{
"$schema": "http://json-schema.org/draft-07/schema#",
"$id": "https://iomega.github.io/paired-data-form/schema.json",
"title": "iOMEGA Paired Omics Data Platform",
"description": "This Paired Omics Data Platform is a community-based initiative standardizing links between genomic and metabolomics data in a computer-readable manner to further the field of natural products discovery. The form below aims to capture sufficient metadata to create informative links between genome sequences on the one hand and metabolomics profiles on the other hand. Note that wherever we could, we have used existing ontology to define terms. When filling out the form below, at any time the inputted data can be saved and downloaded in json format to be reloaded when continuing with the entries. The form below first asks for some personal information to provide proper credits and allow the community to ask the right person information on the linked data. Then, overall information on the metabolomics experiment is captured, before all genomes or metagenomes can be detailed, including creating a unique genome label for easy recall during linking. Then the metabolomics metadata can be saved using labels for sample growth conditions, extraction, and instrument methods. Finally, the data links can be made with references to the actual mass spectral files in MaSSIVE. Optionally, you can save links between known biosynthesis gene clusters and mass spectra or molecular families in the second part of the form. After saving your entries, a table below the form will appear filled with the links you created with experimental labels; you can also expand the table to see all information inputted. Then you can download the filled json schema in which all links are recorded. To accommodate inputting large datasets, you can download the TSV linking table, manually add new links, and re-upload the TSV file. It is important to note that all experimental labels need to be defined in the form and at least one link made before you download and edit the table. We hope you will use our platform to capture your paired data links as this will allow you and the community to efficiently use your data in follow-up studies that rely on the combined use of genome and metabolome data.",
"type": "object",
"required": [
"version",
"personal",
"metabolomics",
"genomes",
"proteomes",
"experimental",
"genome_metabolome_links"
],
"properties": {
"version": {
"type": "string",
"readOnly": true,
"default": "3",
"enum": [
"3"
]
},
"personal": {
"type": "object",
"title": "1. Submitter Information",
"properties": {
"submitter_name": {
"type": "string",
"title": "Name of contact for correspondence",
"description": "This person will be the point of contact for any communication related to this entry."
},
"submitter_orcid": {
"type": "string",
"title": "ORCID identifier",
"description": "ORCID identifier of person who is point of contact. Please use full ORCID iD, e.g. https://orcid.org/0000-0002-1825-0097 .",
"format": "uri",
"pattern": "^https://orcid.org/[0-9]{4}-?[0-9]{4}-?[0-9]{4}-?[0-9]{3}[0-9X]$"
},
"submitter_email": {
"type": "string",
"title": "Submitter contact e-mail address",
"format": "email"
},
"submitter_name_secondary": {
"type": "string",
"title": "Name of second contact for correspondence",
"description": "This person will be the second point of contact for any communication related to this entry."
},
"submitter_email_secondary": {
"type": "string",
"title": "Secondary submitter contact e-mail address",
"format": "email"
},
"PI_name": {
"type": "string",
"title": "Name of the principal investigator of the submitter",
"description": "This person is contacted in case the submitters have moved institutions"
},
"PI_institution": {
"type": "string",
"title": "Academic institution or company name",
"description": "Please use the full, official name of your institute in English. E.g., 'Harvard University'."
},
"PI_email": {
"type": "string",
"title": "PI contact e-mail address",
"format": "email"
}
},
"additionalProperties": false
},
"metabolomics": {
"type": "object",
"title": "2. Metabolomics Information",
"description": "Please provide basic information on the publicly available metabolomics project from which paired data is available. Currently, we allow for links to mass spectrometry data deposited in GNPS-MaSSIVE or MetaboLights.",
"properties": {
"project": {
"oneOf": [
{
"type": "object",
"required": [
"GNPSMassIVE_ID",
"MaSSIVE_URL"
],
"title": "GNPS-MassIVE",
"properties": {
"GNPSMassIVE_ID": {
"type": "string",
"title": "GNPS-MassIVE identifier",
"description": "Please provide the GNPS-MassIVE identifier of your metabolomics data set, e.g., MSV000078839.",
"pattern": "^MSV[0-9]{9}$"
},
"MaSSIVE_URL": {
"type": "string",
"title": "Link to MassIVE upload",
"description": "Please provide the link to the MassIVE upload, e.g., https://gnps.ucsd.edu/ProteoSAFe/result.jsp?task=a507232a787243a5afd69a6c6fa1e508&view=advanced_view. Warning, there cannot be spaces in the URI.",
"format": "uri"
},
"molecular_network": {
"type": "string",
"pattern": "^[0-9a-z]{32}$",
"title": "Molecular Network Task ID",
"description": "If you have run a Molecular Network on GNPS, please provide the task ID of the Molecular Network job. It can be found in the URL of the Molecular Networking job, e.g., in https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=c36f90ba29fe44c18e96db802de0c6b9 the task ID is c36f90ba29fe44c18e96db802de0c6b9."
}
}
},
{
"type": "object",
"title": "MetaboLights",
"required": [
"metabolights_study_id"
],
"properties": {
"metabolights_study_id": {
"type": "string",
"title": "MetaboLights study identifier",
"pattern": "^MTBLS[0-9]{1,}$",
"description": "Please provide the MetaboLights study identifier of your metabolomics data set, e.g. MTBLS307."
