pepr-hal-data / softcite /AStandardsBasedKnowledgeGraphthatBridgesScientificWorkflowsRunTimeProvenanceandToolRegistries.software.json
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"software-type": "software", "software-name": {"rawForm": "ComputationalWorkflow", "normalizedForm": "ComputationalWorkflow", "offsetStart": 6, "offsetEnd": 27}, "context": "a bsc:ComputationalWorkflow ; 4 schema:name ?workflow_name ; 5 schema:step ?step .", "mentionContextAttributes": {"used": {"value": false, "score": 0.007303953170776367}, "created": {"value": false, "score": 2.1457672119140625e-06}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": false, "score": 0.007303953170776367}, "created": {"value": false, "score": 1.1086463928222656e-05}, "shared": {"value": false, "score": 0.00011217594146728516}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 7, "offsetEnd": 12}, "context": "In bio.tools, each tool is annotated with EDAM topics, operations, and type and format of their input and output data.", "mentionContextAttributes": {"used": 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"offsetStart": 10, "offsetEnd": 15}, "context": "Among all tools, 2,159 (7.12%) have no topic or operation annotations.", "mentionContextAttributes": {"used": {"value": false, "score": 0.4227500557899475}, "created": {"value": false, "score": 1.5020370483398438e-05}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.999976634979248}, "created": {"value": true, "score": 0.9999253749847412}, "shared": {"value": true, "score": 0.9572210907936096}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "STRSTARTS", "normalizedForm": "STRSTARTS", "offsetStart": 10, "offsetEnd": 19}, "url": {"rawForm": "https://bio.tools/\"", "normalizedForm": "https://bio.tools/\"", "offsetStart": 41, "offsetEnd": 60}, "context": "20 FILTER(STRSTARTS(STR(?biotools_url), \"https://bio.tools/\"))", "mentionContextAttributes": {"used": {"value": true, "score": 0.9359251260757446}, "created": {"value": false, "score": 2.2649765014648438e-05}, "shared": {"value": false, "score": 3.4570693969726562e-06}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9359251260757446}, "created": {"value": false, "score": 2.2649765014648438e-05}, "shared": {"value": false, "score": 3.4570693969726562e-06}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "CWL", "normalizedForm": "CWL", "offsetStart": 11, "offsetEnd": 14}, "context": "Bioschemas CWL API Provenance Run Crate Schema.org,", "mentionContextAttributes": {"used": {"value": false, "score": 0.0008605718612670898}, "created": {"value": false, "score": 0.0003510713577270508}, "shared": {"value": false, "score": 0.35339784622192383}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9995833039283752}, "created": {"value": false, "score": 0.0019192695617675781}, "shared": {"value": false, "score": 0.35339784622192383}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 11, "offsetEnd": 16}, "context": "We grouped tools into three categories based on an arbitrary threshold applied to the sum of their topic and operation entropy (max(\ud835\udc46 \ud835\udc52 ) = 15.76).", "mentionContextAttributes": {"used": {"value": true, "score": 0.999930739402771}, "created": {"value": false, "score": 1.728534698486328e-05}, "shared": {"value": false, "score": 1.1920928955078125e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.999976634979248}, "created": {"value": true, "score": 0.9999253749847412}, "shared": {"value": true, "score": 0.9572210907936096}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 11, "offsetEnd": 16}, "context": "Only 1,262 tools have an entropy sum above 10.", "mentionContextAttributes": {"used": {"value": false, "score": 0.016934752464294434}, "created": {"value": false, "score": 3.409385681152344e-05}, "shared": {"value": false, "score": 1.1920928955078125e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.999976634979248}, "created": {"value": true, "score": 0.9999253749847412}, "shared": {"value": true, "score": 0.9572210907936096}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "Planemo", "normalizedForm": "Planemo", "offsetStart": 11, "offsetEnd": 18}, "context": "Bioschemas Planemo output file Loaded in the knowledge base Data flow", "mentionContextAttributes": {"used": {"value": true, "score": 0.7121401429176331}, "created": {"value": false, "score": 1.3470649719238281e-05}, "shared": {"value": false, "score": 1.1920928955078125e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9998983144760132}, "created": {"value": false, "score": 0.0019457340240478516}, "shared": {"value": false, "score": 3.5762786865234375e-07}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "Nextflow", "normalizedForm": "Nextflow", "offsetStart": 11, "offsetEnd": 19}, "context": "Bioschemas Nextflow API Workflow RO-Crate Schema.org", "mentionContextAttributes": {"used": {"value": false, "score": 0.0002993345260620117}, "created": {"value": false, "score": 0.0001533031463623047}, "shared": {"value": false, "score": 0.13519150018692017}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999864101409912}, "created": {"value": false, "score": 0.008241117000579834}, "shared": {"value": false, "score": 0.13519150018692017}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 12, "offsetEnd": 17}, "context": "On average, tools have 3.27 \u00b1 1.46 (standard deviation) directly assigned topics and 2.28 \u00b1 1.44 directly assigned operations.", "mentionContextAttributes": {"used": {"value": false, "score": 0.1478305459022522}, "created": {"value": false, "score": 7.987022399902344e-06}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.999976634979248}, "created": {"value": true, "score": 0.9999253749847412}, "shared": {"value": true, "score": 0.9572210907936096}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "Nextflow", "normalizedForm": "Nextflow", "offsetStart": 12, "offsetEnd": 20}, "context": "Some of the Nextflow workflows are part of the nf-core framework, while all galaxy workflows were taken from the Intergalactic Workflow Commission (IWC) library.", "mentionContextAttributes": {"used": {"value": true, "score": 0.9991028308868408}, "created": {"value": false, "score": 2.1219253540039062e-05}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999864101409912}, "created": {"value": false, "score": 0.008241117000579834}, "shared": {"value": false, "score": 0.13519150018692017}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "Crate", "normalizedForm": "Crate", "offsetStart": 13, "offsetEnd": 18}, "context": "Workflow Run Crate metadata files generated by Galaxy were exported.", "mentionContextAttributes": {"used": {"value": true, "score": 0.9999258518218994}, "created": {"value": false, "score": 1.0013580322265625e-05}, "shared": {"value": false, "score": 1.1920928955078125e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999258518218994}, "created": {"value": true, "score": 0.8732197284698486}, "shared": {"value": true, "score": 0.6471108794212341}}, "references": [{"label": "[14]", "normalizedForm": "[14]", "refKey": 14}]}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "MultiQC", "normalizedForm": "MultiQC", "offsetStart": 13, "offsetEnd": 20}, "context": "For example, MultiQC is directly annotated by Sequence analysis (topic_0080), that is associated to Sequence (data_2044) so we can infer that MultiQC is also associated to Sequence (and its ancestors).", "mentionContextAttributes": {"used": {"value": true, "score": 0.9504700303077698}, "created": {"value": false, "score": 5.364418029785156e-06}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9997537732124329}, "created": {"value": false, "score": 0.00755387544631958}, "shared": {"value": true, "score": 0.9572210907936096}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "MultiQC", "normalizedForm": "MultiQC", "offsetStart": 13, "offsetEnd": 20}, "context": "For example, MultiQC is also directly annotated by Sequencing quality control (operation_3218), which inherits an association to Nucleic acid sequence (data_2977) through its ancestor Nucleic acid sequence analysis (operation_2478).", "mentionContextAttributes": {"used": {"value": false, "score": 0.02703416347503662}, "created": {"value": false, "score": 6.67572021484375e-06}, "shared": {"value": false, "score": 1.1920928955078125e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9997537732124329}, "created": {"value": false, "score": 0.00755387544631958}, "shared": {"value": true, "score": 0.9572210907936096}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "BoMiProt", "normalizedForm": "BoMiProt", "offsetStart": 13, "offsetEnd": 21}, "context": "The software BoMiProt 33 also illustrates that some software entries in bio.tools have a very large number of high-quality annotations, although such tools represent only 1,262 tools (4.16%) of the entire registry.", "mentionContextAttributes": {"used": {"value": false, "score": 0.0017449259757995605}, "created": {"value": false, "score": 5.841255187988281e-05}, "shared": {"value": false, "score": 1.3113021850585938e-06}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9937278032302856}, "created": {"value": false, "score": 5.841255187988281e-05}, "shared": {"value": false, "score": 1.3113021850585938e-06}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "ShareFAIR-KG", "normalizedForm": "ShareFAIR-KG", "offsetStart": 13, "offsetEnd": 28}, "context": "The proposed ShareFAIR-KG for tools and workflows makes it possible to query many aspects of the workflows, and especially the specific annotation of tools used in workflow steps.", "mentionContextAttributes": {"used": {"value": false, "score": 8.738040924072266e-05}, "created": {"value": true, "score": 0.5985383987426758}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.992659866809845}, "created": {"value": true, "score": 0.5985383987426758}, "shared": {"value": false, "score": 3.5762786865234375e-07}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "CWL", "normalizedForm": "CWL", "offsetStart": 14, "offsetEnd": 17}, "context": "\u2022 The code of CWL and Nextflow workflows is parsable and analysable with our scripts.", "mentionContextAttributes": {"used": {"value": false, "score": 0.04905742406845093}, "created": {"value": false, "score": 8.130073547363281e-05}, "shared": {"value": false, "score": 1.1920928955078125e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9995833039283752}, "created": {"value": false, "score": 0.0019192695617675781}, "shared": {"value": false, "score": 0.35339784622192383}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "EDAM", "normalizedForm": "EDAM", "offsetStart": 14, "offsetEnd": 18}, "context": "Note that the EDAM ontology recommends 837 candidate annotations for the deprecated ones (and 5 of these 837 have since become deprecated themselves).", "mentionContextAttributes": {"used": {"value": false, "score": 0.007793605327606201}, "created": {"value": false, "score": 2.086162567138672e-05}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999855756759644}, "created": {"value": true, "score": 0.9998804330825806}, "shared": {"value": true, "score": 0.9572210907936096}}, "references": [{"label": "35]", "normalizedForm": "35]", "refKey": 35}, {"label": "[34,", "normalizedForm": "[34", "refKey": 34}]}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 14, "offsetEnd": 19}, "context": "Tool name bio.tools identifier EDAM operation EDAM operation label # workflow steps MultiQC https://bio.tools/multiqc", "mentionContextAttributes": {"used": {"value": false, "score": 0.00015938282012939453}, "created": {"value": false, "score": 8.463859558105469e-06}, "shared": {"value": true, "score": 0.9572210907936096}}, "documentContextAttributes": {"used": {"value": true, "score": 0.999976634979248}, "created": {"value": true, "score": 0.9999253749847412}, "shared": {"value": true, "score": 0.9572210907936096}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "org", "normalizedForm": "org", "offsetStart": 15, "offsetEnd": 18}, "context": "https://www.w3.org/TR/prov-o/", "mentionContextAttributes": {"used": {"value": false, "score": 0.00015342235565185547}, "created": {"value": false, "score": 1.430511474609375e-05}, "shared": {"value": true, "score": 0.9237979054450989}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999961853027344}, "created": {"value": false, "score": 0.10365641117095947}, "shared": {"value": true, "score": 0.9923090934753418}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "org", "normalizedForm": "org", "offsetStart": 15, "offsetEnd": 18}, "context": "https://schema.org/", "mentionContextAttributes": {"used": {"value": 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"software-name": {"rawForm": "org", "normalizedForm": "org", "offsetStart": 18, "offsetEnd": 21}, "context": "15 https://schema.org/additionalType", "mentionContextAttributes": {"used": {"value": false, "score": 0.00030243396759033203}, "created": {"value": false, "score": 1.2159347534179688e-05}, "shared": {"value": true, "score": 0.9910010695457458}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999961853027344}, "created": {"value": false, "score": 0.10365641117095947}, "shared": {"value": true, "score": 0.9923090934753418}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "CWL", "normalizedForm": "CWL", "offsetStart": 18, "offsetEnd": 21}, "context": "Then, the code of CWL workflows was parsed, to extract their prospective provenance and generate corresponding Provenance Run Crate metadata files.", "mentionContextAttributes": {"used": {"value": true, "score": 0.9995833039283752}, "created": {"value": false, "score": 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ease of integration with existing resources.", "mentionContextAttributes": {"used": {"value": false, "score": 0.00021308660507202148}, "created": {"value": false, "score": 0.00018912553787231445}, "shared": {"value": false, "score": 