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s_iri { prefix_id: 8 } p_iri { prefix_id: 15 name_id: 23 } o_literal { lex: "https://orcid.org/0000-0002-1789-1861" } } } rows { quad { p_iri { name_id: 13 } o_literal { lex: "Jean-Marie Burel" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 15 name_id: 20 } } } rows { prefix { value: "https://w3id.org/ro-id/" } } rows { name { value: "0c88387d-3c01-4e1f-a5c6-07793281a80b" } } rows { quad { s_iri { prefix_id: 9 name_id: 26 } p_iri { prefix_id: 15 name_id: 13 } o_literal { lex: "The main objective of this notebook is to demonstrate how public resources such as the IDR can be used to train your neural network or validate software tools." } } } rows { prefix { value: "https://w3id.org/ro/terms/earth-science#" } } rows { name { value: "Sentence" } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 10 name_id: 27 } } } rows { name { value: "normScore" } } rows { quad { p_iri { } o_literal { lex: "13.134851138353765" } } } rows { name { value: 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Cellpose" } } } rows { name { value: "Phrase" } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 10 name_id: 39 } } } rows { quad { p_iri { name_id: 28 } o_literal { lex: "25.542570951585976" } } } rows { quad { p_iri { } o_literal { lex: "15.3" } } } rows { prefix { value: "https://w3id.org/ro-id/356b66d5-921f-41c8-97e3-ebe65ed97084/#" } } rows { name { value: "enrichment_service-account-enrichment" } } rows { quad { s_iri { prefix_id: 11 name_id: 40 } p_iri { prefix_id: 15 name_id: 13 } o_literal { lex: "service-account-enrichment" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 5 name_id: 22 } } } rows { prefix { value: "https://w3id.org/ro-id/356b66d5-921f-41c8-97e3-ebe65ed97084/" } } rows { prefix { value: "http://purl.org/pav/" } } rows { name { value: "importedBy" } } rows { quad { s_iri { prefix_id: 12 name_id: 2 } p_iri { prefix_id: 13 name_id: 41 } o_iri { prefix_id: 4 name_id: 21 } } } rows { name { value: "author" } } rows { quad { p_iri { prefix_id: 15 name_id: 42 } o_iri { prefix_id: 8 name_id: 25 } } } rows { name { value: "contentSize" } } rows { datatype { value: "http://www.w3.org/2001/XMLSchema#integer" } } rows { quad { p_iri { prefix_id: 15 name_id: 43 } o_literal { lex: "898666" datatype: 1 } } } rows { name { value: "contentUrl" } } rows { quad { p_iri { } o_literal { lex: "https://api.rohub.org/api/ros/356b66d5-921f-41c8-97e3-ebe65ed97084/crate/download/" } } } rows { name { value: "creativeWorkStatus" } } rows { quad { p_iri { } o_literal { lex: "Stable" } } } rows { name { value: "creator" } } rows { quad { p_iri { } o_iri { prefix_id: 4 name_id: 21 } } } rows { name { value: "dateCreated" } } rows { quad { p_iri { prefix_id: 15 name_id: 47 } o_literal { lex: "2023-09-06 04:40:29.876060+00:00" } } } rows { name { value: "dateModified" } } rows { quad { p_iri { } o_literal { lex: "2024-03-05 12:23:17.655491+00:00" } } } rows { name { value: "datePublished" } } rows { quad { p_iri { } o_literal { lex: "2023-09-06 04:40:29.876060+00:00" } } } rows { name { value: "description" } } rows { quad { p_iri { } o_literal { lex: "IDR is based on OMERO and thus all what we show in this notebook can be easily adjusted for use against another OMERO server, e.g. your institutional OMERO server instance.\r\n\r\nThe main objective of this notebook is to demonstrate how public resources such as the IDR can be used to train your neural network or validate software tools.\r\n\r\nThe authors of the PLOS Biology paper, \"Nessys: A new set of tools for the automated detection of nuclei within intact tissues and dense 3D cultures\" published in August 2019: https://doi.org/10.1371/journal.pbio.3000388, considered several image segmenation packages, but they did not use the approach described in this notebook.