}
}
}
]
},
"related_GNPSMassIVE_ID": {
"type": "string",
"title": "Related GNPS-Massive identifiers",
"description": "Add other associated GNPS-MassIVE identifiers here, eg. MSV000078836,MSV000078839. For example, if you have data spread out over multiple MASSIVE datasets, reported in the same publication, you can add those related IDs here. If you used the same assays (\"Sample Preparation,\" \"Extraction Methods,\" and/or \"Instrumentation Methods\"), you can clone one project and make slight modifications (e.g. different Genome IDs) instead of entering the assay information again.",
"pattern": "^MSV[0-9]{9}(,\\s*MSV[0-9]{9})*$"
},
"related_metabolights_study_id": {
"type": "string",
"title": "Related Metabolights study identifiers",
"description": "Add other associated MetaboLights study identifiers here, eg. MTBLS727,MTBLS728. Similar to the related GNPS-Massive identifiers.",
"pattern": "^MTBLS[0-9]{1,}(,\\s*MTBLS[0-9]{1,})*$"
},
"publications": {
"type": "string",
"pattern": "[0-9]{1,}",
"title": "Key publications",
"description": "Publications describing the metabolomics experiment and samples. Please input PubMed IDs (PMIDs, not PMCIDs!), separated by commas: e.g., '12000953,8843436'. Only enter numeric characters and commas. If a PMID is not available, a DOI can be entered instead (without the designation 'DOI' itself, e.g. '10.1039/c4sc01927j')"
}
},
"required": [
"project"
],
"additionalProperties": false
},
"genomes": {
"type": "array",
"title": "3. (Meta)genomics Information",
"description": "Please add all genomes and/or metagenomes for which paired data is available as separate entries.",
"items": {
"type": "object",
"required": [
"genome_ID",
"genome_label"
],
"properties": {
"genome_ID": {
"type": "object",
"title": "Genome or Metagenome",
"description": "Please select genome (microbial isolate grown in pure culture), metagenome (microbial mixture or environmental sample), or metagenome-assembled genome (genome assembled from a metagenome with no isolate grown in culture). All genome sequences must first be submitted to a public database with a unique identifier. In the case of a whole genome sequence, please use master records. At least one identifier must be entered.",
"required": [
"genome_type"
],
"properties": {
"genome_type": {
"type": "string",
"title": "Genome type",
"enum": [
"genome",
"metagenome",
"metagenome-assembled genome"
],
"default": "genome"
}
},
"dependencies": {
"genome_type": {
"oneOf": [
{
"properties": {
"genome_type": {
"enum": [
"genome",
"metagenome-assembled genome"
]
},
"GenBank_accession": {
"type": "string",
"title": "GenBank accession number",
"description": "If the publicly available genome got a GenBank accession number assigned, e.g., AL645882, please provide it here. The genome sequence must be submitted to GenBank/ENA/DDBJ (and an accession number must be received) before this form can be filled out. In case of a whole genome sequence, please use master records. At least one identifier must be entered."
},
"RefSeq_accession": {
"type": "string",
"title": "RefSeq accession number",
"description": "For example: NC_003888.3"
},
"JGI_Genome_ID": {
"type": "string",
"title": "JGI IMG genome ID",
"description": "For example: 641228474"
}
}
},
{
"properties": {
"genome_type": {
"enum": [
"metagenome"
]
},
"ENA_NCBI_accession": {
"type": "string",
"title": "ENA/NCBI accession number",
"description": "For example: GCA_900283375"
},
"MGnify_accession": {
"type": "string",
"title": "MGnify accession number",
"description": "For example: MGYS00001053"
},
"JGI_ID": {
"type": "string",
"title": "JGI IMG (meta)genome ID",
"description": "For example: 3300005805"
}
}
}
]
}
}
},
"BioSample_accession": {
"type": "string",
"title": "BioSample accession number",
"description": "If publicly available metadata is available at BioSamples, please provide the BioSample accession number, e.g. SAMEA3648350, here. We encourage depositing metadata following a standardized ontology to enable proper reuse of the data."
},
"publications": {
"type": "string",
"pattern": "[0-9]{1,}",
"title": "Key publications",
"description": "Publications describing the sequencing of the genome or metagenome. Please input PubMed IDs (PMIDs, not PMCIDs!), separated by commas: e.g., '12000953,8843436'. Only enter numeric characters and commas. If a PMID is not available, a DOI can be entered instead (without the designation 'DOI' itself, e.g. '10.1039/c4sc01927j')"
},
"genome_label": {
"type": "string",
"title": "Genome label",
"description": "Please assign a unique Genome Label for this genome or metagenome to help you recall it during the linking step. For example 'Streptomyces sp. CNB091'",
"minLength": 1
}
}
}
},
"experimental": {
"type": "object",
"title": "4. Experimental Details",
"description": "Please provide basic information about the Sample Preparation, Extraction Methods, and Instrumentation Methods used. If different Sample Preparation, Extraction Methods, and/or Instrumentation Methods were used leading to different metabolomics data, please use separate entries for each experimental change and create a label that will help you recall the experimental parameters during the linking step. Experimental details can be attached to a metabolomics data file or a proteome.",
"properties": {
"sample_preparation": {
"type": "array",
"title": "Sample Growth Conditions",
"description": "For strains grown in culture, please fill in the first five sections. For metagenomic samples, only metagenomic source is necessary.",
"items": {
"type": "object",
"properties": {
"medium_details": {
"type": "object",
"title": "Medium details",
"properties": {
"medium_type": {
"type": "string",
"title": "Medium type",
"description": "Please select liquid or solid medium.",
"enum": [
"liquid",
"solid",
"metagenome"
],
"default": "liquid"
}
},
"dependencies": {
"medium_type": {
"oneOf": [
{
"properties": {
"medium_type": {
"enum": [
"metagenome"
]
},
"metagenomic_sample_description": {
"type": "string",
"title": "Metagenomic sample description",
"description": "Please describe your metagenomic sample preparation prior to extraction. This can include cell sorting or enrichment, drying, filtering, or other treatments."
