has the comment text

Tobias Kuhn

2023-08-16T11:04:32.221Z

This is just a test with a long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long long comment.

Tobias Kuhn

2023-08-16T10:46:24.119Z

has the comment text

Tobias Kuhn

2023-08-16T10:41:01.767Z

Yes, and as expressed in http://purl.org/np/RAANP7AWgyZRaS2WgNcGDfp8-4bXv0blhKapMcUrrWvos , it would be nice to have a way to quantify the solidity.

Cristina-Iulia Bucur

2021-12-17T10:42:04.007Z

Yes, and it would be nice to have a way to assess how well the formalization corresponds to the original claim.

Cristina-Iulia Bucur

2021-12-17T10:33:10.257Z

Yes, and maybe we should clarify the procedure for doing this systematically.

Cristina-Iulia Bucur

2021-12-17T10:29:59.594Z

Yes, it would be useful to specify how the sources should be referred to.

Cristina-Iulia Bucur

2021-12-17T10:24:40.300Z

Thank you for your suggestion, which was addressed.

Cristina-Iulia Bucur

2021-11-17T19:50:51.725Z

Thank you.

Cristina-Iulia Bucur

2021-11-17T19:45:57.799Z

Thank you.

Cristina-Iulia Bucur

2021-11-17T19:45:21.231Z

Thank you.

Cristina-Iulia Bucur

2021-11-17T19:44:46.412Z

Thank you.

Cristina-Iulia Bucur

2021-11-17T19:44:43.500Z

In another review comment (http://purl.org/np/RALWxVELKuqrkcO9ud2eXr0E2-ot5bl-0NpOIQi1ktrgI) it is specified that this naming is ok.

Cristina-Iulia Bucur

2021-11-17T19:44:11.450Z

In another review comment (http://purl.org/np/RALWxVELKuqrkcO9ud2eXr0E2-ot5bl-0NpOIQi1ktrgI) it is specified that this naming is ok.

Cristina-Iulia Bucur

2021-11-17T19:43:28.590Z

In another review comment (http://purl.org/np/RALWxVELKuqrkcO9ud2eXr0E2-ot5bl-0NpOIQi1ktrgI) it is specified that this naming is ok.

Cristina-Iulia Bucur

2021-11-17T19:41:33.173Z

Thank you for your suggestion, which was addressed.

Cristina-Iulia Bucur

2021-11-17T19:37:00.187Z

Thank you for your suggestion, which was addressed.

Cristina-Iulia Bucur

2021-11-17T19:35:59.839Z

Thank you for your suggestion, which was addressed.

Cristina-Iulia Bucur

2021-11-17T19:29:32.702Z

Looking at this again, I think this formalization can be made more precise (and in a way simpler) by not using the universal context, but instead biodiversity data (Q28946370) as context and data reuse (Q58023280) as object.

Tobias Kuhn

2021-11-09T14:37:39.607Z

Thank you.

Cristina-Iulia Bucur

2021-11-04T08:29:43.987Z

Thank you for your suggestion which has been implemented.

Cristina-Iulia Bucur

2021-11-04T08:29:13.197Z

Thank you for the suggestion which was implemented.

Cristina-Iulia Bucur

2021-11-04T08:27:07.342Z

Thank you for the suggestion which was implemented.

Cristina-Iulia Bucur

2021-11-04T08:26:28.261Z

Thank you for your suggestion which has been implemented.

Cristina-Iulia Bucur

2021-11-04T08:25:41.076Z

Thank you for your valuable suggestion.

Cristina-Iulia Bucur

2021-11-04T08:19:30.326Z

Thank you.

Mariya Dimitrova

2021-10-28T06:36:54.931Z

The modelling of the formalization looks good.

Cristina-Iulia Bucur

2021-10-19T19:20:01.242Z

Apart from the object class link, this is a very convincing formalization.

Tobias Kuhn

2021-10-18T14:24:34.468Z

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).

Tobias Kuhn

2021-10-18T14:19:13.802Z

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.

Tobias Kuhn

2021-10-14T08:51:32.113Z

This looks like a very good formalization to me.

