forms such as this Draft Sequence Repository Contextual Data Standard (takes a few seconds to load).  I acknowledge however that there are a number of other RDF/ schema.org compatible vocabularies (e.g. GS1) for us to integrate with. It seems LinkML is enabling this flexibility of vocabulary reuse.

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[Michael DeBellis]

Bruce, on Yosemite:I'm curious why RDF rather than OWL? Also, how does what Yosemite is doing differ from (or fit with/compliment) SNOMED? 

Michael

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[Steve Ray]

Hmm, it has been a while since I installed it, but as I recall I just use the vanilla, default Visual Studio. Then I went to "preferences" and searched the marketplace for the SHACL language server (there are language servers for many many languages), and it installed with a single click.

VS has really evolved over the past few years, and is the editor of choice for many people I am in touch with. Also, by the way, GitHub is beta-testing Codespaces, which is basically a web-resident version of Visual Studio integrated into the GitHub environment. Looks interesting. Eventually they say they will charge for compute time and storage when using it though.

Steve

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[Michael DeBellis]

Thanks again Steve. The last time I used Visual Studio Bill Gates was still CEO of Microsoft! But I remember even then it had a pretty impressive environment. Looking forward to using it again. 

Michael

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