1.0728836059570312e-06}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999961853027344}, "created": {"value": false, "score": 0.005827009677886963}, "shared": {"value": false, "score": 0.05262273550033569}}, "references": [{"label": "[15]", "normalizedForm": "[15]", "refKey": 15, "offsetStart": 8186, "offsetEnd": 8190}, {"label": "[15]", "normalizedForm": "[15]", "refKey": 15, "offsetStart": 8186, "offsetEnd": 8190}]}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "org", "normalizedForm": "org", "offsetStart": 27, "offsetEnd": 30}, "context": "https://www.researchobject.org/ro-crate/", "mentionContextAttributes": {"used": {"value": false, "score": 0.0001537799835205078}, "created": {"value": false, 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{"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 89, "offsetEnd": 94}, "context": "When possible, a link was established between the tools executed in Galaxy and their bio.tools", "mentionContextAttributes": {"used": {"value": true, "score": 0.9993481040000916}, "created": {"value": false, "score": 0.005827009677886963}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.999976634979248}, "created": {"value": true, "score": 0.9999253749847412}, "shared": {"value": true, "score": 0.9572210907936096}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "WMS", "normalizedForm": "WMS", "offsetStart": 90, "offsetEnd": 93}, "context": "Workflow Run Crate describes the execution of a workflow by a Workflow Management System (WMS), including its inputs and outputs, but not its individual steps nor the software used.", "mentionContextAttributes": {"used": {"value": false, "score": 0.0005130767822265625}, "created": {"value": false, "score": 0.00042432546615600586}, "shared": {"value": false, "score": 4.76837158203125e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9994499087333679}, "created": {"value": false, "score": 0.024468600749969482}, "shared": {"value": true, "score": 0.9611940979957581}}, "references": [{"label": "[15]", "normalizedForm": "[15]", "refKey": 15}, {"label": "[15]", "normalizedForm": "[15]", "refKey": 15}]}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "Nextflow", "normalizedForm": "Nextflow", "offsetStart": 90, "offsetEnd": 98}, "context": "Workflows from three different WMS were selected: Common Workflow Language (CWL) , Nextflow and Galaxy.", "mentionContextAttributes": {"used": {"value": true, "score": 0.9995304346084595}, "created": {"value": false, "score": 8.797645568847656e-05}, "shared": {"value": false, "score": 1.1920928955078125e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999864101409912}, "created": {"value": false, "score": 0.008241117000579834}, "shared": {"value": false, "score": 0.13519150018692017}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "bio.tools", "normalizedForm": "bio.tools", "offsetStart": 90, "offsetEnd": 99}, "context": "In this fourth use case, information about workflow output data formats is extracted from bio.tools, which contains EDAM annotation on the type and format of tool outputs.", "mentionContextAttributes": {"used": {"value": false, "score": 0.22012680768966675}, "created": {"value": false, "score": 2.5510787963867188e-05}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.999983549118042}, "created": {"value": false, "score": 0.00015306472778320312}, "shared": {"value": false, "score": 1.6808509826660156e-05}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "Provenance", "normalizedForm": "Provenance", "offsetStart": 90, "offsetEnd": 100}, "context": "Thus, it can integrate ontologies or vocabularies from external sources to complement the Provenance Run Crate's workflow descriptions.", "mentionContextAttributes": {"used": {"value": false, "score": 7.390975952148438e-05}, "created": {"value": false, "score": 0.00013530254364013672}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.999825656414032}, "created": {"value": false, "score": 0.01495349407196045}, "shared": {"value": false, "score": 0.35339784622192383}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "Sub-workflow 2", "normalizedForm": "Sub-workflow 2", "offsetStart": 90, "offsetEnd": 104}, "context": "Input Data Output Data i Scale ii iii iv Process 3 Tool 3 Process 2 Tool 2 Sub-workflow 2 Sub-workflow 2 Process 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false, "score": 0.0019058585166931152}, "created": {"value": false, "score": 0.00755387544631958}, "shared": {"value": false, "score": 1.0728836059570312e-06}}, "documentContextAttributes": {"used": {"value": true, "score": 0.999976634979248}, "created": {"value": true, "score": 0.9999253749847412}, "shared": {"value": true, "score": 0.9572210907936096}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "EDAM", "normalizedForm": "EDAM", "offsetStart": 92, "offsetEnd": 96}, "context": "The properties encodingFormat 14 and additionalType 15 refer to standards like EDAM Data or EDAM Format, for data description.", "mentionContextAttributes": {"used": {"value": true, "score": 0.8950000405311584}, "created": {"value": false, "score": 2.384185791015625e-06}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999855756759644}, "created": {"value": true, "score": 0.9998804330825806}, "shared": {"value": true, "score": 0.9572210907936096}}, "references": [{"label": "35]", "normalizedForm": "35]", "refKey": 35}, {"label": "[34,", "normalizedForm": "[34", "refKey": 34}]}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 92, "offsetEnd": 97}, "context": "With citation counts exceeding 9,000 and 32,000 respectively, it is unsurprising that these tools are widely integrated into numerous workflows.", "mentionContextAttributes": {"used": {"value": false, "score": 7.641315460205078e-05}, "created": {"value": false, "score": 0.00020128488540649414}, "shared": {"value": false, "score": 3.5762786865234375e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.999976634979248}, "created": {"value": true, "score": 0.9999253749847412}, "shared": {"value": true, "score": 0.9572210907936096}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "org", "normalizedForm": "org", "offsetStart": 93, "offsetEnd": 96}, "context": "Finally, Galaxy workflow repositories were cloned and their tests were executed on usegalaxy.org", "mentionContextAttributes": {"used": {"value": true, "score": 0.9999961853027344}, "created": {"value": false, "score": 1.1563301086425781e-05}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999961853027344}, "created": {"value": false, "score": 0.10365641117095947}, "shared": {"value": true, "score": 0.9923090934753418}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "Crate", "normalizedForm": "Crate", "offsetStart": 93, "offsetEnd": 98}, "context": "One such approach, the Provenance Run RO-Crate profile (Provenance Run Crate) [14] of the RO-Crate standardfoot_1 , emerges as a robust solution for representing comprehensive pipelines.", "mentionContextAttributes": {"used": {"value": false, "score": 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"normalizedForm": "tools", "offsetStart": 104, "offsetEnd": 109}, "context": "Tool name bio.tools identifier EDAM operation EDAM operation label # workflow steps MultiQC https://bio.tools/multiqc", "mentionContextAttributes": {"used": {"value": false, "score": 0.00015938282012939453}, "created": {"value": false, "score": 8.463859558105469e-06}, "shared": {"value": true, "score": 0.9572210907936096}}, "documentContextAttributes": {"used": {"value": true, "score": 0.999976634979248}, "created": {"value": true, "score": 0.9999253749847412}, "shared": {"value": true, "score": 0.9572210907936096}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "Crate", "normalizedForm": "Crate", "offsetStart": 105, "offsetEnd": 110}, "context": "Thus, it can integrate ontologies or vocabularies from external sources to complement the Provenance Run Crate's workflow descriptions.", "mentionContextAttributes": {"used": {"value": false, "score": 7.390975952148438e-05}, "created": {"value": false, "score": 0.00013530254364013672}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999258518218994}, "created": {"value": true, "score": 0.8732197284698486}, "shared": {"value": true, "score": 0.6471108794212341}}, "references": [{"label": "[14]", "normalizedForm": "[14]", "refKey": 14}]}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "Process 1 Tool 1", "normalizedForm": "Process 1 Tool 1", "offsetStart": 105, "offsetEnd": 121}, "context": "Input Data Output Data i Scale ii iii iv Process 3 Tool 3 Process 2 Tool 2 Sub-workflow 2 Sub-workflow 2 Process 1 Tool 1 Process 5 Tool 6 Process 4 Tool 4 Tool 5 Process 6 Tool 2 Process 4 Tool 4 Tool 5", "mentionContextAttributes": {"used": {"value": true, "score": 0.9968697428703308}, "created": {"value": false, "score": 1.990795135498047e-05}, "shared": {"value": false, "score": 4.76837158203125e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9968697428703308}, "created": {"value": false, "score": 1.990795135498047e-05}, "shared": {"value": false, "score": 4.76837158203125e-07}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 106, "offsetEnd": 111}, "context": "(iii) Domain specific ontologies like EDAM, EFO and SIO, as well as the content of WorkflowHub and of bio.tools repositories, ensuring unique software and annotation referencing and annotation.", "mentionContextAttributes": {"used": {"value": false, "score": 0.015488028526306152}, "created": {"value": false, "score": 5.924701690673828e-05}, "shared": {"value": false, "score": 2.1457672119140625e-06}}, "documentContextAttributes": {"used": {"value": true, "score": 0.999976634979248}, "created": {"value": true, "score": 0.9999253749847412}, "shared": {"value": true, "score": 0.9572210907936096}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 107, "offsetEnd": 112}, "context": "EDAM operations indicates the label of the EDAM term qualifying the operation performed by the tool in bio.tools.", "mentionContextAttributes": {"used": {"value": true, "score": 0.5080110430717468}, "created": {"value": false, "score": 0.00029021501541137695}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.999976634979248}, "created": {"value": true, "score": 0.9999253749847412}, "shared": {"value": true, "score": 0.9572210907936096}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "MultiQC", "normalizedForm": "MultiQC", "offsetStart": 108, "offsetEnd": 115}, "context": "This highlights the need to detect and improve annotation quality, particularly for a widely used tool like MultiQC, which plays a key role in many workflows.", "mentionContextAttributes": {"used": {"value": false, "score": 4.4226646423339844e-05}, "created": {"value": false, "score": 0.0009721517562866211}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9997537732124329}, "created": {"value": false, "score": 0.00755387544631958}, "shared": {"value": true, "score": 0.9572210907936096}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 109, "offsetEnd": 114}, "context": "They were extracted from WorkflowHub, well-known by the community for promoting workflow FAIRness using open tools and standards like bio.tools and EDAM.", "mentionContextAttributes": {"used": {"value": true, "score": 0.9998958110809326}, "created": {"value": false, "score": 0.002504587173461914}, "shared": {"value": false, "score": 2.3365020751953125e-05}}, "documentContextAttributes": {"used": {"value": true, "score": 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"offsetStart": 111, "offsetEnd": 121}, "context": "Then, the code of CWL workflows was parsed, to extract their prospective provenance and generate corresponding Provenance Run Crate metadata files.", "mentionContextAttributes": {"used": {"value": true, "score": 0.9995833039283752}, "created": {"value": false, "score": 4.839897155761719e-05}, "shared": {"value": false, "score": 1.1920928955078125e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.999825656414032}, "created": {"value": false, "score": 0.01495349407196045}, "shared": {"value": false, "score": 0.35339784622192383}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "GATK", "normalizedForm": "GATK", "offsetStart": 112, "offsetEnd": 116}, "context": "\u2022 Researchers can locate every workflow that implements a specific analytical step (e.g., \"variant calling with GATK\") across all supported languages, compare implementations, and reuse the most appropriate one.", "mentionContextAttributes": {"used": {"value": false, "score": 0.00010085105895996094}, "created": {"value": false, "score": 0.0001024007797241211}, "shared": {"value": false, "score": 4.76837158203125e-07}}, "documentContextAttributes": {"used": {"value": false, "score": 0.00010085105895996094}, "created": {"value": false, "score": 0.0001024007797241211}, "shared": {"value": false, "score": 4.76837158203125e-07}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "CWL", "normalizedForm": "CWL", "offsetStart": 113, "offsetEnd": 116}, "context": "Once populated, the knowledge graph contains prospective provenance information for 49 Nextflow workflows and 73 CWL workflows, and Provenance Run Crate metadata on the structure and execution traces of 102 Galaxy workflows (Table 2).", "mentionContextAttributes": {"used": {"value": true, "score": 0.6823556423187256}, "created": {"value": false, "score": 3.337860107421875e-06}, "shared": {"value": false, "score": 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"software", "software-type": "software", "software-name": {"rawForm": "PROV", "normalizedForm": "PROV", "offsetStart": 114, "offsetEnd": 118}, "context": "Ontologies extending the W3C PROVenance Ontologyfoot_0 (PROV-O) for provenance description, such as P-PLAN [9], D-PROV [10] and PROV-One [11] support the representation of workflow plans and their executions.", "mentionContextAttributes": {"used": {"value": false, "score": 0.00042814016342163086}, "created": {"value": false, "score": 8.940696716308594e-06}, "shared": {"value": false, "score": 