@prefix this: . @prefix sub: . @prefix np: . @prefix dct: . @prefix nt: . @prefix npx: . @prefix xsd: . @prefix rdfs: . @prefix orcid: . @prefix prov: . @prefix ns1: . @prefix foaf: . sub:Head { this: a np:Nanopublication; np:hasAssertion sub:assertion; np:hasProvenance sub:provenance; np:hasPublicationInfo sub:pubinfo . } sub:assertion { rdfs:comment """We have the nanopub tutorial page: https://nanopub.net/docs/tutorials/ And this gentle intro: https://saranjeetkaur.github.io/nanopub_101/#/title-slide also expressed as fair training material: https://w3id.org/np/RAz25iqVXH4PWBENKSqdUBAif3oDVgUa2-GVU30HD1lLE - and probably other resources.""" . } sub:provenance { sub:assertion prov:wasAttributedTo orcid:0000-0003-2408-7588 . } sub:pubinfo { orcid:0000-0003-2408-7588 foaf:name "Christian Meesters" . this: dct:created "2026-05-16T07:39:34.689Z"^^xsd:dateTime; dct:creator orcid:0000-0003-2408-7588; dct:license ; npx:wasCreatedAt ; rdfs:label "Comment on: RAZHJmoLra"; nt:wasCreatedFromProvenanceTemplate ; nt:wasCreatedFromPubinfoTemplate , ; nt:wasCreatedFromTemplate ns1:RA3gQDMnYbKCTiQeiUYJYBaH6HUhz8f3HIg71itlsZDgA . sub:sig npx:hasAlgorithm "RSA"; npx:hasPublicKey "MIGfMA0GCSqGSIb3DQEBAQUAA4GNADCBiQKBgQC+DVJTSCzdJUJMzlwRfb2Qm2NZpuZ932RpVliWxMAhmZ6ZkeeibmJlW/Z0q51YkFArJIWbJ0f7rLQWM5epuZV4I5cjMqepOWGey6LrPolMs8lI9dJf9zW9lJsneV+py3U8WsrB6mg//pkEeXnVDd+WscADyXJ5EeLwoZjCkPn8/QIDAQAB"; npx:hasSignature "KkeTYZZ2noSup913+AaLqw6UiO5q/wMG2jn7MQYCVrLIOkfvTbVisbK+PMIK9I2zcV0NjTWlAj0Eg5WemKmp+EF+hLWL1K0F5xHFsqZ8n8++UcOz/NLY0hoWdTm61iOAL+3G4PxWxa1uK6Fw4a7RQ4haLwdCwoMvyeuKQF7scNo="; npx:hasSignatureTarget this:; npx:signedBy orcid:0000-0003-2408-7588 . } @prefix this: . @prefix sub: . @prefix np: . @prefix rdf: . @prefix prov: . @prefix npx: . @prefix dc: . @prefix xsd: . sub:Head { this: a np:Nanopublication; np:hasAssertion sub:assertion; np:hasProvenance sub:provenance; np:hasPublicationInfo sub:pubinfo . } sub:assertion { "Same FORRT Claim can be investigated at HEALPix nside=128." . } sub:provenance { sub:assertion prov:wasAttributedTo . } sub:pubinfo { " Anne Fouilloux" . this: dc:created "2026-05-11T19:21:05.801Z"^^xsd:dateTime; dc:creator ; dc:license ; npx:wasCreatedAt ; "Comment on: RAh7NYjme8dajwxnoBfbOjsd1L76LQfN-pMEajIwiRDJE"; . sub:sig npx:hasAlgorithm "RSA"; npx:hasPublicKey "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"; npx:hasSignature "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"; npx:hasSignatureTarget this:; npx:signedBy . } @prefix this: . @prefix sub: . @prefix np: . @prefix rdf: . @prefix prov: . @prefix npx: . @prefix dc: . @prefix xsd: . sub:Head { this: a np:Nanopublication; np:hasAssertion sub:assertion; np:hasProvenance sub:provenance; np:hasPublicationInfo sub:pubinfo . } sub:assertion { "Some of the topics are incorrect in this nanopublication. For instance meta learning. So I disapprove it and create a new one with the correct information." . } sub:provenance { sub:assertion prov:wasAttributedTo . } sub:pubinfo { " Anne Fouilloux" . this: dc:created "2026-04-18T15:16:40.475Z"^^xsd:dateTime; dc:creator ; dc:license ; npx:wasCreatedAt ; "Comment on: RAMica_BoBV-OHaTZzdFCLK1bh76wIarqr2aQoTRqczMo"; . sub:sig npx:hasAlgorithm "RSA"; npx:hasPublicKey "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"; 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The problems you describe are definitely real, and we need to address them. It's great to see big entities like Astera and Arcadia taking such a clear