Nanopublications LDF server

Matches in Nanopublications for { ?s <https://w3id.org/linkflows/reviews/hasCommentText> ?o ?g. }

• comment hasCommentText "We have adapted the formalization accordingly." assertion.
• comment hasCommentText "Yes, and it would be nice to have a way to assess how well the formalization corresponds to the original claim." assertion.
• comment hasCommentText "Yes, and as expressed in http://purl.org/np/RAANP7AWgyZRaS2WgNcGDfp8-4bXv0blhKapMcUrrWvos , it would be nice to have a way to quantify the solidity." assertion.
• comment hasCommentText "I think the article is relevant for the (intended) audience of FAIR Connect. It is well-written and mostly clear, although some concepts may be expanded, as they are not straightforward for data stewards at the beginning of their career. As also suggested by the other reviewer, it could be useful to add a section reporting more practical examples. I also added some comments in the text and edited the text where I felt necessary, but please feel free to ignore changes if I misunderstood." assertion.
• comment hasCommentText "Nice article on a really nice, relevant topic. Here and there the structure/argument could be strengthened a bit, I made some suggestions for that (please ignore if not useful). Not sure how/if you can use it, but at Radboud uni (my previous jobs), we actually started DMPs that reflect this process, not so much with regard to FAIR but regarding what the researcher is expected to do according to the RDM policy of his/her faculty. The DMP included pre-given answers but with blank spots for details and indeed room to deviate if explained. If you are curious, I can bring you into contact with my Radboud uni successor to explore." assertion.
• comment hasCommentText "Here a 'cancer cell engaged in extracellular matrix' is defined as the intersection between the classes 'cancer cell' and 'extracellular matrix', but as the latter is defined as 'structure external to cells' this intersection is empty. I think this should rather be defined as a subclass of 'cancer cell' with some (possibly informal) link to the concept of 'extracellular matrix'." assertion.
• comment hasCommentText "Maybe using "mostly" as qualifier would be best." assertion.
• comment hasCommentText "The name of the class contains the word "with" misspelled." assertion.
• comment hasCommentText "A link to a publication might be useful to be added in the provenance" assertion.
• comment hasCommentText "Very good information provided" assertion.
• comment hasCommentText "The label of the spi has a small typo or encoding error: it now appears as STX1B rather than STX1B. I suggest changing that" assertion.
• comment hasCommentText "I cannot find the original quote 'In the context of Digital Humanities research, usage of the Linked Data Scopes ontology contributes to transparency of the research.' in the given paper https://link.springer.com/chapter/10.1007%2F978-3-030-71903-6_32" assertion.
• comment hasCommentText "Since it is a legal issue, wouldn't https://w3id.org/linkflows/superpattern/latest/alwaysQualifier work better?" assertion.
• comment hasCommentText "The subject class has a related to sub:bulk, but this is undefined in the subject class nanopublication." assertion.
• comment hasCommentText "Good formalization of an existing scientific paper with a wikipedia identifier. This also raises the question as to how publications should be referenced - e.g. by their DOI, pubmed, or indeed a wikipedia ID." assertion.
• comment hasCommentText "while this class nanopub is a subclass of size from wikipedia, it doesn't make a formal relation to the neocortex (e.g. that it specifically an attribute of the neocortex). thus, the class formalization could be improved." assertion.
• comment hasCommentText "This class definition could be made more precise and more valuable by referring to an identifier for 'regulatory element' (as superclass) and to 'intron' and 'human gene FTO' (with skos:relatedMatch)." assertion.
• comment hasCommentText "The label 'expression of genes IRX3 AND IRX5' unnecessarily capitalizes 'AND', which seems wrong and could be confusing." assertion.
• comment hasCommentText "It would be good to add a skos:relatedMatch reference to an identifier for PCI." assertion.
• comment hasCommentText "The usage of dx.doi.org type of DOIs has been deprecated. Instead, the author should use doi.org such as https://doi.org/10.1007%2F978-3-030-71903-6_32 ." assertion.
• comment hasCommentText "The exact quote from the article should be specified, not the text of the scientific claim in the formalization." assertion.
• comment hasCommentText "The formalization in the assertion reflects very well the chosen scientific claim." assertion.
• comment hasCommentText "The literal for the rdfs:label of the super-pattern instantiation should contain the actual (rephrased) scientific claim (ideally in an AIDA sentence), not the doi to the article. This should be changed." assertion.
• comment hasCommentText "The subject id http://identifiers.org/omim/610805 does not seem to resolve. Maybe using https://www.omim.org/entry/610805 is better?" assertion.
• comment hasCommentText "I believe the modelling of the formalization reflects the content of the scientific claim very well." assertion.
• comment hasCommentText "The resulting formalization has as a provenance the "FormalizationActivity", which is correct. Moreover, all fields are correctly filled in." assertion.
• comment hasCommentText "The provenance of the nanopub is as a result of a "FormalizationActivity", as was chosen." assertion.