\r\n\r\nWe will analyse the data using Cellpose and compare the output with the original segmentation produced by the authors. StarDist was not considered by the authors. Our workflow shows how public repository can be accessed and data inside it used to validate software tools or new algorithms.\r\n\r\nWe will use an image (id=6001247) referenced in the paper. The image can be viewed online in the Image Data Resource (IDR).\r\n\r\nWe will use a predefined model from Cellpose as a starting point. Steps to access data from IDR could be re-used if you wish to create a new model (outside the scope of this notebook).\r\n\r\n## Launch\r\nThis notebook uses the [environment_cellpose.yml](https://github.com/ome/EMBL-EBI-imaging-course-05-2023/blob/main/Day_4/environment_cellpose.yml) file.\r\n\r\nSee [Setup](https://github.com/ome/EMBL-EBI-imaging-course-05-2023/blob/main/Day_4/setup.md)." } } } rows { name { value: "encodingFormat" } } rows { quad { p_iri { } o_literal { lex: "application/ld+json" } } } rows { name { value: "hasPart" } } rows { prefix { id: 1 value: "https://w3id.org/ro-id/356b66d5-921f-41c8-97e3-ebe65ed97084/resources/" } } rows { name { value: "23516bda-79ff-42f3-8e01-19d832e48bf2" } } rows { quad { p_iri { } o_iri { prefix_id: 1 } } } rows { name { value: "678a9a7c-7f20-4b16-8639-e40f0130f17d" } } rows { quad { o_iri { } } } rows { name { value: "d7444133-eaf9-4f60-86e6-c1f37c97126b" } } rows { quad { o_iri { } } } rows { quad { p_iri { prefix_id: 15 name_id: 23 } o_literal { lex: "https://w3id.org/ro-id/356b66d5-921f-41c8-97e3-ebe65ed97084" } } } rows { name { value: "isBasedOn" } } rows { quad { p_iri { name_id: 56 } o_literal { lex: "https://github.com/ome/EMBL-EBI-imaging-course-05-2023/blob/main/Day_4/Cellpose.ipynb" } } } rows { name { value: "license" } } rows { prefix { id: 3 value: "https://choosealicense.com/no-permission/" } } rows { quad { p_iri { } o_iri { prefix_id: 3 name_id: 2 } } } rows { name { value: "mainEntity" } } rows { quad { p_iri { prefix_id: 15 name_id: 58 } o_literal { lex: "Cellpose.ipynb" } } } rows { quad { p_iri { name_id: 13 } o_literal { lex: "Research Object Crate for Validate a tool against IDR data: Load Image with labels from IDR, re-analyze using Cellpose" } } } rows { quad { p_iri { } o_literal { lex: "https://workflowhub.eu/workflows/489/ro_crate?version=1" } } } rows { prefix { id: 14 value: "http://purl.org/wf4ever/ro#" } } rows { name { value: "ResearchObject" } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 14 name_id: 59 } } } rows { prefix { id: 2 value: "http://purl.org/wf4ever/roevo#" } } rows { name { value: "LiveRO" } } rows { quad { o_iri { prefix_id: 2 } } } rows { name { value: "Dataset" } } rows { quad { o_iri { prefix_id: 15 } } } rows { prefix { id: 16 value: "https://w3id.org/contentdesc#" } } rows { name { value: "Domain" } } rows { quad { p_iri { prefix_id: 16 } o_literal { lex: "https://w3id.org/ro-id/8830b06c-03a0-44b9-8d18-1d6d5b594bb6" } } } rows { quad { p_iri { prefix_id: 10 name_id: 33 } o_literal { lex: "https://w3id.org/ro-id/18cc8dfa-eb1f-4630-98f8-b896cf0aa517" } } } rows { quad { o_literal { lex: "https://w3id.org/ro-id/23894926-e9ec-4d7a-b7aa-5a20f2aa7d36" } } } rows { quad { o_literal { lex: "https://w3id.org/ro-id/4806fa6e-eafb-445a-a146-4541eb1fc111" } } } rows { quad { o_literal { lex: "https://w3id.org/ro-id/4c7e0947-1ab0-48bb-906a-48965a739ef0" } } } rows { quad { o_literal { lex: 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"https://w3id.org/ro-id/a07db792-1d4f-4537-9cca-9b469542387e" } } } rows { quad { o_literal { lex: "https://w3id.org/ro-id/b38e6b6b-7758-4404-8041-a3d90a0263fe" } } } rows { quad { o_literal { lex: "https://w3id.org/ro-id/d2ab79ab-d870-47b7-90f8-6203c629f8f2" } } } rows { name { value: "NASA" } } rows { quad { p_iri { name_id: 65 } o_literal { lex: "https://w3id.org/ro-id/6c2c06b8-a3c4-4034-8cb4-497da5e21f46" } } } rows { quad { o_literal { lex: "https://w3id.org/ro-id/9766b451-0737-495f-844d-ce59d8edd307" } } } rows { quad { p_iri { name_id: 39 } o_literal { lex: "https://w3id.org/ro-id/32d2d471-7a7f-4d67-8a0a-fd4385f42fc3" } } } rows { quad { o_literal { lex: "https://w3id.org/ro-id/5852d3f1-ad25-43b7-830b-0821d6823bd4" } } } rows { quad { o_literal { lex: "https://w3id.org/ro-id/987fe02e-cd3e-4b79-b8a2-9d8fabf1817d" } } } rows { quad { o_literal { lex: "https://w3id.org/ro-id/e4f43df9-5857-4ff7-aa9e-61768f8a03d9" } } } rows { quad { o_literal { lex: "https://w3id.org/ro-id/f48ff04d-e41c-4df6-973d-41fe178fd2f1" } } } rows { quad { p_iri { name_id: 27 } o_literal { lex: "https://w3id.org/ro-id/0c88387d-3c01-4e1f-a5c6-07793281a80b" } } } rows { quad { o_literal { lex: "https://w3id.org/ro-id/113e942c-efd3-494a-9ab0-dbe57b83efac" } } } rows { quad { o_literal { lex: "https://w3id.org/ro-id/179556f3-4098-4bf9-809d-443eaf174cdf" } } } rows { name { value: "TimeReference" } } rows { quad { p_iri { name_id: 66 } o_literal { lex: "https://w3id.org/ro-id/84ddb21f-6abc-45c3-85d2-33a543cebbeb" } } } rows { prefix { id: 7 value: "https://www.w3.org/ns/iana/link-relations/relation#" } } rows { name { value: "cite-as" } } rows { quad { p_iri { prefix_id: 7 } o_literal { lex: "Jean-Marie Burel. \"Research Object Crate for Validate a tool against IDR data: Load Image with labels from IDR, re-analyze using Cellpose.\" ROHub. Sep 06 ,2023. https://w3id.org/ro-id/356b66d5-921f-41c8-97e3-ebe65ed97084." } } } rows { quad { s_iri { prefix_id: 1 name_id: 53 } p_iri { prefix_id: 15 name_id: 42 } o_iri { prefix_id: 4 name_id: 21 } } } rows { quad { p_iri { prefix_id: 15 name_id: 43 } o_literal { lex: "513401" } } } rows { quad { p_iri { } o_literal { lex: "https://api.rohub.org/api/resources/23516bda-79ff-42f3-8e01-19d832e48bf2/download/" } } } rows { quad { p_iri { name_id: 46 } o_iri { prefix_id: 4 name_id: 21 } } } rows { quad { p_iri { prefix_id: 15 name_id: 47 } o_literal { lex: "2023-09-06 04:40:30.769117+00:00" } } } rows { quad { p_iri { } o_literal { lex: "2023-09-06 04:40:31.562846+00:00" } } } rows { quad { p_iri { name_id: 51 } o_literal { lex: "image/png" } } } rows { quad { p_iri { name_id: 57 } o_iri { prefix_id: 3 name_id: 2 } } } rows { quad { p_iri { prefix_id: 15 name_id: 13 } o_literal { lex: "CellposeIDR.png" } } } rows { name { value: "sdDatePublished" } } rows { quad { p_iri { name_id: 68 } o_literal { lex: "2023-09-06 04:40:30.769117+00:00" } } } rows { quad { p_iri { name_id: 14 } o_literal { lex: "https://github.com/ome/EMBL-EBI-imaging-course-05-2023/blob/main/Day_4/includes/CellposeIDR.png" } } } rows { prefix { id: 9 value: "http://purl.org/wf4ever/wf4ever#" } } rows { name { value: "Resource" } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 9 name_id: 69 } } } rows { name { value: "ImageObject" } } rows { quad { o_iri { prefix_id: 15 } } } rows { name { value: "MediaObject" } } rows { quad { o_iri { } } } rows { name { value: "WorkflowSketch" } } rows { quad { o_iri { prefix_id: 12 } } } rows { name { value: "about" } } rows { quad { s_iri { prefix_id: 1 name_id: 54 } p_iri { prefix_id: 15 name_id: 73 } o_literal { lex: "https://ror.org/https://doi.org/10.48546/workflowhub.workflow.489.1" } } } rows { quad { p_iri { name_id: 42 } o_iri { prefix_id: 4 name_id: 21 } } } rows { quad { p_iri { prefix_id: 15 name_id: 43 } o_literal { lex: "11251" datatype: 1 } } } rows { quad { p_iri { } o_literal { lex: "https://api.rohub.org/api/resources/678a9a7c-7f20-4b16-8639-e40f0130f17d/download/" } } } rows { quad { p_iri { name_id: 46 } o_iri { prefix_id: 4 name_id: 21 } } } rows { quad { p_iri { prefix_id: 15 name_id: 47 } o_literal { lex: "2023-09-06 04:40:30.774304+00:00" } } } rows { quad { p_iri { } o_literal { lex: "2023-09-06 04:40:34.357123+00:00" } } } rows { quad { p_iri { name_id: 51 } o_literal { lex: "text/html" } } } rows { quad { p_iri { name_id: 57 } o_iri { prefix_id: 3 name_id: 2 } } } rows { quad { p_iri { prefix_id: 15 name_id: 13 } o_literal { lex: "ro-crate-preview.html" } } } rows { quad { p_iri { name_id: 68 } o_literal { lex: "2023-09-06 04:40:30.774304+00:00" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 9 name_id: 69 } } } rows { quad { o_iri { prefix_id: 15 name_id: 18 } } } rows { quad { o_iri { name_id: 71 } } } rows { prefix { id: 11 value: "http://purl.org/dc/terms/" } } rows { name { value: "conformsTo" } } rows { quad { s_iri { prefix_id: 1 name_id: 55 } p_iri { prefix_id: 11 name_id: 74 } o_literal { lex: "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/" } } } rows { quad { p_iri { prefix_id: 15 name_id: 42 } o_iri { prefix_id: 4 name_id: 19 } } } rows { quad { p_iri { prefix_id: 15 name_id: 43 } o_literal { lex: "525382" } } } rows { quad { p_iri { } o_literal { lex: "https://api.rohub.org/api/resources/d7444133-eaf9-4f60-86e6-c1f37c97126b/download/" } } } rows { quad { p_iri { name_id: 46 } o_iri { prefix_id: 4 name_id: 19 } } } rows { quad { p_iri { prefix_id: 15 name_id: 47 } o_literal { lex: "2023-06-01 09:47:01+00:00" } } } rows { quad { p_iri { } o_literal { lex: "2023-09-06 04:40:35.261149+00:00" } } } rows { quad { p_iri { name_id: 50 } o_literal { lex: "IDR is based on OMERO and thus all what we show in this notebook can be easily adjusted for use against another OMERO server, e.g. your institutional OMERO server instance.\r\n\r\nThe main objective of this notebook is to demonstrate how public resources such as the IDR can be used to train your neural network or validate software tools.\r\n\r\nThe authors of the PLOS Biology paper, \"Nessys: A new set of tools for the automated detection of nuclei within intact tissues and dense 3D cultures\" published in August 2019: https://doi.org/10.1371/journal.pbio.3000388, considered several image segmenation packages, but they did not use the approach described in this notebook.\r\n\r\nWe will analyse the data using Cellpose and compare the output with the original segmentation produced by the authors. StarDist was not considered by the authors. Our workflow shows how public repository can be accessed and data inside it used to validate software tools or new algorithms.\r\n\r\nWe will use an image (id=6001247) referenced in the paper. The image can be viewed online in the Image Data Resource (IDR).\r\n\r\nWe will use a predefined model from Cellpose as a starting point. Steps to access data from IDR could be re-used if you wish to create a new model (outside the scope of this notebook).\r\n\r\n## Launch\r\nThis notebook uses the [environment_cellpose.yml](https://github.com/ome/EMBL-EBI-imaging-course-05-2023/blob/main/Day_4/environment_cellpose.yml) file.\r\n\r\nSee [Setup](https://github.com/ome/EMBL-EBI-imaging-course-05-2023/blob/main/Day_4/setup.md)." } } } rows { name { value: "image" } } rows { quad { p_iri { name_id: 75 } o_literal { lex: "CellposeIDR.png" } } } rows { name { value: "isPartOf" } } rows { quad { p_iri { } o_literal { lex: "https://workflowhub.eu/collections/4" } } } rows { name { value: "keywords" } } rows { quad { p_iri { } o_literal { lex: "imaging, Machine Learning, Python" } } } rows { quad { p_iri { name_id: 57 } o_iri { prefix_id: 3 name_id: 2 } } } rows { quad { p_iri { prefix_id: 15 name_id: 13 } o_literal { lex: "Validate a tool against IDR data: Load Image with labels from IDR, re-analyze using Cellpose" } } } rows { name { value: "producer" } } rows { quad { p_iri { name_id: 78 } o_literal { lex: "https://workflowhub.eu/projects/69" } } } rows { name { value: "programmingLanguage" } } rows { quad { p_iri { } o_literal { lex: "#jupyter" } } } rows { quad { p_iri { name_id: 68 } o_literal { lex: "2023-06-01 09:47:01+00:00" } } } rows { name { value: "sdPublisher" } } rows { quad { p_iri { name_id: 80 } o_literal { lex: "https://about.workflowhub.eu/" } } } rows { quad { p_iri { name_id: 14 } o_literal { lex: "https://github.com/ome/EMBL-EBI-imaging-course-05-2023/blob/main/Day_4/Cellpose.ipynb" } } } rows { quad { p_iri { name_id: 17 } o_literal { lex: "1" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 