Thanks for the quick reply. I feel like there is a misunderstanding here. I didn't modify the system file, I created my own shacl file and built my own namespace. I only modified the source code for one property which is a function I believe.
在 2020年7月12日星期日 UTC-5下午10:24:10，Irene Polikoff写道： > > > Please see below > > On Jul 12, 2020, at 10:42 PM, Emily Zhang <zxy10...@gmail.com > <javascript:>> wrote: > > Hi Irene, > I was trying to learn the key concepts while managing to finish this task. > I've read all the tutorials I could find before I start posting on this > forum. I wish there are documents that explain how TopBraid Composer works > in a more general way. For example, you said "I should never modify > shacl.ttl", I guess I won't learn that from any tutorials or classes. Even > if I am familiar with all the RDF concepts, I still wouldn't know that. > > > Yes, I believe you would. A general best practice and convention with RDF > is that you do not modify other people’s namespaces and files. You create > your own. > > In case of SHACL.ttl, if you looked at its description, you would see "This > vocabulary defines terms used in SHACL, the W3C Shapes Constraint Language." > > This is a standard ontology of SHACL language elements. It would be quite > peculiar to think that one should or even could put their own domain > specific shapes into it. > > Further, certain files in the TBC namespace are locked - because they are > system files. This includes shacl.ttl and a number of others. Users should > not be unlocking locked files and changing them. > > And when you create new files you should not put them into projects that > are pre-built - those that are in the workspace after install. You should > create your own project and use it for your artifacts. > > And I don't know anyone else who has experience with TopBraid Composer. If > you think I need other training, please point me to. > > > Many thanks, > Emily > > 在 2020年7月9日星期四 UTC-5上午8:44:21，Irene Polikoff写道： >> >> Hi Emily, >> >> There are too many misunderstandings and things to correct. We will not >> be able to help you through this on the mailing list. The learning gap is >> too large. >> >> My recommendation, if you want to continue with this, is to go back to >> basics and do this step by step - learn RDF, including key concepts and >> terminology, learn how to work in TopBraid Composer, including managing >> graphs, understand modeling, etc. For example, you should never modify >> shacl.ttl. All the documentation I have been pointing you to is readily >> available - both on the web and in TBC itself under Help. You need to take >> some time to study these topics, go through tutorials, etc. If you are at a >> university, get help from your professors. If you are doing this from work, >> try to find a training class. >> >> Then, may be you can try to progress to more technically advanced topics >> like SHACL rules. >> >> Regards, >> >> Irene >> >> On Jul 9, 2020, at 12:55 AM, Emily Zhang <zxy10...@gmail.com> wrote: >> >> Hi Irene, >> >> Thanks for the reply! The documents were really helpful! I think I >> understand the concept "graph" now. I've attached my answers to some of >> your questions below. >> >> 1. What do you mean by “under”. How can an instance be under a property? >> So clearly, property shouldn't have instance. I wasn't sure what is the >> relationship between "diagnosis" and "melanoma" when you give this >> comment: "create a new property e.g., :diagnosis and infer :diagnosis >> :Melanoma". Is "melanoma" a label of the property "diagnosis"? >> >> >> 2. How do your data triples look like? >> >> Is your data graph separate from the graph containing your model and the >> rule or are they together? If