rows { options { physical_type: PHYSICAL_STREAM_TYPE_QUADS max_name_table_size: 128 max_prefix_table_size: 16 max_datatype_table_size: 16 logical_type: LOGICAL_STREAM_TYPE_DATASETS version: 2 } } rows { prefix { value: "http://purl.org/dc/terms/" } } rows { name { } } rows { namespace { name: "dcterms" value { prefix_id: 1 } } } rows { prefix { value: "http://www.nanopub.org/nschema#" } } rows { namespace { name: "np" value { prefix_id: 2 name_id: 1 } } } rows { prefix { value: "http://purl.org/nanopub/x/" } } rows { namespace { name: "npx" value { prefix_id: 3 name_id: 1 } } } rows { prefix { value: "https://w3id.org/np/snakemake/" } } rows { namespace { name: "ns1" value { prefix_id: 4 name_id: 1 } } } rows { prefix { value: "https://orcid.org/" } } rows { namespace { name: "orcid" value { prefix_id: 5 name_id: 1 } } } rows { prefix { value: "http://www.w3.org/ns/prov#" } } rows { namespace { name: "prov" value { prefix_id: 6 name_id: 1 } } } rows { prefix { value: "http://www.w3.org/2000/01/rdf-schema#" } } rows { namespace { name: "rdfs" value { prefix_id: 7 name_id: 1 } } } rows { prefix { value: "https://schema.org/" } } rows { namespace { name: "schema" value { prefix_id: 8 name_id: 1 } } } rows { prefix { value: "https://w3id.org/np/RAl-YXmaNyU7wRmmOGrmVugTqHe36Z-txlh4aPXPIeWU8/" } } rows { namespace { name: "sub" value { prefix_id: 9 name_id: 1 } } } rows { prefix { value: "https://w3id.org/np/" } } rows { name { value: "RAl-YXmaNyU7wRmmOGrmVugTqHe36Z-txlh4aPXPIeWU8" } } rows { namespace { name: "this" value { prefix_id: 10 } } } rows { prefix { value: "http://www.w3.org/2001/XMLSchema#" } } rows { namespace { name: "xsd" value { prefix_id: 11 name_id: 1 } } } rows { name { value: "hasAssertion" } } rows { name { value: "assertion" } } rows { name { value: "Head" } } rows { quad { s_iri { prefix_id: 10 } p_iri { prefix_id: 2 } o_iri { prefix_id: 9 } g_iri { } } } rows { name { value: "hasProvenance" } } rows { name { value: "provenance" } } rows { quad { p_iri { prefix_id: 2 } o_iri { prefix_id: 9 } } } rows { name { value: "hasPublicationInfo" } } rows { name { value: "pubinfo" } } rows { quad { p_iri { prefix_id: 2 } o_iri { prefix_id: 9 } } } rows { prefix { value: "http://www.w3.org/1999/02/22-rdf-syntax-ns#" } } rows { name { value: "type" } } rows { name { value: "Nanopublication" } } rows { quad { p_iri { prefix_id: 12 } o_iri { prefix_id: 2 } } } rows { name { value: "config-1" } } rows { name { value: "identifier" } } rows { quad { s_iri { prefix_id: 9 } p_iri { prefix_id: 1 } o_literal { lex: "config.yml" } g_iri { prefix_id: 9 name_id: 4 } } } rows { name { value: "text" } } rows { quad { p_iri { prefix_id: 8 name_id: 14 } o_literal { lex: "samples: samples.csv\n\nref:\n species: \"Drosophila melanogaster\"\n genome: \"\"\n annotation: \"\"\n accession: \"GCF_000001215.4\"\n ensembl_species: \"\" # e.g., \"homo_sapiens\"\n build: \"\" # e.g., \"GRCh38\"\n release: \"\" # e.g., \"105\"\n\nread_filter:\n min_length: 200\n\nminimap2:\n index_opts: \"\"\n opts: \"\"\n maximum_secondary: 100\n secondary_score_ratio: 1.0\n\nsamtools:\n samtobam_opts: \"-b\"\n bamsort_opts: \"\"\n bamindex_opts: \"\"\n bamstats_opts: \"\"\n\nquant:\n salmon_libtype: \"U\"\n\ndeseq2:\n fit_type: \"\"\n design_factors:\n - \"condition\"\n lfc_null: 1.0\n alt_hypothesis: \"greaterAbs\"\n point_width: 20\n mincount: 10\n alpha: 0.05\n threshold_plot: 10\n colormap: \"Blues\"\n figtype: \"png\"\n batch_effect:\n - \"\"\n\nisoform_analysis:\n FLAIR: true\n qscore: 1\n exp_thresh: 10\n col_opts: \"--annotation_reliant generate --generate_map --stringent\"\n\nprotein_annotation:\n lambda: false\n uniref: \"https://ftp.imp.fu-berlin.de/pub/lambda/index/lambda3/gen_0/uniref50_20230713.lba.gz\"\n num_matches: 3" } } } rows { name { value: "dataset" } } rows { name { value: "Dataset" } } rows { quad { s_iri { prefix_id: 9 } p_iri { prefix_id: 12 name_id: 10 } o_iri { prefix_id: 8 name_id: 16 } } } rows { name { value: "describesWorkflow" } } rows { quad { p_iri { prefix_id: 4 } o_literal { lex: "RAjHDlPDghZzc9ZvQ3uJQNJ9Jd_KAYzZt7dk5PXKgjRyE" } } } rows { name { value: "description" } } rows { quad { p_iri { } o_literal { lex: "This workflow performs differential expression analysis of RNA-seq data obtained from Oxford Nanopore long-read sequencing technology.