Nanopublications LDF server

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

• comment hasCommentText "We thank the reviewer for this comment and have changed the formalization accordingly." assertion.
• comment hasCommentText "Yes, it would be useful to specify how the sources should be referred to." assertion.
• comment hasCommentText "We have adapted the formalization accordingly." 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 "I believe the exact quote from the article of the scientific claim is "Our data show that pharmacogenomics-guided clopidogrel treatment strategy may represent a cost-effective choice compared with non-pharmacogenomics-guided strategy for patients undergoing PCI." and not the actual scientific claim stated there, which is a reformulation of this phrase from the article." assertion.
• comment hasCommentText "The provenance of this formalization is indeed a special type of activity named "FormalizationActivity". So, this is a good chouce for the provenance field." 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 "I have some doubts about the context class used, as I am not sure if, from a biological point of view, the interpretation of the formalization makes sense." 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 "A small thing: to start the sentence containing the scientific claim with an uppercase letter." assertion.
• comment hasCommentText "Something small: starting the sentence containing the scientific claim of the super-pattern with a capital letter." 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 is good." assertion.
• comment hasCommentText "The modeling of the formalization reflects very well the scientific claim." assertion.
• comment hasCommentText "The scientific claim does not seem to be atomic, as it mentions two genes, IRX3 and IRX5. I think it should be broken into two different claims, one for each of these genes." 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 creation and also the related term in Wikidata seem correct." 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 "I am not sure that this is a correctly chosen Wikidata class in this case, as this is a scientific article." assertion.
• comment hasCommentText "I would replace the object class of skos:related with https://www.wikidata.org/wiki/Q29032644." assertion.
• comment hasCommentText "The class definition is good." assertion.
• comment hasCommentText "The way the class is defined is good." 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 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 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 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 "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 "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 "I think a correct subclass would be "therapy" (https://www.wikidata.org/wiki/Q179661)." assertion.
• comment hasCommentText "I think a correct subclass would be "treatment" (https://www.wikidata.org/wiki/Q179661)." assertion.
• comment hasCommentText "Good class definition and declaration." assertion.
• comment hasCommentText "Great usage of a new nested class." assertion.
• comment hasCommentText "The definition and declaration of the class look good." assertion.
• comment hasCommentText "I think a skos:related class can be added here. It can be either "pharmacogenomics " (https://www.wikidata.org/wiki/Q1152227) or "clopidogrel" (https://www.wikidata.org/wiki/Q410237)." 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 general structure is good, but some improvements can be made to make it more complete, like adding a class of which the current one is a subclass of and also adding related classes." assertion.
• comment hasCommentText "The class definition and declaration seems good." assertion.
• comment hasCommentText "The capitalization of the "AND" in the class name should be removed and replaced with "and"." assertion.
• comment hasCommentText "The name of the class needs to be corrected. The general convention when creating a new class in Nanobench is for the individual elements (words) of the class to be separated by a "-" and use capital letters only when the elements are acronyms." assertion.
• comment hasCommentText "I believe the correct qualifier here would be "generally"." 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 name of the class was updated according to the Nanobench convention." assertion.
• comment hasCommentText "I couldn't find that exact quote from the original paper. It seems that this is a paraphrase whereas it should be the verbatim quote." assertion.
• comment hasCommentText "Very nice that all classes are defined in WikiData." assertion.
• comment hasCommentText "The provenance part should use the template 'generated from a formalization activity'." assertion.
• comment hasCommentText "The context class 'chemical to gene association' doesn't make sense to me here. I suppose we are talking about individual patients here, so then the context class 'human' would make sense, meaning whenever a human has this condition then it is sometimes related to that other condition *of the same human*." assertion.
• comment hasCommentText "Overall, I think this is a good formalization." assertion.
• comment hasCommentText "I am a bit uncertain about the subject class. It is defined as a subclass of 'knowledge graph' but seems to be treated more like an instance. I think it would be good to better specify (in the formalization nanopub or the class definition one) what the instances of the class 'OpenBiodiv knowledge graph' really are (maybe the different versions/branches?)." assertion.