they are separate, does your data graph >> owl:imports your shapes graph? >> >> https://topbraidcomposer.org/html/Imports_Panel.htm >> <https://www.google.com/url?q=https%3A%2F%2Ftopbraidcomposer.org%2Fhtml%2FImports_Panel.htm&sa=D&sntz=1&usg=AFQjCNGJPp2YFNPQD7OfwXFtE3gMBNJGug> >> >> By "data triples", my understanding is the classes, properties I defined >> in a graph, which in my case in "shacl.ttl". I've attached a screenshot of >> all the classes, properties I've created so far. >> And they are all in the same graph. My rule was defined in the "source >> code" of "patient" class. >> >> <Screenshot 2020-07-08 23.47.20.png> >> Appreciate a lot! >> Best, >> Emily >> >> 在 2020年7月7日星期二 UTC-5下午11:29:14，Irene Polikoff写道： >>> >>> >>> >>> On Jul 8, 2020, at 12:04 AM, Emily Zhang <zxy10...@gmail.com> wrote: >>> >>> Hi Irene, >>> Great suggestions on creating a property for "Diagnosis". I've done that >>> but I am not exactly sure: 1) If I want to infer a patient has Melanoma, >>> should Melanoma be an instance under the property "Diagnosis”? >>> >>> >>> What do you mean by “under”. How can an instance be under a property? >>> >>> 2) You mentioned "I need to run it on a graph that has data and it must >>> include your model and rules.", I am not really familiar with the concept >>> "graph" in the Top Braid Composer. >>> >>> >>> https://topbraidcomposer.org/html/NamedGraphsAndBaseURIs.htm >>> >>> 3) For the inferred results, since you mentioned I don't have to use >>> tosh:value for sparql in this case, I was expecting to "run inference" >>> against the instance of "Patient" and got a returned label for " Melanoma"? >>> But there was still nothing returned. The inference run successfully, >>> >>> >>> Not sure what is going wrong for you. >>> >>> 4) I even tried to add sparql query attached below, the "execute SPARQL" >>> button was grey somehow. >>> Here is the source code I used: >>> >>> p3point_validation:Patient >>> >>> rdf:type owl:Class ; >>> >>> rdf:type sh:NodeShape ; >>> >>> rdfs:subClassOf rdfs:Resource ; >>> >>> sh:rule [ >>> >>> rdf:type sh:TripleRule ; >>> >>> sh:condition [ >>> >>> sh:property [ >>> >>> sh:path < >>> http://example.org/3point_validation#Diagnosis:Melanoma> ; >>> >>> sh:in ( >>> >>> p3point_validation:Atypical >>> >>> p3point_validation:Asymmetry >>> >>> p3point_validation:Blue_white_structure >>> >>> ) ; >>> >>> sh:maxCount 3 ; >>> >>> sh:minCount 2 ; >>> >>> ] ; >>> >>> ] ; >>> >>> sh:object p3point_validation:Melanoma ; >>> >>> sh:predicate rdf:type ; >>> >>> sh:subject sh:this ; >>> >>> ] ; >>> >>> . >>> >>> >>> How do your data triples look like? >>> >>> Is your data graph separate from the graph containing your model and the >>> rule or are they together? If they are separate, does your data graph >>> owl:imports your shapes graph? >>> >>> https://topbraidcomposer.org/html/Imports_Panel.htm >>> >>> Here is the SPARQL query: >>> >>> *SELECT* * >>> >>> *WHERE* { >>> >>> ?Patient a schema: Patient . >>> >>> (?Patient schema: Diagnosis) *tosh:values* ?Diagnosis . >>> >>> } >>> >>> >>> Appreciate a lot! >>> >>> Best, >>> >>> Emily >>> 在 2020年6月30日星期二 UTC-5下午5:34:47，Irene Polikoff写道： >>>> >>>> Yes, if you are in Composer, then clicking on Run Inferencing would >>>> normally run SHACL rules. You will need to run it on a graph that has data >>>> and it must include your model and rules. >>>> >>>> I do not know if Composer will run Property Value rules when Run >>>> Inferencing is pressed. Holger will know. >>>> >>>> The whole point with Property Value rules is that values are calculated >>>> dynamically at query time, they are not stored any where. When you press >>>> Run Inferencing, however, inferred triples actually get materialized in a >>>> graph. >>>> >>>> The page I sent you has a section entitled *Use of Inferred Values >>>> using SPARQL*. This is for dynamic inferencing. >>>> >>>> If you Run Inferencing and get triples persisted/materialized, then you >>>> can query for them as you would for any other triple - nothing special is >>>> required. >>>> >>>> On Jun 30, 2020, at 5:47 PM, Emily Zhang <zxy10...