stance because solving these problems is difficult. People don't like to let go of their habits, particularly if those habits made them \"successful\" researchers. It will also be a big transition, and those are difficult and take time, particularly when collective incentives are involved, where individuals are punished by the system if they deviate. I hope this helps gain momentum and that we can all work together to eliminate these vast inefficiencies in current science communication (and thereby science itself). As a specific remark, I would add one point to your \"structural features\" list. You allude to this point when you mention \"linked data\" and \"narratives\", but I think it would deserve to feature as a separate point in this list: - Unstructured information: The scientific findings as well as their context are not represented in a structured manner that would allow for things like automatic and precise aggregations, updates, and question answering. For example, when evidence (or counter-evidence) for a particular relation between a given gene and a certain disease is presented, the entities (gene and disease) and the relation (e.g. \"tends to contribute to\") should be formally expressed with community-agreed identifiers, and this statement should be linked in an equally structured way to the equiment, scientific method, raw data, significance values, and researchers involved in arriving at that finding. Only then, we can reliably aggregate all these findings (like live literature reviews!), have all researchers interested in these topics be updated in real-time, provide these data as input for future neuro-symbolic AIs, and generally build reliable and provenance-aware tools on top of this (for researchers as well as the general public).""" . } sub:provenance { sub:assertion prov:wasAttributedTo orcid:0000-0002-1267-0234 . } sub:pubinfo { orcid:0000-0002-1267-0234 foaf:name "Tobias Kuhn" . this: dct:created "2025-06-16T14:43:28.126Z"^^xsd:dateTime; dct:creator orcid:0000-0002-1267-0234; dct:license ; npx:wasCreatedAt ; rdfs:label "Comment on: scientific-publishing-enough-is-enough"; nt:wasCreatedFromProvenanceTemplate ; nt:wasCreatedFromPubinfoTemplate , ; nt:wasCreatedFromTemplate ns1:RA3gQDMnYbKCTiQeiUYJYBaH6HUhz8f3HIg71itlsZDgA . sub:sig npx:hasAlgorithm "RSA"; npx:hasPublicKey "MIGfMA0GCSqGSIb3DQEBAQUAA4GNADCBiQKBgQD4Wj537OijfOWVtsHMznuXKISqBhtGDQZfdO6pbb4hg9EHMcUFGTLbWaPrP783PHv8HMAAPjvEkHLaOHMIknqhaIa5236lfBO3r+ljVdYBElBcLvROmwG+ZGtmPNZf7lMhI15xf5TfoaSa84AFRd5J2EXekK6PhaFQhRm1IpSYtwIDAQAB"; npx:hasSignature "lQ1/648LC+DjNN4v6ljd0rOkwyF2VlsPJJ47BXhsPxh1/cyr0bcsUuJYrgJuUUQwuz59z+twUF9TgKO53jus4GCbk9XBnRN5h4Vm+xn9u37xs2h4SHu61ky36mgpFvX7bX2hzafpIsB3iCeULiQe66S241g+TO4W8vhcTl7oL8o="; npx:hasSignatureTarget this:; npx:signedBy orcid:0000-0002-1267-0234 . } @prefix this: . @prefix sub: . @prefix np: . @prefix dct: . @prefix nt: . @prefix npx: . @prefix xsd: . @prefix rdfs: . @prefix orcid: . @prefix prov: . @prefix ns1: . @prefix foaf: . sub:Head { this: a np:Nanopublication; np:hasAssertion sub:assertion; np:hasProvenance sub:provenance; np:hasPublicationInfo sub:pubinfo . } sub:assertion { rdfs:comment "It was really cool! Thanks Tobias for organizing this." . } sub:provenance { sub:assertion prov:wasAttributedTo orcid:0000-0002-2543-9461 . } sub:pubinfo { orcid:0000-0002-2543-9461 foaf:name "Piotr Sowiński" . this: dct:created "2025-06-09T08:12:32.983Z"^^xsd:dateTime; dct:creator orcid:0000-0002-2543-9461; dct:license ; npx:wasCreatedAt ; rdfs:label "Comment on: RATX060iPk"; nt:wasCreatedFromProvenanceTemplate ; nt:wasCreatedFromPubinfoTemplate , ; nt:wasCreatedFromTemplate ns1:RA3gQDMnYbKCTiQeiUYJYBaH6HUhz8f3HIg71itlsZDgA . sub:sig npx:hasAlgorithm "RSA"; npx:hasPublicKey "MIGfMA0GCSqGSIb3DQEBAQUAA4GNADCBiQKBgQCTHgk4F1Fuj1WT3rb97R451KIDLjCwb0dyVD4BQEii7FqUMNjVsfH2oU19Tvkopmt/OVaOI/7khWR/NtiIhXJTekIZYh9Ccop527GwZVlwtvJT4LGtMrcXNK8E6/6i7HCR2UEMbM1AhzEdo9FOwXyjAgw+qWjo1XNpkXIGfqHEeQIDAQAB"; npx:hasSignature "C5gjAj1EXowMPSG60UwfYabKy0Kvl1w4MQMyO5OE/ZOV2Lh0XfPso2RhG4OxEtbQaBLQbFl7lRgMZ3r8NlAgqHCDBNye4nBfoI5d/N8Lnu+zsRT0DOq7fKqlYEpBL0jAXcTqxD5uniMlAV0ZOXy3h5KSX9BTUv62z5/behtA748="; npx:hasSignatureTarget this:; 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It is a groundbreaking album that showcases his unique ability to blend various musical genres, including rock, R&B, and traditional Chinese elements." . } sub:provenance { sub:assertion prov:wasAttributedTo orcid:0009-0006-7468-8612 . } sub:pubinfo { orcid:0009-0006-7468-8612 foaf:name "Guanghe Xie" . sub:sig npx:hasAlgorithm "RSA"; npx:hasPublicKey "MIGfMA0GCSqGSIb3DQEBAQUAA4GNADCBiQKBgQCUdMG+7pEPHDalkSCV/ABYfNfi959c/KYLvf4+3emb+KThgeVaWPYsTYATvSRN0AEZ4TIM2iCZR1zv6xd6+W3lX5lh5KYckUX0IDUZcmsn6A7EYjubS7j+OMVg1Vln9EGXzcsjIAXqWYifbH6f2q3O9tvlxqTHafVR/90boxm4kQIDAQAB"; npx:hasSignature "jFfl1Rk8qM09F2GCN5M/HSqU1YuPB6fqt48p7dVbMEuwWHYx575rKa8R+PaQV7L0fhxLUWTbpzQO9eP2jZdrED+CV6uqLvCn9hKpRaQ1JaPUoD5Fs7RXfsQBPpaF/awCxCqv6gwvLVsr3R7S6da+CEC9BTq1/zqsLOaM2glEY74="; npx:hasSignatureTarget this:; npx:signedBy orcid:0009-0006-7468-8612 . this: dct:created "2024-10-04T15:15:10.134Z"^^xsd:dateTime; dct:creator orcid:0009-0006-7468-8612; dct:license ; npx:wasCreatedAt ; rdfs:label "Comment on: Black_Tangerine"; nt:wasCreatedFromProvenanceTemplate ; nt:wasCreatedFromPubinfoTemplate , ; nt:wasCreatedFromTemplate . } @prefix this: . @prefix sub: . @prefix np: . @prefix dct: . @prefix nt: . @prefix npx: . @prefix xsd: . @prefix rdfs: . @prefix orcid: . @prefix prov: . @prefix ns1: . @prefix foaf: . sub:Head { this: a np:Nanopublication; np:hasAssertion sub:assertion; np:hasProvenance sub:provenance; np:hasPublicationInfo sub:pubinfo . } sub:assertion { rdfs:comment "This book is an enjoyable read." . } sub:provenance { sub:assertion prov:wasAttributedTo orcid:0009-0005-5152-6832 . } sub:pubinfo { orcid:0009-0005-5152-6832 foaf:name "Zsofia Gugan" . sub:sig npx:hasAlgorithm "RSA"; npx:hasPublicKey "MIGfMA0GCSqGSIb3DQEBAQUAA4GNADCBiQKBgQCli5hvNyennNxd8cRf6R0uw/UEOlZ08MQ+ZHeEoq5TCQiMDxeibE81dBjfzYCCAJ45dddVLAhYEiayikeTDKhVy8fnZ8YwIXsXmvB+jlu8Z3FMa46h3khtBG9PFBWgS8s8qcil8IrGBhhnXTTRkKBPdphEdbRdCb/XyjHXx+Fq8wIDAQAB"; npx:hasSignature "cnRYtEnnYl6IuBnNfH5aiYjUuHj7NyricnVE1JDNU/TtsK5lURiWjBC/ygUERmGx5HMx+NUvpd+pmTRCI7yLSEq0783xB71SXqBASjgW4vhVtH21ugLWeRu8HN/egwQrHTiwXRY1tW7d6vv/hx7zuxYz+g2o5XQtWaMFHQhzUuY="; npx:hasSignatureTarget this:; npx:signedBy orcid:0009-0005-5152-6832 . this: a npx:ExampleNanopub; dct:created "2024-10-03T16:50:54.092Z"^^xsd:dateTime; dct:creator orcid:0009-0005-5152-6832; dct:license ; npx:supersedes ; npx:wasCreatedAt ; rdfs:label "Comment on: Q101438737"; nt:wasCreatedFromProvenanceTemplate ns1:RANwQa4ICWS5SOjw7gp99nBpXBasapwtZF1fIM3H2gYTM; nt:wasCreatedFromPubinfoTemplate ns1:RAA2MfqdBCzmz9yVWjKLXNbyfBNcwsMmOqcNUxkk1maIM, ns1:RATtBNB9Rj1cIwxJyoHBgNn8eeIR06m0H6C6RTRVqSy3E, ns1:RAh1gm83JiG5M6kDxXhaYT1l49nCzyrckMvTzcPn-iv90, ns1:RAjpBMlw3owYhJUBo3DtsuDlXsNAJ8cnGeWAutDVjuAuI; nt:wasCreatedFromTemplate