},
"metagenomic_environment": {
"type": "string",
"title": "Metagenome host or isolation source",
"description": "For metagenomic samples, please select the source host or isolation source. If it is not available, please select Other and type it in.",
"oneOf": [
{
"type": "string",
"title": "Human",
"enum": [
"https://bioportal.bioontology.org/ontologies/MEO/?p=classes&conceptid=http%3A%2F%2Fpurl.jp%2Fbio%2F11%2Fmeo%2FMEO_0000393"
]
},
{
"type": "string",
"title": "Other mammal",
"enum": [
"https://bioportal.bioontology.org/ontologies/MEO/?p=classes&conceptid=http%3A%2F%2Fpurl.jp%2Fbio%2F11%2Fmeo%2FMEO_0000395"
]
},
{
"type": "string",
"title": "Aquatic invertebrate",
"enum": [
"https://bioportal.bioontology.org/ontologies/MEO/?p=classes&conceptid=http%3A%2F%2Fpurl.jp%2Fbio%2F11%2Fmeo%2FMEO_0000871"
]
},
{
"type": "string",
"title": "Insect",
"enum": [
"https://bioportal.bioontology.org/ontologies/MEO/?p=classes&conceptid=http%3A%2F%2Fpurl.jp%2Fbio%2F11%2Fmeo%2FMEO_0000058"
]
},
{
"type": "string",
"title": "Other animal",
"enum": [
"https://bioportal.bioontology.org/ontologies/MEO/?p=classes&conceptid=http%3A%2F%2Fpurl.jp%2Fbio%2F11%2Fmeo%2FMEO_0000421"
]
},
{
"type": "string",
"title": "Biofilm / Microbial mat",
"enum": [
"https://bioportal.bioontology.org/ontologies/MEO/?p=classes&conceptid=http%3A%2F%2Fpurl.jp%2Fbio%2F11%2Fmeo%2FMEO_0000116"
]
},
{
"type": "string",
"title": "Plant",
"enum": [
"https://bioportal.bioontology.org/ontologies/MEO/?p=classes&conceptid=http%3A%2F%2Fpurl.jp%2Fbio%2F11%2Fmeo%2FMEO_0000057"
]
},
{
"type": "string",
"title": "Soil",
"enum": [
"https://bioportal.bioontology.org/ontologies/MEO/?p=classes&conceptid=http%3A%2F%2Fpurl.jp%2Fbio%2F11%2Fmeo%2FMEO_0000007"
]
},
{
"type": "string",
"title": "Sediment",
"enum": [
"https://bioportal.bioontology.org/ontologies/MEO/?p=classes&conceptid=http%3A%2F%2Fpurl.jp%2Fbio%2F11%2Fmeo%2FMEO_0000066"
]
},
{
"type": "string",
"title": "Ocean",
"enum": [
"https://bioportal.bioontology.org/ontologies/MEO/?p=classes&conceptid=http%3A%2F%2Fpurl.jp%2Fbio%2F11%2Fmeo%2FMEO_0000022"
]
},
{
"type": "string",
"title": "Air",
"enum": [
"https://bioportal.bioontology.org/ontologies/MEO/?p=classes&conceptid=http%3A%2F%2Fpurl.jp%2Fbio%2F11%2Fmeo%2FMEO_0000006"
]
},
{
"type": "string",
"title": "Other",
"enum": [
"other"
]
}
]
}
}
},
{
"properties": {
"medium_type": {
"enum": [
"solid"
]
},
"medium": {
"type": "string",
"title": "Growth medium",
"description": "Please select a growth medium used in the experiment. If it is not present, please select Other and type it in.",
"anyOf": [
{
"type": "string",
"title": "LB (Luria-Bertani) medium",
"enum": [
"http://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium381.pdf"
]
},
{
"type": "string",
"title": "Tryptic-Soy Broth (TSB)",
"enum": [
"http://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium545.pdf"
]
},
{
"type": "string",
"title": "Nutrient Agar",
"enum": [
"http://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1.pdf"
]
},
{
"type": "string",
"title": "Oat Flake agar",
"enum": [
"http://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium189.pdf"
]
},
{
"type": "string",
"title": "Marine Broth (Difco 2216)",
"enum": [
"http://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium514.pdf"
]
},
{
"type": "string",
"title": "Mannitol Yeast extract Peptone (MYE)",
"enum": [
"http://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1087.pdf"
]
},
{
"type": "string",
"title": "ISP2 medium",
"enum": [
"http://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium987.pdf"
]
},
{
"type": "string",
"title": "ISP4 medium",
"enum": [
"http://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium547.pdf"
]
},
{
"type": "string",
"title": "A1 medium",
"enum": [
"http://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1054.pdf"
]
},
{
"type": "string",
"title": "Mannitol soy flour medium (MS)",
"enum": [
"https://www.elabprotocols.com/protocols/#!protocol=469"
]
},
{
"type": "string",
"title": "R5 medium",
"enum": [
"https://www.elabprotocols.com/protocols/#!protocol=486"
]
},
{
"type": "string",
"title": "Yeast extract-malt extract (YEME) medium",
"enum": [
"https://www.elabprotocols.com/protocols/#!protocol=464"
]
},
{
"type": "string",
"title": "Minimal medium (MM)",
"enum": [
"https://www.elabprotocols.com/protocols/#!protocol=484"
]
},
{
"type": "string",
"title": "Supplemented minimal medium (SMM)",
"enum": [
"https://openwetware.org/wiki/M9_medium/minimal"
]
},
{
"type": "string",
"title": "Maltose Yeast Malt media (MYM)",
"enum": [
"https://s3-eu-west-1.amazonaws.com/pfigshare-u-files/1805982/MYMmedium.pdf"
]
},
{
"type": "string",
"title": "R2YE medium",
"enum": [
"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2950629/pdf/nihms234294.pdf"
]
},
{
"type": "string",
