{ "version": "https://jsonfeed.org/version/1.1", "title": "chem-bla-ics", "description": "Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.", "home_page_url": "https://chem-bla-ics.linkedchemistry.info/", "feed_url": "https://chem-bla-ics.linkedchemistry.info/2018/12/27/creating-nanopublications-with-groovy.json", "icon": "https://chem-bla-ics.linkedchemistry.info/assets/images/chem-bla-ics_logo.png", "language": "en", "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286", "_orcid": "0000-0001-7542-0286" } ], "items": [ { "id": "https://doi.org/10.59350/v3szx-3jk73", "url": "https://chem-bla-ics.linkedchemistry.info/2018/12/27/creating-nanopublications-with-groovy.html", "title": "Creating nanopublications with Groovy", "content_html": "

\nYesterday, I struggled some with creating nanopublications with Groovy.\nMy first attempt was an utter failure, but then I discovered Thomas Kuhn’s\nNanopubCreator\nand it was downhill from there.

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On the right, a depiction is given of a compound found in Taphrorychus bicolor (doi:10.1002/JLAC.199619961005).\nPublished in Liebigs Annalen, see this post\nabout the history of that journal.

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There are two good things about this. First, I now have a code base\nthat I can easily repurpose to make trusty nanopublications (doi:10.1007/978-3-319-07443-6_27)\nabout anything structured as a table (so can you).

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Second, I now about almost 1200 CCZero nanopublications that tell you in which species a certain metabolite\nhas been found. Sourced from Wikidata, using their SPARQL end point.\nThis collection is a bit boring that this moment, and most of them are human metabolites, where the source is either\nRecon 2.2 or WikiPathways.\nBut I expect (hope) to see more DOIs to show up. Think\nWe challenge you to reuse Additional Files.

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Finally, you are probably interested in learning what one of the created nanopublications looks like, to I put\na Gist online:

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@prefix this: <http://www.bigcat.unimaas.nl/nanopubs/wikidata/tmp/np742.RAwXcetTykN6UPVzBOyatKm30mbT6endXfDrxnarRysL0> .\n@prefix sub: <http://www.bigcat.unimaas.nl/nanopubs/wikidata/tmp/np742.RAwXcetTykN6UPVzBOyatKm30mbT6endXfDrxnarRysL0#> .\n@prefix wd: <http://www.wikidata.org/entity/> .\n@prefix np: <http://www.nanopub.org/nschema#> .\n@prefix has-source: <http://semanticscience.org/resource/SIO_000253> .\n@prefix has-inchikey: <http://semanticscience.org/resource/CHEMINF_000399> .\n@prefix orcid: <http://orcid.org/> .\n@prefix wdt: <http://www.wikidata.org/prop/direct/> .\n@prefix owl: <http://www.w3.org/2002/07/owl#> .\n@prefix pav: <http://purl.org/pav/> .\n@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .\n@prefix skos: <http://www.w3.org/2004/02/skos/core#> .\n\nsub:Head {\n        this: np:hasAssertion sub:assertion ;\n                np:hasProvenance sub:provenance ;\n                np:hasPublicationInfo sub:pubinfo ;\n                a np:Nanopublication .\n}\n\nsub:assertion {\n        wd:Q15978631 rdfs:label \"Homo sapiens\"@en ;\n                skos:exactMatch <http://purl.obolibrary.org/obo/NCBITaxon_9606> .\n\n        wd:Q27125029 has-inchikey: \"APJYDQYYACXCRM-UHFFFAOYSA-O\" ;\n                rdfs:label \"tryptaminium\"@en ;\n                wdt:P703 wd:Q15978631 .\n}\n\nsub:provenance {\n        sub:assertion has-source: wd:Q2013 , wd:Q28601559 .\n\n        wd:Q28601559 rdfs:label \"Recon 2.2: from reconstruction to model of human metabolism\"@en ;\n                owl:sameAs <https://doi.org/10.1007/S11306-016-1051-4> .\n}\n\nsub:pubinfo {\n        this: pav:createdBy orcid:0000-0001-7542-0286 .\n}\n
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References

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Francke, W., Schröder, F., Kohnle, U., & Simon, M. (1996). Synthesis of (1S,2R,5R)‐2‐Ethyl‐1,5‐dimethyl‐6,8‐dioxabicyclo[3.2.1]octane, the Aggregation Pheromone of Male Beech Bark Beetles, Taphrorychus bicolor (Col., Scol.). Liebigs Annalen, 1996(10), 1523–1527. https://doi.org/10.1002/jlac.199619961005 CrossRef Scholia
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Kuhn, T., & Dumontier, M. (2014). Trusty URIs: Verifiable, Immutable, and Permanent Digital Artifacts for Linked Data. In Lecture Notes in Computer Science (pp. 395–410). Springer International Publishing. https://doi.org/10.1007/978-3-319-07443-6_27 CrossRef Scholia
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", "summary": "Yesterday, I struggled some with creating nanopublications with Groovy. My first attempt was an utter failure, but then I discovered Thomas Kuhn’s NanopubCreator and it was downhill from there.", "image": "https://chem-bla-ics.linkedchemistry.info/assets/images/Screenshot_20181227_075006.png", "date_published": "2018-12-27T00:00:00+00:00", "date_modified": "2025-02-16T00:00:00+00:00", "tags": ["nanopub","wikidata","groovy"], "_references": [ { "url": "https://doi.org/10.1007/978-3-319-07443-6_27", "doi": "10.1007/978-3-319-07443-6_27" } , { "url": "https://doi.org/10.1002/JLAC.199619961005", "doi": "10.1002/JLAC.199619961005" } ], "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ] } ] }