Hi Tony, > On 8 Aug 2015, at 10:19, Hammond, Tony <[email protected]> wrote: > > Hi Hugh: > > Many thanks for the comments. This is exactly the kind of thing we need to > hear. Thanks you for your responses, and the manner in which your received my comments. > > So, I think you may have raised four separate points which I'll try to > answer in turn: > > == > 1. Examples > > You are right. We've been sloppy. These were intended more for reading > than parsing. So we took liberties with omitting common namespaces, > abbreviating strings, etc. Punctuation, we were just careless. Sure thing. > > But I agree there is real value in making these examples complete. We will > address this in our next release. > > 2. Dereference > > We really have no defence here. **We do not support dereference at this > time.** The datasets are outputs from our production systems and HTTP URIs > are used for namespacing only. We need to figure out a strategy for > supporting dereference. > > So, if that means we are Bad Guys for violating Principle 2, then so be > it. We are not trying to claim that this is true Linked Data - it's only > common-or-garden linked data (of the RDF kind). > > That's not to say that we are not interested in adding in dereference. > Only that these things take time to implement and we are proceeding with > our data publishing in an incremental manner. Again, sure thing.
What you have done is lovely Semantic Web stuff - it is only the Linked Data bit that seems to be missing. However, looking at the site, I think you may be being hard on yourself. Were you to have used the term Semantic Web instead of Linked Data on http://www.nature.com/ontologies/ and the other explanation pages, I think it would have been less misleading. I certainly would not have then gone to the data with the expectation of URIs resolving. > > > So, for now, sorry! > > 3. URNs, etc > > Note that the RDF you obtained from dereferencing the DOI is from CrossRef > - not from ourselves. So we cannot properly answer for something retrieved > from a third party. That said, CrossRef are also in the early stages of > data publishing, and may not themselves have reached the Linked Data > standard. Again, seems like it's only RDF at this time. OK - got that. Not your RDF. (I would rename your DOCS dir to be VoID, by the way, as it makes it more attractive to people like me :-) ) > > 4. Mappings > > Am a little perplexed as to the distinction between mappings and links, > although maybe I can see where you're coming from. Note that we're anyway > planning to decouple our ontology mappings and put those in separate files > and list then under Mappings. Sounds good. A personal view: A mapping is something that says to things are pretty much the same (in some sense we won’t go into); A link is the use of a URI that comes from as different source, such as your use of the dbpedia URIs. So I would say that something like <http://dx.doi.org/10.1038/003022a0> <http://xmlns.com/foaf/0.1/topic> <http://dbpedia.org/resource/Thomas_Henry_Huxley> is a link from your dataset to dbpedia. If you also had a URI for http://dbpedia.org/resource/Thomas_Henry_Huxley that you wanted to say was the same, then you would say so using a skos or owl predicate, and that would be a mapping. > Our core and domain ontologies generally > have SKOS mappings, i.e. we use skos:closeMatch, skos:broadMatch, > skos:exactMatch, skos:relatedMatch, etc. This feels appropriate for the > ontology and the taxonomies. > > I guess we are cautiously feeling our way forward and want to be a little > careful about using owl:sameAs. I’m happy to get those as well :-) > > == > > So, I hope we've clarified some things here. There's a couple obvious > things we can do/are doing (examples, mappings). Some other things are out > of our hands (DOI dereference). And some will need more time for us to > implement (dereference generally). > > Anyway, many thanks again for all your comments. It's really good to hear > back from real users. Otherwise it can feel like we are whistling in the > wind. Pleasure. Hugh > > Tony > > > > > > On 07/08/2015 12:48, "Hugh Glaser" <[email protected]> wrote: > >> Hi Tony, >> Great stuff! >> So I start exploring, looking for more fodder for sameAs.org Š :-) >> >> It may be that my questions are too specific for the list - feel free to >> go off-list in response, and then we can summarise. >> And there