"title": "Bottromycin Production Medium (BPM)",
"enum": [
"https://www.nature.com/articles/s41467-017-01975-6"
]
},
{
"type": "string",
"title": "Potato Dextrose (PD) medium",
"enum": [
"https://www.sigmaaldrich.com/catalog/product/sial/70139?lang=en®ion=NL"
]
},
{
"type": "string",
"title": "Yeast Powder-Soluble Starch (YPSS) medium",
"enum": [
"http://www.mycobank.org/BioloMICS.aspx?TableKey=14682616000000058&Rec=254&Fields=All"
]
},
{
"type": "string",
"title": "Czapek-Dox medium",
"enum": [
"https://en.wikipedia.org/wiki/Czapek_medium"
]
},
{
"type": "string",
"title": "Malt Extract medium",
"enum": [
"http://cshprotocols.cshlp.org/content/2016/3/pdb.rec091454.full"
]
},
{
"type": "string",
"title": "Other",
"enum": [
"other"
]
}
]
}
}
},
{
"properties": {
"medium_type": {
"enum": [
"liquid"
]
},
"medium_volume": {
"type": "number",
"title": "Volume of culture (millilitre)"
},
"medium": {
"type": "string",
"title": "Growth medium",
"description": "Please select a growth medium used in the experiment. If it is not present, please select Other and type it in.",
"anyOf": [
{
"type": "string",
"title": "LB (Luria-Bertani) medium",
"enum": [
"http://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium381.pdf"
]
},
{
"type": "string",
"title": "Tryptic-Soy Broth (TSB)",
"enum": [
"http://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium545.pdf"
]
},
{
"type": "string",
"title": "Nutrient Agar",
"enum": [
"http://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1.pdf"
]
},
{
"type": "string",
"title": "Oat Flake agar",
"enum": [
"http://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium189.pdf"
]
},
{
"type": "string",
"title": "Marine Broth (Difco 2216)",
"enum": [
"http://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium514.pdf"
]
},
{
"type": "string",
"title": "Mannitol Yeast extract Peptone (MYE)",
"enum": [
"http://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1087.pdf"
]
},
{
"type": "string",
"title": "ISP2 medium",
"enum": [
"http://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium987.pdf"
]
},
{
"type": "string",
"title": "ISP4 medium",
"enum": [
"http://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium547.pdf"
]
},
{
"type": "string",
"title": "A1 medium",
"enum": [
"http://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1054.pdf"
]
},
{
"type": "string",
"title": "Mannitol soy flour medium (MS)",
"enum": [
"https://www.elabprotocols.com/protocols/#!protocol=469"
]
},
{
"type": "string",
"title": "R5 medium",
"enum": [
"https://www.elabprotocols.com/protocols/#!protocol=486"
]
},
{
"type": "string",
"title": "Yeast extract-malt extract (YEME) medium",
"enum": [
"https://www.elabprotocols.com/protocols/#!protocol=464"
]
},
{
"type": "string",
"title": "Minimal medium (MM)",
"enum": [
"https://www.elabprotocols.com/protocols/#!protocol=484"
]
},
{
"type": "string",
"title": "Supplemented minimal medium (SMM)",
"enum": [
"https://openwetware.org/wiki/M9_medium/minimal"
]
},
{
"type": "string",
"title": "Maltose Yeast Malt media (MYM)",
"enum": [
"https://s3-eu-west-1.amazonaws.com/pfigshare-u-files/1805982/MYMmedium.pdf"
]
},
{
"type": "string",
"title": "R2YE medium",
"enum": [
"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2950629/pdf/nihms234294.pdf"
]
},
{
"type": "string",
"title": "Bottromycin Production Medium (BPM)",
"enum": [
"https://www.nature.com/articles/s41467-017-01975-6"
]
},
{
"type": "string",
"title": "Potato Dextrose (PD) medium",
"enum": [
"https://www.sigmaaldrich.com/catalog/product/sial/70139?lang=en®ion=NL"
]
},
{
"type": "string",
"title": "Yeast Powder-Soluble Starch (YPSS) medium",
"enum": [
"http://www.mycobank.org/BioloMICS.aspx?TableKey=14682616000000058&Rec=254&Fields=All"
]
},
{
"type": "string",
"title": "Czapek-Dox medium",
"enum": [
"https://en.wikipedia.org/wiki/Czapek_medium"
]
},
{
"type": "string",
"title": "Malt Extract medium",
"enum": [
"http://cshprotocols.cshlp.org/content/2016/3/pdb.rec091454.full"
]
},
{
"type": "string",
"title": "Other",
"enum": [
"other"
]
}
]
}
}
}
]
},
"medium": {
"oneOf": [
{
"properties": {
"medium": {
"enum": [
"http://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium381.pdf",
"http://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium545.pdf",
"http://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1.pdf",
"http://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium189.pdf",
"http://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium514.pdf",
"http://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1087.pdf",
"http://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium987.pdf",
"http://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium547.pdf",
"http://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1054.pdf",