• comment hasCommentText "I was wondering if a better context class would be "Digital Humanities research", instead of just "Digital Humanities"." assertion.
• comment hasCommentText "The scientific claim "mutations in STX1B are associated with epilepsy" contains an unknown or wrong character for the "STX1B" subunit. This should be corrected." assertion.
• comment hasCommentText "The modelling of the formalization looks good." assertion.
• comment hasCommentText "The correct provenance here is a "FormalizationActivity", as the formalization was derived after such a specific activity. There the original article (http://dx.doi.org/10.1038/ng.3130) and the exact quote from the article that contained the scientific claim, together with the ORCID of the creator(s) should be specified." assertion.
• comment hasCommentText "The modelling of the formalization is good." assertion.
• comment hasCommentText "The provenance of the formalization needs to be a "FormalizationActivity", but at the moment the "sub:quote" field is missing. There a link to the article from which the scientific claim was taken needs to be specified ("sub:quote prov:wasQuotedFrom <https://royalsocietypublishing.org/doi/10.1098/rsbl.2021.0158>"), together with the quote from the article from which the scientific claim was derived ("sub:quote prov:value "add phrase from original article from which the scientific claim was extracted or rephrased" ")." assertion.
• comment hasCommentText "The provenance of the formalization should be a "FormalizationActivity". As such, more details can be given about the original article from which the scientific claim was derived, the original content from the article (the quote) of the phrase from which the scientific claim was derived (can be the same as the scientific claim itself if it was not rephrased) and the author of the formalization." assertion.
• comment hasCommentText "The content of the scientific claim that is modeled in the formalization should be something like "Adherence of a dataset to the FAIR Guiding Principles enables its automated discovery.", instead of containing the interpretation of the mentioned scientific claim." assertion.
• comment hasCommentText "The modeling of the formalization reflects very well the scientific claim." assertion.
• comment hasCommentText "The provenance indicates that this is a joint-authored formalization." assertion.
• comment hasCommentText "The modeling of the formalization reflects very well the scientific claim." assertion.
• comment hasCommentText "If the formalization has multiple authors, then these need to be specified in this part, after choosing the "FormalizationActivity" as provenance of the formalization." assertion.
• comment hasCommentText "Something small: starting the sentence containing the scientific claim of the super-pattern with a capital letter." assertion.
• comment hasCommentText "The modelling of the formalization looks good." assertion.
• comment hasCommentText "The content of the scientific claim that is modeled in the formalization should be something like "Adherence of a dataset to the FAIR Guiding Principles enables its automated discovery.", instead of containing the interpretation of the mentioned scientific claim." assertion.
• comment hasCommentText "Maybe the scientific claim should be rephrased a bit to reflect the growth effect more, instead of just using "mechanically drives"." assertion.
• comment hasCommentText "The modeling of the formalization reflects very well the scientific claim." assertion.
• comment hasCommentText "The modelling of the formalization is very good." assertion.
• comment hasCommentText "The modelling of the formalization reflects very well the scientific claim." assertion.
• comment hasCommentText "I think the object class needs to be "autosomal-recessive-disorder-of-ERAD-pathway" instead of just the "ERAD-pathway"." assertion.
• comment hasCommentText "The class looks good." assertion.
• comment hasCommentText "The modelling of the class seems ok." assertion.
• comment hasCommentText "I am not sure this is a correct choice. I would choose the skos:related property instead and use as an object the "neocortex" class, for example." assertion.
• comment hasCommentText "I believe this should be removed. Instead, the Wikidata class that is in the object would go well as an object of the skos:related to property." assertion.
• comment hasCommentText "The class definition looks ok." assertion.
• comment hasCommentText "I believe the intersection between the "extracellular matrix" and "cancer cell" is empty. Instead, I would just mention that this class is a subclassOf "cancer cell"." assertion.
• comment hasCommentText "I would replace the object class of skos:related with https://www.wikidata.org/wiki/Q29032644." assertion.
• comment hasCommentText "The general convention when specifying the name of a new class in Nanobench is to separate the individual elements by a "-", instead of using camel case." assertion.
• comment hasCommentText "The way the class is defined is good." assertion.
• comment hasCommentText "I believe a skos:related field should be added as well, having as an object PCI (https://www.wikidata.org/wiki/Q2008344)." assertion.
• comment hasCommentText "The general declaration of the class seems ok." assertion.
• comment hasCommentText "The general convention when specifying the name of a new class in Nanobench is to separate the individual elements by a "-", instead of using "_"." assertion.
• comment hasCommentText "The general convention when specifying the name of a new class in Nanobench is to separate the individual elements by a "-", instead of using "_"." assertion.
• comment hasCommentText "The general convention when specifying the name of a new class in Nanobench is to separate the individual elements by a "-", instead of using camel case." assertion.