ns1:RA3gQDMnYbKCTiQeiUYJYBaH6HUhz8f3HIg71itlsZDgA . } @prefix this: . @prefix sub: . @prefix np: . @prefix dct: . @prefix nt: . @prefix npx: . @prefix xsd: . @prefix rdfs: . @prefix orcid: . @prefix prov: . @prefix foaf: . sub:Head { this: a np:Nanopublication; np:hasAssertion sub:assertion; np:hasProvenance sub:provenance; np:hasPublicationInfo sub:pubinfo . } sub:assertion { rdfs:comment """Thanks for your reply. Yes, we seem to be in agreement then :) Except possibly some details on the order in which certain steps should be taken. We have focussed on the technology (but always with the users in the longer term in our mind), because the technology needs to be at a certain level of maturity to start doing actual things with it. How to represent scientific content as a knowledge graph has been studied academically, and to make the next step to move this to practice we need a suitable technology first. And now that the technology is \"ready enough\", we can start doing this, but we won't get it right on the first try. So, in my view, what you point out are valid points, but they are not fundamental shortcomings but rather practical mistakes and rough edges that are part of the process. Right, the last two query links were broken. Somehow they got truncated. I fixed the links in my post above, and now they should work. Indeed persistence isn't free. But for nanopublications, as long as we stay in the range of thousands to millions, the costs are actually small. In particular if we separate the storage/archiving from the querying layer, as we do, where only the first is crucial for persistence. Then the persistence is more of an organizational/coordination problem than a cost problem, and with a decentralized redundant network as we have it, this task can be distributed and managed at low cost (on university servers, for example). Maybe URIs don't always resolve, but there is always a well-defined procedure to find the nanopubs at other locations. Things change if we talk about hundreds of millions to billions of nanopublications and more. Given the versatility of nanopublications, it's possible we will get there. For this we need a model where the mass creators of nanopublications also carry the associated costs. We are working on next-generation nanopublication services that will allow for exactly that. Nodes in the nanopublication network can then assert restrictions and quotas on users and types of nanopublications they replicate/accept, and so for publishing large quantities one would have to convince (with money, probably) a few of the nodes to co-host the nanopublications. Just as a quick summary of these plans; happy to explain more. And it's great that your post has triggered these discussions. Thanks for that :)""" . } sub:provenance { sub:assertion prov:wasAttributedTo orcid:0000-0002-1267-0234 . } sub:pubinfo { orcid:0000-0002-1267-0234 foaf:name "Tobias Kuhn" . sub:sig npx:hasAlgorithm "RSA"; npx:hasPublicKey "MIGfMA0GCSqGSIb3DQEBAQUAA4GNADCBiQKBgQD4Wj537OijfOWVtsHMznuXKISqBhtGDQZfdO6pbb4hg9EHMcUFGTLbWaPrP783PHv8HMAAPjvEkHLaOHMIknqhaIa5236lfBO3r+ljVdYBElBcLvROmwG+ZGtmPNZf7lMhI15xf5TfoaSa84AFRd5J2EXekK6PhaFQhRm1IpSYtwIDAQAB"; npx:hasSignature "uSuWHs0RDQfWRcmsckUcuo4iw7kTD4hQmwgMjvv0hUrAc870ba706vTSY/C+dElcL6fGDNS1S776yWO8oAdOZvzHi97SmRDgZvox8TEx9Fp2lpL3rVQwuJyzAWuwDBh1ml9fif+9WqzIHCUuQcpoi1Ed4Q9RU8HI3bjhNtPrKhs="; npx:hasSignatureTarget this:; npx:signedBy orcid:0000-0002-1267-0234 . this: dct:created "2024-06-20T08:56:31.960Z"^^xsd:dateTime; dct:creator