"https://www.elabprotocols.com/protocols/#!protocol=469",
"https://www.elabprotocols.com/protocols/#!protocol=486",
"https://www.elabprotocols.com/protocols/#!protocol=464",
"https://www.elabprotocols.com/protocols/#!protocol=484",
"https://openwetware.org/wiki/M9_medium/minimal",
"https://s3-eu-west-1.amazonaws.com/pfigshare-u-files/1805982/MYMmedium.pdf",
"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2950629/pdf/nihms234294.pdf",
"https://www.nature.com/articles/s41467-017-01975-6",
"https://www.sigmaaldrich.com/catalog/product/sial/70139?lang=en®ion=NL",
"http://www.mycobank.org/BioloMICS.aspx?TableKey=14682616000000058&Rec=254&Fields=All",
"https://en.wikipedia.org/wiki/Czapek_medium",
"http://cshprotocols.cshlp.org/content/2016/3/pdb.rec091454.full"
]
}
}
},
{
"properties": {
"medium": {
"enum": [
"other"
]
},
"Other_medium": {
"type": "string",
"title": "Name of other medium"
},
"Other_medium_link": {
"type": "string",
"title": "URL for definition of other medium"
}
}
}
]
},
"metagenomic_environment": {
"oneOf": [
{
"properties": {
"metagenomic_environment": {
"enum": [
"https://bioportal.bioontology.org/ontologies/MEO/?p=classes&conceptid=http%3A%2F%2Fpurl.jp%2Fbio%2F11%2Fmeo%2FMEO_0000393",
"https://bioportal.bioontology.org/ontologies/MEO/?p=classes&conceptid=http%3A%2F%2Fpurl.jp%2Fbio%2F11%2Fmeo%2FMEO_0000395",
"https://bioportal.bioontology.org/ontologies/MEO/?p=classes&conceptid=http%3A%2F%2Fpurl.jp%2Fbio%2F11%2Fmeo%2FMEO_0000871",
"https://bioportal.bioontology.org/ontologies/MEO/?p=classes&conceptid=http%3A%2F%2Fpurl.jp%2Fbio%2F11%2Fmeo%2FMEO_0000058",
"https://bioportal.bioontology.org/ontologies/MEO/?p=classes&conceptid=http%3A%2F%2Fpurl.jp%2Fbio%2F11%2Fmeo%2FMEO_0000421",
"https://bioportal.bioontology.org/ontologies/MEO/?p=classes&conceptid=http%3A%2F%2Fpurl.jp%2Fbio%2F11%2Fmeo%2FMEO_0000116",
"https://bioportal.bioontology.org/ontologies/MEO/?p=classes&conceptid=http%3A%2F%2Fpurl.jp%2Fbio%2F11%2Fmeo%2FMEO_0000057",
"https://bioportal.bioontology.org/ontologies/MEO/?p=classes&conceptid=http%3A%2F%2Fpurl.jp%2Fbio%2F11%2Fmeo%2FMEO_0000007",
"https://bioportal.bioontology.org/ontologies/MEO/?p=classes&conceptid=http%3A%2F%2Fpurl.jp%2Fbio%2F11%2Fmeo%2FMEO_0000066",
"https://bioportal.bioontology.org/ontologies/MEO/?p=classes&conceptid=http%3A%2F%2Fpurl.jp%2Fbio%2F11%2Fmeo%2FMEO_0000022",
"https://bioportal.bioontology.org/ontologies/MEO/?p=classes&conceptid=http%3A%2F%2Fpurl.jp%2Fbio%2F11%2Fmeo%2FMEO_0000006"
]
}
}
},
{
"properties": {
"metagenomic_environment": {
"enum": [
"other"
]
},
"metagenomic_other_environment": {
"type": "string",
"title": "Name of other environment or host"
}
}
}
]
}
}
},
"growth_parameters": {
"type": "object",
"title": "Growth parameters",
"properties": {
"growth_temperature": {
"type": "number",
"title": "Temperature (℃)",
"description": "Please enter the temperature of growth in degrees Celsius."
},
"growth_duration": {
"type": "number",
"title": "Duration (h)",
"description": "Please enter the growth duration in hours."
},
"growth_phase_OD": {
"type": "string",
"title": "Phase or OD",
"description": "Please enter the growth phase or optical density (OD) if you know it."
}
},
"additionalProperties": false
},
"aeration": {
"type": "object",
"title": "Aeration",
"properties": {
"aeration_type": {
"type": "string",
"title": "Type",
"description": "Please select aeration type.",
"enum": [
"shaking",
"fermenter",
"not shaking"
]
}
},
"dependencies": {
"aeration_type": {
"oneOf": [
{
"properties": {
"aeration_type": {
"enum": [
"shaking"
]
},
"aeration_vessel": {
"type": "string",
"title": "Vessel",
"description": "Select vessel used for shaking",
"enum": [
"Erlenmeyer flask",
"spring flask",
"baffled flask",
"conical tubes",
"deep-well plates",
"other"
]
},
"aeration_rpm": {
"type": "number",
"title": "RPM",
"description": "Rotations per minute of shaker or fermenter"
}
}
},
{
"properties": {
"aeration_type": {
"enum": [
"fermenter"
]
},
"aeration_rpm": {
"type": "number",
"title": "RPM",
"description": "Rotations per minute of shaker or fermenter"
}
}
},
{
"properties": {
"aeration_type": {
"enum": [
"not shaking"
]
}
}
}
]
},
"aeration_vessel": {
"oneOf": [
{
"properties": {
"aeration_vessel": {
"enum": [
"other"
]
},
"aeration_other_vessel": {
"type": "string",
"title": "Other vessel"
}
}
},
{
"properties": {
"aeration_vessel": {
"enum": [
"Erlenmeyer flask",
"spring flask",
"baffled flask",
"conical tubes",
"deep-well plates"
]
}
}
}
]
}
}
},
"other_growth_conditions": {
"type": "string",
"title": "Other growth conditions",
"description": "Please describe any other relevant or distinguishing growth conditions e.g. light 12h, dark 12h. You can also define custom media here, indicate if purity checks were made, and provide more specific details."
