Matches in Nanopublications for { ?s <https://w3id.org/linkflows/reviews/hasCommentText> ?o ?g. }
- comment hasCommentText "We discussed that and agree to change the context (and the classes) so that "universal context" fits best." assertion.
- comment hasCommentText "Chris Evelo added as author as agreed." assertion.
- comment hasCommentText "Replaced by new class." assertion.
- comment hasCommentText "The publication is about overlapping genes in the disease networks of CAKUT and in the vitamin A targets. There is no causality involved." assertion.
- comment hasCommentText "Changed according to suggestion." assertion.
- comment hasCommentText "We discussed that and agreed to "universal context" together with a change of subject and object classes." assertion.
- comment hasCommentText "The formalization in the assertion reflects very well the chosen scientific claim." assertion.
- comment hasCommentText "A small thing: to start the sentence containing the scientific claim with an uppercase letter." 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 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 "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 "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 "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.
- comment hasCommentText "Maybe the use of a causal relation like "contributes to" can also be used here." 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 modelling of the formalization seems to reflect well the content of the scientific claim." 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 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 "The modelling of the class seems ok." assertion.
- comment hasCommentText "The general definition 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 am not sure that this is a correctly chosen Wikidata class in this case, as this is a scientific article." 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 "The description of the class seems ok." assertion.
- comment hasCommentText "The class definition 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 camel case." 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 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 "I think a correct subclass would be "therapy" (https://www.wikidata.org/wiki/Q179661)." 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 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 "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 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 general class definition and declaration looks good. If some related classes would be added, it would be even better." assertion.
- comment hasCommentText "I believe the chosen qualifier here should 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 structure of the formalization seems to reflect very well the chosen scientific claim, except for the qualifier, which can be chosen better." 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 "This is not a subclassof obesity (http://www.wikidata.org/entity/Q12174), but a skos:relatedTo class. This should be corrected." assertion.
- comment hasCommentText "The name of the class was updated according to the Nanobench convention." assertion.
- comment hasCommentText "Obesity was added as a relatedTo class." 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 "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 "You are now stating that the given deficiency is caused by the ERAD pathway, which doesn't sound right. I suppose it should be something like: it is caused by the dysfunction of the ERAD pathway. So, it would mean to mint a new class 'dysfunction of ERAD pathway' and then use this class in object position." assertion.
- comment hasCommentText "The provenance part should use the template 'generated from a formalization activity'." assertion.
- comment hasCommentText "The formalization looks solid to me." 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 "I am not sure about the isSameAs relation. This might be fine depending on how the other classes are filled in in the final version, but I have the impression that it should rather be something like isCausedBy." 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 "This looks like a good formalization to me." assertion.
- comment hasCommentText "Overall, I think this is a very good formalization." assertion.
- comment hasCommentText "With a protein class in the object position and a gene in the context, this raises for me the question what it means for a protein to be in the context of a gene. Maybe a class like 'presence of TAR DNA binding protein' in object position might make it clearer? But I am not sure..." assertion.
- comment hasCommentText "The modeling of the formalization for the specific scientific claim looks good." assertion.
- comment hasCommentText "Something small: I would start the scientific claim with an upper case and end it with a period." assertion.
- comment hasCommentText "The provenance section does not contain a reference to the original article" assertion.
- comment hasCommentText "Reference to the original article is missing." assertion.
- comment hasCommentText "I agree that it was not clear that this is an instance. To address this review comment, I have created a new class (latest-release-of-openbiodiv), which is a subclass of software release (Q20631656) and related to openbiodiv-knowledge-graph, and I have updated the formalisation nanopub to say that 'The latest release of the OpenBiodiv knowledge graph contains semantic triples extracted from biodiversity literature'. Thank you for your review!" assertion.
- comment hasCommentText "Thank you!" assertion.
- comment hasCommentText "Thank you! In response to your other review comment we made small changes to the formalisation." assertion.
- comment hasCommentText "Thank you for your review! While we agree that when it comes to legal issues a more concrete language should be used, our formalisation is of a statement which expresses an opinion rather than a legal fact. Licenses with a non-commercial clause do not inhibit reuse of biodiversity data because of legal reasons but as a consequence of the difficulty to reuse data." assertion.
- comment hasCommentText "Thank you for your review!" assertion.
- comment hasCommentText "Thank you!" assertion.
- comment hasCommentText "I updated the class description to use skos:related to for glycocalyx" assertion.
- comment hasCommentText "The qualifier should be "frequently" instead of "generally"." assertion.
- comment hasCommentText "The general class definition is good." assertion.
- comment hasCommentText "Thank you for your suggestion which has been implemented." assertion.
- comment hasCommentText "Thank you for the suggestion which was implemented." assertion.
- comment hasCommentText "Thank you for your suggestion which has been implemented." assertion.
- comment hasCommentText "Thank you." assertion.
- comment hasCommentText "Changed according to suggestion." assertion.
- comment hasCommentText "Changed according to suggestion." assertion.
- comment hasCommentText "Changed according to suggestion." assertion.
- comment hasCommentText "No excess or deficiency involved here, that is just a statement that Vitamin A targets and CAKUT related proteins overlap (are sometimes the same)." assertion.
- 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 "Yes, and maybe we should clarify the procedure for doing this systematically." 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 "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 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 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 modelling of the formalization is very good." assertion.
- comment hasCommentText "The original quote from the article that contains the scientific claim that is formalized should be written here, instead of the sentence with the scientific claim." assertion.
- comment hasCommentText "I was wondering if a better context class would be "Digital Humanities research", instead of just "Digital Humanities"." 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 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.