• comment hasCommentText "I would add a more detailed definition of the class, or just modify slightly the literal label of it and put it in the form of a sentence. Something along the lines of "A clopidrogel therapy whose use is guided by pharmacogenomics."." assertion.
• comment hasCommentText "I think a correct subclass would be "therapy" (https://www.wikidata.org/wiki/Q179661)." assertion.
• comment hasCommentText "The general structures is mostly ok." assertion.
• comment hasCommentText "The definition and declaration of the class is good." assertion.
• comment hasCommentText "The definition and declaration of the class look good." assertion.
• comment hasCommentText "The subclass of and related to classes should be added to this class. For instance, the subclass can be "regulatory element" (http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C13734) and some related classes could be "intron"(https://www.wikidata.org/wiki/Q207551) and "FTO" (https://www.wikidata.org/wiki/Q14912501)." assertion.
• comment hasCommentText "The capitalization of the "AND" in the class name should be removed and replaced with "and"." assertion.
• comment hasCommentText "The general class definition and declaration looks good. If some related classes would be added, it would be even better." assertion.
• comment hasCommentText "The context class chosen here is wrong as we are not referring to humanity as a whole, but to the individuals that comprise it. As such choosing the class "human" would be correct." assertion.
• comment hasCommentText "The chosen superclass here is wrong. Instead, the "obesity" class can be used in the skos:related field, which I advise." assertion.
• comment hasCommentText "I believe the correct qualifier here would be "generally"." assertion.
• comment hasCommentText "The provenance of this formalization should be a "FormalizationActivity". There the original article and the original quote from the article need to be specified, together with the author(s) of the formalization." assertion.
• comment hasCommentText "The general convention when specifying the name of a new class in Nanobench is to separate the individual elements by a "-", instead of using camel case." assertion.
• comment hasCommentText "Obesity was added as a relatedTo class." assertion.
• comment hasCommentText "I feel that the context class of 'clinical entity' doesn't add anything. It's a very general class. Just leaving it empty (= universal class) might make more sense." assertion.
• comment hasCommentText "Very nice that all classes are defined in WikiData." assertion.
• comment hasCommentText "The formalization looks solid to me." assertion.
• comment hasCommentText "The label of the superpattern instance should be a short human-readable sentence, not the DOI of the original paper." assertion.
• comment hasCommentText "It seems to me that the object class should be something like 'excess or deficiency of vitamin A' and not just 'vitamin A'." assertion.
• comment hasCommentText "Referring to another reviewer's comments, I think having underscores '_' instead of hythens '-' for class URIs is perfectly fine. So, I think no action is required on this." assertion.
• comment hasCommentText "I think the label of the superpattern instance, in particular the 'essential regulator' part, is a bit stronger than what the superpattern is actually expressing. I suggest to revise the label a bit such that it better reflects what the formalization says." assertion.
• comment hasCommentText "The quote provided in the provenance seems to be a general quote from the source rather than the specific passage on which this formalization is based." assertion.
• comment hasCommentText "Overall, I think this is a good formalization." assertion.
• comment hasCommentText "The provenance part should be using the template 'generated from a formalization activity'." assertion.
• comment hasCommentText "As humans typically belong to many different groups of different kinds, I am inclined to think that the context class should more specifically be 'social group of humans' (possibly with a quite technical and precise definition) and not just 'group of humans'." assertion.
• comment hasCommentText "The provenance part should refer to the original publication by using the template 'generated from a formalization activity'." assertion.
• comment hasCommentText "I find the context class 'Digital Humanities' a bit confusing, as it is unclear to me what the instances of this class are. WikiData is not always very precise about this, but the superpattern is. I believe that a context class like 'Digital Humanities research' (as mentioned in the label) would make more sense." assertion.
• comment hasCommentText "The modeling of the formalization for the specific scientific claim looks good." assertion.
• comment hasCommentText "Reference to the original article is missing" assertion.
• comment hasCommentText "Reference to the original article is missing." assertion.
• comment hasCommentText "Reference to the original article is missing." assertion.
• comment hasCommentText "The object slot of the superpattern refers to the nanopublication that defines the class, instead of the class itself (http://purl.org/np/RAiUYY1dbEDbcsscapEmbMMHsgJmjEJ1yUoNsxZIH1r90#transcription-of-stmn2)." assertion.
• comment hasCommentText "The relation subClassOf was replaced with skos:related as it matches better the intended meaning. The new class is now related to both - the neocortex and size - classes." assertion.
• comment hasCommentText "Thank you for the review" assertion.
• comment hasCommentText "Indeed https://www.wikidata.org/wiki/Q874405 (social group) matches better than https://www.wikidata.org/wiki/Q16334295 (group of humans) and thus was replaced." assertion.
• comment hasCommentText "The missing information have been added." assertion.
• comment hasCommentText "Thank you for your comment." assertion.
• comment hasCommentText "I agree with the style adopted for this representation." assertion.
• comment hasCommentText "Good claim representation" assertion.

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