orcid:0000-0002-1267-0234; dct:license ; npx:supersedes ; npx:wasCreatedAt ; rdfs:label "Comment on: comment-6484057602"; nt:wasCreatedFromProvenanceTemplate ; nt:wasCreatedFromPubinfoTemplate , , ; nt:wasCreatedFromTemplate . } @prefix this: . @prefix sub: . @prefix np: . @prefix dct: . @prefix nt: . @prefix npx: . @prefix xsd: . @prefix rdfs: . @prefix orcid: . @prefix prov: . @prefix foaf: . sub:Head { this: a np:Nanopublication; np:hasAssertion sub:assertion; np:hasProvenance sub:provenance; np:hasPublicationInfo sub:pubinfo . } sub:assertion { rdfs:comment """Hi Roderic, Great to see that you decided to look into nanopublications and get to the bottom of it. Let me respond to some of the points you raised and clarify a few misunderstandings and inaccuracies. > Nanopubs, a way to create even more silos The title is highly misleading in my view. You can use any kind of URI-based identifiers in nanopublications, so any silo-ness on the conceptual level is user-generated and not a shortcoming of the nanopublication technology. And on the data storage level, nanopublications are born in the global decentralized nanopublication network and never live in just one location, so they are as anti-silo as you can be in that respect. The nanopublication you mention can be found at all these places: - https://server.np.trustyuri.net/RAXCvEZfCcjYuH5DWOIujBehGQt61y_nRHWssw9u6aYig - http://130.60.24.146:7880/RAXCvEZfCcjYuH5DWOIujBehGQt61y_nRHWssw9u6aYig - https://server.np.dumontierlab.com/RAXCvEZfCcjYuH5DWOIujBehGQt61y_nRHWssw9u6aYig - http://rdf.disgenet.org/nanopub-server/RAXCvEZfCcjYuH5DWOIujBehGQt61y_nRHWssw9u6aYig - https://np.knowledgepixels.com/RAXCvEZfCcjYuH5DWOIujBehGQt61y_nRHWssw9u6aYig And you can query it at all these places (and more): - https://query.np.trustyuri.net/tools/full/yasgui.html#query=SELECT+%3Fs+%3Fp+%3Fo+WHERE+%7B+GRAPH+%3Chttps%3A%2F%2Fw3id.org%2Fnp%2FRAXCvEZfCcjYuH5DWOIujBehGQt61y_nRHWssw9u6aYig%23assertion%3E+%7B+%3Fs+%3Fp+%3Fo+%7D+%7D+&contentTypeConstruct=text%2Fturtle&contentTypeSelect=application%2Fsparql-results%2Bjson&endpoint=%2Frepo%2Ffull&requestMethod=POST&tabTitle=Query&headers=%7B%7D&outputFormat=table - https://nanopub.sdsc.edu/tools/full/yasgui.html#query=SELECT+%3Fs+%3Fp+%3Fo+WHERE+%7B+GRAPH+%3Chttps%3A%2F%2Fw3id.org%2Fnp%2FRAXCvEZfCcjYuH5DWOIujBehGQt61y_nRHWssw9u6aYig%23assertion%3E+%7B+%3Fs+%3Fp+%3Fo+%7D+%7D+&contentTypeConstruct=text%2Fturtle&contentTypeSelect=application%2Fsparql-results%2Bjson&endpoint=%2Frepo%2Ffull&requestMethod=POST&tabTitle=Query&headers=%7B%7D&outputFormat=table - https://query.np.kpxl.org/tools/full/yasgui.html#query=SELECT+%3Fs+%3Fp+%3Fo+WHERE+%7B+GRAPH+%3Chttps%3A%2F%2Fw3id.org%2Fnp%2FRAXCvEZfCcjYuH5DWOIujBehGQt61y_nRHWssw9u6aYig%23assertion%3E+%7B+%3Fs+%3Fp+%3Fo+%7D+%7D+&contentTypeConstruct=text%2Fturtle&contentTypeSelect=application%2Fsparql - https://query.knowledgepixels.com/tools/full/yasgui.html#query=SELECT+%3Fs+%3Fp+%3Fo+WHERE+%7B+GRAPH+%3Chttps%3A%2F%2Fw3id.org%2Fnp%2FRAXCvEZfCcjYuH5DWOIujBehGQt61y_nRHWssw9u6aYig%23assertion%3E+%7B+%3Fs+%3Fp+%3Fo+%7D+%7D+&contentTypeConstruct=text%2Fturtle&contentTypeSelect=application%2Fsparql Can you point me to any technology that is *less* silo than this? > there are reasons not to be optimistic about nanopubs (or text-mining in general) Nanopublications are *not* a special case of text mining. In fact, they were conceived to make sure we don't need text mining in the first place (\"Why bury it first and then mine it again?