3.5762786865234375e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9652681946754456}, "created": {"value": false, "score": 0.0019728541374206543}, "shared": {"value": false, "score": 3.5762786865234375e-07}}, "references": [{"label": "[10]", "normalizedForm": "[10]", "refKey": 10, "offsetStart": 6536, "offsetEnd": 6540}, {"label": "[10]", "normalizedForm": "[10]", "refKey": 10, "offsetStart": 6536, "offsetEnd": 6540}]}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 114, "offsetEnd": 119}, "context": "More specifically, the EDAM format of some outputs of the Galaxy workflow ATACseq [48] can be retrieved using bio.tools", "mentionContextAttributes": {"used": {"value": false, "score": 0.2124198079109192}, "created": {"value": false, "score": 3.337860107421875e-06}, "shared": {"value": false, "score": 1.1920928955078125e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.999976634979248}, "created": {"value": true, "score": 0.9999253749847412}, "shared": {"value": true, "score": 0.9572210907936096}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "Crate", "normalizedForm": "Crate", "offsetStart": 115, "offsetEnd": 120}, "context": "The Planemo output files and Workflow Run Crate metadata files were combined, to produce a complete Provenance Run Crate record.", "mentionContextAttributes": {"used": {"value": true, "score": 0.999825656414032}, "created": {"value": false, "score": 1.6808509826660156e-05}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999258518218994}, "created": {"value": true, "score": 0.8732197284698486}, "shared": {"value": true, "score": 0.6471108794212341}}, "references": [{"label": "[14]", "normalizedForm": "[14]", "refKey": 14}]}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "EDAM", "normalizedForm": "EDAM", "offsetStart": 116, "offsetEnd": 120}, "context": "In this fourth use case, information about workflow output data formats is extracted from bio.tools, which contains EDAM annotation on the type and format of tool outputs.", "mentionContextAttributes": {"used": {"value": false, "score": 0.22012680768966675}, "created": {"value": false, "score": 2.5510787963867188e-05}, "shared": {"value": false, "score": 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false, "score": 0.00755387544631958}, "shared": {"value": true, "score": 0.9572210907936096}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "Intergalactic Workflow Commission (IWC)", "normalizedForm": "Intergalactic Workflow Commission (IWC)", "offsetStart": 116, "offsetEnd": 158}, "context": "Some of the Nextflow workflows are part of the nf-core framework, while all galaxy workflows were taken from the Intergalactic Workflow Commission (IWC) library.", "mentionContextAttributes": {"used": {"value": true, "score": 0.9991028308868408}, "created": {"value": false, "score": 2.1219253540039062e-05}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9991028308868408}, "created": {"value": false, "score": 2.1219253540039062e-05}, "shared": {"value": false, "score": 2.384185791015625e-07}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "Docker", "normalizedForm": "Docker", "offsetStart": 118, "offsetEnd": 127}, "context": "(ii) To query this knowledge base, a SPARQL endpoint was deployed into a Jena Fuseki server, inside a dedicated Docker container.", "mentionContextAttributes": {"used": {"value": true, "score": 0.9998923540115356}, "created": {"value": false, "score": 0.00012671947479248047}, "shared": {"value": false, "score": 1.1920928955078125e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9998923540115356}, "created": {"value": false, "score": 0.00012671947479248047}, "shared": {"value": false, "score": 1.1920928955078125e-07}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "EDAM", "normalizedForm": "EDAM", "offsetStart": 120, "offsetEnd": 124}, "context": "Bioconda [27], Biocontainers [28], De-bianMed 8 [29]) Operations: OBI, EDAM operation Data type (ad-ditionalType): OBI, EDAM data, NIDM results [30], SIO Metadata RO-Crate with Bioschema and Schema.org", "mentionContextAttributes": {"used": {"value": true, "score": 0.992515504360199}, "created": {"value": false, "score": 2.86102294921875e-06}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999855756759644}, "created": {"value": true, "score": 0.9998804330825806}, "shared": {"value": true, "score": 0.9572210907936096}}, "references": [{"label": "35]", "normalizedForm": "35]", "refKey": 35}, {"label": "[34,", "normalizedForm": "[34", "refKey": 34}]}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "EDAM", "normalizedForm": "EDAM", "offsetStart": 120, "offsetEnd": 124}, "context": "In that domain, bio.tools [36,37] provides a solution to uniquely identify scientific software, and annotate them using EDAM.", "mentionContextAttributes": {"used": {"value": false, "score": 2.384185791015625e-05}, "created": {"value": false, "score": 0.000754237174987793}, "shared": {"value": false, 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{"value": true, "score": 0.9968697428703308}, "created": {"value": false, "score": 1.990795135498047e-05}, "shared": {"value": false, "score": 4.76837158203125e-07}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "EDAM", "normalizedForm": "EDAM", "offsetStart": 123, "offsetEnd": 127}, "context": "As an example, for MultiQC, we are now able to enrich the direct annotations stated in bio.tools with inferred transversal EDAM data and format annotation, thus addressing the \"Tool adoption\", \"Workflow input formats\" as well as the \"Workflow tools output formats\" use cases.", "mentionContextAttributes": {"used": {"value": false, "score": 0.0019058585166931152}, "created": {"value": false, "score": 0.00755387544631958}, "shared": {"value": false, "score": 1.0728836059570312e-06}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999855756759644}, "created": {"value": true, "score": 0.9998804330825806}, "shared": {"value": true, "score": 0.9572210907936096}}, "references": [{"label": "35]", "normalizedForm": "35]", "refKey": 35}, {"label": "[34,", "normalizedForm": "[34", "refKey": 34}]}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "WMS", "normalizedForm": "WMS", "offsetStart": 124, "offsetEnd": 127}, "context": "Five of the resulting workflows are detailed in Table 4, along some metadata, such as their name, source code, license, and WMS.", "mentionContextAttributes": {"used": {"value": false, "score": 0.06610959768295288}, "created": {"value": false, "score": 0.0001226663589477539}, "shared": {"value": false, "score": 3.0994415283203125e-06}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9994499087333679}, "created": {"value": false, "score": 0.024468600749969482}, "shared": {"value": true, "score": 0.9611940979957581}}, "references": [{"label": "[15]", "normalizedForm": "[15]", "refKey": 15}, {"label": "[15]", "normalizedForm": "[15]", "refKey": 15}]}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "Crate", "normalizedForm": "Crate", "offsetStart": 126, "offsetEnd": 131}, "context": "Then, the code of CWL workflows was parsed, to extract their prospective provenance and generate corresponding Provenance Run Crate metadata files.", "mentionContextAttributes": {"used": {"value": true, "score": 0.9995833039283752}, "created": {"value": false, "score": 4.839897155761719e-05}, "shared": {"value": false, "score": 1.1920928955078125e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999258518218994}, "created": {"value": true, "score": 0.8732197284698486}, "shared": {"value": true, "score": 0.6471108794212341}}, "references": [{"label": "[14]", "normalizedForm": "[14]", "refKey": 14}]}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "PROV", "normalizedForm": "PROV", "offsetStart": 128, "offsetEnd": 132}, "context": "Ontologies extending the W3C PROVenance Ontology (PROV-O) for provenance description, such as P-PLAN , D-PROV and PROV-One support the representation of workflow plans and their executions.", "mentionContextAttributes": {"used": {"value": false, "score": 0.0001583099365234375}, "created": {"value": false, "score": 1.4185905456542969e-05}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9652681946754456}, "created": {"value": false, "score": 0.0019728541374206543}, "shared": {"value": false, "score": 3.5762786865234375e-07}}, "references": [{"label": "[11]", "normalizedForm": "[11]", "refKey": 11, "offsetStart": 6554, "offsetEnd": 6558}, {"label": "[11]", "normalizedForm": "[11]", "refKey": 11, "offsetStart": 6554, "offsetEnd": 6558}]}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 129, "offsetEnd": 134}, "context": "Among these tool annotations, the EDAM annotations as provided by bio.tools constitute an important source of information on the tools' topics, operations, data, and format.", "mentionContextAttributes": {"used": {"value": false, "score": 0.001583695411682129}, "created": {"value": false, "score": 8.380413055419922e-05}, "shared": {"value": false, "score": 3.5762786865234375e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.999976634979248}, "created": {"value": true, "score": 0.9999253749847412}, "shared": {"value": true, "score": 0.9572210907936096}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 131, "offsetEnd": 136}, "context": "EDAMannot can be particularly useful both: for registry data curators, helping them maintaining a minimal, yet informative, set of tools and workflow annotations; as well as for software agents aiming at searching, re-using, composing, or analyzing scientific workflows.", "mentionContextAttributes": {"used": {"value": false, "score": 3.1948089599609375e-05}, "created": {"value": false, "score": 0.00032007694244384766}, "shared": {"value": false, "score": 2.1457672119140625e-06}}, "documentContextAttributes": {"used": {"value": true, "score": 0.999976634979248}, "created": {"value": true, "score": 0.9999253749847412}, "shared": {"value": true, "score": 0.9572210907936096}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "Provenance", "normalizedForm": "Provenance", "offsetStart": 132, "offsetEnd": 142}, "context": "Once populated, the knowledge graph contains prospective provenance information for 49 Nextflow workflows and 73 CWL workflows, and Provenance Run Crate metadata on the structure and execution traces of 102 Galaxy workflows (Table 2).", "mentionContextAttributes": {"used": {"value": true, "score": 0.6823556423187256}, "created": {"value": false, "score": 3.337860107421875e-06}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.999825656414032}, "created": {"value": false, "score": 0.01495349407196045}, "shared": {"value": false, "score": 0.35339784622192383}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "One", "normalizedForm": "One", "offsetStart": 133, "offsetEnd": 141}, "context": "Ontologies extending the W3C PROVenance Ontology (PROV-O) for provenance description, such as P-PLAN , D-PROV and PROV-One support the representation of workflow plans and their executions.", "mentionContextAttributes": {"used": {"value": false, "score": 0.0001583099365234375}, "created": {"value": false, "score": 1.4185905456542969e-05}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": false, "score": 0.0001583099365234375}, "created": {"value": false, "score": 1.4185905456542969e-05}, "shared": {"value": false, "score": 2.384185791015625e-07}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "ComputationalWorkflow", "normalizedForm": "ComputationalWorkflow", "offsetStart": 133, "offsetEnd": 154}, "context": "3 PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> 4 5 SELECT ?format_label ?format ?input_name 6 WHERE { 7 ?workflow a bsc:ComputationalWorkflow ; 8 schema:name ?workflow_name ; 9 <https://bioschemas.org/ComputationalWorkflow#input> ?wf_input .", "mentionContextAttributes": {"used": {"value": false, "score": 0.0005404353141784668}, "created": {"value": false, "score": 2.1457672119140625e-06}, "shared": {"value": false, "score": 0.00011217594146728516}}, "documentContextAttributes": {"used": {"value": false, "score": 0.007303953170776367}, "created": {"value": false, "score": 1.1086463928222656e-05}, "shared": {"value": false, "score": 0.00011217594146728516}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "org", "normalizedForm": "org", "offsetStart": 134, "offsetEnd": 137}, "context": "EDAM format label EDAM format BED http://edamontology.org/format_3003 WIG http://edamontology.org/format_3005 TSV http://edamontology.org/format_3475 HTML http://edamontology.org/format_2331 JSON http://edamontology.org/format_3464 YAML http://edamontology.org/format_3750 CSV http://edamontology.org/format_3752 7. Availability and implementation The datasets and the code used to generate the results are available in the following repositories: i) https://gitlab.liris.cnrs.fr/sharefair/knowledge_base_workflow_annotations/ShareFAIR-KG", "mentionContextAttributes": {"used": {"value": false, "score": 0.005739808082580566}, "created": {"value": false, "score": 3.0994415283203125e-06}, "shared": {"value": false, "score": 4.315376281738281e-05}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999961853027344}, "created": {"value": false, "score": 0.10365641117095947}, "shared": {"value": true, "score": 0.9923090934753418}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "MultiQC", "normalizedForm": "MultiQC", "offsetStart": 136, "offsetEnd": 143}, "context": "Figure 9 illustrates how simple count, information content and Shannon entropy provide different perspectives on the annotations of the MultiQC tool.", "mentionContextAttributes": {"used": 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{"type": "software", "software-type": "software", "software-name": {"rawForm": "org", "normalizedForm": "org", "offsetStart": 138, "offsetEnd": 141}, "context": "We have enriched these profiles with further information on processes, by specifying their inputs/outputs and their order with the