\nFirst a transcriptome FASTA is constructed using gffread [https://github.com/gpertea/gffread]. Reads are then mapped to the transcriptome with the long-read optimized alignment tool minimap2 [https://github.com/lh3/minimap2].\nNext quantification is performed using salmon [https://github.com/COMBINE-lab/salmon] before normalization and differential expression analysis are conducted by PyDESeq2 [https://github.com/owkin/PyDESeq2].\nThe workflow can optionally analyze splice-isoforms through integrating the FLAIR [https://github.com/BrooksLabUCSC/flair] workflow.\nAdditionaly, NanoPlot [https://github.com/wdecoster/NanoPlot] is employed to analyze initial sequencing data and QualiMap [https://github.com/EagleGenomics-cookbooks/QualiMap] is used to evaluate mapping results." } } } rows { name { value: "generatedAt" } } rows { datatype { value: "http://www.w3.org/2001/XMLSchema#dateTime" } } rows { quad { p_iri { } o_literal { lex: "2026-04-17T14:07:59.954639+00:00" datatype: 1 } } } rows { name { value: "hasConfigurationSection" } } rows { name { value: "workflow-configuration" } } rows { quad { p_iri { } o_iri { prefix_id: 9 } } } rows { name { value: "label" } } rows { quad { s_iri { name_id: 21 } p_iri { prefix_id: 7 } o_literal { lex: "from workflow configuration" } } } rows { name { value: "hasConfigurationFile" } } rows { quad { p_iri { prefix_id: 4 } o_iri { prefix_id: 9 name_id: 12 } } } rows { name { value: "generatedAtTime" } } rows { quad { s_iri { name_id: 4 } p_iri { prefix_id: 6 name_id: 24 } o_literal { lex: "2026-04-17T16:08:02.401532" datatype: 1 } g_iri { prefix_id: 9 name_id: 7 } } } rows { name { value: "wasAttributedTo" } } rows { name { value: "0000-0003-2408-7588" } } rows { quad { p_iri { prefix_id: 6 name_id: 25 } o_iri { prefix_id: 5 } } } rows { name { value: "created" } } rows { quad { s_iri { prefix_id: 10 name_id: 2 } p_iri { prefix_id: 1 name_id: 27 } o_literal { lex: "2026-04-17T14:07:59.954639+00:00" datatype: 1 } g_iri { prefix_id: 9 name_id: 9 } } } rows { name { value: "creator" } } rows { quad { p_iri { prefix_id: 1 name_id: 28 } o_iri { prefix_id: 5 name_id: 26 } } } rows { name { value: "hasNanopubType" } } rows { quad { p_iri { prefix_id: 3 name_id: 29 } o_iri { prefix_id: 8 name_id: 16 } } } rows { name { value: "signedBy" } } rows { quad { p_iri { prefix_id: 3 name_id: 30 } o_iri { prefix_id: 5 name_id: 26 } } } rows { quad { p_iri { prefix_id: 7 name_id: 22 } o_literal { lex: "Snakemake workflow metadata: RAjHDlPDghZzc9ZvQ3uJQNJ9Jd_KAYzZt7dk5PXKgjRyE" } } } rows { quad { p_iri { prefix_id: 6 name_id: 24 } o_literal { lex: "2026-04-17T16:08:02.401532" datatype: 1 } } } rows { quad { p_iri { } o_iri { prefix_id: 5 } } } rows { name { value: "sig" } } rows { name { value: "hasAlgorithm" } } rows { quad { s_iri { prefix_id: 9 name_id: 31 } p_iri { prefix_id: 3 } o_literal { lex: "RSA" } } } rows { name { value: "hasPublicKey" } } rows { quad { p_iri { } o_literal { lex: "MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAkOFUnnRCp/k9/0ugvx8zQJ+Qc675W1Ug6F839+xvJ2QsSBu4iOJ1O2kJCmb3tALp3gJOt8sffRot3VrfY1hbgXxL7BVtDsfHHmXVff4YCeg5Ycdn5cDpLawDpAdYwMhK0LwIkZ3fwH9/o9JniYKXLV/jpF9bMKyiw/6tqlCHaMW1r8gzZzoxVIAakwvlABoY0iNoToLTlBRXEI4mLUNjDMnMwQgfh1KXMxMruNjW3wJyeDEIfa2ooAt0E4CRM9pkrEb37NzD9Jz8aSUFFY6BvIxF4ixK7rm6IUDvQ76LqXkEmgSeRv1kw7gnCe9wV/wHd0ZeW4heoBXmLHX3MvHfjwIDAQAB" } } } rows { name { value: "hasSignature" } } rows { quad { p_iri { } o_literal { lex: "MnZwY2UY0hXpwknx/9zq+JMX5sGjP3cQ+O54k3MwtJwIvs5rivLKybiZBOtHyREfrejXGhE+YfObQtcZWzl6yZVjT5h6V/EE7dVJGvFUAJnexX3Z41JSvMD2bdtGOn+somvIJ3tVAL+Jiw8YF01Zzr/jFZzjfAu32UI/jBABUnbPFlqTknC9KuxWPDw0r0De5UD4Ngn7vX0lioXt84UEPaTUfxcWVcuOUqAnB2cxcwe6gO0m4r06rx7g1k1YB18zUMeUaP1Qn+s+MHAoAOCNn97inTWmbu458xGyaCWjY1EXaaTXveVsAv0AjL5B2vI9FSJqjNF7V6MLZCeRs3LFyg==" } } } rows { name { value: "hasSignatureTarget" } } rows { quad { p_iri { } o_iri { prefix_id: 10 name_id: 2 } } } rows { quad { p_iri { prefix_id: 3 name_id: 30 } o_iri { prefix_id: 5 name_id: 26 } } }