@gmail.com> wrote: >>>> >>>> Thanks, Irene! It's a great suggestion to create a new property for >>>> diagnosis:Melanoma. I will try to add sh:values for the new property. Just >>>> to clarify, I was using TopBraid Composer instead of EDG, and >>>> according to the tutorial, I should "press the Run Inferences button >>>> to materialize the inferences." >>>> For the materials you've provided so far, I've only seen the example >>>> GraphQL query to fetch the results. But I guess that's okay since I found >>>> another type of file in composer that I can create which is >>>> "GraphQL/SHACL" >>>> file. I could try to move my source code, write a GraphQL to query the >>>> results and press the Run Inferences button. Hopefully I can get the >>>> returned label "Melanoma" for that "patient". >>>> >>>> >>>> 在 2020年6月30日星期二 UTC-5下午1:10:42，Irene Polikoff写道： >>>>> >>>>> Emily, >>>>> >>>>> If you have a shape like this >>>>> >>>>> p3point_validation:Patient a owl:Class, sh:NodeShape >>>>>> sh:rule [ >>>>>> a sh:TripleRule ; >>>>>> sh:subject sh:this; >>>>>> sh:predicate rdf:type ; >>>>>> sh:objectp3point_validation:Melanoma; >>>>>> >>>>> sh:condition [ >>>>>> sh:property [ >>>>>> >>>>>> sh:path p3point_validation:point_dermfeatures ; >>>>>> >>>>>> sh:in ( >>>>>> >>>>>> p3point_validation:Atypical >>>>>> >>>>>> p3point_validation:Asymmetry >>>>>> >>>>>> p3point_validation:Blue_white_structure >>>>>> >>>>>> ) ; >>>>>> >>>>>> sh:minCount 2 ; >>>>>> >>>>>> ] ; >>>>>> ] >>>>>> ] >>>>>> >>>>> >>>>> >>>>> And you have an instance of p3point_validation:Patient with some of >>>>> the listed values for the p3point_validation:point_dermfeatures property, >>>>> you will get this inference - provided that the patient has at least 2 >>>>> values for the property. >>>>> >>>>> I do not understand what you meant by "it only provided examples for >>>>> the EDG version”. EDG version of what? >>>>> >>>>> EDG performs these inferences so yes, everything you see is for EDG. >>>>> >>>>> How are you running the inferences? You need to go to the Transform >>>>> tab in EDG to execute. >>>>> >>>>> If you wanting to invoke inference execution programmatically, then, >>>>> as explained in the slides, you need to script it. You will need to write >>>>> a >>>>> script that will call the SPARQLMotion module - again, explained in the >>>>> slides. This would be either SWP or SPARQLMotion script, but to do so, >>>>> you >>>>> will need to get familiar with these scripting technologies and it will >>>>> take you some time. I doubt that we will be able to get you >>>>> successfully through this learning curve just by using this mailing list. >>>>> It will need you to take some training/mentoring. >>>>> >>>>> GraphQL example in the slides was to show that if you are using >>>>> sh:values to infer property values, a dynamically inferred value of a >>>>> property will be available to the GraphQL query. Sh:values inferences get >>>>> computed on the fly and they do not need any triggering. For your >>>>> example, >>>>> however, we are not using sh:values. So, this is irrelevant to >>>>> your particular example. >>>>> >>>>> Inferred values will be available to SPARQL queries as well. But >>>>> again, this is unconnected to what you are currently trying to accomplish. >>>>> >>>>> One reason we are not using sh:values for your example is that you are >>>>> trying to infer the type of