schema.org", "mentionContextAttributes": {"used": {"value": true, "score": 0.995517909526825}, "created": {"value": false, "score": 0.10365641117095947}, "shared": {"value": false, "score": 1.1920928955078125e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999961853027344}, "created": {"value": false, "score": 0.10365641117095947}, "shared": {"value": true, "score": 0.9923090934753418}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 138, "offsetEnd": 143}, "context": "They were extracted from WorkflowHub, well-known by the community for promoting workflow FAIRness using open tools and standards like bio.tools and EDAM.", "mentionContextAttributes": {"used": {"value": true, "score": 0.9998958110809326}, "created": {"value": false, "score": 0.002504587173461914}, "shared": {"value": false, "score": 2.3365020751953125e-05}}, "documentContextAttributes": {"used": {"value": true, "score": 0.999976634979248}, "created": {"value": true, "score": 0.9999253749847412}, "shared": {"value": true, "score": 0.9572210907936096}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "WorkflowHub", "normalizedForm": "WorkflowHub", "offsetStart": 139, "offsetEnd": 150}, "context": "WorkflowHub and Galaxy server come with the added benefit of using or generating RO-Crate for workflow description, following respectively WorkflowHub's workflow profile and Workflow Run Crate profile.", "mentionContextAttributes": {"used": {"value": false, "score": 0.020892620086669922}, "created": {"value": false, "score": 2.8967857360839844e-05}, "shared": {"value": false, 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"tools", "offsetStart": 150, "offsetEnd": 155}, "context": "The software BoMiProt 33 also illustrates that some software entries in bio.tools have a very large number of high-quality annotations, although such tools represent only 1,262 tools (4.16%) of the entire registry.", "mentionContextAttributes": {"used": {"value": false, "score": 0.0017449259757995605}, "created": {"value": false, "score": 5.841255187988281e-05}, "shared": {"value": false, "score": 1.3113021850585938e-06}}, "documentContextAttributes": {"used": {"value": true, "score": 0.999976634979248}, "created": {"value": true, "score": 0.9999253749847412}, "shared": {"value": true, "score": 0.9572210907936096}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "Crate", "normalizedForm": "Crate", "offsetStart": 152, "offsetEnd": 157}, "context": "Provenance Run Crate includes two other, less detailed profiles: (i) Process Run Crate characterises software used for file creation, (ii) Workflow Run Crate combines Process Run Crate and WorkflowHub's [4] Workflow RO-Crate profile 3 for the representation of a workflow, its datasets and metadata.", "mentionContextAttributes": {"used": {"value": false, "score": 0.0012350082397460938}, "created": {"value": false, "score": 9.059906005859375e-06}, "shared": {"value": false, "score": 1.5497207641601562e-06}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999258518218994}, "created": {"value": true, "score": 0.8732197284698486}, "shared": {"value": true, "score": 0.6471108794212341}}, "references": [{"label": "[14]", "normalizedForm": "[14]", "refKey": 14}]}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 152, "offsetEnd": 157}, "context": "direct annotations that are also ancestor annotations, therefore more general than a direct annotation -in 3,787 tools (12.45%) for topics and in 2,060 tools (6.79%) for operations.", "mentionContextAttributes": {"used": {"value": true, "score": 0.9551804661750793}, "created": {"value": false, "score": 5.364418029785156e-06}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.999976634979248}, "created": {"value": true, "score": 0.9999253749847412}, "shared": {"value": true, "score": 0.9572210907936096}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "org", "normalizedForm": "org", "offsetStart": 153, "offsetEnd": 156}, "context": "While PROV-based approaches support fine-grained and logically sound provenance descriptions, more recent approaches, based on the widely adopted Schema.org", "mentionContextAttributes": {"used": {"value": false, "score": 7.11679458618164e-05}, "created": {"value": false, "score": 0.019134044647216797}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 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"software-type": "software", "software-name": {"rawForm": "Workflow Run", "normalizedForm": "Workflow Run", "offsetStart": 174, "offsetEnd": 186}, "context": "WorkflowHub and Galaxy server come with the added benefit of using or generating RO-Crate for workflow description, following respectively WorkflowHub's workflow profile and Workflow Run Crate profile.", "mentionContextAttributes": {"used": {"value": false, "score": 0.020892620086669922}, "created": {"value": false, "score": 2.8967857360839844e-05}, "shared": {"value": false, "score": 1.6689300537109375e-06}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999258518218994}, "created": {"value": false, "score": 0.002969026565551758}, "shared": {"value": false, "score": 0.05262273550033569}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "org", "normalizedForm": "org", "offsetStart": 175, "offsetEnd": 178}, "context": "EDAM format label EDAM format BED http://edamontology.org/format_3003 WIG http://edamontology.org/format_3005 TSV http://edamontology.org/format_3475 HTML http://edamontology.org/format_2331 JSON http://edamontology.org/format_3464 YAML http://edamontology.org/format_3750 CSV http://edamontology.org/format_3752 7. Availability and implementation The datasets and the code used to generate the results are available in the following repositories: i) https://gitlab.liris.cnrs.fr/sharefair/knowledge_base_workflow_annotations/ShareFAIR-KG", "mentionContextAttributes": {"used": {"value": false, "score": 0.005739808082580566}, "created": {"value": false, "score": 3.0994415283203125e-06}, "shared": {"value": false, "score": 4.315376281738281e-05}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999961853027344}, "created": {"value": false, "score": 0.10365641117095947}, "shared": {"value": true, "score": 0.9923090934753418}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 177, "offsetEnd": 182}, "context": "The software BoMiProt 33 also illustrates that some software entries in bio.tools have a very large number of high-quality annotations, although such tools represent only 1,262 tools (4.16%) of the entire registry.", "mentionContextAttributes": {"used": {"value": false, "score": 0.0017449259757995605}, "created": {"value": false, "score": 5.841255187988281e-05}, "shared": {"value": false, "score": 1.3113021850585938e-06}}, "documentContextAttributes": {"used": {"value": true, "score": 0.999976634979248}, "created": {"value": true, "score": 0.9999253749847412}, "shared": {"value": true, "score": 0.9572210907936096}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 181, "offsetEnd": 186}, "context": "Conversely, Information Content (the opposite of logarithm of the proportion of tools annotated by an annotation or one of its descendants) highlights annotations that annotate few tools.", "mentionContextAttributes": {"used": {"value": false, "score": 0.0003185272216796875}, "created": {"value": false, "score": 9.5367431640625e-06}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.999976634979248}, "created": {"value": true, "score": 0.9999253749847412}, "shared": {"value": true, "score": 0.9572210907936096}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 181, "offsetEnd": 186}, "context": "The describe-viz alternative command generates a graph representing these annotations, colors them according to their informativeness, and highlights intersections between multiple tools.", "mentionContextAttributes": {"used": {"value": false, "score": 0.0017123818397521973}, "created": {"value": false, "score": 8.225440979003906e-06}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.999976634979248}, "created": {"value": true, "score": 0.9999253749847412}, "shared": {"value": true, "score": 0.9572210907936096}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "WorkflowHub", "normalizedForm": "WorkflowHub", "offsetStart": 185, "offsetEnd": 196}, "context": "Once the representation model defined, we built ShareFAIR-KG , the knowledge base, made of the following components: (i) The workflows extracted from the main workflow repositories (WorkflowHub, Galaxy IWC), and corresponding to the main WMSs (Nextflow, CWL, Galaxy, see Figure ).", "mentionContextAttributes": {"used": {"value": true, "score": 0.992659866809845}, "created": {"value": false, "score": 0.0005767345428466797}, "shared": {"value": false, "score": 3.5762786865234375e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9998958110809326}, "created": {"value": false, "score": 0.008241117000579834}, "shared": {"value": false, "score": 2.3365020751953125e-05}}, "references": [{"label": "[4]", "normalizedForm": "[4]", "refKey": 4}, {"label": "[4]", "normalizedForm": "[4]", "refKey": 4}]}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "Crate", "normalizedForm": "Crate", "offsetStart": 187, "offsetEnd": 192}, "context": "WorkflowHub and Galaxy server come with the added benefit of using or generating RO-Crate for workflow description, following respectively WorkflowHub's workflow profile and Workflow Run Crate profile.", "mentionContextAttributes": {"used": {"value": false, "score": 0.020892620086669922}, "created": {"value": false, "score": 2.8967857360839844e-05}, "shared": {"value": false, "score": 1.6689300537109375e-06}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999258518218994}, "created": {"value": true, "score": 0.8732197284698486}, "shared": {"value": true, "score": 0.6471108794212341}}, "references": [{"label": "[14]", "normalizedForm": "[14]", "refKey": 14}]}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "WorkflowHub", "normalizedForm": "WorkflowHub", "offsetStart": 189, "offsetEnd": 200}, "context": "Provenance Run Crate includes two other, less detailed profiles: (i) Process Run Crate characterises software used for file creation, (ii) Workflow Run Crate combines Process Run Crate and WorkflowHub's Workflow RO-Crate profile for the representation of a workflow, its datasets and metadata.", "mentionContextAttributes": {"used": {"value": false, "score": 0.0010417699813842773}, "created": {"value": false, "score": 6.35385513305664e-05}, "shared": {"value": false, "score": 1.9073486328125e-06}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9998958110809326}, "created": {"value": false, "score": 0.008241117000579834}, "shared": {"value": false, "score": 2.3365020751953125e-05}}, "references": [{"label": "[4]", "normalizedForm": "[4]", "refKey": 4, "offsetStart": 7796, "offsetEnd": 7799}, {"label": "[4]", "normalizedForm": "[4]", "refKey": 4, "offsetStart": 7796, "offsetEnd": 7799}]}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "org", "normalizedForm": "org", "offsetStart": 198, "offsetEnd": 201}, "context": "Bioconda [27], Biocontainers [28], De-bianMed 8 [29]) Operations: OBI, EDAM operation Data type (ad-ditionalType): OBI, EDAM data, NIDM results [30], SIO Metadata RO-Crate with Bioschema and Schema.org", "mentionContextAttributes": {"used": {"value": true, "score": 0.992515504360199}, "created": {"value": false, "score": 2.86102294921875e-06}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999961853027344}, "created": {"value": false, "score": 0.10365641117095947}, "shared": {"value": true, "score": 0.9923090934753418}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "Galaxy IWC", "normalizedForm": "Galaxy IWC", "offsetStart": 198, "offsetEnd": 208}, "context": "Once the representation model defined, we built ShareFAIR-KG , the knowledge base, made of the following components: (i) The workflows extracted from the main workflow repositories (WorkflowHub, Galaxy IWC), and corresponding to the main WMSs (Nextflow, CWL, Galaxy, see Figure ).", "mentionContextAttributes": {"used": {"value": true, "score": 0.992659866809845}, "created": {"value": false, "score": 0.0005767345428466797}, "shared": {"value": false, "score": 3.5762786865234375e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.992659866809845}, "created": {"value": false, "score": 0.0005767345428466797}, "shared": {"value": false, "score": 3.5762786865234375e-07}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 204, "offsetEnd": 209}, "context": "Even without considering spurious annotations, the informativeness of a tool's description can be affected by three aspects: incompleteness, vagueness and obsolescence (due either to the evolution of the tools, or the evolution of the EDAM ontology itself).", "mentionContextAttributes": {"used": {"value": false, "score": 0.0003052949905395508}, "created": {"value": false, "score": 9.548664093017578e-05}, "shared": {"value": false, "score": 7.152557373046875e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.999976634979248}, "created": {"value": true, "score": 0.9999253749847412}, "shared": {"value": true, "score": 0.9572210907936096}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 205, "offsetEnd": 210}, "context": "Using the previously selected standards, we have then developed a comprehensive workflow representation model (Figure 2) capable of representing the multiple granularity levels needed, from the individual tools to the entire workflows.", "mentionContextAttributes": {"used": {"value": false, "score": 0.11288511753082275}, "created": {"value": true, "score": 0.9980207681655884}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.999976634979248}, "created": {"value": true, "score": 0.9999253749847412}, "shared": {"value": true, "score": 0.9572210907936096}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "Galaxy", "normalizedForm": "Galaxy", "offsetStart": 207, "offsetEnd": 213}, "context": "Once populated, the knowledge graph contains prospective