},
"sample_preparation_method": {
"type": "string",
"title": "Sample Growth Conditions Label",
"description": "Please assign a Sample Growth Conditions Label for this set of sample preparation details. If more than one sample growth conditions was used, please create a new Sample Growth Conditions Label for each condition by clicking on the plus.",
"minLength": 1
}
},
"required": [
"sample_preparation_method",
"medium_details",
"growth_parameters",
"aeration"
]
}
},
"extraction_methods": {
"type": "array",
"title": "Extraction Methods",
"description": "Please provide basic details about the extraction solvents and procedures used.",
"items": {
"type": "object",
"properties": {
"solvents": {
"type": "array",
"title": "Extraction solvent",
"description": "Please select the organic solvent used to extract the sample. If your sovent is not listed, please select Other and specify the solvent. If you used multiple solvents, please select them all and indicate the ratio.",
"items": {
"type": "object",
"required": [
"solvent",
"ratio"
],
"properties": {
"solvent": {
"title": "Solvent",
"type": "string",
"anyOf": [
{
"type": "string",
"title": "Methanol",
"enum": [
"http://purl.obolibrary.org/obo/CHEBI_17790"
]
},
{
"type": "string",
"title": "Methylene Chloride / Dichloromethane",
"enum": [
"http://purl.obolibrary.org/obo/CHEBI_15767"
]
},
{
"type": "string",
"title": "Ethyl acetate",
"enum": [
"http://purl.obolibrary.org/obo/CHEBI_27750"
]
},
{
"type": "string",
"title": "Chloroform",
"enum": [
"http://purl.obolibrary.org/obo/CHEBI_35255"
]
},
{
"type": "string",
"title": "Acetone",
"enum": [
"http://purl.obolibrary.org/obo/CHEBI_15347"
]
},
{
"type": "string",
"title": "Isopropanol",
"enum": [
"http://purl.obolibrary.org/obo/CHEBI_17824"
]
},
{
"type": "string",
"title": "Butanol",
"enum": [
"http://purl.obolibrary.org/obo/CHEBI_28885"
]
},
{
"type": "string",
"title": "Acetonitrile",
"enum": [
"http://purl.obolibrary.org/obo/CHEBI_38472"
]
},
{
"type": "string",
"title": "Ethanol",
"enum": [
"http://purl.obolibrary.org/obo/CHEBI_16236"
]
},
{
"type": "string",
"title": "Diethyl ether",
"enum": [
"http://purl.obolibrary.org/obo/CHEBI_35702"
]
},
{
"type": "string",
"title": "Hexane",
"enum": [
"http://purl.obolibrary.org/obo/CHEBI_29021"
]
},
{
"type": "string",
"title": "Water",
"enum": [
"http://purl.obolibrary.org/obo/CHEBI_15377"
]
},
{
"type": "string",
"title": "Other solvent",
"enum": [
"http://purl.obolibrary.org/obo/CHEBI_46787"
]
}
]
},
"ratio": {
"type": "number",
"title": "Ratio",
"description": "When a mixture of solvents was used, specify in which ratio each solvent was used. The ratios should sum up to 1.",
"default": 1,
"exclusiveMinimum": 0,
"maximum": 1
}
},
"dependencies": {
"solvent": {
"oneOf": [
{
"properties": {
"solvent": {
"enum": [
"http://purl.obolibrary.org/obo/CHEBI_17790",
"http://purl.obolibrary.org/obo/CHEBI_15767",
"http://purl.obolibrary.org/obo/CHEBI_27750",
"http://purl.obolibrary.org/obo/CHEBI_35255",
"http://purl.obolibrary.org/obo/CHEBI_15347",
"http://purl.obolibrary.org/obo/CHEBI_17824",
"http://purl.obolibrary.org/obo/CHEBI_28885",
"http://purl.obolibrary.org/obo/CHEBI_38472",
"http://purl.obolibrary.org/obo/CHEBI_16236",
"http://purl.obolibrary.org/obo/CHEBI_35702",
"http://purl.obolibrary.org/obo/CHEBI_29021",
"http://purl.obolibrary.org/obo/CHEBI_15377"
]
}
}
},
{
"properties": {
"solvent": {
"enum": [
"http://purl.obolibrary.org/obo/CHEBI_46787"
]
},
"Other_solvent": {
"type": "string",
"title": "Name of other solvent"
}
},
"required": [
"Other_solvent"
]
}
]
}
}
}
},
"extracted_material": {
"title": "Extracted material",
"description": "Material used for extraction",
"type": "string",
"oneOf": [
{
"title": "Cells",
"enum": [
"cells"
]
},
{
"title": "Supernatant",
"enum": [
"supernatant"
]
},
{
"title": "Cells & supernatant",
"enum": [
"cells_supernatant"
]
},
{
"title": "Complex mixture (metagenome)",
"enum": [
"complex"
]
}
]
},
"resins": {
"type": "string",
"title": "Resins",
"description": "Did you use resins in your extraction? If so, add the name of the resin here (e.g. XAD-2 or XAD-4). Otherwise, leave this section blank."