a resource. A property backed by sh:values >>>>> rule >>>>> is protected from edits. It is always system generated on a fly. We would >>>>> not want this for rdf:type since when you create a new resource, you >>>>> specify its type. >>>>> >>>>> Another approach is not to infer rdf:type Melanoma for the patient. >>>>> Instead, create a new property e.g., :diagnosis and infer :diagnosis >>>>> :Melanoma. After all, a patient is not melanoma, he has melanoma, but he >>>>> is >>>>> not a disease, he is a person. >>>>> >>>>> If you do this, then you will be able to use sh:values. And then, the >>>>> inference will happen on the fly. You will be able to get the inferred >>>>> value in a GraphQL query as explained in the slides. To get it in a >>>>> SPARQL >>>>> query, you need to use tosh:values. See >>>>> https://www.topquadrant.com/graphql/values.html for an example of a >>>>> SPARQL query to retrieve dynamically inferred values. >>>>> >>>>> >>>>> >>>>> >>>>> On Jun 30, 2020, at 12:40 PM, Emily Zhang <zxy10...@gmail.com> wrote: >>>>> >>>>> Thanks, Hogler! I've revised the code accordingly, however, when I >>>>> "Run Inference" against the instance of "Patient", still nothing >>>>> returned. >>>>> I am wondering whether that's because I should write a GraphQL/SPARQL >>>>> query >>>>> for inference? I've read the slides provided by Irene, very helpful, >>>>> thank >>>>> you! But it only provided examples for the EDG version. It did provide >>>>> example for GraphQL query, but I am using SHACL file right now, and I >>>>> think >>>>> it only contains the SPARQL query function. >>>>> >>>>> 在 2020年6月29日星期一 UTC-5下午10:54:59，Holger Knublauch写道： >>>>> Oh I guess I made a copy and paste mistake. Change the line >>>>> to sh:object p3point_validation:Melanoma because that's the rdf:type you >>>>> want to infer? >>>>> >>>>> Holger >>>>> >>>>> >>>>> >>>>> On 30/06/2020 13:53, Emily Zhang wrote: >>>>> >>>>> Thank for the quick reply, Holger! It make sense that I should define >>>>> the rule under Patient class. However, how can I link the rule to >>>>> "Melanoma" since its the the instance of patient should be inferred as? >>>>> Should I define the "melanoma" as the sh:node under sh:filtershape? >>>>> Thanks again, >>>>> Emily >>>>> >>>>> 在 2020年6月29日星期一 UTC-5下午10:30:58，Holger Knublauch写道： >>>>> Hi Emily, >>>>> >>>>> the definition below doesn't look correct: you can only use sh:values >>>>> rules in a property shape, not in a class or node shape. Also, any such >>>>> rule would need to be attached to the class Patient because you want to >>>>> apply it to all instances of that class to infer an additional triple. It >>>>> may work better if you have something like >>>>> >>>>> :Patient >>>>> sh:rule [ >>>>> a sh:TripleRule ; >>>>> sh:subject sh:this; >>>>> sh:predicate rdf:type ; >>>>> sh:object p3point_validation:Patient ; >>>>> sh:condition [ >>>>> # your sh:filterShape, i.e. start with sh:property >>>>> sh:property [ >>>>> >>>>> sh:path p3point_validation:point_dermfeatures ; >>>>> >>>>> sh:in ( >>>>> >>>>> p3point_validation:Atypical >>>>> >>>>> p3point_validation:Asymmetry >>>>> >>>>> p3point_validation:Blue_white_structure >>>>> >>>>> ) ; >>>>> >>>>> sh:maxCount 3 ; # Are those constraints really needed? >>>>> >>>>> sh:minCount 2 ; >>>>> >>>>> ] ; >>>>> ] >>>>> ] >>>>> >>>>> HTH >>>>> Holger >>>>> >>>>> >>>>> On 30/06/2020 13:14, Emily Zhang wrote: >>>>> >>>>> Thanks so much for the detailed reply! I actually found out that sh:in >>>>> might be a better choice for me. >>>>> To give a summary of my question: >>>>> It's a inference question that all the instances of "Patient" who has >>>>> the property of "3point_dermfeatures" that satisfy the constrain: (a): >>>>> their features are within the