provenance information for 49 Nextflow workflows and 73 CWL workflows, and Provenance Run Crate metadata on the structure and execution traces of 102 Galaxy workflows (Table 2).", "mentionContextAttributes": {"used": {"value": true, "score": 0.6823556423187256}, "created": {"value": false, "score": 3.337860107421875e-06}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999961853027344}, "created": {"value": false, "score": 0.005827009677886963}, "shared": {"value": false, "score": 0.05262273550033569}}, "references": [{"label": "[15]", "normalizedForm": "[15]", "refKey": 15}, {"label": "[15]", "normalizedForm": "[15]", "refKey": 15}]}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 208, "offsetEnd": 213}, "context": "In this section we propose a toolbox, for the knowledge graph, aimed at better exploiting the domain-specific reasoning capabilities provided by EDAM to identify the informativeness of semantically annotated tools and workflows.", "mentionContextAttributes": {"used": {"value": false, "score": 5.447864532470703e-05}, "created": {"value": true, "score": 0.9998804330825806}, "shared": {"value": false, "score": 7.152557373046875e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.999976634979248}, "created": {"value": true, "score": 0.9999253749847412}, "shared": {"value": true, "score": 0.9572210907936096}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "org", "normalizedForm": "org", "offsetStart": 210, "offsetEnd": 213}, "context": "3 PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> 4 5 SELECT ?format_label ?format ?input_name 6 WHERE { 7 ?workflow a bsc:ComputationalWorkflow ; 8 schema:name ?workflow_name ; 9 <https://bioschemas.org/ComputationalWorkflow#input> ?wf_input .", "mentionContextAttributes": {"used": {"value": false, "score": 0.0005404353141784668}, "created": {"value": false, "score": 2.1457672119140625e-06}, "shared": {"value": false, "score": 0.00011217594146728516}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999961853027344}, "created": {"value": false, "score": 0.10365641117095947}, "shared": {"value": true, "score": 0.9923090934753418}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "org", "normalizedForm": "org", "offsetStart": 216, "offsetEnd": 219}, "context": "EDAM format label EDAM format BED http://edamontology.org/format_3003 WIG http://edamontology.org/format_3005 TSV http://edamontology.org/format_3475 HTML http://edamontology.org/format_2331 JSON http://edamontology.org/format_3464 YAML http://edamontology.org/format_3750 CSV http://edamontology.org/format_3752 7. Availability and implementation The datasets and the code used to generate the results are available in the following repositories: i) https://gitlab.liris.cnrs.fr/sharefair/knowledge_base_workflow_annotations/ShareFAIR-KG", "mentionContextAttributes": {"used": {"value": false, "score": 0.005739808082580566}, "created": {"value": false, "score": 3.0994415283203125e-06}, "shared": {"value": false, "score": 4.315376281738281e-05}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999961853027344}, "created": {"value": false, "score": 0.10365641117095947}, "shared": {"value": true, "score": 0.9923090934753418}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 216, "offsetEnd": 221}, "context": "Based on the bio.tools dataset described in the previous section, the EDAMannot toolbox identifies 264 unique topics (99,159 topic annotations) and 529 unique operations (69,106 operation annotations) for the 30,328 tools registered.", "mentionContextAttributes": {"used": {"value": false, "score": 0.19737350940704346}, "created": {"value": false, "score": 7.62939453125e-06}, "shared": {"value": false, "score": 2.384185791015625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.999976634979248}, "created": {"value": true, "score": 0.9999253749847412}, "shared": {"value": true, "score": 0.9572210907936096}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "-Crate", "normalizedForm": "-Crate", "offsetStart": 218, "offsetEnd": 224}, "context": "Provenance Run Crate includes two other, less detailed profiles: (i) Process Run Crate characterises software used for file creation, (ii) Workflow Run Crate combines Process Run Crate and WorkflowHub's Workflow RO-Crate profile for the representation of a workflow, its datasets and metadata.", "mentionContextAttributes": {"used": {"value": false, "score": 0.0010417699813842773}, "created": {"value": false, "score": 6.35385513305664e-05}, "shared": {"value": false, "score": 1.9073486328125e-06}}, "documentContextAttributes": {"used": {"value": false, "score": 0.0010417699813842773}, "created": {"value": false, "score": 6.35385513305664e-05}, "shared": {"value": false, "score": 1.9073486328125e-06}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "EDAM", "normalizedForm": "EDAM", "offsetStart": 224, "offsetEnd": 228}, "context": "Granularity Workflows Process Software Data Domain Context (about): OBI [17], SIO, EFO, EDAM topics, SO [18], GO [19,20], NCIT [21], STATO 7 , CHEBI [22], ISSVA [23,24], CVDO [25], NIFSTD [26] Operations (po-tentialAction): EDAM operation, OBI Operations: EDAM operation, OBI Repositories (bio.tools,", "mentionContextAttributes": {"used": {"value": false, "score": 0.4087156653404236}, "created": {"value": false, "score": 4.172325134277344e-06}, "shared": {"value": false, "score": 3.5762786865234375e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999855756759644}, "created": {"value": true, "score": 0.9998804330825806}, "shared": {"value": true, "score": 0.9572210907936096}}, "references": [{"label": "35]", "normalizedForm": "35]", "refKey": 35}, {"label": "[34,", "normalizedForm": "[34", "refKey": 34}]}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 227, "offsetEnd": 232}, "context": "Therefore, three main directions can be overtaken in future work: (i) Adding richer, structural metadata and enhancing annotation depth and coverage by integrating a larger diversity of established standards and completing bio.tools annotations, including domain-specific annota-tions, (ii) Increasing the scale of workflow integration, especially with their execution traces by extending retrospective provenance beyond Galaxy (e.g. to Nextflow, CWL, Snakemake), (iii) Addressing annotation quality, for example by leveraging Large Language Models (LLMs) for semi-automated annotation extraction and standardisation [50], in addition to communitydriven curation efforts, e.g., through platforms like WorkflowHub, in collaboration with existing initiatives such as ELIXIR services, WorkflowsCommunity 35 and other community-based efforts.", "mentionContextAttributes": {"used": {"value": false, "score": 0.000279843807220459}, "created": {"value": false, "score": 0.0019192695617675781}, "shared": {"value": false, "score": 2.9802322387695312e-06}}, "documentContextAttributes": {"used": {"value": true, "score": 0.999976634979248}, "created": {"value": true, "score": 0.9999253749847412}, "shared": {"value": true, "score": 0.9572210907936096}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "EDAM", "normalizedForm": "EDAM", "offsetStart": 235, "offsetEnd": 239}, "context": "Even without considering spurious annotations, the informativeness of a tool's description can be affected by three aspects: incompleteness, vagueness and obsolescence (due either to the evolution of the tools, or the evolution of the EDAM ontology itself).", "mentionContextAttributes": {"used": {"value": false, "score": 0.0003052949905395508}, "created": {"value": false, "score": 9.548664093017578e-05}, "shared": {"value": false, "score": 7.152557373046875e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999855756759644}, "created": {"value": true, "score": 0.9998804330825806}, "shared": {"value": true, "score": 0.9572210907936096}}, "references": [{"label": "35]", "normalizedForm": "35]", "refKey": 35}, {"label": "[34,", "normalizedForm": "[34", "refKey": 34}]}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 243, "offsetEnd": 248}, "context": "As an example, for MultiQC, we are now able to enrich the direct annotations stated in bio.tools with inferred transversal EDAM data and format annotation, thus addressing the \"Tool adoption\", \"Workflow input formats\" as well as the \"Workflow tools output formats\" use cases.", "mentionContextAttributes": {"used": {"value": false, "score": 0.0019058585166931152}, "created": {"value": false, "score": 0.007553756237030029}, "shared": {"value": false, "score": 1.0728836059570312e-06}}, "documentContextAttributes": {"used": {"value": true, "score": 0.999976634979248}, "created": {"value": true, "score": 0.9999253749847412}, "shared": {"value": true, "score": 0.9572210907936096}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "Nextflow", "normalizedForm": "Nextflow", "offsetStart": 247, "offsetEnd": 255}, "context": "Once the representation model defined, we built ShareFAIR-KG , the knowledge base, made of the following components: (i) The workflows extracted from the main workflow repositories (WorkflowHub, Galaxy IWC), and corresponding to the main WMSs (Nextflow, CWL, Galaxy, see Figure ).", "mentionContextAttributes": {"used": {"value": true, "score": 0.992659866809845}, "created": {"value": false, "score": 0.0005767345428466797}, "shared": {"value": false, "score": 3.5762786865234375e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999864101409912}, "created": {"value": false, "score": 0.008241117000579834}, "shared": {"value": false, "score": 0.13519150018692017}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "EDAM", "normalizedForm": "EDAM", "offsetStart": 256, "offsetEnd": 260}, "context": "Granularity Workflows Process Software Data Domain Context (about): OBI [17], SIO, EFO, EDAM topics, SO [18], GO [19,20], NCIT [21], STATO 7 , CHEBI [22], ISSVA [23,24], CVDO [25], NIFSTD [26] Operations (po-tentialAction): EDAM operation, OBI Operations: EDAM operation, OBI Repositories (bio.tools,", "mentionContextAttributes": {"used": {"value": false, "score": 0.4087156653404236}, "created": {"value": false, "score": 4.172325134277344e-06}, "shared": {"value": false, "score": 3.5762786865234375e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999855756759644}, "created": {"value": true, "score": 0.9998804330825806}, "shared": {"value": true, "score": 0.9572210907936096}}, "references": [{"label": "35]", "normalizedForm": "35]", "refKey": 35}, {"label": "[34,", "normalizedForm": "[34", "refKey": 34}]}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "CWL", "normalizedForm": "CWL", "offsetStart": 257, "offsetEnd": 260}, "context": "Once the representation model defined, we built ShareFAIR-KG , the knowledge base, made of the following components: (i) The workflows extracted from the main workflow repositories (WorkflowHub, Galaxy IWC), and corresponding to the main WMSs (Nextflow, CWL, Galaxy, see Figure ).", "mentionContextAttributes": {"used": {"value": true, "score": 0.992659866809845}, "created": {"value": false, "score": 0.0005767345428466797}, "shared": {"value": false, "score": 3.5762786865234375e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9995833039283752}, "created": {"value": false, "score": 0.0019192695617675781}, "shared": {"value": false, "score": 0.35339784622192383}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "org", "normalizedForm": "org", "offsetStart": 257, "offsetEnd": 260}, "context": "EDAM format label EDAM format BED http://edamontology.org/format_3003 WIG http://edamontology.org/format_3005 TSV http://edamontology.org/format_3475 HTML http://edamontology.org/format_2331 JSON http://edamontology.org/format_3464 YAML http://edamontology.org/format_3750 CSV http://edamontology.org/format_3752 7. Availability and implementation The datasets and the code used to generate the results are available in the following repositories: i) https://gitlab.liris.cnrs.fr/sharefair/knowledge_base_workflow_annotations/ShareFAIR-KG", "mentionContextAttributes": {"used": {"value": false, "score": 0.005739927291870117}, "created": {"value": false, "score": 3.0994415283203125e-06}, "shared": {"value": false, "score": 4.315376281738281e-05}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999961853027344}, "created": {"value": false, "score": 0.10365641117095947}, "shared": {"value": true, "score": 0.9923090934753418}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "Galaxy", "normalizedForm": "Galaxy", "offsetStart": 262, "offsetEnd": 268}, "context": "Once the representation model defined, we built ShareFAIR-KG , the knowledge base, made of the following components: (i) The workflows extracted from the main workflow repositories (WorkflowHub, Galaxy IWC), and corresponding to the main WMSs (Nextflow, CWL, Galaxy, see Figure ).", "mentionContextAttributes": {"used": {"value": true, "score": 0.992659866809845}, "created": {"value": false, "score": 0.0005767345428466797}, "shared": {"value": false, "score": 3.5762786865234375e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999961853027344}, "created": {"value": false, "score": 0.005827009677886963}, "shared": {"value": false, "score": 0.05262273550033569}}, "references": [{"label": "[15]", "normalizedForm": "[15]", "refKey": 15}, {"label": "[15]", "normalizedForm": "[15]", "refKey": 15}]}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 294, "offsetEnd": 299}, "context": "Granularity Workflows Process Software Data Domain Context (about): OBI [17], SIO, EFO, EDAM topics, SO [18], GO [19,20], NCIT [21], STATO 7 , CHEBI [22], ISSVA [23,24], CVDO [25], NIFSTD [26] Operations (po-tentialAction): EDAM operation, OBI Operations: EDAM operation, OBI Repositories (bio.tools,", "mentionContextAttributes": {"used": {"value": false, "score": 0.4087156653404236}, "created": {"value": false, "score": 4.172325134277344e-06}, "shared": {"value": false, "score": 3.5762786865234375e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.999976634979248}, "created": {"value": true, "score": 