Nanopublications LDF server

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

• comment hasCommentText "Maybe using "mostly" as qualifier would be best." assertion.
• comment hasCommentText "The provenance looks really good." assertion.
• 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 "Very good information provided" assertion.
• comment hasCommentText "The content is very good" 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 "The provenance part of this SPI looks good. The content of the paper matches the content of the nanopublication." 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 "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 "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 looks OK." 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 "This class definition looks good." 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 "It would be good to add a skos:relatedMatch reference to an identifier for PCI." assertion.
• comment hasCommentText "This formalisation paper captures excellently one of the main claims made in the original article. I have a small comment regarding the style of the formalisation paper itself. There is no quote from the original paper and instead the paraphrased claim was inserted (sub:quote triple in the Provenance section)." assertion.
• comment hasCommentText "I agree with the way the class was defined and commend the author for linking it to a parent Wikidata class (gene expression). The only thing I would change is the uppercase 'and' within the class identifier between the two gene names." 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 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 "I believe the modelling of the formalization reflects the content of the scientific claim very well." assertion.
• comment hasCommentText "The modelling of the formalization is very good." assertion.
• comment hasCommentText "The provenance of the nanopub is as a result of a "FormalizationActivity", as was chosen." 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 "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 "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 "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 (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 modeling of the formalization reflects very well the scientific claim." assertion.
• comment hasCommentText "The modeling of the formalization reflects very well the scientific claim." 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 reflects very well the scientific claim." 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 believe the formalization structure is good, reflecting almost all the details of the scientific claim. If the missing details about the "autosomal recessive disorder" were to be included, this would make the formalization complete in my view." assertion.
• comment hasCommentText "The class looks good." 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 the skos:related object should be <http://www.wikidata.org/entity/Q898356>." assertion.
• comment hasCommentText "The general definition seems ok." 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 "The description of the class seems ok." 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 "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 "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 "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 "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 "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 correct qualifier here would be "generally"." 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 "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 provenance should use the 'Generated by a formalization activity' template." 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 "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 "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 "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 formalization looks solid to me." assertion.
• comment hasCommentText "The provenance part should use the template 'generated from a formalization activity'." 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 "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 "Overall, I think this is a very good formalization." assertion.
• comment hasCommentText "The provided label for the superpattern instance refers to 'licenses with a non-commertial clause' in general, whereas the actual formalization has the specific kind of license 'Creative Commons NonCommercial' in subject position. This should be make consistent in one way or the other." assertion.
• comment hasCommentText "The provenance part should refer to the original publication by using the template 'generated from a formalization activity'." assertion.
• comment hasCommentText "This looks like a very good formalization to me." 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 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. It has been changed in the formal definition of class which is now skos:related to both - the cortex class and the size class in Wikidata." 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 "I do have to agree. However, I changed it to affects instead of causes since it is a negation and leaves the option open to find a positive correlation in the future." assertion.
• comment hasCommentText "The missing information have been added." 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 "The original quote from the article has been replaced with a more specific one" assertion.
• comment hasCommentText "Thanks! m." assertion.
• comment hasCommentText "Thanks! m." assertion.
• comment hasCommentText "Thanks for the positive review on the class definition." assertion.
• comment hasCommentText "Provenance changed to show generated by a formalization activity." assertion.

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