From 9709eca5c76aabe823ba34d976c5d11a9d150b76 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Sat, 7 Nov 2020 10:06:30 +0000 Subject: RDF: use URIs --- bh20sequploader/bh20seq-schema.yml | 8 ++++- bh20sequploader/bh20seq-shex.rdf | 5 +-- test/data/input/TN_UT2.yaml | 2 +- test/data/regression/TN_UT2.rdf | 64 +++++++++++++++++++------------------- 4 files changed, 43 insertions(+), 36 deletions(-) diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml index 861a5ca..645be5e 100644 --- a/bh20sequploader/bh20seq-schema.yml +++ b/bh20sequploader/bh20seq-schema.yml @@ -1,6 +1,6 @@ $base: http://biohackathon.org/bh20-seq-schema $namespaces: - cc: http://creativecommons.org/ns# + cc: https://creativecommons.org/ns# dc: http://purl.org/metadata/dublin_core_elements# sch: https://schema.org/ efo: http://www.ebi.ac.uk/efo/ @@ -19,6 +19,8 @@ $graph: type: string jsonldPredicate: _id: https://creativecommons.org/ns#License + _type: "@id" + noLinkCheck: true title: doc: Attribution title related to data license type: string? @@ -34,11 +36,15 @@ $graph: type: string? jsonldPredicate: _id: https://creativecommons.org/ns#attributionURL + _type: "@id" + noLinkCheck: true attribution_source: doc: Attribution source URL related to data license type: string? jsonldPredicate: _id: https://creativecommons.org/ns#attributionSource + _type: "@id" + noLinkCheck: true - name: hostSchema type: record diff --git a/bh20sequploader/bh20seq-shex.rdf b/bh20sequploader/bh20seq-shex.rdf index fa765dd..1b15c58 100644 --- a/bh20sequploader/bh20seq-shex.rdf +++ b/bh20sequploader/bh20seq-shex.rdf @@ -2,6 +2,7 @@ PREFIX : PREFIX hostSchema: PREFIX cc: +PREFIX cclicenses: PREFIX dc: PREFIX xsd: PREFIX obo: @@ -71,9 +72,9 @@ PREFIX wikidata: } :licenseShape{ - cc:License xsd:string ; + cc:License [ cclicenses:~ ] ; dc:Title xsd:string ?; cc:attributionName xsd:string ?; - cc:attributionURL xsd:string ?; + cc:attributionURL /^http/ ; cc:attributionSource xsd:string ?; } diff --git a/test/data/input/TN_UT2.yaml b/test/data/input/TN_UT2.yaml index 2c5f987..9c4370d 100644 --- a/test/data/input/TN_UT2.yaml +++ b/test/data/input/TN_UT2.yaml @@ -1,7 +1,7 @@ id: placeholder license: - license_type: http://creativecommons.org/licenses/by/4.0/ + license_type: https://creativecommons.org/licenses/by/4.0/ title: "TN_UT2 - Pegram, Tennessee, USA" attribution_name: "Mariah Taylor, Colleen Jonsson" attribution_url: https://www.uthsc.edu/medicine/molecular-sciences/faculty-directory/jonsson.php diff --git a/test/data/regression/TN_UT2.rdf b/test/data/regression/TN_UT2.rdf index aa1356a..84353a5 100644 --- a/test/data/regression/TN_UT2.rdf +++ b/test/data/regression/TN_UT2.rdf @@ -1,33 +1,33 @@ -_:Nc519408f538a4bb39ea09f56ce9bb88e "TN_UT2" . -_:N299826fb66794f11991cebc5f8d8b24a "https://bio.tools/BWA#!" . -_:N982774a13a39474aae39272447a09574 "https://www.uthsc.edu/medicine/molecular-sciences/faculty-directory/jonsson.php" . -_:N7857c4718ab741169bae9fafa9b47c75 "2020-04-26" . -_:N708d19e87323455c9f9bb317538f742d "Pjotr Prins" . -_:N95d4a000e14d4bd99b46d6ec84989aaf "SARS-CoV-2/human/USA/TN_UT2/2020" . - _:N982774a13a39474aae39272447a09574 . -_:N95d4a000e14d4bd99b46d6ec84989aaf . -_:Nc519408f538a4bb39ea09f56ce9bb88e . -_:N708d19e87323455c9f9bb317538f742d "Colleen Jonsson" . -_:N982774a13a39474aae39272447a09574 "Mariah Taylor, Colleen Jonsson" . - _:N7857c4718ab741169bae9fafa9b47c75 . -_:N708d19e87323455c9f9bb317538f742d "Regional Biocontainment Laboratory, Memphis, TN" . -_:N299826fb66794f11991cebc5f8d8b24a . -_:N708d19e87323455c9f9bb317538f742d "UTHSC, Memphis, Tennessee 38163, USA" . -_:N7857c4718ab741169bae9fafa9b47c75 . -_:N708d19e87323455c9f9bb317538f742d "TN_UT2" . -_:N7857c4718ab741169bae9fafa9b47c75 "TN_UT2" . -_:N708d19e87323455c9f9bb317538f742d . - _:N708d19e87323455c9f9bb317538f742d . - _:N299826fb66794f11991cebc5f8d8b24a . -_:N982774a13a39474aae39272447a09574 "TN_UT2 - Pegram, Tennessee, USA" . -_:N299826fb66794f11991cebc5f8d8b24a "Oxford Nanopore MiniIon RNA long reads" . -_:N7857c4718ab741169bae9fafa9b47c75 . - _:Nc519408f538a4bb39ea09f56ce9bb88e . -_:N708d19e87323455c9f9bb317538f742d "Mariah Taylor" . -_:N708d19e87323455c9f9bb317538f742d . - _:N95d4a000e14d4bd99b46d6ec84989aaf . -_:N708d19e87323455c9f9bb317538f742d "Colleen B. Jonsson" . -_:N708d19e87323455c9f9bb317538f742d "TN_UT2" . -_:N982774a13a39474aae39272447a09574 "http://creativecommons.org/licenses/by/4.0/" . -_:N708d19e87323455c9f9bb317538f742d "Mariah Taylor" . +_:N850430bbc537473e8fbab09c300daf2b . +_:Ncab40e8bd4b84431aa6782f7e7480ef3 . +_:N3c28bc8014134d77823451de114c6085 "Mariah Taylor" . +_:Ncab40e8bd4b84431aa6782f7e7480ef3 "TN_UT2" . + _:N850430bbc537473e8fbab09c300daf2b . +_:N3c28bc8014134d77823451de114c6085 "TN_UT2" . +_:N850430bbc537473e8fbab09c300daf2b . +_:N3c28bc8014134d77823451de114c6085 "UTHSC, Memphis, Tennessee 38163, USA" . +_:Nebe62f68542a47d0936e953195cf25d7 . +_:N3c28bc8014134d77823451de114c6085 "Colleen B. Jonsson" . +_:N78bfdbe9d12745e99164d619cb125277 . +_:Nbf9e7b47381b4965926a47bf5b34e489 "Oxford Nanopore MiniIon RNA long reads" . + _:Ncab40e8bd4b84431aa6782f7e7480ef3 . +_:Nbf9e7b47381b4965926a47bf5b34e489 "https://bio.tools/BWA#!" . +_:Nebe62f68542a47d0936e953195cf25d7 "TN_UT2" . + _:Nebe62f68542a47d0936e953195cf25d7 . +_:N850430bbc537473e8fbab09c300daf2b "Mariah Taylor, Colleen Jonsson" . +_:N78bfdbe9d12745e99164d619cb125277 "SARS-CoV-2/human/USA/TN_UT2/2020" . +_:N3c28bc8014134d77823451de114c6085 "Colleen Jonsson" . +_:N3c28bc8014134d77823451de114c6085 . +_:Nebe62f68542a47d0936e953195cf25d7 "2020-04-26" . +_:Nebe62f68542a47d0936e953195cf25d7 . +_:N850430bbc537473e8fbab09c300daf2b "TN_UT2 - Pegram, Tennessee, USA" . +_:Nbf9e7b47381b4965926a47bf5b34e489 . +_:N3c28bc8014134d77823451de114c6085 "Mariah Taylor" . +_:N3c28bc8014134d77823451de114c6085 "TN_UT2" . +_:N3c28bc8014134d77823451de114c6085 "Pjotr Prins" . + _:N3c28bc8014134d77823451de114c6085 . +_:N3c28bc8014134d77823451de114c6085 . + _:N78bfdbe9d12745e99164d619cb125277 . +_:N3c28bc8014134d77823451de114c6085 "Regional Biocontainment Laboratory, Memphis, TN" . + _:Nbf9e7b47381b4965926a47bf5b34e489 . -- cgit v1.2.3