0.9999253749847412}, "shared": {"value": true, "score": 0.9572210907936096}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "org", "normalizedForm": "org", "offsetStart": 297, "offsetEnd": 300}, "context": "EDAM format label EDAM format BED http://edamontology.org/format_3003 WIG http://edamontology.org/format_3005 TSV http://edamontology.org/format_3475 HTML http://edamontology.org/format_2331 JSON http://edamontology.org/format_3464 YAML http://edamontology.org/format_3750 CSV http://edamontology.org/format_3752 7. Availability and implementation The datasets and the code used to generate the results are available in the following repositories: i) https://gitlab.liris.cnrs.fr/sharefair/knowledge_base_workflow_annotations/ShareFAIR-KG", "mentionContextAttributes": {"used": {"value": false, "score": 0.005739927291870117}, "created": {"value": false, "score": 3.0994415283203125e-06}, "shared": {"value": false, "score": 4.315376281738281e-05}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999961853027344}, "created": {"value": false, "score": 0.10365641117095947}, "shared": {"value": true, "score": 0.9923090934753418}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "tools", "normalizedForm": "tools", "offsetStart": 300, "offsetEnd": 305}, "context": "Shannon entropy (the product of the information content of an annotation and the proportion of tools annotated by this annotation) offers a compromise by being low for the most general annotations (they have a small information content), and for the most precise (they annotate a small proportion of tools).", "mentionContextAttributes": {"used": {"value": false, "score": 0.0025788545608520508}, "created": {"value": false, "score": 5.650520324707031e-05}, "shared": {"value": false, "score": 5.960464477539062e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.999976634979248}, "created": {"value": true, "score": 0.9999253749847412}, "shared": {"value": true, "score": 0.9572210907936096}}}, {"type": "software", "software-type": "implicit", "software-name": {"rawForm": "code", "normalizedForm": "code", "offsetStart": 369, "offsetEnd": 373}, "context": "EDAM format label EDAM format BED http://edamontology.org/format_3003 WIG http://edamontology.org/format_3005 TSV http://edamontology.org/format_3475 HTML http://edamontology.org/format_2331 JSON http://edamontology.org/format_3464 YAML http://edamontology.org/format_3750 CSV http://edamontology.org/format_3752 7. Availability and implementation The datasets and the code used to generate the results are available in the following repositories: i) https://gitlab.liris.cnrs.fr/sharefair/knowledge_base_workflow_annotations/ShareFAIR-KG", "mentionContextAttributes": {"used": {"value": false, "score": 0.005739927291870117}, "created": {"value": false, "score": 3.0994415283203125e-06}, "shared": {"value": false, "score": 4.315376281738281e-05}}, "documentContextAttributes": {"used": {"value": false, "score": 0.04905742406845093}, "created": {"value": false, "score": 8.130073547363281e-05}, "shared": {"value": false, "score": 4.315376281738281e-05}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "Galaxy", "normalizedForm": "Galaxy", "offsetStart": 421, "offsetEnd": 427}, "context": "Therefore, three main directions can be overtaken in future work: (i) Adding richer, structural metadata and enhancing annotation depth and coverage by integrating a larger diversity of established standards and completing bio.tools annotations, including domain-specific annota-tions, (ii) Increasing the scale of workflow integration, especially with their execution traces by extending retrospective provenance beyond Galaxy (e.g. to Nextflow, CWL, Snakemake), (iii) Addressing annotation quality, for example by leveraging Large Language Models (LLMs) for semi-automated annotation extraction and standardisation , in addition to communitydriven curation efforts, e.g., through platforms like WorkflowHub, in collaboration with existing initiatives such as ELIXIR services, WorkflowsCommunity 35 and other community-based efforts.", "mentionContextAttributes": {"used": {"value": false, "score": 0.000279843807220459}, "created": {"value": false, "score": 0.0019192695617675781}, "shared": {"value": false, "score": 2.9802322387695312e-06}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999961853027344}, "created": {"value": false, "score": 0.005827009677886963}, "shared": {"value": false, "score": 0.05262273550033569}}, "references": [{"label": "[15]", "normalizedForm": "[15]", "refKey": 15}, {"label": "[15]", "normalizedForm": "[15]", "refKey": 15}]}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "Nextflow", "normalizedForm": "Nextflow", "offsetStart": 437, "offsetEnd": 445}, "context": "Therefore, three main directions can be overtaken in future work: (i) Adding richer, structural metadata and enhancing annotation depth and coverage by integrating a larger diversity of established standards and completing bio.tools annotations, including domain-specific annota-tions, (ii) Increasing the scale of workflow integration, especially with their execution traces by extending retrospective provenance beyond Galaxy (e.g. to Nextflow, CWL, Snakemake), (iii) Addressing annotation quality, for example by leveraging Large Language Models (LLMs) for semi-automated annotation extraction and standardisation , in addition to communitydriven curation efforts, e.g., through platforms like WorkflowHub, in collaboration with existing initiatives such as ELIXIR services, WorkflowsCommunity 35 and other community-based efforts.", "mentionContextAttributes": {"used": {"value": false, "score": 0.000279843807220459}, "created": {"value": false, "score": 0.0019192695617675781}, "shared": {"value": false, "score": 2.9802322387695312e-06}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9999864101409912}, "created": {"value": false, "score": 0.008241117000579834}, "shared": {"value": false, "score": 0.13519150018692017}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "CWL", "normalizedForm": "CWL", "offsetStart": 447, "offsetEnd": 450}, "context": "Therefore, three main directions can be overtaken in future work: (i) Adding richer, structural metadata and enhancing annotation depth and coverage by integrating a larger diversity of established standards and completing bio.tools annotations, including domain-specific annota-tions, (ii) Increasing the scale of workflow integration, especially with their execution traces by extending retrospective provenance beyond Galaxy (e.g. to Nextflow, CWL, Snakemake), (iii) Addressing annotation quality, for example by leveraging Large Language Models (LLMs) for semi-automated annotation extraction and standardisation , in addition to communitydriven curation efforts, e.g., through platforms like WorkflowHub, in collaboration with existing initiatives such as ELIXIR services, WorkflowsCommunity 35 and other community-based efforts.", "mentionContextAttributes": {"used": {"value": false, "score": 0.000279843807220459}, "created": {"value": false, "score": 0.0019192695617675781}, "shared": {"value": false, "score": 2.9802322387695312e-06}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9995833039283752}, "created": {"value": false, "score": 0.0019192695617675781}, "shared": {"value": false, "score": 0.35339784622192383}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "MultiQC", "normalizedForm": "MultiQC", "offsetStart": 451, "offsetEnd": 458}, "context": "Bioinformatics (topic_0091) Sequencing (topic_3168) Genomics (topic_0622) Sequence analysis (topic_0080) Validation (operation_2428) Sequencing quality control (operation_3218) Informatics topic_0605 Data acquisition topic_3077 Omics topic_3391 Computational biology topic_3307 Operation operation_0004 Nucleic acid sequence analysis operation_2478 Topic topic_0003 Biosciences topic_4019 Sequence analysis operation_2403 Data analysis operation_2945 MultiQC Bioinformatics (topic_0091) Sequencing (topic_3168) Genomics (topic_0622) Sequence analysis (topic_0080) Validation (operation_2428) Sequencing quality control (operation_3218) Informatics topic_0605 Data acquisition topic_3077 Omics topic_3391 Computational biology topic_3307 Operation operation_0004 Nucleic acid sequence analysis operation_2478 Topic topic_0003 Biosciences topic_4019 Sequence analysis operation_2403 Data analysis operation_2945 MultiQC Bioinformatics (topic_0091) Sequencing (topic_3168) Genomics (topic_0622) Sequence analysis (topic_0080) Validation (operation_2428) Sequencing quality control (operation_3218) Informatics topic_0605 Data acquisition topic_3077 Omics topic_3391 Computational biology topic_3307 Operation operation_0004 Nucleic acid sequence analysis operation_2478 Topic topic_0003 Biosciences topic_4019 Sequence analysis operation_2403 Data analysis operation_2945 In addition, EDAMannot reveals annotation redundancies -i.e.", "mentionContextAttributes": {"used": {"value": true, "score": 0.620009183883667}, "created": {"value": false, "score": 3.6954879760742188e-06}, "shared": {"value": false, "score": 1.3113021850585938e-06}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9997537732124329}, "created": {"value": 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operation_0004 Nucleic acid sequence analysis operation_2478 Topic topic_0003 Biosciences topic_4019 Sequence analysis operation_2403 Data analysis operation_2945 As an example, following the same principle as in table 3, the tool MultiQC has six direct topic and operation annotations, but when leveraging the EDAM class hierarchy, a total of sixteen annotations are retrieved as shown in Figure .", "mentionContextAttributes": {"used": {"value": false, "score": 0.47936558723449707}, "created": {"value": false, "score": 3.2186508178710938e-06}, "shared": {"value": false, "score": 9.5367431640625e-07}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9997537732124329}, "created": {"value": false, "score": 0.00755387544631958}, "shared": {"value": true, "score": 0.9572210907936096}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "EDAM", "normalizedForm": "EDAM", "offsetStart": 607, "offsetEnd": 611}, "context": "MultiQC Bioinformatics 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0.9998804330825806}, "shared": {"value": true, "score": 0.9572210907936096}}, "references": [{"label": "35]", "normalizedForm": "35]", "refKey": 35}, {"label": "[34,", "normalizedForm": "[34", "refKey": 34}]}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "WorkflowHub", "normalizedForm": "WorkflowHub", "offsetStart": 701, "offsetEnd": 712}, "context": "Therefore, three main directions can be overtaken in future work: (i) Adding richer, structural metadata and enhancing annotation depth and coverage by integrating a larger diversity of established standards and completing bio.tools annotations, including domain-specific annota-tions, (ii) Increasing the scale of workflow integration, especially with their execution traces by extending retrospective provenance beyond Galaxy (e.g. to Nextflow, CWL, Snakemake), (iii) Addressing annotation quality, for example by leveraging Large Language Models (LLMs) for semi-automated annotation extraction and standardisation , in addition to communitydriven curation efforts, e.g., through platforms like WorkflowHub, in collaboration with existing initiatives such as ELIXIR services, WorkflowsCommunity 35 and other community-based efforts.", "mentionContextAttributes": {"used": {"value": false, "score": 0.000279843807220459}, "created": {"value": false, "score": 0.0019192695617675781}, "shared": {"value": false, "score": 2.9802322387695312e-06}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9998958110809326}, "created": {"value": false, "score": 0.008241117000579834}, "shared": {"value": false, "score": 2.3365020751953125e-05}}, "references": [{"label": "[4]", "normalizedForm": "[4]", "refKey": 4}, {"label": "[4]", "normalizedForm": "[4]", "refKey": 4}]}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "WorkflowsCommunity", "normalizedForm": "WorkflowsCommunity", "offsetStart": 782, "offsetEnd": 800}, "context": "Therefore, three main directions can be overtaken in future work: (i) Adding richer, structural metadata and enhancing annotation depth and coverage by integrating a larger diversity of established standards and completing bio.tools annotations, including domain-specific annota-tions, (ii) Increasing the scale of workflow integration, especially with their execution traces by extending retrospective provenance beyond Galaxy (e.g. to Nextflow, CWL, Snakemake), (iii) Addressing annotation quality, for example by leveraging Large Language Models (LLMs) for semi-automated annotation extraction and standardisation , in addition to communitydriven curation efforts, e.g., through platforms like WorkflowHub, in collaboration with existing initiatives such as ELIXIR services, WorkflowsCommunity 35 and other community-based efforts.", "mentionContextAttributes": {"used": {"value": false, "score": 0.000279843807220459}, "created": {"value": false, "score": 0.0019192695617675781}, "shared": {"value": false, "score": 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Sequencing quality control (operation_3218) Informatics topic_0605 Data acquisition topic_3077 Omics topic_3391 Computational biology topic_3307 Operation operation_0004 Nucleic acid sequence analysis operation_2478 Topic topic_0003 Biosciences topic_4019 Sequence analysis operation_2403 Data analysis operation_2945 MultiQC Bioinformatics (topic_0091) Sequencing (topic_3168) Genomics (topic_0622) Sequence analysis (topic_0080) Validation (operation_2428) Sequencing quality control (operation_3218) Informatics topic_0605 Data acquisition topic_3077 Omics topic_3391 Computational biology topic_3307 Operation operation_0004 Nucleic acid sequence analysis operation_2478 Topic topic_0003 Biosciences topic_4019 