{
  "@context": "https://w3id.org/ro/crate/1.1/context",
  "@graph": [
    {
      "@id": "ro-crate-metadata.json",
      "@type": "CreativeWork",
      "about": {
        "@id": "./"
      },
      "conformsTo": [
        {
          "@id": "https://w3id.org/ro/crate/1.1"
        },
        {
          "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"
        }
      ]
    },
    {
      "@id": "ro-crate-preview.html",
      "@type": "CreativeWork",
      "about": {
        "@id": "./"
      }
    },
    {
      "@id": "./",
      "@type": "Dataset",
      "mainEntity": {
        "@id": "cwl/maw.cwl"
      },
      "datePublished": "2023-08-01 15:15:02 +0100",
      "author": [
        {
          "@id": "https://orcid.org/0000-0002-8330-4071"
        },
        {
          "@id": "https://orcid.org/0000-0002-2961-9670"
        },
        {
          "@id": "https://orcid.org/0000-0002-8122-9522"
        }
      ],
      "license": "MIT",
      "identifier": "https://doi.org/10.48546/workflowhub.workflow.510.2",
      "url": "https://workflowhub.eu/workflows/510/ro_crate?version=2",
      "name": "Research Object Crate for Metabolome Annotation Workflow (MAW)",
      "description": "\nThis repository hosts Metabolome Annotation Workflow (MAW). The workflow takes MS2 .mzML format data files as an input in R. It performs spectral database dereplication using R Package Spectra and compound database dereplication using SIRIUS OR MetFrag . Final candidate selection is done in Python using RDKit and PubChemPy.",
      "isBasedOn": "https://github.com/zmahnoor14/MAW",
      "sdDatePublished": "2026-04-21 15:17:15 +0100",
      "creativeWorkStatus": "Stable",
      "hasPart": [
        {
          "@id": "cwl/maw.cwl"
        },
        {
          "@id": "workflow-510-2da7fbaab0e2e4ebbff3f36d631336690fb318b0-diagram.svg"
        }
      ]
    },
    {
      "@id": "cwl/maw.cwl",
      "@type": [
        "File",
        "SoftwareSourceCode",
        "ComputationalWorkflow"
      ],
      "contentSize": 1506,
      "programmingLanguage": {
        "@id": "#cwl"
      },
      "image": {
        "@id": "workflow-510-2da7fbaab0e2e4ebbff3f36d631336690fb318b0-diagram.svg"
      },
      "dct:conformsTo": {
        "@id": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/"
      },
      "description": "\nThis repository hosts Metabolome Annotation Workflow (MAW). The workflow takes MS2 .mzML format data files as an input in R. It performs spectral database dereplication using R Package Spectra and compound database dereplication using SIRIUS OR MetFrag . Final candidate selection is done in Python using RDKit and PubChemPy.",
      "name": "Metabolome Annotation Workflow (MAW)",
      "url": "https://workflowhub.eu/workflows/510?version=2",
      "keywords": "Metabolomics, Annotation, mass-spectrometry, identification, Bioinformatics, FAIR workflows, workflow, gnps, massbank, hmdb, spectra, rdkit, Cheminformatics",
      "version": 2,
      "license": "https://spdx.org/licenses/MIT",
      "creator": [
        {
          "@id": "https://workflowhub.eu/people/423"
        },
        {
          "@id": "https://workflowhub.eu/people/70"
        },
        {
          "@id": "https://workflowhub.eu/people/469"
        },
        {
          "@id": "https://orcid.org/0000-0001-6966-0814"
        },
        {
          "@id": "https://orcid.org/0000-0001-9359-7149"
        },
        {
          "@id": "https://orcid.org/0000-0002-4321-0257"
        }
      ],
      "producer": {
        "@id": "https://workflowhub.eu/projects/151"
      },
      "dateCreated": "2023-08-01T14:21:50Z",
      "dateModified": "2023-08-01T14:22:09Z",
      "isPartOf": [

      ],
      "identifier": "https://doi.org/10.48546/workflowhub.workflow.510.2",
      "isBasedOn": "https://workflowhub.eu/workflows/510?version=1",
      "input": [
        {
          "@id": "#metabolome_annotation_workflow__maw_-inputs-python_script"
        },
        {
          "@id": "#metabolome_annotation_workflow__maw_-inputs-r_script"
        },
        {
          "@id": "#metabolome_annotation_workflow__maw_-inputs-mzml_files"
        },
        {
          "@id": "#metabolome_annotation_workflow__maw_-inputs-gnps_file"
        },
        {
          "@id": "#metabolome_annotation_workflow__maw_-inputs-hmdb_file"
        },
        {
          "@id": "#metabolome_annotation_workflow__maw_-inputs-mbank_file"
        },
        {
          "@id": "#metabolome_annotation_workflow__maw_-inputs-ppmx"
        },
        {
          "@id": "#metabolome_annotation_workflow__maw_-inputs-collision_info"
        },
        {
          "@id": "#metabolome_annotation_workflow__maw_-inputs-db_name"
        },
        {
          "@id": "#metabolome_annotation_workflow__maw_-inputs-db_path"
        }
      ],
      "output": [
        {
          "@id": "#metabolome_annotation_workflow__maw_-outputs-candidate_files"
        },
        {
          "@id": "#metabolome_annotation_workflow__maw_-outputs-result"
        }
      ],
      "sdPublisher": {
