Nanopublications LDF server

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

• comment hasCommentText "The name of the class contains the word "with" misspelled." assertion.
• comment hasCommentText "Maybe changing the "_" into a "-" for newly generated classes" assertion.
• comment hasCommentText "A link to a publication might be useful to be added in the provenance" assertion.
• comment hasCommentText "There is no link to the original publication" 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 "Thanks for adding the class as automatic discovery is missing in Wikidata." assertion.
• comment hasCommentText "Since it is a legal issue, wouldn't https://w3id.org/linkflows/superpattern/latest/alwaysQualifier work better?" assertion.
• comment hasCommentText "I learned a lot from this formalization. In particular, about nesting object classes." assertion.
• comment hasCommentText "looks good!" 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 skos:relatedMatch references to identifiers for the genes IRX3 and IRX5." assertion.
• comment hasCommentText "The subject class has a related to sub:bulk, but this is undefined in the subject class nanopublication." assertion.
• comment hasCommentText "The class 'cancer cell engaged in extracellular matrix' is defined as an intersection between 'extracellular matrix' and 'cancer cell'. But these two things are different, and cannot be formally intersected. instead, I might suggest that the subject type is a cancer cell that has a relation of 'located in' to an 'extracellular matrix'" 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 "A provenance source is provided but it does not have the correct link. Instead of the article URL, the author should put the DOI in the form https://doi.org/10.1056/NEJMoa1502214. There is also a superfluous comma before the provenance URL." 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 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 "Something small: starting the sentence containing the scientific claim of the super-pattern with a capital letter." assertion.
• comment hasCommentText "The correct provenance here is a "FormalizationActivity", as the formalization was derived after such a specific activity. There the original article (https://www.nature.com/articles/nature13535) 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 "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 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 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 "The provenance of the formalization is the result of a "FormalizationAcitvity", which is correctly chosen and filled in." assertion.
• comment hasCommentText "The modeling of the formalization reflects very well the scientific claim." assertion.
• comment hasCommentText "The provenance of the formalization is a "FormalizationActivity" as was correctly chosen and filled in." assertion.
• comment hasCommentText "The provenance indicates that this is a joint-authored formalization." assertion.
• comment hasCommentText "The rephrasing of the scientific claim is clear and in an AIDA-form." 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 "A small thing: to start the sentence containing the scientific claim with an uppercase 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 looks good." assertion.
• comment hasCommentText "The modelling of the formalization is good." 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 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 provenance of this formalization should be a "FormalizationActivity". As such, the source of the scientific claim (the original scientific article) can be specified, together with the quote from the article that contains the scientific claim and the orcid of the author of the formalization." 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 class creation and also the related term in Wikidata seem correct." assertion.
• comment hasCommentText "I would replace the object class of skos:related with https://www.wikidata.org/wiki/Q29032644." assertion.
• comment hasCommentText "Check again if this is a good fit, if not remove the subclass entirely." 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 "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 "Maybe a skos:related term can be added in the form of https://www.wikidata.org/wiki/Q1754768 as an object." 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 class declaration looks good." 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 "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 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 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 "IRX3" (https://www.wikidata.org/wiki/Q18046058) and "IRX5" (https://www.wikidata.org/wiki/Q18035174) classes should be added as related classes." assertion.
• comment hasCommentText "my pleasure!" 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 "I believe the correct qualifier here would be "generally"." 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 "The provenance should use the 'Generated by a formalization activity' template." assertion.
• comment hasCommentText "The provenance of this formalization is a "FormalizationActivity" where the link to the article and the actual quote from the same article from which the scientific claim was derived need to be specified together with the orcid of the formalization author. This should be changed accordingly." 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 "I believe the label in itself represents the meaning of the original article, but the qualifier wasn't the suitable one to express it. I have modified the qualifier from "generally" to "mostly" to specify that the original article claims that Shh is an essential regulator." assertion.
• comment hasCommentText "Thanks for the feedback" assertion.
• comment hasCommentText "Thanks for the feedback" assertion.
• comment hasCommentText "Thanks for the feedback" assertion.
• comment hasCommentText "Provenance changed to show generated by a formalization activity." assertion.
• comment hasCommentText "Provenance was changed to show that it was generated by a formalization activity, and the necessary attributes of that template were added." assertion.
• comment hasCommentText "Whether we consider a protein in the context of a gene or the PRESENCE of the protein in that context is a subtle distinction whose need here eludes me. This requires further discussion." assertion.
• comment hasCommentText "no review needed, but was completed anyway" assertion.
• comment hasCommentText "An exact quote from the article was added" assertion.
• comment hasCommentText "The paper refers to both genes and both genes are regulated. Not sure if it should be split into two claims or remain as one" assertion.
• comment hasCommentText "no action needed" 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 "Thank you!" assertion.
• comment hasCommentText "We agree with this review comment and have addressed it by defining a new class license-with-non-commercial-clause which is a subclass of software license (Q79719) and is related to Q65071627 and have used this new class as the subject of our updated formalisation." assertion.
• comment hasCommentText "Thank you!" assertion.
• comment hasCommentText "Thank you!" assertion.
• comment hasCommentText "done" assertion.
• comment hasCommentText "no modification requested" 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 "This issue has been resolved as indicated." assertion.
• comment hasCommentText "addressed in previous comment" assertion.
• comment hasCommentText "Addressed in previous correction" assertion.
• comment hasCommentText "We have adapted the formalization accordingly." assertion.
• comment hasCommentText "Yes, and we have also added the full stop at the end." 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.

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