is rather a lot here, I¹m afraid. >> >> Some possible problemettes I hit: >> http://www.nature.com/ontologies/datasets/articles/#data_example >> might be confusing for people (and awkward when I tried to rapper it). >> Since quite a few prefixes are not declared, most notably one of yours: >> npg, but also the usual suspects (xsd, dc, bibo, foaf and also prism). >> There is also a missing foaf:homepage that causes a syntax error. >> And some semi-colons missing off the last few lines. >> >> A slightly more challenging problem is that the URI for that example >> doesn¹t resolve. >> It unqualifies to http://ns.nature.com/articles/nrg3870 (I assume it is a >> namespace problem.) >> >> But I managed to find a resolving URI: http://dx.doi.org/10.1038/246015a0 >> (from http://www.nature.com/ontologies/mappings/articles-dbpedia/) >> And successfully got some RDF :-) >> Looking at the owl:sameAs triples in there, I then start to worry - they >> are urn:, doi: and info: URIs. >> This is fine for a Semantic Web publishing, but means (in my opinion) >> that it is not Linked Data (violating principle 2) - all URIs for Things >> have to be http: for that. So you could use another predicate, but >> owl:sameAs seems wrong. >> >> Having found http://www.nature.com/ontologies/mappings/, I excitedly went >> off to http://www.nature.com/ontologies/mappings/articles-dbpedia/ and >> downloaded the files. >> However, I found that the file contains only triples with foaf:topic and >> cito:isCitedBy - no mappings between your URIs and DBpedia, Mesh, etcŠ, >> which is what I was expecting. It seems to me that this is more of a >> ³links² file than a ³mappings² file. >> Even more frustrating, many URIs that I tried, such as >> http://dx.doi.org/10.1038/ng1285, don¹t resolve (give an invalid doi: >> message), so I wouldn¹t be able to use them in any case. >> >> SoŠ :-) >> Apart from any fixing you may want to do; and maybe having some example >> Linked Data URIs for People and Publications sprinkled around (it really >> was quite a challenge to find any RDF!). >> I suspect that you do have some mappings between your URIs and dbpedia >> URIs, for example. >> Is there any chance you would like to send me (or link to a file) any >> Linked Data owl:sameAs triples that I could add to sameAs.org, please? >> And also, do you have an interesting owl:differentFrom dataset that I >> could add to differentFrom.org? This might be your regression test, where >> you have done mappings that you later found were wrong. >> >> Sorry if I have made some basic errors in failing to find things. >> Very best >> Hugh >>> On 28 Jul 2015, at 12:41, Hammond, Tony <[email protected]> >>> wrote: >>> >>> Hi: >>> >>> As promised in a couple posts to the list earlier this year [1,2] we >>> have now resumed dataset publishing (following on from the 2012 releases >>> on data.nature.com [3,4]) and have added a new snapshot of bibliography >>> metadata for nature.com articles to the Nature.com Ontologies portal: >>> >>> http://nature.com/ontologies/ >>> >>> Specifically, as announced yesterday [5], we have released 170 years of >>> bib data for all nature.com articles and contributors over the period >>> 1845-2015. We expect to release new snapshots periodically. >>> >>> The release notes are copied below. >>> >>> Tony >>> >>> >>> == >>> Release: >>> >>> * We've resumed publishing of datasets. We're now making available >>> complete instance datasets for articles (1.2 m) and contributors (2.7 >>> m). These datsets are linked to the DOI and ORCID datasets. (These >>> datasets replace the historic datasets from 2012.) >>> >>> * We've now added our core and domain models to GitHub projects and >>> brought them under version control: public-npg-core-ontology GitHub and >>> public-npg-domain-ontology GitHub >>> >>> * We've improved our documentation. A whole new Technical Notes section >>> has been added. Some material from the homepage (e.g. Background, >>> Licenses, Namespaces) has been moved there, and new material has been >>> added (e.g. Annotations, Mappings, Naming Policy, Versions). >>> >>> * We've improved our data mappings. The Subjects Ontology is now 100% >>> mapped to DBpedia. See Mappings. >>> >>> * We've added a reference in our Links section to our new colleagues at >>> Springer and their LOD for Conferences in Computer Science. >>> == >>> >>> >>> [1] https://lists.w3.org/Archives/Public/public-lod/2015Apr/0005.html >>> [2] https://lists.w3.org/Archives/Public/public-lod/2015May/0002.html >>> [3] https://lists.w3.org/Archives/Public/public-lod/2012Apr/0061.html >>> [4] https://lists.w3.org/Archives/Public/public-lod/2012Jul/0130.html >>> [5] https://twitter.com/tonyhammond/status/625641560676409345 >>> >>> >>> ************************************************************************* >>> ******* >>> DISCLAIMER: This e-mail is confidential and should not be used by >>> anyone who is not the original intended recipient. If you have received >>> this e-mail in error please inform the sender and delete it from your >>> mailbox or any other storage mechanism. Neither Macmillan Publishers >>> Limited nor Macmillan Publishers International Limited nor any of their >>> agents accept liability for any statements made which are clearly the >>> sender's own and not expressly made on behalf of Macmillan Publishers >>> Limited or Macmillan Publishers International Limited or one of their >>> agents. >>> Please note that neither Macmillan Publishers Limited nor Macmillan >>> Publishers International Limited nor any of their agents accept any >>> responsibility for viruses that may be contained in this e-mail or its >>> attachments and it is your responsibility to scan the e-mail and >>> attachments (if any). No contracts may be concluded on behalf of >>> Macmillan Publishers Limited or Macmillan Publishers International >>> Limited or their agents by means of e-mail communication. >>> Macmillan Publishers Limited. Registered in England and Wales with >>> registered number 785998. Macmillan Publishers International Limited. >>> Registered in England and Wales with registered number 02063302. >>> Registered Office Brunel Road, Houndmills, Basingstoke RG21 6XS >>> Pan Macmillan, Priddy and MDL are divisions of Macmillan Publishers >>> International Limited. >>> Macmillan Science and Education, Macmillan Science and Scholarly, >>> Macmillan Education, Language Learning, Schools, Palgrave, Nature >>> Publishing Group, Palgrave Macmillan, Macmillan Science Communications >>> and Macmillan Medical Communications are divisions of Macmillan >>> Publishers Limited. >>> >>> ************************************************************************* >>> ******* >>> >> >> -- >> Hugh Glaser >> 20 Portchester Rise >> Eastleigh >> SO50 4QS >> Mobile: +44 75 9533 4155, Home: +44 23 8061 5652 >> >> > > ******************************************************************************** > > DISCLAIMER: This e-mail is confidential and should not be used by anyone who > is not the original intended recipient. If you have received this e-mail in > error please inform the sender and delete it from your mailbox or any other > storage mechanism. Neither Macmillan Publishers Limited nor Macmillan > Publishers International Limited nor any of their agents accept liability for > any statements made which are clearly the sender's own and not expressly made > on behalf of Macmillan Publishers Limited or Macmillan Publishers > International Limited or one of their agents. > Please note that neither Macmillan Publishers Limited nor Macmillan > Publishers International Limited nor any of their agents accept any > responsibility for viruses that may be contained in this e-mail or its > attachments and it is your responsibility to scan the e-mail and > attachments (if any). No contracts may be concluded on behalf of Macmillan > Publishers Limited or Macmillan Publishers International Limited or their > agents by means of e-mail communication. > Macmillan Publishers Limited. Registered in England and Wales with registered > number 785998. Macmillan Publishers International Limited. Registered in > England and Wales with registered number 02063302. > Registered Office Brunel Road, Houndmills, Basingstoke RG21 6XS > Pan Macmillan, Priddy and MDL are divisions of Macmillan Publishers > International Limited. > Macmillan Science and Education, Macmillan Science and Scholarly, Macmillan > Education, Language Learning, Schools, Palgrave, Nature Publishing Group, > Palgrave Macmillan, Macmillan Science Communications and Macmillan Medical > Communications are divisions of Macmillan Publishers Limited. > ******************************************************************************** > > -- Hugh Glaser 20 Portchester Rise Eastleigh SO50 4QS Mobile: +44 75 9533 4155, Home: +44 23 8061 5652