\"; see https://doi.org/10.1186/1471-2105-6-142 ). > In other words, > [Helictopleurus dorbignyi] -> [isSynonymOf] -> [Helictopleurus halffteri] > This seems a fairly simple thing to say, ... Yes, it always looks simple until you dig into the details, and then it gets more complicated. This modeling was the result form extended discussions with people at Pensoft and other biodiversity experts. I might not be using the right domain terms here, but as you know, taxons have names and these names have URI-based identifiers even, but these names have often been used in different ways. So, the same names (even with identifiers) can refer to different taxon *concepts*. For these concepts, there aren't universally available and acceptable identifiers yet, unfortunately. But they can be constructed form a taxon name and a reference to a publication or \"treatment\" where this interpretation is explained. There are others who can explain better the domain side of this reasoning, which you can probably piece together from your own expertise in the domain, but that was how we arrived at this semantic model. > indeed we could say it with a single triple, but the corresponding nanopub requires 33 RDF triples to say this. 33 doesn't seem like a very large number to me. And I can explain in detail the purpose of every single one of these triples. Provenance and metadata are important, and they need a bit of space, that's all. > By itself this isn’t terribly useful because neither of the two taxa are “things” that have identifiers, they are blank nodes. Yes, but that's a result of the modeling decision above. Nanopublications as a technology don't force you to do it this way. > cannot have interoperability unless you use the same identifiers for the same things No, that's not true. We should indeed *minimize* the use of different identifiers for the same thing, but we can very well achieve interoperability with multiple identifiers. Approaches like linksets and scientific lenses, among others, can do this. We are working on concrete solutions for this within the nanopublication ecosystem too. On an open and distributed system like the Web, it's in fact *impossible* to enforce unique identifiers for the same things. You cannot prevent different people defining different identifiers for the same thing at different ends of the Web, and it has actually happened many many times, so we have to deal with this whether we want to or not. > That means persistent identifiers, identifiers that you have some confidence will be around in ten, 20, or 50 years (at least). That's a completely separate issue from the previous sentence. Yes, but what does \"to be around\" mean? Will catalogueoflife.org still be up in 2074? We don't know! But we can design systems where this doesn't even matter. What matters is that we can keep using the identifier and have an agreement of what it means. And you can do that with nanopublications and their ecosystem, and we are working on the concrete methods and tools. > I find it alarming that the link to the source of the statement that these two names are synonyms is not the DOI for the paper 10.3897/BDJ.12.e120304, No need to be alarmed. But yes, it should refer to the DOI and this should be fixed. We are looking into it with Pensoft. The reason is that this nanopublication was created before the DOI was minted. And the last step of making final versions of nanopublications upon formal article publication isn't fully