        "@id": "https://about.workflowhub.eu/"
      }
    },
    {
      "@id": "workflow-510-2da7fbaab0e2e4ebbff3f36d631336690fb318b0-diagram.svg",
      "@type": [
        "File",
        "ImageObject"
      ],
      "contentSize": 10427
    },
    {
      "@id": "https://orcid.org/0000-0002-8330-4071",
      "@type": "Person",
      "name": "Mahnoor Zulfiqar",
      "identifier": "https://orcid.org/0000-0002-8330-4071"
    },
    {
      "@id": "https://orcid.org/0000-0002-2961-9670",
      "@type": "Person",
      "name": "Michael R. Crusoe",
      "identifier": "https://orcid.org/0000-0002-2961-9670"
    },
    {
      "@id": "https://orcid.org/0000-0002-8122-9522",
      "@type": "Person",
      "name": "Luiz Gadelha",
      "identifier": "https://orcid.org/0000-0002-8122-9522"
    },
    {
      "@id": "https://workflowhub.eu/people/423",
      "@type": "Person",
      "name": "Mahnoor Zulfiqar"
    },
    {
      "@id": "https://workflowhub.eu/people/70",
      "@type": "Person",
      "name": "Michael R. Crusoe"
    },
    {
      "@id": "https://workflowhub.eu/people/469",
      "@type": "Person",
      "name": "Luiz Gadelha"
    },
    {
      "@id": "https://orcid.org/0000-0001-6966-0814",
      "@type": "Person",
      "name": "Christoph  Steinbeck"
    },
    {
      "@id": "https://orcid.org/0000-0001-9359-7149",
      "@type": "Person",
      "name": "Maria Sorokina"
    },
    {
      "@id": "https://orcid.org/0000-0002-4321-0257",
      "@type": "Person",
      "name": "Kristian Peters"
    },
    {
      "@id": "https://workflowhub.eu/projects/151",
      "@type": [
        "Project",
        "Organization"
      ],
      "name": "Metabolomics-Reproducibility"
    },
    {
      "@id": "#cwl",
      "@type": "ComputerLanguage",
      "name": "Common Workflow Language",
      "alternateName": "CWL",
      "identifier": {
        "@id": "https://w3id.org/cwl/v1.0/"
      },
      "url": {
        "@id": "https://www.commonwl.org/"
      }
    },
    {
      "@id": "#metabolome_annotation_workflow__maw_-inputs-python_script",
      "@type": "FormalParameter",
      "name": "python_script",
      "dct:conformsTo": {
        "@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/"
      }
    },
    {
      "@id": "#metabolome_annotation_workflow__maw_-inputs-r_script",
      "@type": "FormalParameter",
      "name": "r_script",
      "dct:conformsTo": {
        "@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/"
      }
    },
    {
      "@id": "#metabolome_annotation_workflow__maw_-inputs-mzml_files",
      "@type": "FormalParameter",
      "name": "mzml_files",
      "dct:conformsTo": {
        "@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/"
      }
    },
    {
      "@id": "#metabolome_annotation_workflow__maw_-inputs-gnps_file",
      "@type": "FormalParameter",
      "name": "gnps_file",
      "dct:conformsTo": {
        "@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/"
      }
    },
    {
      "@id": "#metabolome_annotation_workflow__maw_-inputs-hmdb_file",
      "@type": "FormalParameter",
      "name": "hmdb_file",
      "dct:conformsTo": {
        "@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/"
      }
    },
    {
      "@id": "#metabolome_annotation_workflow__maw_-inputs-mbank_file",
      "@type": "FormalParameter",
      "name": "mbank_file",
      "dct:conformsTo": {
        "@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/"
      }
    },
    {
      "@id": "#metabolome_annotation_workflow__maw_-inputs-ppmx",
      "@type": "FormalParameter",
      "name": "ppmx",
      "dct:conformsTo": {
        "@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/"
      }
    },
    {
      "@id": "#metabolome_annotation_workflow__maw_-inputs-collision_info",
      "@type": "FormalParameter",
      "name": "collision_info",
      "dct:conformsTo": {
        "@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/"
      }
    },
    {
      "@id": "#metabolome_annotation_workflow__maw_-inputs-db_name",
      "@type": "FormalParameter",
      "name": "db_name",
      "dct:conformsTo": {
        "@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/"
      }
    },
    {
      "@id": "#metabolome_annotation_workflow__maw_-inputs-db_path",
      "@type": "FormalParameter",
      "name": "db_path",
      "dct:conformsTo": {
        "@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/"
      }
    },
    {
      "@id": "#metabolome_annotation_workflow__maw_-outputs-candidate_files",
      "@type": "FormalParameter",
      "name": "candidate_files",
      "dct:conformsTo": {
        "@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/"
      }
    },
    {
      "@id": "#metabolome_annotation_workflow__maw_-outputs-result",
      "@type": "FormalParameter",
      "name": "result",
      "dct:conformsTo": {
        "@id": "https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE/"
      }
    },
    {
      "@id": "https://about.workflowhub.eu/",
      "@type": "Organization",
      "name": "WorkflowHub",
      "url": "https://about.workflowhub.eu/"
    }
  ]
}