Sequence analysis operation_2403 Data analysis operation_2945 In addition, EDAMannot reveals annotation redundancies -i.e.", "mentionContextAttributes": {"used": {"value": true, "score": 0.620009183883667}, "created": {"value": false, "score": 3.6954879760742188e-06}, "shared": {"value": false, "score": 1.3113021850585938e-06}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9997537732124329}, "created": {"value": false, "score": 0.00755387544631958}, "shared": {"value": true, "score": 0.9572210907936096}}}, {"type": "software", "software-type": "software", "software-name": {"rawForm": "EDAMannot", "normalizedForm": "EDAMannot", "offsetStart": 1382, "offsetEnd": 1391}, "version": {"rawForm": "0", "normalizedForm": "0"}, "context": "Bioinformatics (topic_0091) Sequencing (topic_3168) Genomics (topic_0622) Sequence analysis (topic_0080) Validation (operation_2428) Sequencing quality control (operation_3218) Informatics topic_0605 Data acquisition topic_3077 Omics topic_3391 Computational biology topic_3307 Operation operation_0004 Nucleic acid sequence analysis operation_2478 Topic topic_0003 Biosciences topic_4019 Sequence analysis operation_2403 Data analysis operation_2945 MultiQC Bioinformatics (topic_0091) Sequencing (topic_3168) Genomics (topic_0622) Sequence analysis (topic_0080) Validation (operation_2428) Sequencing quality control (operation_3218) Informatics topic_0605 Data acquisition topic_3077 Omics topic_3391 Computational biology topic_3307 Operation operation_0004 Nucleic acid sequence analysis operation_2478 Topic topic_0003 Biosciences topic_4019 Sequence analysis operation_2403 Data analysis operation_2945 MultiQC Bioinformatics (topic_0091) Sequencing (topic_3168) Genomics (topic_0622) Sequence analysis (topic_0080) Validation (operation_2428) Sequencing quality control (operation_3218) Informatics topic_0605 Data acquisition topic_3077 Omics topic_3391 Computational biology topic_3307 Operation operation_0004 Nucleic acid sequence analysis operation_2478 Topic topic_0003 Biosciences topic_4019 Sequence analysis operation_2403 Data analysis operation_2945 In addition, EDAMannot reveals annotation redundancies -i.e.", "mentionContextAttributes": {"used": {"value": true, "score": 0.620009183883667}, "created": {"value": false, "score": 3.6954879760742188e-06}, "shared": {"value": false, "score": 1.3113021850585938e-06}}, "documentContextAttributes": {"used": {"value": true, "score": 0.9992945194244385}, "created": {"value": true, "score": 0.9992551207542419}, "shared": {"value": true, "score": 0.9869785308837891}}}], "references": [{"refKey": 11, "tei": "<biblStruct status=\"consolidated\" source=\"crossref\" xml:id=\"b11\">\n\t<analytic>\n\t\t<title level=\"a\" type=\"main\">ProvONE+: A Provenance Model for Scientific Workflows</title>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Anila</forename><forename type=\"middle\">Sahar</forename><surname>Butt</surname></persName>\n\t\t\t<idno type=\"ORCID\">0000-0002-3508-6049</idno>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Peter</forename><surname>Fitch</surname></persName>\n\t\t\t<idno type=\"ORCID\">0000-0002-9813-0588</idno>\n\t\t</author>\n\t\t<idno type=\"DOI\">10.1007/978-3-030-62008-0_30</idno>\n\t</analytic>\n\t<monogr>\n\t\t<title level=\"m\">Lecture Notes in Computer Science</title>\n\t\t<editor>\n\t\t\t<persName><forename type=\"first\">Z</forename><surname>Huang</surname></persName>\n\t\t</editor>\n\t\t<editor>\n\t\t\t<persName><forename type=\"first\">W</forename><surname>Beek</surname></persName>\n\t\t</editor>\n\t\t<editor>\n\t\t\t<persName><forename type=\"first\">H</forename><surname>Wang</surname></persName>\n\t\t</editor>\n\t\t<editor>\n\t\t\t<persName><forename type=\"first\">R</forename><surname>Zhou</surname></persName>\n\t\t</editor>\n\t\t<editor>\n\t\t\t<persName><forename type=\"first\">Y</forename><surname>Zhang</surname></persName>\n\t\t</editor>\n\t\t<imprint>\n\t\t\t<publisher>Springer International Publishing</publisher>\n\t\t\t<date type=\"published\" when=\"2020\">2020</date>\n\t\t\t<biblScope unit=\"page\" from=\"431\" to=\"444\" />\n\t\t</imprint>\n\t</monogr>\n</biblStruct>\n"}, {"refKey": 35, "tei": "<biblStruct status=\"consolidated\" source=\"crossref\" xml:id=\"b35\">\n\t<analytic>\n\t\t<title level=\"a\" type=\"main\">EDAM: the bioscientific data analysis ontology (update 2021)</title>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Melissa</forename><surname>Black</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Lucie</forename><surname>Lamothe</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Hager</forename><surname>Eldakroury</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Mads</forename><surname>Kierkegaard</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Ankita</forename><surname>Priya</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Anne</forename><surname>Machinda</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Uttam</forename><surname>Singh Khanduja</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Drashti</forename><surname>Patoliya</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Rashika</forename><surname>Rathi</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Tawah</forename><forename type=\"middle\">Peggy</forename><surname>Che Nico</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Gloria</forename><surname>Umutesi</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Claudia</forename><surname>Blankenburg</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Anita</forename><surname>Op</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Precious</forename><surname>Chieke</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Omodolapo</forename><surname>Babatunde</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Steve</forename><surname>Laurie</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Steffen</forename><surname>Neumann</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Veit</forename><surname>Schw\u00e4mmle</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Ivan</forename><surname>Kuzmin</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Chris</forename><surname>Hunter</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Jonathan</forename><surname>Karr</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Jon</forename><surname>Ison</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Alban</forename><surname>Gaignard</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Bryan</forename><surname>Brancotte</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Herv\u00e9</forename><surname>M\u00e9nager</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Mat\u00fa\u0161</forename><surname>Kala\u0161</surname></persName>\n\t\t</author>\n\t\t<idno type=\"DOI\">10.7490/f1000research.1118900.1</idno>\n\t</analytic>\n\t<monogr>\n\t\t<title level=\"j\">Research</title>\n\t\t<imprint>\n\t\t\t<biblScope unit=\"volume\">11</biblScope>\n\t\t\t<date type=\"published\" when=\"2022-01-01\">update 2021. 1000. 2021</date>\n\t\t\t<publisher>F1000 Research Ltd</publisher>\n\t\t</imprint>\n\t</monogr>\n</biblStruct>\n"}, {"refKey": 34, "tei": "<biblStruct status=\"consolidated\" source=\"crossref\" xml:id=\"b34\">\n\t<analytic>\n\t\t<title level=\"a\" type=\"main\">EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats</title>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Jon</forename><surname>Ison</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Mat\u00fa\u0161</forename><surname>Kala\u0161</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Inge</forename><surname>Jonassen</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Dan</forename><surname>Bolser</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Mahmut</forename><surname>Uludag</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Hamish</forename><surname>Mcwilliam</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">James</forename><surname>Malone</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Rodrigo</forename><surname>Lopez</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Steve</forename><surname>Pettifer</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Peter</forename><surname>Rice</surname></persName>\n\t\t</author>\n\t\t<idno type=\"DOI\">10.1093/bioinformatics/btt113</idno>\n\t</analytic>\n\t<monogr>\n\t\t<title level=\"j\">Bioinformatics</title>\n\t\t<idno type=\"ISSN\">1367-4803</idno>\n\t\t<idno type=\"ISSNe\">1367-4811</idno>\n\t\t<imprint>\n\t\t\t<biblScope unit=\"volume\">29</biblScope>\n\t\t\t<biblScope unit=\"issue\">10</biblScope>\n\t\t\t<biblScope unit=\"page\" from=\"1325\" to=\"1332\" />\n\t\t\t<date type=\"published\" when=\"2013-03-11\">2013</date>\n\t\t\t<publisher>Oxford University Press (OUP)</publisher>\n\t\t</imprint>\n\t</monogr>\n</biblStruct>\n"}, {"refKey": 31, "tei": "<biblStruct status=\"consolidated\" source=\"crossref\" xml:id=\"b31\">\n\t<analytic>\n\t\t<title level=\"a\" type=\"main\">The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation</title>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">James</forename><surname>Malone</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Andy</forename><surname>Brown</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Allyson</forename><forename type=\"middle\">L</forename><surname>Lister</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Jon</forename><surname>Ison</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Duncan</forename><surname>Hull</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Helen</forename><surname>Parkinson</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Robert</forename><surname>Stevens</surname></persName>\n\t\t</author>\n\t\t<idno type=\"DOI\">10.1186/2041-1480-5-25</idno>\n\t</analytic>\n\t<monogr>\n\t\t<title level=\"j\">Journal of Biomedical Semantics</title>\n\t\t<title level=\"j\" type=\"abbrev\">J Biomed Semant</title>\n\t\t<idno type=\"ISSNe\">2041-1480</idno>\n\t\t<imprint>\n\t\t\t<biblScope unit=\"volume\">5</biblScope>\n\t\t\t<biblScope unit=\"issue\">1</biblScope>\n\t\t\t<biblScope unit=\"page\">25</biblScope>\n\t\t\t<date type=\"published\" when=\"2014-06-02\">2014</date>\n\t\t\t<publisher>Springer Science and Business Media LLC</publisher>\n\t\t</imprint>\n\t</monogr>\n</biblStruct>\n"}, {"refKey": 32, "tei": "<biblStruct status=\"consolidated\" source=\"crossref\" xml:id=\"b32\">\n\t<analytic>\n\t\t<title level=\"a\" type=\"main\">The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments</title>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Krzysztof</forename><forename type=\"middle\">J</forename><surname>Gorgolewski</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Tibor</forename><surname>Auer</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Vince</forename><forename type=\"middle\">D</forename><surname>Calhoun</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">R</forename><forename type=\"middle\">Cameron</forename><surname>Craddock</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Samir</forename><surname>Das</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Eugene</forename><forename type=\"middle\">P</forename><surname>Duff</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Guillaume</forename><surname>Flandin</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Satrajit</forename><forename type=\"middle\">S</forename><surname>Ghosh</surname></persName>\n\t\t\t<idno type=\"ORCID\">0000-0002-5312-6729</idno>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Tristan</forename><surname>Glatard</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Yaroslav</forename><forename type=\"middle\">O</forename><surname>Halchenko</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Daniel</forename><forename type=\"middle\">A</forename><surname>Handwerker</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Michael</forename><surname>Hanke</surname></persName>\n\t\t\t<idno type=\"ORCID\">0000-0001-6398-6370</idno>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">David</forename><surname>Keator</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Xiangrui</forename><surname>Li</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Zachary</forename><surname>Michael</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Camille</forename><surname>Maumet</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">B</forename><forename type=\"middle\">Nolan</forename><surname>Nichols</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Thomas</forename><forename type=\"middle\">E</forename><surname>Nichols</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">John</forename><surname>Pellman</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Jean-Baptiste</forename><surname>Poline</surname></persName>\n\t\t\t<idno type=\"ORCID\">0000-0002-9794-749X</idno>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Ariel</forename><surname>Rokem</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Gunnar</forename><surname>Schaefer</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Vanessa</forename><surname>Sochat</surname></persName>\n\t\t\t<idno type=\"ORCID\">0000-0002-4387-3819</idno>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">William</forename><surname>Triplett</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Jessica</forename><forename type=\"middle\">A</forename><surname>Turner</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Ga\u00ebl</forename><surname>Varoquaux</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Russell</forename><forename type=\"middle\">A</forename><surname>Poldrack</surname></persName>\n\t\t</author>\n\t\t<idno type=\"DOI\">10.1038/sdata.2016.44</idno>\n\t</analytic>\n\t<monogr>\n\t\t<title level=\"j\">Scientific Data</title>\n\t\t<title level=\"j\" type=\"abbrev\">Sci Data</title>\n\t\t<idno type=\"ISSNe\">2052-4463</idno>\n\t\t<imprint>\n\t\t\t<biblScope unit=\"volume\">3</biblScope>\n\t\t\t<biblScope