• comment hasCommentText "The provenance part should be using the template 'generated from a formalization activity'." assertion.
• comment hasCommentText "I agree that the object 'ERAD pathway' is not the appropiate. I addressed this minting a new class 'dysfunction of ERAD pathway' which is more accurate." assertion.
• comment hasCommentText "I changed the context with the more specific class 'genetic disorder' that is stated in the assertion but was not included in the first version, which is 'autosomal recessive disorder' thus declaring the congenital characteristic of this disorder." assertion.
• comment hasCommentText "The provenance of this formalization is a specific type of provenance, namely, it is the result of a "formalization activity". This should be used in the provenance field with all the corresponding details pertaining to this "formalization activity"." assertion.
• comment hasCommentText "The formalization in the assertion reflects very well the chosen scientific claim." assertion.
• comment hasCommentText "The modelling of the formalization looks good." assertion.
• comment hasCommentText "The modelling of the formalization reflects very well the scientific claim." 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 "I believe the modelling of the formalization reflects the content of the scientific claim very well." assertion.
• comment hasCommentText "The modelling of the formalization seems to reflect well the content of the scientific claim." assertion.
• comment hasCommentText "The modelling of the formalization is very good." 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 chosen superclass here is wrong. Instead, the "obesity" class can be used in the skos:related field, which I advise." 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 "Apart from the object class link, this is a very convincing formalization." assertion.
• comment hasCommentText "Thanks, I updated the object class to http://purl.org/np/RAiUYY1dbEDbcsscapEmbMMHsgJmjEJ1yUoNsxZIH1r90#transcription-of-stmn2" assertion.
• comment hasCommentText "Thanks, I updated the object slot to http://purl.org/np/RAiUYY1dbEDbcsscapEmbMMHsgJmjEJ1yUoNsxZIH1r90#transcription-of-stmn2" assertion.
• comment hasCommentText ""autosomal recessive disorder" has been added as "genetic disorder" to declare the context of the assertion" 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 "The scientific claim does not seem to be atomic, as it mentions two genes, IRX3 and IRX5. I think it should be broken into two different claims, one for each of these genes." 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 modelling of the scientific claim (if we assume the claim is rephrased in an atomic way) seems correct." assertion.
• comment hasCommentText "The modelling of the formalization looks good." assertion.
• comment hasCommentText "Indeed, I misunderstood the quote part. The quote now comes from (the abstract of) the original article" assertion.
• comment hasCommentText "no review needed, but was completed anyway" assertion.
• comment hasCommentText "an exact quote from the article was added" assertion.
• comment hasCommentText "Thanks for the positive review on the class definition." assertion.
• comment hasCommentText "Thanks for the positive review on the class definition." assertion.
• comment hasCommentText "Thanks for the positive review on the class definition." assertion.
• comment hasCommentText "I updated the class description to use skos:related to for glycocalyx" assertion.
• comment hasCommentText "done" assertion.
• comment hasCommentText "no modification requested" assertion.
• comment hasCommentText "done" assertion.
• comment hasCommentText "should be fixed hopefully. not sure as it's not clear how the problem appeared in the first place." assertion.
• comment hasCommentText "should be fixed hopefully. not sure as it's not clear how the problem appeared in the first place." assertion.
• comment hasCommentText "I don't think the original publication shows a causal relationship. It seems to me only a correlation is proven." assertion.
• comment hasCommentText "no modification requested" assertion.
• comment hasCommentText "The qualifier should be "frequently" instead of "generally"." assertion.
• comment hasCommentText "This issue has been resolved as indicated." assertion.
• comment hasCommentText "Thank you for the suggestion." assertion.
• comment hasCommentText "Thank you for the comment." assertion.
• comment hasCommentText "Thank you for your suggestion which has been implemented." assertion.
• comment hasCommentText "class updated" assertion.
• comment hasCommentText "A small thing: to start the sentence containing the scientific claim with an uppercase letter." assertion.
• comment hasCommentText "The provenance of this formalization is a specific type of provenance, namely, it is the result of a "formalization activity". This should be used in the provenance field with all the corresponding details pertaining to this "formalization activity". This is the place where the DOI of the article from which the quoted scientific claim was extracted should be specified." 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 "The provenance, which is a "FormalizationActivity" should also include the actual quote from the article from which the scientific claim was derived. As such, the "sub:quote prov:value <quote_from_article_from_which_the_scientific_claim_was_derived>" and "prov:wasQuotedFrom <http://doi.org/10.1038/ng.3130>" should be added." assertion.

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