range of "Atypical, >>>>> Asymmetry, blue_white_structure"; (b): the number of all the features >>>>> are in the range [2,3]; should be inferred to as having the disease of >>>>> "Melanoma". >>>>> However, when I tried to "Run Inferences" for the instance of >>>>> "Patient", nothing returned. Do you think it has something to do with my >>>>> source code? >>>>> Here is the source code I've edited according to to tutorial. >>>>> p3point_validation:Melanoma >>>>> >>>>> rdf:type owl:Class ; >>>>> >>>>> rdf:type sh:NodeShape ; >>>>> >>>>> rdfs:subClassOf owl:Thing ; >>>>> >>>>> sh:values [ >>>>> >>>>> sh:filterShape [ >>>>> >>>>> sh:property [ >>>>> >>>>> sh:path p3point_validation:point_dermfeatures ; >>>>> >>>>> sh:in ( >>>>> >>>>> p3point_validation:Atypical >>>>> >>>>> p3point_validation:Asymmetry >>>>> >>>>> p3point_validation:Blue_white_structure >>>>> >>>>> ) ; >>>>> >>>>> sh:maxCount 3 ; >>>>> >>>>> sh:minCount 2 ; >>>>> >>>>> ] ; >>>>> >>>>> ] ; >>>>> >>>>> sh:nodes [ >>>>> >>>>> sh:path p3point_validation:Patient ; >>>>> >>>>> ] ; >>>>> >>>>> ] ; >>>>> >>>>> . >>>>> >>>>> >>>>> 在 2020年6月29日星期一 UTC-5下午7:04:49，Irene Polikoff写道： >>>>> Hi Emily, >>>>> >>>>> I am not sure I understand the question. OWL is OWL and SHACL is >>>>> SHACL. They are different languages with different semantics. OWL is >>>>> based >>>>> on the Open World Assumption and SHACL is not. >>>>> >>>>> You can combine OWL axioms and SHACL constraints and rules in the same >>>>> RDF graph if this is what you mean by “using together”. >>>>> >>>>> There are similarities between SHACL and OWL and you can find >>>>> constraint components in SHACL that are similar to certain >>>>> OWL restrictions. If your question is “what in SHACL would be similar to >>>>> the OWL allValueFrom and someValuesFrom restrictions", then: >>>>> >>>>> For allValuesFrom, if values are resources, use sh:class - this means >>>>> that all values must be members of the specified class. If values are >>>>> literals, use sh:datatype. >>>>> >>>>> OWL someValuesFrom is simply a short hand for a qualified cardinality >>>>> restriction with min = 1. In other words, at least one value must satisfy >>>>> the restriction, others could be different. In SHACL, you could use >>>>> qualified value shapes for something similar to the qualified cardinality >>>>> restrictions. See https://www.w3.org/TR/ >>>>> shacl/#QualifiedValueShapeConstraintComponent. >>>>> >>>>> There is no short hand for someValuesFrom in the spec, we we have >>>>> defined dash:hasValueWithClass in the dash (http://datashapes.org/dash) >>>>> namespace. >>>>> You can find it at http://datashapes.org/dash.ttl and some >>>>> documentation at http://datashapes.org/dash. >>>>> >>>>> You can also take a look at the mapping from OWL to SHACL that is used >>>>> by TopBraid to auto-generate SHACL from RDFS/OWL. It is described in >>>>> https://www.topquadrant.com/from-owl-to-shacl-in-an-automated-way/. For >>>>> the most up to date version of the rules, see the file in the workspace. >>>>> >>>>> Regards, >>>>> >>>>> Irene >>>>> >>>>> >>>>> On Jun 29, 2020, at 6:47 PM, Emily Zhang <zxy10...@gmail.com> wrote: >>>>> >>>>> Hi Irene, >>>>> Just wondering if I can use SHACL and the OWL function >>>>> "allvaluesfrom" or "somevaluesfrom" together? I do see there is >>>>> "hasvalue" >>>>> function embedded in the SHACL file, however, I didn't find the other >>>>> two functions. >>>>> Thanks, >>>>> Emily >>>>> >>>>> -- >>>>> You received this message because you are subscribed to the Google >>>>> Groups "TopBraid Suite Users" group. >>>>> To unsubscribe from this group and stop receiving emails from it, send >>>>> an email to topbrai...