![\"\"](\"/assets/images/citoPub.png\")
During the Open Science Retreat I organized\na short session where we looking into typing citation intentions using a new nanopublication template. First, let’s describe\nnanopublications (originally used in doi:10.3233/ISU-2010-0613) a bit.\nScholia gives a nice overview of (macro?)publications on the topic .\nThe nanopub.net\nwebsite describes that [a nanopublication is a small knowledge graph snippet with metadata that is treated as an\nindependent (scientific) publication.]. The knowledge graph, it continues, can be anything from an opinion to the link\nbetween a disease and a gene (doi:10.1109/ESCIENCE.2018.00024).
\n\nNow, in this post I will document an update of how we can use nanopublications for citation intention annotation, and\ncompare this to existing solutions. I have been collecting and indexing the CiTO intention annotations in Wikidata and\nvisualizing the corpus with Scholia at qlever.scholia.wiki/cito/ . There are\ncurrently 22 journal articles with explicit CiTO annoation, largely thanks to a Journal of Cheminformatics pilot\n(e.g. see doi:10.1186/s13321-023-00683-2). Recently,\nthe preprint/report server BioHackrXiv started\nCiTO support too, also visible in the statistics\non Scholia with another 17 papers. A third source is data sets from bibliometric-like studies, as explained\nin this post . Nanopublications\nwould be a fourth solution.
\n\nSo, why another solutions? Like the datasets, assuming DataCite approaches, have clear provenance, but the overhead\nof and needed time for creating a dataset with citation intent annotations can be limiting. And because nanopublications\ncan be linked to ORCID identifiers, we can even discover which citation intent annotations are created by the original\nauthors of articles. Another advantage is that nanopubs are basically RDF and we can query them easily, allowing\nthe citation intentions to migrate to Wikidata. Scholia already saw an update to recognize nanopublications as\na unique kind reference (see the new Wikidata property Nanopublication identifier (P12545)).
\n\nSo, if we can make it easy for people to define nanopublications with CiTO citation intent annotations, than we can\nstart formalizing intent annotations from a much wider range of use cases. For example, we can annotate historically\nimportant discussions. Anyone can retrospectively annotate all their own articles, making them more FAIR. And if we\nuse DOI links, then it no longer is limited to journal articles, but we can use of for software and data citations too.\nThis is where a recent template comes in created by\nTobias Kuhn, one of the main nanopub developers:
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This nanopublication template defines the minimal needs of the assumptions, along with useful provenance and nanopub\ninfo. Basically, the assertion defines that one DOI is a ScholarlyWork and using the CiTO, defines that it cites\none or more article works (with DOI). For each citations, one can select any of the known CiTO intent types,\ne.g. ‘extends’ or ‘uses method’ in, as in this nanopublication\ncreated with this template:
\n\n![\"\"](\"/assets/images/citoPub2.png\")
Besides the template, Tobias also started a SPARQL query to which I added restrictions that the citing and cited\nresources needs to have a DOI, giving us this query:
\n\nprefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>\nprefix np: <http://www.nanopub.org/nschema#>\nprefix npa: <http://purl.org/nanopub/admin/>\nprefix npx: <http://purl.org/nanopub/x/>\nprefix xsd: <http://www.w3.org/2001/XMLSchema#>\nprefix dct: <http://purl.org/dc/terms/>\n\nselect ?np ?label ?subj ?citationrel ?obj ?date where {\n graph npa:graph {\n ?np npa:hasValidSignatureForPublicKey ?pubkey .\n ?np dct:created ?date .\n ?np np:hasAssertion ?assertion .\n optional { ?np rdfs:label ?label . }\n filter not exists { ?npx npx:invalidates ?np ; npa:hasValidSignatureForPublicKey ?pubkey . }\n filter not exists { ?np npx:hasNanopubType npx:ExampleNanopub . }\n }\n graph ?assertion {\n ?subj ?citationrel ?obj .\n filter(regex(str(?citationrel), \"^http://purl.org/spar/cito/.*$\"))\n filter(regex(str(?subj), \"doi.org/10\"))\n filter(regex(str(?obj), \"doi.org/10\"))\n }\n}\nThis includes 6 citation intentions defined by 4 nanopublications added during the Open Science Retreat:
\n\nNow, this query also provides me with enough information to propagate the citation intent (a fact?) to Wikidata\nand cite the original nanopublication as reference. With a variation of the above SPARQL query, I can get the\nfive most recent new nanopublications, convert them to QuickStatements, and then enjoy them in Wikidata. This\nis written up in this Bacting script.
\n\nThe script needs to handle some situations. For example, it will not add items for DOIs not already in Wikidata.\nSo, if neither of the two DOIs are known in Wikidata, then nothing gets added. If they both are, then it will\nadd the citation intent. There are alternative solutions, but in practice that doesn’t matter and the QuickStatements\nis in all situations the same, and QuickStatements will only add the new information.
\n\nThis is what it will look like in Wikidata:
\n\n![\"\"](\"/assets/images/citoPub3.png\")
And this is what it looks (yellow) when we compare the contributions\nfrom nanopublications now with the other sources:
\n\n![\"\"](\"/assets/images/citoPubs4.png\")