},
"other_extraction_parameters": {
"type": "string",
"title": "Other extraction details",
"description": "Please describe any other relevant extraction methods, e.g. partitioned against water, fractionated with 20% acetonitrile, sequential extractions, used resins or storage manner (dried, liquid)."
},
"extraction_method": {
"type": "string",
"title": "Extraction Method Label",
"description": "Please assign an Extraction Method Label for this set of extraction details. If more than one extraction method was used, please create a new Extraction Method Label for each method by clicking on the plus.",
"minLength": 1
}
},
"required": [
"extraction_method"
]
}
},
"instrumentation_methods": {
"type": "array",
"title": "Instrumentation Methods",
"description": "Please provide basic information on the type of LCMS instrumentation and protocols used in this experiment. More detailed information can go in the 'Other' box. Including both metabolomics and proteomics (if proteomics data is included) instruments",
"items": {
"type": "object",
"properties": {
"instrumentation": {
"type": "object",
"title": "Instrumentation",
"properties": {
"instrument": {
"type": "string",
"title": "Instrument type",
"description": "Please select the type of LCMS instrument used. If your instrument type is not listed here, please select Other and specify.",
"anyOf": [
{
"type": "string",
"title": "Quadrupole",
"enum": [
"http://purl.obolibrary.org/obo/MS_1000081"
]
},
{
"type": "string",
"title": "Time-of-flight (TOF)",
"enum": [
"http://purl.obolibrary.org/obo/MS_1000084"
]
},
{
"type": "string",
"title": "Ion trap (IT)",
"enum": [
"http://purl.obolibrary.org/obo/MS_1000264"
]
},
{
"type": "string",
"title": "Quadrupol-IT",
"enum": [
"http://purl.obolibrary.org/obo/MS_1000082"
]
},
{
"type": "string",
"title": "Orbitrap (Q-Exactive, LTQ-Orbitrap, etc.)",
"enum": [
"http://purl.obolibrary.org/obo/MS_1000484"
]
},
{
"type": "string",
"title": "Fourier Transform Ion Cyclotron Resonance (FTICR)",
"enum": [
"http://purl.obolibrary.org/obo/MS_1000079"
]
},
{
"type": "string",
"title": "Magnetic Sector",
"enum": [
"http://purl.obolibrary.org/obo/MS_1000080"
]
},
{
"type": "string",
"title": "Electrostatic Energy Analyzer",
"enum": [
"http://purl.obolibrary.org/obo/MS_1000254"
]
},
{
"type": "string",
"title": "Stored Waveform Inverse Fourier Transform",
"enum": [
"http://purl.obolibrary.org/obo/MS_1000284"
]
},
{
"type": "string",
"title": "Cyclotron",
"enum": [
"http://purl.obolibrary.org/obo/MS_1000288"
]
},
{
"type": "string",
"title": "Other Mass Spectrometer",
"enum": [
"http://purl.obolibrary.org/obo/MS_1000443"
]
}
]
}
},
"dependencies": {
"instrument": {
"oneOf": [
{
"properties": {
"instrument": {
"enum": [
"http://purl.obolibrary.org/obo/MS_1000081",
"http://purl.obolibrary.org/obo/MS_1000084",
"http://purl.obolibrary.org/obo/MS_1000264",
"http://purl.obolibrary.org/obo/MS_1000082",
"http://purl.obolibrary.org/obo/MS_1000484",
"http://purl.obolibrary.org/obo/MS_1000079",
"http://purl.obolibrary.org/obo/MS_1000080",
"http://purl.obolibrary.org/obo/MS_1000254",
"http://purl.obolibrary.org/obo/MS_1000284",
"http://purl.obolibrary.org/obo/MS_1000288"
]
}
}
},
{
"properties": {
"instrument": {
"enum": [
"http://purl.obolibrary.org/obo/MS_1000443"
]
},
"other_instrument": {
"type": "string",
"title": "Name of other instrument type"
}
}
}
]
}
}
},
"column": {
"type": "string",
"title": "Column phase",
"description": "Please select column phase. You can add additional column details in the Other Instrumentation Information section below.",
"enum": [
"Reverse Phase",
"Normal Phase",
"Hydrophilic interaction (HILIC)",
"Strong cation exchange (SCX)"
],
"default": "Reverse Phase"
},
"mode": {
"type": "string",
"title": "Ionization mode",
"description": "Please select ionization mode.",
"anyOf": [
{
"type": "string",
"title": "Positive",
"enum": [
"http://purl.obolibrary.org/obo/MS_1000130"
]
},
{
"type": "string",
"title": "Negative",
"enum": [
"http://purl.obolibrary.org/obo/MS_1000129"
]
},
{
"type": "string",
"title": "Both",
"enum": [
"http://purl.obolibrary.org/obo/CHMO_0002262"
]
}
],
"default": [
"http://purl.obolibrary.org/obo/MS_1000129"
]
},
"ionization": {
"type": "object",
"title": "Ionization type",
"properties": {
"ionization_type": {
"type": "string",
"title": "Ionization type",
"description": "Please select the type of ionization used. If your ionization type is not listed here, please select Other and specify.",
"anyOf": [
{
"type": "string",
"title": "Electrospray Ionization (ESI)",
"enum": [
"http://purl.obolibrary.org/obo/MS_1000073"
]
},
{
"type": "string",
"title": "Matrix-assisted laser desorption ionization (MALDI)",
"enum": [
"http://purl.obolibrary.org/obo/MS_1000075"
]
},
{
"type": "string",
"title": "Atmospheric pressure chemical ionization (APCI)",
"enum": [
"http://purl.obolibrary.org/obo/MS_1000070"
]
},
{
"type": "string",
"title": "Other ionization type",
"enum": [
"http://purl.obolibrary.org/obo/MS_1000008"
]
}
]
}
},
"dependencies": {
"ionization_type": {
"oneOf": [
{
"properties": {
"ionization_type": {
"enum": [
"http://purl.obolibrary.org/obo/MS_1000073",
"http://purl.obolibrary.org/obo/MS_1000075",
"http://purl.obolibrary.org/obo/MS_1000070"
]
}
}
},
{
"properties": {
"ionization_type": {
"enum": [
"http://purl.obolibrary.org/obo/MS_1000008"
]
},
"other_ionization_type": {
"type": "string",
"title": "Name of other ionization type"
}
}
}
]
}
}
},
"range": {
"type": "string",
"title": "Mass range",
"description": "Please enter the mass range collected in Da. For example `100-800` for a range from 100 Da to 800 Da"
},
"collision_energy": {
"type": "string",
"title": "Collision energy",
"description": "Please enter the collision energy. Do not forget the unit like KeV or NCE"
},
"buffering": {
"type": "string",
"title": "Mobile phase conditions",
"description": "Did you add anything to your mobile phase, e.g. 0.1% formic acid."