Tobias Kuhn

2021-10-14T08:47:57.503Z

The provenance part should refer to the original publication by using the template 'generated from a formalization activity'.

Tobias Kuhn

2021-10-14T08:45:01.748Z

I am wondering whether the "never causes" is a bit too strong a relation, also given the natural language sentence. "Never affects" might be more precise than "never causes". (This is also a stronger statement, more likely to be wrong, but that's not necessarily a bad thing.)

Tobias Kuhn

2021-10-14T08:42:32.604Z

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'.

Tobias Kuhn

2021-10-14T08:40:29.441Z

This looks like a very good formalization to me.

Tobias Kuhn

2021-10-14T08:29:23.662Z

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...

Tobias Kuhn

2021-10-14T08:27:07.167Z

The provenance part should be using the template 'generated from a formalization activity'.

Tobias Kuhn

2021-10-14T08:12:44.665Z

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?).

Tobias Kuhn

2021-10-14T08:09:34.403Z

Overall, I think this is a good formalization.

Tobias Kuhn

2021-10-14T08:03:50.967Z

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.

Tobias Kuhn

2021-10-14T08:02:49.190Z

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.

Tobias Kuhn

2021-10-14T07:57:55.467Z

Overall, I think this is a very good formalization.

Tobias Kuhn

2021-10-14T07:42:52.597Z

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.

Tobias Kuhn

2021-10-14T07:42:14.313Z

This looks like a good formalization to me.

Tobias Kuhn

2021-10-14T07:37:51.087Z

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.

Tobias Kuhn

2021-10-14T07:35:58.569Z

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.

Tobias Kuhn

2021-10-14T07:33:47.896Z

It seems to me that the object class should be something like 'excess or deficiency of vitamin A' and not just 'vitamin A'.

Tobias Kuhn

2021-10-14T07:32:24.704Z

The provenance part should use the template 'generated from a formalization activity'.

Tobias Kuhn

2021-10-14T07:30:30.183Z

The label of the superpattern instance should be a short human-readable sentence, not the DOI of the original paper.

Tobias Kuhn

2021-10-14T07:29:37.044Z

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*.

Tobias Kuhn

2021-10-14T07:28:45.501Z

The formalization looks solid to me.

Tobias Kuhn

2021-10-14T07:20:04.914Z

The provenance part should use the template 'generated from a formalization activity'.

Tobias Kuhn

2021-10-14T07:18:51.277Z

Very nice that all classes are defined in WikiData.

Tobias Kuhn

2021-10-14T07:17:23.237Z

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.

Tobias Kuhn

2021-10-14T07:14:08.481Z

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.

Tobias Kuhn

2021-10-14T07:11:40.397Z

The provenance should use the 'Generated by a formalization activity' template.

Tobias Kuhn

2021-10-14T07:05:51.453Z

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.

Tobias Kuhn

2021-10-12T14:16:05.597Z

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.

Cristina-Iulia Bucur

2021-10-11T07:47:36.147Z

The "IRX3" (https://www.wikidata.org/wiki/Q18046058) and "IRX5" (https://www.wikidata.org/wiki/Q18035174) classes should be added as related classes.

Cristina-Iulia Bucur

2021-10-07T00:24:42.724Z

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.

Cristina-Iulia Bucur

2021-10-07T00:18:50.448Z

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).

Cristina-Iulia Bucur

2021-10-07T00:17:25.659Z

The definition and declaration of the class is good.

Cristina-Iulia Bucur

2021-10-07T00:07:09.233Z

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).

Cristina-Iulia Bucur

2021-10-06T23:59:04.849Z

I think a correct subclass would be "treatment" (https://www.wikidata.org/wiki/Q179661).

Cristina-Iulia Bucur

2021-10-06T23:58:37.152Z

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).

Cristina-Iulia Bucur

2021-10-06T23:55:54.332Z

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.".

Cristina-Iulia Bucur

2021-10-06T23:49:44.776Z

Maybe a skos:related term can be added in the form of https://www.wikidata.org/wiki/Q1754768 as an object.