developed yet. We have a long journey ahead of us, so we decided to move fast and allow ourselves to make mistakes on the way. This is one of them and it will be fixed. > The taxon names have as their identifiers https://www.checklistbank.org/dataset/9880/taxon/3K9T4 and https://www.checklistbank.org/dataset/9880/taxon/3K9ST. These identifiers are also local to a particular dataset. Why not use identifiers such as the Catalogue of Life entries for these names (i.e., e.g. https://www.catalogueoflife.org/data/taxon/3K9T4, Checklistbank has broader coverage and is therefore more universal, and includes Catalogueoflife. To me Checklistbank seemed at least as persistent and long-term as Catalogueoflife, so overall preferable, but I am not familiar with the details and policies behind these platforms. In any case, this is a just a modeling decision we made, which we could have just as well done differently. It just shows we can use any kind of URI-based identifier, and consequently some tools/people will sometimes make modeling mistakes, but that's part of the process. > This is nice, but where is the equivalent for linking the publication to the nanopub via its DOI, or the taxon names to the nanopub? It should and can be there. See my answer above. > For example, http://purl.obolibrary.org/obo/NOMEN_0000285 is used to define the relation between. I confess it’s unclear to me why NOMEN_0000285 isn’t used to directly link the two ChecklistBank records, rather than the indirection via #subjtaxon and #objtaxon, given that is a relationship between names (isn’t it?). See above. > It amazes me how readily people create new ontologies We just defined terms where needed, and didn't necessarily group them together in ontologies, applying the thinking of \"breaking things into nano-pieces\" to ontologies and their terms, in a sense. > especially as in the wider world there is a trend towards one vocabuary to rule them all (schema.org). Not all trends are good. Just saying :) > I find it disheartening that the bulk of the information in a nanopub is administrivia about that nanopub. Again, it all has a purpose, which I can explain in more detail if you like. > I understand the desire to establish provenance and to cryptographically sign the information, but all this is of limited use if the actual scientific information is poorly expressed. This is a false dichotomy. Of course we want both: provenance/validity, as well as properly expressed assertions. Nanopublications don't tell you upfront which ontologies to use (so no conceptual silo) or how to formulate your statements, but then of course modeling mistakes can happen. There is no way to prevent that, but that doesn't mean the technology or the ecosystem is flawed. I hope these responses and clarifications are helpful. Tobias""" . } sub:provenance { sub:assertion prov:wasAttributedTo orcid:0000-0002-1267-0234 . } sub:pubinfo { orcid:0000-0002-1267-0234 foaf:name "Tobias Kuhn" . sub:sig npx:hasAlgorithm "RSA"; npx:hasPublicKey "MIGfMA0GCSqGSIb3DQEBAQUAA4GNADCBiQKBgQD4Wj537OijfOWVtsHMznuXKISqBhtGDQZfdO6pbb4hg9EHMcUFGTLbWaPrP783PHv8HMAAPjvEkHLaOHMIknqhaIa5236lfBO3r+ljVdYBElBcLvROmwG+ZGtmPNZf7lMhI15xf5TfoaSa84AFRd5J2EXekK6PhaFQhRm1IpSYtwIDAQAB"; npx:hasSignature "d1GNDDcKeUKVk41JU9WqjBiB9luhapGJY3VYOIPxR9hayjkUxX3hcQVKPkrbfAul3bgnjS5oj3FiWqxMBSZzOhpkGLvtSPYv3Bv5HBGXra+f7fbDvc1SpImWuDMqKZGAyOdnxqoXVhdPlTL1w8KalxSo15t71xgNk3QJVNRT/Z4="; npx:hasSignatureTarget this:; npx:signedBy orcid:0000-0002-1267-0234 . this: dct:created "2024-06-19T12:09:27.022Z"^^xsd:dateTime; dct:creator orcid:0000-0002-1267-0234; dct:license ; npx:wasCreatedAt ; rdfs:label "Comment on: nanopubs-way-to-create-even-more-silos.html"; nt:wasCreatedFromProvenanceTemplate ; nt:wasCreatedFromPubinfoTemplate , ; nt:wasCreatedFromTemplate . } @prefix this: . @prefix sub: . @prefix np: . @prefix dct: . @prefix nt: . @prefix npx: . @prefix xsd: . @prefix rdfs: . @prefix orcid: . @prefix prov: . @prefix ns1: . @prefix foaf: . sub:Head { this: a np:Nanopublication; np:hasAssertion sub:assertion; np:hasProvenance sub:provenance; np:hasPublicationInfo sub:pubinfo . } sub:assertion { rdfs:comment "a well-preserved wolf" . } sub:provenance { sub:assertion prov:wasAttributedTo orcid:0000-0002-1267-0234 . } sub:pubinfo { orcid:0000-0002-1267-0234 foaf:name "Tobias Kuhn" . sub:sig npx:hasAlgorithm "RSA"; npx:hasPublicKey "MIGfMA0GCSqGSIb3DQEBAQUAA4GNADCBiQKBgQD4Wj537OijfOWVtsHMznuXKISqBhtGDQZfdO6pbb4hg9EHMcUFGTLbWaPrP783PHv8HMAAPjvEkHLaOHMIknqhaIa5236lfBO3r+ljVdYBElBcLvROmwG+ZGtmPNZf7lMhI15xf5TfoaSa84AFRd5J2EXekK6PhaFQhRm1IpSYtwIDAQAB"; npx:hasSignature "5+/IkcoKmbf683+4gaLKZSX1pChI18loPkggNNqEu6HW5wFUsv/IQ2hsmpNKKPYBdcUQBbgtYtm2H+lv+KwEu1e6eSN9nqf4u+jhcNULAx9nu0xXLc9hbufzq53tEPU6LNWSAssmrLwviaGNNpu9ZYk5NL0pCW1hyH6102aqe9M="; npx:hasSignatureTarget this:; npx:signedBy orcid:0000-0002-1267-0234 . this: a npx:ExampleNanopub; dct:created "2024-04-17T11:11:00.121Z"^^xsd:dateTime; dct:creator orcid:0000-0002-1267-0234; dct:license ; npx:wasCreatedAt ; rdfs:label "Comment on: RGM.1287389"; nt:wasCreatedFromProvenanceTemplate ns1:RANwQa4ICWS5SOjw7gp99nBpXBasapwtZF1fIM3H2gYTM; nt:wasCreatedFromPubinfoTemplate ns1:RAA2MfqdBCzmz9yVWjKLXNbyfBNcwsMmOqcNUxkk1maIM, ns1:RATtBNB9Rj1cIwxJyoHBgNn8eeIR06m0H6C6RTRVqSy3E, ns1:RAh1gm83JiG5M6kDxXhaYT1l49nCzyrckMvTzcPn-iv90; nt:wasCreatedFromTemplate ns1:RA3gQDMnYbKCTiQeiUYJYBaH6HUhz8f3HIg71itlsZDgA . } @prefix this: . @prefix sub: . @prefix np: . @prefix dct: . @prefix nt: . @prefix npx: . @prefix xsd: . @prefix rdfs: . @prefix orcid: . @prefix prov: . @prefix foaf: . sub:Head { this: a np:Nanopublication; np:hasAssertion sub:assertion; np:hasProvenance sub:provenance; np:hasPublicationInfo sub:pubinfo . } sub:assertion { rdfs:comment "Frontiers for Young Mind article to introduce budding scientists on the story of Sir James Black, reknowned pharmacologist. 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npx:hasSignatureTarget this: . this: a npx:ExampleNanopub; dct:created "2023-10-03T12:38:16.113Z"^^xsd:dateTime; dct:creator orcid:0009-0003-0301-3405; dct:license ; rdfs:label "Comment on: Volcano"; nt:wasCreatedFromProvenanceTemplate ; nt:wasCreatedFromPubinfoTemplate , , ; nt:wasCreatedFromTemplate . } @prefix this: . @prefix sub: . @prefix np: . @prefix dct: . @prefix nt: . @prefix npx: . @prefix xsd: . @prefix rdfs: . @prefix orcid: . @prefix prov: . sub:Head { this: a np:Nanopublication; np:hasAssertion sub:assertion; np:hasProvenance sub:provenance; np:hasPublicationInfo sub:pubinfo . } sub:assertion { rdfs:comment "next example" . } sub:provenance { sub:assertion prov:wasAttributedTo orcid:0000-0002-1267-0234 . } sub:pubinfo { sub:sig npx:hasAlgorithm "RSA"; npx:hasPublicKey "MIGfMA0GCSqGSIb3DQEBAQUAA4GNADCBiQKBgQCwUtewGCpT5vIfXYE1bmf/Uqu1ojqnWdYxv+ySO80ul8Gu7m8KoyPAwuvaPj0lvPtHrg000qMmkxzKhYknEjq8v7EerxZNYp5B3/3+5ZpuWOYAs78UnQVjbHSmDdmryr4D4VvvNIiUmd0yxci47dTFUj4DvfHnGd6hVe5+goqdcwIDAQAB"; 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