unit=\"issue\">1</biblScope>\n\t\t\t<biblScope unit=\"page\">160044</biblScope>\n\t\t\t<date type=\"published\" when=\"2016-06-21\">2016</date>\n\t\t\t<publisher>Springer Science and Business Media LLC</publisher>\n\t\t</imprint>\n\t</monogr>\n</biblStruct>\n"}, {"refKey": 33, "tei": "<biblStruct status=\"consolidated\" source=\"crossref\" xml:id=\"b33\">\n\t<analytic>\n\t\t<title level=\"a\" type=\"main\">The Neurodata Without Borders ecosystem for neurophysiological data science</title>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Oliver</forename><surname>R\u00fcbel</surname></persName>\n\t\t\t<idno type=\"ORCID\">0000-0001-9902-1984</idno>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Andrew</forename><surname>Tritt</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Ryan</forename><surname>Ly</surname></persName>\n\t\t\t<idno type=\"ORCID\">0000-0001-9238-0642</idno>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Benjamin</forename><forename type=\"middle\">K</forename><surname>Dichter</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Satrajit</forename><surname>Ghosh</surname></persName>\n\t\t\t<idno type=\"ORCID\">0000-0002-5312-6729</idno>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Lawrence</forename><surname>Niu</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Pamela</forename><surname>Baker</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Ivan</forename><surname>Soltesz</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Lydia</forename><surname>Ng</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Karel</forename><surname>Svoboda</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Loren</forename><surname>Frank</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Kristofer</forename><forename type=\"middle\">E</forename><surname>Bouchard</surname></persName>\n\t\t\t<idno type=\"ORCID\">0000-0002-1974-4603</idno>\n\t\t</author>\n\t\t<idno type=\"DOI\">10.7554/elife.78362</idno>\n\t</analytic>\n\t<monogr>\n\t\t<title level=\"j\">eLife</title>\n\t\t<idno type=\"ISSNe\">2050-084X</idno>\n\t\t<imprint>\n\t\t\t<biblScope unit=\"volume\">11</biblScope>\n\t\t\t<biblScope unit=\"page\">78362</biblScope>\n\t\t\t<date type=\"published\" when=\"2022-10-04\">2022</date>\n\t\t\t<publisher>eLife Sciences Publications, Ltd</publisher>\n\t\t</imprint>\n\t</monogr>\n</biblStruct>\n"}, {"refKey": 4, "tei": "<biblStruct status=\"extracted\" xml:id=\"b4\">\n\t<monogr>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">O</forename><forename type=\"middle\">J R</forename><surname>Gustafsson</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">S</forename><forename type=\"middle\">R</forename><surname>Wilkinson</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">F</forename><surname>Bacall</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">L</forename><surname>Pireddu</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">S</forename><surname>Soiland-Reyes</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">S</forename><surname>Leo</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">S</forename><surname>Owen</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">N</forename><surname>Juty</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">J</forename><forename type=\"middle\">M</forename><surname>Fern\u00e1ndez</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">B</forename><surname>Gr\u00fcning</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">T</forename><surname>Brown</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">H</forename><surname>M\u00e9nager</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">S</forename><surname>Capella-Gutierrez</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">F</forename><surname>Coppens</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">C</forename><surname>Goble</surname></persName>\n\t\t</author>\n\t\t<idno type=\"DOI\">10.48550/arXiv.2410.06941</idno>\n\t\t<idno>arXiv:2410.06941</idno>\n\t\t<title level=\"m\">WorkflowHub: a registry for computational workflows</title>\n\t\t<imprint>\n\t\t\t<date>2024</date>\n\t\t</imprint>\n\t</monogr>\n</biblStruct>\n"}, {"refKey": 15, "tei": "<biblStruct status=\"consolidated\" source=\"crossref\" xml:id=\"b15\">\n\t<analytic>\n\t\t<title level=\"a\" type=\"main\">The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update</title>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Enis</forename><surname>Afgan</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Anton</forename><surname>Nekrutenko</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Bj\u00f3rn</forename><forename type=\"middle\">A</forename><surname>Gr\u00fcning</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Daniel</forename><surname>Blankenberg</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Jeremy</forename><surname>Goecks</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Michael</forename><forename type=\"middle\">C</forename><surname>Schatz</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Alexander</forename><forename type=\"middle\">E</forename><surname>Ostrovsky</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Alexandru</forename><surname>Mahmoud</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Andrew</forename><forename type=\"middle\">J</forename><surname>Lonie</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Anna</forename><surname>Syme</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Anne</forename><surname>Fouilloux</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Anthony</forename><surname>Bretaudeau</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Anton</forename><surname>Nekrutenko</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Anup</forename><surname>Kumar</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Arthur</forename><forename type=\"middle\">C</forename><surname>Eschenlauer</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Assunta</forename><forename type=\"middle\">D</forename><surname>Desanto</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Aysam</forename><surname>Guerler</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Beatriz</forename><surname>Serrano-Solano</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">B\u00e9r\u00e9nice</forename><surname>Batut</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Bj\u00f6rn</forename><forename type=\"middle\">A</forename><surname>Gr\u00fcning</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Bradley</forename><forename type=\"middle\">W</forename><surname>Langhorst</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Bridget</forename><surname>Carr</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Bryan</forename><forename type=\"middle\">A</forename><surname>Raubenolt</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Cameron</forename><forename type=\"middle\">J</forename><surname>Hyde</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Catherine</forename><forename type=\"middle\">J</forename><surname>Bromhead</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Christopher</forename><forename type=\"middle\">B</forename><surname>Barnett</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Coline</forename><surname>Royaux</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Crist\u00f3bal</forename><surname>Gallardo</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Daniel</forename><surname>Blankenberg</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Daniel</forename><forename 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type=\"first\">Michael</forename><forename type=\"middle\">C</forename><surname>Schatz</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Michael</forename><forename type=\"middle\">R</forename><surname>Crusoe</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Miguel</forename><surname>Roncoroni</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Natalie</forename><surname>Kucher</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Nate</forename><surname>Coraor</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Nicholas</forename><surname>Stoler</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Nick</forename><surname>Rhodes</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename 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type=\"first\">Shilpa</forename><surname>Garg</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Simon</forename><forename type=\"middle\">A</forename><surname>Bray</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Simon</forename><forename type=\"middle\">L</forename><surname>Gladman</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Simone</forename><surname>Leo</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Subina</forename><forename type=\"middle\">P</forename><surname>Mehta</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Timothy</forename><forename type=\"middle\">J</forename><surname>Griffin</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Vahid</forename><surname>Jalili</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Vandenbrouck</forename><surname>Yves</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Victor</forename><surname>Wen</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Vijay</forename><forename type=\"middle\">K</forename><surname>Nagampalli</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Wendi</forename><forename type=\"middle\">A</forename><surname>Bacon</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Willem</forename><surname>De Koning</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Wolfgang</forename><surname>Maier</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Peter</forename><forename type=\"middle\">J</forename><surname>Briggs</surname></persName>\n\t\t</author>\n\t\t<idno type=\"DOI\">10.1093/nar/gkac247</idno>\n\t</analytic>\n\t<monogr>\n\t\t<title level=\"j\">Nucleic Acids Research</title>\n\t\t<idno type=\"ISSN\">0305-1048</idno>\n\t\t<idno type=\"ISSNe\">1362-4962</idno>\n\t\t<imprint>\n\t\t\t<biblScope unit=\"volume\">50</biblScope>\n\t\t\t<biblScope unit=\"issue\">W1</biblScope>\n\t\t\t<biblScope unit=\"page\" from=\"W345\" to=\"W351\" />\n\t\t\t<date type=\"published\" when=\"2022-04-21\">2022</date>\n\t\t\t<publisher>Oxford University Press (OUP)</publisher>\n\t\t</imprint>\n\t</monogr>\n</biblStruct>\n"}, {"refKey": 14, "tei": "<biblStruct status=\"extracted\" xml:id=\"b14\">\n\t<monogr>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">S</forename><surname>Leo</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">M</forename><forename type=\"middle\">R</forename><surname>Crusoe</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">L</forename><surname>Rodr\u00edguez-Navas</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">R</forename><surname>Sirvent</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">A</forename><surname>Kanitz</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">P</forename><surname>De Geest</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">R</forename><surname>Wittner</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">L</forename><surname>Pireddu</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">D</forename><surname>Garijo</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">J</forename><forename type=\"middle\">M</forename><surname>Fern\u00e1ndez</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">I</forename><surname>Colonnelli</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">M</forename><surname>Gallo</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">T</forename><surname>Ohta</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">H</forename><surname>Suetake</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">S</forename><surname>Capella-Gutierrez</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">R</forename><surname>De Wit</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">B</forename><forename type=\"middle\">P</forename><surname>Kinoshita</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">S</forename><surname>Soiland-Reyes</surname></persName>\n\t\t</author>\n\t\t<idno type=\"DOI\">10.48550/arXiv.2312.07852</idno>\n\t\t<idno>arXiv:2312.07852</idno>\n\t\t<title level=\"m\">Recording provenance of workflow runs with RO-Crate</title>\n\t\t<imprint>\n\t\t\t<date>2024</date>\n\t\t</imprint>\n\t</monogr>\n</biblStruct>\n"}, {"refKey": 48, "tei": "<biblStruct status=\"extracted\" xml:id=\"b48\">\n\t<monogr>\n\t\t<title/>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">L</forename><surname>Lopez-Delisle</surname></persName>\n\t\t</author>\n\t\t<idno type=\"DOI\">10.5281/zenodo.15078780</idno>\n\t\t<imprint>\n\t\t\t<date>2025</date>\n\t\t</imprint>\n\t</monogr>\n</biblStruct>\n"}, {"refKey": 10, "tei": "<biblStruct status=\"consolidated\" source=\"crossref\" xml:id=\"b10\">\n\t<analytic>\n\t\t<title level=\"a\" type=\"main\">The W3C PROV family of specifications for modelling provenance metadata</title>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Paolo</forename><surname>Missier</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">Khalid</forename><surname>Belhajjame</surname></persName>\n\t\t</author>\n\t\t<author>\n\t\t\t<persName><forename type=\"first\">James</forename><surname>Cheney</surname></persName>\n\t\t</author>\n\t\t<idno type=\"DOI\">10.1145/2452376.2452478</idno>\n\t</analytic>\n\t<monogr>\n\t\t<title level=\"m\">Proceedings of the 16th International Conference on Extending Database Technology</title>\n\t\t<meeting>the 16th International Conference on Extending Database Technology</meeting>\n\t\t<imprint>\n\t\t\t<publisher>ACM</publisher>\n\t\t\t<date type=\"published\" when=\"2013-03-18\">2013</date>\n\t\t\t<biblScope unit=\"page\" from=\"773\" to=\"776\" />\n\t\t</imprint>\n\t</monogr>\n</biblStruct>\n"}], "runtime": 61942, "id": 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