Cristina-Iulia Bucur

2021-10-06T23:31:18.481Z

The general declaration of the class seems ok.

Cristina-Iulia Bucur

2021-10-06T23:26:21.658Z

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".

Cristina-Iulia Bucur

2021-10-06T22:55:14.853Z

The general definition seems ok.

Cristina-Iulia Bucur

2021-10-06T22:44:24.290Z

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.

Cristina-Iulia Bucur

2021-10-06T22:43:35.827Z

The general definition of the class seems ok.

Cristina-Iulia Bucur

2021-10-06T22:35:02.696Z

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.

Cristina-Iulia Bucur

2021-10-06T21:59:52.304Z

The modelling of the formalization reflects very well the scientific claim.

Cristina-Iulia Bucur

2021-10-06T19:53:22.786Z

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.

Cristina-Iulia Bucur

2021-10-06T19:51:12.581Z

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.

Cristina-Iulia Bucur

2021-10-06T19:49:15.990Z

The modelling of the formalization seems to reflect well the content of the scientific claim.

Cristina-Iulia Bucur

2021-10-06T19:46:04.316Z

The modeling of the formalization reflects very well the scientific claim.

Cristina-Iulia Bucur

2021-10-06T19:44:57.531Z

The modelling of the formalization is good.

Cristina-Iulia Bucur

2021-10-06T19:39:49.858Z

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.

Cristina-Iulia Bucur

2021-10-06T19:38:40.403Z

The modelling of the formalization looks good.

Cristina-Iulia Bucur

2021-10-06T19:34:11.255Z

Something small: starting the sentence containing the scientific claim of the super-pattern with a capital letter.

Cristina-Iulia Bucur

2021-10-06T19:28:36.565Z

A small thing: to start the sentence containing the scientific claim with an uppercase letter.

Cristina-Iulia Bucur

2021-10-06T19:26:42.403Z

If the formalization has multiple authors, then these need to be specified in this part, after choosing the "FormalizationActivity" as provenance of the formalization.

Cristina-Iulia Bucur

2021-10-05T23:26:59.591Z

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.

Cristina-Iulia Bucur

2021-10-05T22:55:02.611Z

The modeling of the formalization reflects very well the scientific claim.

Cristina-Iulia Bucur

2021-10-05T22:49:33.579Z

The provenance of the formalization is the result of a "FormalizationAcitvity", which is correctly chosen and filled in.

Cristina-Iulia Bucur

2021-10-05T22:15:05.459Z

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.

Cristina-Iulia Bucur

2021-10-05T13:55:56.487Z

The resulting formalization has as a provenance the "FormalizationActivity", which is correct. Moreover, all fields are correctly filled in.

Cristina-Iulia Bucur

2021-10-04T15:58:45.302Z

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.

Cristina-Iulia Bucur

2021-10-04T13:24:33.935Z

The formalization in the assertion reflects very well the chosen scientific claim.

Cristina-Iulia Bucur

2021-10-04T10:36:09.460Z

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".

Cristina-Iulia Bucur

2021-10-04T10:20:40.154Z

The exact quote from the article should be specified, not the text of the scientific claim in the formalization.

Cristina-Iulia Bucur

2021-09-27T13:43:33.194Z

It would be good to add a skos:relatedMatch reference to an identifier for PCI.

Tobias Kuhn

2021-08-11T13:37:33.909Z

It would be good to add skos:relatedMatch references to identifiers for the genes IRX3 and IRX5.

Tobias Kuhn

2021-08-11T13:36:09.363Z

The label 'expression of genes IRX3 AND IRX5' unnecessarily capitalizes 'AND', which seems wrong and could be confusing.

Tobias Kuhn

2021-08-11T13:34:51.657Z

This class definition looks good.

Tobias Kuhn

2021-08-11T13:32:14.040Z

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).

Tobias Kuhn

2021-08-11T13:30:28.390Z

This class definition looks OK.

Tobias Kuhn

2021-08-11T13:26:47.349Z

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'.

Tobias Kuhn

2021-06-23T05:05:18.750Z