@googlegroups.com. >>>>> To view this discussion on the web visit >>>>> https://groups.google.com/d/msgid/topbraid-users/89d3bec0-016d-4696-80a0-73fa467cdf98o%40googlegroups.com >>>>> . >>>>> >>>>> >>>>> -- >>>>> You received this message because you are subscribed to the Google >>>>> Groups "TopBraid Suite Users" group. >>>>> To unsubscribe from this group and stop receiving emails from it, send >>>>> an email to topbrai...@googlegroups.com. >>>>> To view this discussion on the web visit >>>>> https://groups.google.com/d/msgid/topbraid-users/300044d2-bec1-49a5-85d2-c2de44bfd74fo%40googlegroups.com >>>>> . >>>>> >>>>> -- >>>>> You received this message because you are subscribed to the >>>>> Google Groups "TopBraid Suite Users" group. >>>>> To unsubscribe from this group and stop receiving emails from it, send >>>>> an email to topbrai...@googlegroups.com. >>>>> To view this discussion on the web visit >>>>> https://groups.google.com/d/msgid/topbraid-users/d5d89d89-0fb2-4af6-883d-a453c5f6257do%40googlegroups.com >>>>> . >>>>> >>>>> >>>>> -- >>>>> You received this message because you are subscribed to the Google >>>>> Groups "TopBraid Suite Users" group. >>>>> To unsubscribe from this group and stop receiving emails from it, send >>>>> an email to topbrai...@googlegroups.com. >>>>> To view this discussion on the web visit >>>>> https://groups.google.com/d/msgid/topbraid-users/49c2c4eb-85dc-4009-b52d-a4c73a3e2e74o%40googlegroups.com >>>>> . >>>>> >>>>> >>>>> >>>> -- >>>> You received this message because you are subscribed to the Google >>>> Groups "TopBraid Suite Users" group. >>>> To unsubscribe from this group and stop receiving emails from it, send >>>> an email to topbrai...@googlegroups.com. >>>> To view this discussion on the web visit >>>> https://groups.google.com/d/msgid/topbraid-users/475dcb32-2794-4c11-8955-cbd64bb1a9c7o%40googlegroups.com >>>> >>>> <https://groups.google.com/d/msgid/topbraid-users/475dcb32-2794-4c11-8955-cbd64bb1a9c7o%40googlegroups.com?utm_medium=email&utm_source=footer> >>>> . >>>> >>>> >>>> >>> -- >>> You received this message because you are subscribed to the Google >>> Groups "TopBraid Suite Users" group. >>> To unsubscribe from this group and stop receiving emails from it, send >>> an email to topbrai...@googlegroups.com. >>> To view this discussion on the web visit >>> https://groups.google.com/d/msgid/topbraid-users/74a5ec44-6f12-4c0d-a591-2d2d0c343e44o%40googlegroups.com >>> >>> <https://groups.google.com/d/msgid/topbraid-users/74a5ec44-6f12-4c0d-a591-2d2d0c343e44o%40googlegroups.com?utm_medium=email&utm_source=footer> >>> . >>> >>> >>> >> -- >> You received this message because you are subscribed to the Google Groups >> "TopBraid Suite Users" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to topbrai...@googlegroups.com. >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/topbraid-users/78ca7f0c-baeb-4391-b7af-dc529fde5c72o%40googlegroups.com >> >> <https://groups.google.com/d/msgid/topbraid-users/78ca7f0c-baeb-4391-b7af-dc529fde5c72o%40googlegroups.com?utm_medium=email&utm_source=footer> >> . >> <Screenshot 2020-07-08 23.47.20.png> >> >> >> > -- > You received this message because you are subscribed to the Google Groups > "TopBraid Suite Users" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to topbrai...@googlegroups.com <javascript:>. > To view this discussion on the web visit > https://groups.google.com/d/msgid/topbraid-users/64aeb414-0b53-40af-9528-1fba08d35ad0o%40googlegroups.com > > <https://groups.google.com/d/msgid/topbraid-users/64aeb414-0b53-40af-9528-1fba08d35ad0o%40googlegroups.com?utm_medium=email&utm_source=footer> > . > > > -- You received this message because you are subscribed to the Google Groups "TopBraid Suite Users" group. 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