9 name_id: 69 } } } rows { quad { o_iri { prefix_id: 15 name_id: 71 } } } rows { name { value: "SoftwareSourceCode" } } rows { quad { o_iri { name_id: 81 } } } rows { prefix { id: 5 value: "https://bioschemas.org/" } } rows { name { value: "ComputationalWorkflow" } } rows { quad { o_iri { prefix_id: 5 } } } rows { name { value: "ro-crate-metadata.json" } } rows { prefix { id: 13 value: "https://w3id.org/ro/crate/" } } rows { name { value: "1.1" } } rows { quad { s_iri { prefix_id: 12 } p_iri { prefix_id: 11 name_id: 74 } o_iri { prefix_id: 13 name_id: 84 } } } rows { quad { p_iri { prefix_id: 15 name_id: 73 } o_iri { prefix_id: 12 name_id: 2 } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 15 name_id: 18 } } } rows { prefix { id: 8 value: "https://w3id.org/ro-id/" } } rows { name { value: "4806fa6e-eafb-445a-a146-4541eb1fc111" } } rows { quad { s_iri { prefix_id: 8 name_id: 85 } p_iri { prefix_id: 15 name_id: 13 } o_literal { lex: "author" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 10 name_id: 33 } } } rows { quad { p_iri { name_id: 28 } o_literal { lex: "6.456456456456457" } } } rows { quad { p_iri { } o_literal { lex: "4.3" } } } rows { name { value: "4c7e0947-1ab0-48bb-906a-48965a739ef0" } } rows { quad { s_iri { prefix_id: 8 name_id: 86 } p_iri { prefix_id: 15 name_id: 13 } o_literal { lex: "workflow" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 10 name_id: 33 } } } rows { quad { p_iri { name_id: 28 } o_literal { lex: "5.105105105105106" } } } rows { quad { p_iri { } o_literal { lex: "3.4" } } } rows { name { value: "4d11bd60-6e1b-4c94-9abc-e66823307fe6" } } rows { quad { s_iri { prefix_id: 8 name_id: 87 } p_iri { prefix_id: 15 name_id: 13 } o_literal { lex: "Restaurant and catering" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 10 name_id: 64 } } } rows { name { value: "path" } } rows { quad { p_iri { name_id: 88 } o_literal { lex: "Economy, business and finance/Economic sector/Tourism and leisure/Restaurant and catering" } } } rows { name { value: "56f05825-650c-48e5-9b2a-4396562ba762" } } rows { quad { s_iri { prefix_id: 8 } p_iri { prefix_id: 15 name_id: 13 } o_literal { lex: "information" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 10 name_id: 33 } } } rows { quad { p_iri { name_id: 28 } o_literal { lex: "10.210210210210212" } } } rows { quad { p_iri { } o_literal { lex: "6.8" } } } rows { name { value: "5852d3f1-ad25-43b7-830b-0821d6823bd4" } } rows { quad { s_iri { prefix_id: 8 name_id: 90 } p_iri { prefix_id: 15 name_id: 13 } o_literal { lex: "authors of the PLOS biology paper" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 10 name_id: 39 } } } rows { quad { p_iri { name_id: 28 } o_literal { lex: "11.185308848080133" } } } rows { quad { p_iri { } o_literal { lex: "6.7" } } } rows { name { value: "6c2c06b8-a3c4-4034-8cb4-497da5e21f46" } } rows { quad { s_iri { prefix_id: 8 name_id: 91 } p_iri { prefix_id: 15 name_id: 13 } o_literal { lex: "computer operations and hardware" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 10 name_id: 65 } } } rows { quad { p_iri { name_id: 28 } o_literal { lex: "100.0" } } } rows { quad { p_iri { } o_literal { lex: "0.37114787101745605" } } } rows { name { value: "6ea1af0a-0ba3-43b3-acf8-0c7990c0e0b7" } } rows { quad { s_iri { prefix_id: 8 name_id: 92 } p_iri { prefix_id: 15 name_id: 13 } o_literal { lex: "parcel" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 10 name_id: 33 } } } rows { quad { p_iri { name_id: 28 } o_literal { lex: "7.207207207207208" } } } rows { quad { p_iri { } o_literal { lex: "4.8" } } } rows { name { value: "7a024ba8-43ca-430a-b730-270e6d19d513" } } rows { quad { s_iri { prefix_id: 8 name_id: 93 } p_iri { prefix_id: 15 name_id: 13 } o_literal { lex: "Image Data Resource" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 10 name_id: 36 } } } rows { quad { p_iri { name_id: 28 } o_literal { lex: "20.903954802259886" } } } rows { quad { p_iri { } o_literal { lex: "11.1" } } } rows { name { value: "7f6f5244-2bbb-459f-8545-53dd8a5851df" } } rows { quad { s_iri { prefix_id: 8 name_id: 94 } p_iri { prefix_id: 15 name_id: 13 } o_literal { lex: "repository" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 10 name_id: 36 } } } rows { quad { p_iri { name_id: 28 } o_literal { lex: "9.416195856873824" } } } rows { quad { p_iri { } o_literal { lex: "5.0" } } } rows { name { value: "84ddb21f-6abc-45c3-85d2-33a543cebbeb" } } rows { quad { s_iri { prefix_id: 8 name_id: 95 } p_iri { prefix_id: 15 name_id: 13 } o_literal { lex: "in Aug-2019" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 10 name_id: 66 } } } rows { name { value: "882bc2df-8929-43ff-bcfa-efd8ab3f8dd7" } } rows { quad { s_iri { prefix_id: 8 name_id: 96 } p_iri { prefix_id: 15 name_id: 13 } o_literal { lex: "Biology" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 10 name_id: 64 } } } rows { quad { p_iri { name_id: 88 } o_literal { lex: "Science and technology/Natural science/Biology" } } } rows { name { value: "8830b06c-03a0-44b9-8d18-1d6d5b594bb6" } } rows { quad { s_iri { prefix_id: 8 name_id: 97 } p_iri { prefix_id: 15 name_id: 13 } o_literal { lex: "computer science" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 16 name_id: 62 } } } rows { quad { p_iri { prefix_id: 10 name_id: 28 } o_literal { lex: "100.0" } } } rows { quad { p_iri { } o_literal { lex: "14.6" } } } rows { name { value: "8ffef8d0-c22d-453a-8f12-2f10e2ac93b7" } } rows { quad { s_iri { prefix_id: 8 name_id: 98 } p_iri { prefix_id: 15 name_id: 13 } o_literal { lex: "image" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 10 name_id: 33 } } } rows { quad { p_iri { name_id: 28 } o_literal { lex: "9.15915915915916" } } } rows { quad { p_iri { } o_literal { lex: "6.1" } } } rows { name { value: "9766b451-0737-495f-844d-ce59d8edd307" } } rows { quad { s_iri { prefix_id: 8 name_id: 99 } p_iri { prefix_id: 15 name_id: 13 } o_literal { lex: "mathematical and computer sciences" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 10 name_id: 65 } } } rows { quad { p_iri { name_id: 28 } o_literal { lex: "100.0" } } } rows { quad { p_iri { } o_literal { lex: "0.37114787101745605" } } } rows { name { value: "987fe02e-cd3e-4b79-b8a2-9d8fabf1817d" } } rows { quad { s_iri { prefix_id: 8 name_id: 100 } p_iri { prefix_id: 15 name_id: 13 } o_literal { lex: "IDR data" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 10 name_id: 39 } } } rows { quad { p_iri { name_id: 28 } o_literal { lex: "14.023372287145243" } } } rows { quad { p_iri { } o_literal { lex: "8.4" } } } rows { name { value: "9ffbc6c7-491a-462a-9f88-714629a53223" } } rows { quad { s_iri { prefix_id: 8 name_id: 101 } p_iri { prefix_id: 15 name_id: 13 } o_literal { lex: "using" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 10 name_id: 33 } } } rows { quad { p_iri { name_id: 28 } o_literal { lex: "4.804804804804805" } } } rows { quad { p_iri { } o_literal { lex: "3.2" } } } rows { name { value: "a07db792-1d4f-4537-9cca-9b469542387e" } } rows { quad { s_iri { prefix_id: 8 name_id: 102 } p_iri { prefix_id: 15 name_id: 13 } o_literal { lex: "software tool" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 10 name_id: 36 } } } rows { quad { p_iri { name_id: 28 } o_literal { lex: "11.11111111111111" } } } rows { quad { p_iri { } o_literal { lex: "5.9" } } } rows { name { value: "b38e6b6b-7758-4404-8041-a3d90a0263fe" } } rows { quad { s_iri { prefix_id: 8 name_id: 103 } p_iri { prefix_id: 15 name_id: 13 } o_literal { lex: "OMERO" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 10 name_id: 36 } } } rows { quad { p_iri { name_id: 28 } o_literal { lex: "13.935969868173258" } } } rows { quad { p_iri { } o_literal { lex: "7.4" } } } rows { name { value: "b9ed8a51-ce8c-4585-b8fa-b3447a292541" } } rows { quad { s_iri { prefix_id: 8 name_id: 104 } p_iri { prefix_id: 15 name_id: 13 } o_literal { lex: "Hardware" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 10 name_id: 64 } } } rows { quad { p_iri { name_id: 88 } o_literal { lex: "Economy, business and finance/Economic sector/Computing and information technology/Hardware" } } } rows { name { value: "cafbfdae-a280-482c-86f7-ad7b68bd7ace" } } rows { quad { s_iri { prefix_id: 8 name_id: 105 } p_iri { prefix_id: 15 name_id: 13 } o_literal { lex: "repository" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 10 name_id: 33 } } } rows { quad { p_iri { name_id: 28 } o_literal { lex: "9.00900900900901" } } } rows { quad { p_iri { } o_literal { lex: "6.0" } } } rows { name { value: "d2ab79ab-d870-47b7-90f8-6203c629f8f2" } } rows { quad { s_iri { prefix_id: 8 name_id: 106 } p_iri { prefix_id: 15 name_id: 13 } o_literal { lex: "data" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 10 name_id: 36 } } } rows { quad { p_iri { name_id: 28 } o_literal { lex: "12.617702448210922" } } } rows { quad { p_iri { } o_literal { lex: "6.7" } } } rows { name { value: "d2d5269a-b664-464b-a47b-7db9f6eddf74" } } rows { quad { s_iri { prefix_id: 8 name_id: 107 } p_iri { prefix_id: 15 name_id: 13 } o_literal { lex: "data" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 10 name_id: 33 } } } rows { quad { p_iri { name_id: 28 } o_literal { lex: "11.411411411411413" } } } rows { quad { p_iri { } o_literal { lex: "7.6" } } } rows { name { value: "d7483f86-4fd6-4742-8aef-6615c3fa847b" } } rows { quad { s_iri { prefix_id: 8 name_id: 108 } p_iri { prefix_id: 15 name_id: 13 } o_literal { lex: "earth sciences" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 10 name_id: 63 } } } rows { quad { p_iri { name_id: 28 } o_literal { lex: "100.0" } } } rows { quad { p_iri { } o_literal { lex: "0.5329017639160156" } } } rows { name { value: "dd1a0658-81d9-40b1-834d-eef12c2cc341" } } rows { quad { s_iri { prefix_id: 8 name_id: 109 } p_iri { prefix_id: 15 name_id: 13 } o_literal { lex: "laptop" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 10 name_id: 33 } } } rows { quad { p_iri { name_id: 28 } o_literal { lex: "13.063063063063062" } } } rows { quad { p_iri { } o_literal { lex: "8.7" } } } rows { name { value: "e4f43df9-5857-4ff7-aa9e-61768f8a03d9" } } rows { quad { s_iri { prefix_id: 8 name_id: 110 } p_iri { prefix_id: 15 name_id: 13 } o_literal { lex: "server instance" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 10 name_id: 39 } } } rows { quad { p_iri { name_id: 28 } o_literal { lex: "28.046744574290486" } } } rows { quad { p_iri { } o_literal { lex: "16.8" } } } rows { name { value: "e5131be0-2470-41c2-9710-89a09b67483d" } } rows { quad { s_iri { prefix_id: 8 name_id: 111 } p_iri { prefix_id: 15 name_id: 13 } o_literal { lex: "geology" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 10 name_id: 63 } } } rows { quad { p_iri { name_id: 28 } o_literal { lex: "100.0" } } } rows { quad { p_iri { } o_literal { lex: "0.5329017639160156" } } } rows { name { value: "f48ff04d-e41c-4df6-973d-41fe178fd2f1" } } rows { quad { s_iri { prefix_id: 8 name_id: 112 } p_iri { prefix_id: 15 name_id: 13 } o_literal { lex: "segmenation package" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 10 name_id: 39 } } } rows { quad { p_iri { name_id: 28 } o_literal { lex: "21.202003338898162" } } } rows { quad { p_iri { } o_literal { lex: "12.7" } } } rows { name { value: "faaf5c17-d4b7-4e6c-932f-c7f497af6cab" } } rows { quad { s_iri { prefix_id: 8 name_id: 113 } p_iri { prefix_id: 15 name_id: 13 } o_literal { lex: "Restaurant" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 10 name_id: 64 } } } rows { quad { p_iri { name_id: 88 } o_literal { lex: "Lifestyle and leisure/Leisure/Leisure venue/Restaurant" } } } rows { name { value: "fb61604a-2e68-41f9-807b-124bfd095008" } } rows { quad { s_iri { prefix_id: 8 name_id: 114 } p_iri { prefix_id: 15 name_id: 13 } o_literal { lex: "notebook" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 10 name_id: 33 } } } rows { quad { p_iri { name_id: 28 } o_literal { lex: "4.954954954954955" } } } rows { quad { p_iri { } o_literal { lex: "3.3" } } } rows { prefix { id: 14 value: "https://workflowhub.eu/collections/" } } rows { name { value: "4" } } rows { quad { s_iri { prefix_id: 14 name_id: 115 } p_iri { prefix_id: 15 name_id: 13 } o_literal { lex: "IDR" } } } rows { name { value: "Collection" } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 15 name_id: 116 } } } rows { prefix { id: 2 value: "https://workflowhub.eu/people/" } } rows { name { value: "144" } } rows { quad { s_iri { prefix_id: 2 } p_iri { prefix_id: 15 name_id: 13 } o_literal { lex: "Jean-Marie Burel" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 15 name_id: 20 } } } rows { prefix { id: 7 value: "https://workflowhub.eu/projects/" } } rows { name { value: "69" } } rows { quad { s_iri { prefix_id: 7 name_id: 118 } p_iri { prefix_id: 15 name_id: 13 } o_literal { lex: "OME" } } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 15 name_id: 15 } } } rows { name { value: "Project" } } rows { quad { o_iri { name_id: 119 } } } rows { prefix { id: 1 value: "https://w3id.org/np/RAKKHlme6Pw_5flNQx7gZH7fJlAlXozuegMbuURzkT1j8/" } } rows { prefix { id: 4 value: "http://www.w3.org/ns/prov#" } } rows { name { value: "wasDerivedFrom" } } rows { prefix { id: 3 value: "https://api.rohub.org/api/ros/356b66d5-921f-41c8-97e3-ebe65ed97084/crate/download/" } } rows { quad { s_iri { prefix_id: 1 name_id: 4 } p_iri { prefix_id: 4 name_id: 120 } o_iri { prefix_id: 3 name_id: 83 } g_iri { prefix_id: 1 name_id: 7 } } } rows { prefix { id: 9 value: "https://w3id.org/np/" } } rows { name { value: "created" } } rows { datatype { value: "http://www.w3.org/2001/XMLSchema#dateTime" } } rows { quad { s_iri { prefix_id: 9 name_id: 1 } p_iri { prefix_id: 11 name_id: 121 } o_literal { lex: "2025-11-11T16:09:23.639+01:00" datatype: 2 } g_iri { prefix_id: 1 name_id: 9 } } } rows { prefix { id: 5 value: "http://purl.org/nanopub/x/" } } rows { name { value: "introduces" } } rows { quad { p_iri { prefix_id: 5 name_id: 122 } o_iri { prefix_id: 12 name_id: 2 } } } rows { name { value: "RoCrateNanopub" } } rows { quad { p_iri { prefix_id: 6 name_id: 10 } o_iri { prefix_id: 5 name_id: 123 } } } rows { prefix { id: 13 value: "http://www.w3.org/2000/01/rdf-schema#" } } rows { name { value: "label" } } rows { quad { p_iri { prefix_id: 13 } o_literal { lex: "Research Object Crate for Validate a tool against IDR data: Load Image with labels from IDR, re-analyze using Cellpose" } } } rows { name { value: "sig" } } rows { name { value: "hasAlgorithm" } } rows { quad { s_iri { prefix_id: 1 } p_iri { prefix_id: 5 } o_literal { lex: "RSA" } } } rows { name { value: "hasPublicKey" } } rows { quad { p_iri { } o_literal { lex: "MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEA4pPaESKwmC6l37P86K6TNLq6yeQtc7m9CvcqauLs/1FC0viHvQnFBgxj0a+loPDv/Egwe6OqFpa0iW9Ypnyz9YPoh+pxbRXonbuMOb+8Ry9hXZ+TEKfWjhjVDGEaClwfRwglh2HI/xfV4CD9AgvDOEoZQiyta8a90PYwJ3G6e70oCHTn61+OWTkI9KRYHOYgg3btdy2Z7q/30PTFawb2ZT5aIfIJYobUYv2a7yhtcqWCHZeKv0bxGnRjTFNx1rscBMlLJSzvRtpQc1cCRVEPFZHo1adaXCI9tGvn4cxeNQ96y8dxkN1XhpaJairde+23MDzf42Oe97KG2HYzKiyVnQIDAQAB" } } } rows { name { value: "hasSignature" } } rows { quad { p_iri { } o_literal { lex: "yITpr5LO9QcfloJ0G0nOrawcbu4FxmRcByU3Td+VtM4KAXu5nPbLJIdoecv1R5GfruhNvsDNaY+JOhPKNV7cWyTXlCCh0tAntZEaZicmmMbl+A1vjoBi7leZ15i8Fgy7iY6cUiovzDl+w7Sghae1ru2gIyMPbZ+HWSGdd5+WIWMqTT58V41gOJ1E12P1kZpdrodgaRF5sqapo25W1A2zpu1XM0LSuUxvh7OUQqnQ5Lh4la3UnLjFkrNDlgSRItSzrN7JXwZJvle7hL9gHjeWxMYsAhxQjm5D5KsoYGqUxqG9Mb+oG8lUhE8ErfW8Y+HeBXwWVhJatMbFrkImvZvoZg==" } } } rows { name { id: 3 value: "hasSignatureTarget" } } rows { quad { p_iri { name_id: 3 } o_iri { prefix_id: 9 name_id: 1 } } } rows { name { id: 5 value: "signedBy" } } rows { prefix { id: 16 value: "https://w3id.org/kpxl/gen/terms/" } } rows { name { value: "RoCrateBot" } } rows { quad { p_iri { prefix_id: 5 name_id: 5 } o_iri { prefix_id: 16 } } }