},
"other_instrumentation": {
"type": "string",
"title": "Other instrumentation information",
"description": "Please enter any other relevant instrument or method details, such as gradient used, more column details, or any other relevant information."
},
"instrumentation_method": {
"type": "string",
"title": "Instrumentation method label",
"description": "Please assign an Instrumentation Method Label for this set of instrumentation details. If more than one LCMS instrumentation method was used, please create a new Instrumentation Method Label for each condition by clicking on the plus.",
"minLength": 1
}
},
"required": [
"instrumentation_method"
]
}
}
},
"additionalProperties": false
},
"proteomes": {
"type": "array",
"title": "5. Proteomics information",
"description": "Please add all proteomes for which paired data is available as separate entries. Create an entry for each different condition in your sample set",
"items": {
"type": "object",
"required": [
"proteome_ID",
"raw_data",
"method",
"identification",
"experimental_details",
"more_info",
"proteome_label"
],
"additionalProperties": false,
"properties": {
"proteome_ID": {
"title": "Full proteome or enriched",
"description": "If proteomics experiment includes any enrichment processes in favour of target proteins, please select `Enriched` and provide target(s).",
"type": "object",
"required": [
"proteome_type"
],
"properties": {
"proteome_type": {
"type": "string",
"title": "Type",
"enum": [
"Full proteome", "Enriched"
],
"default": "Full proteome"
}
},
"dependencies": {
"proteome_type": {
"oneOf": [{
"properties": {
"proteome_type": {
"enum": ["Full proteome"]
}
}
}, {
"properties": {
"proteome_type": {
"enum": ["Enriched"]
},
"targets": {
"type": "array",
"title": "Targets",
"minItems": 1,
"items": {
"type": "object",
"required": ["target"],
"properties": {
"target": {
"title": "Target",
"type": "string",
"oneOf": [
{
"title": "PKS machinery",
"enum": [
"pks"
]
},
{
"title": "NRPS machinery",
"enum": [
"nrps"
]
},
{
"title": "Other",
"enum": [
"other"
]
}
]
}
},
"dependencies": {
"target": {
"oneOf": [{
"properties": {
"target": {
"enum": [
"pks",
"nrps"
]
}
}
}, {
"properties": {
"target": {
"enum": [
"other"
]
},
"other_target": {
"type": "string",
"title": "Name of other target"
}
}
}]
}
}
}
}
}
}]
}
}
},
"raw_data": {
"type": "object",
"title": "Raw data link",
"required": ["database", "proteome_data_link"],
"additionalProperties": false,
"properties": {
"database": {
"type": "object",
"required": ["database_name"],
"properties": {
"database_name": {
"title": "Proteome database",
"type": "string",
"enum": [
"ProteomeXchange",
"PRIDE",
"iProX",
"JPOST",
"PeptideAtlas",
"MassIVE",
"Other"
],
"default": "ProteomeXchange"
}
},
"dependencies": {
"database_name": {
"oneOf": [{
"properties": {
"database_name": {
"enum": ["Other"]
},
"other_database_name": {
"type": "string",
"title": "Name of other database"
}
}
}, {
"properties": {
"database_name": {
"enum": [
"ProteomeXchange",
"PRIDE",
"iProX",
"JPOST",
"PeptideAtlas",
"MassIVE"
]
}
}
}]
}
}
},
"proteome_data_link": {
"type": "string",
"title": "Location of raw proteomics data",
"description": "Please provide link to public data depository where the proteomics data and metadata can be found. If the experiment is quantitative, please provide link to the expression table.",
"format": "uri"
}
}
},
"method": {
"type": "object",
"title": "Basic method",
"description": "Please provide basic criteria of proteomics experiment.",
"required": ["analysis_mode", "peptide_labelling"],
"properties": {
"analysis_mode": {
"type": "string",
"title": "Analysis mode",
"enum": [
"Data-dependent acquisition (DDA)",
"Data-independent acquisition (DIA)"
]
},
"peptide_labelling": {
"type": "string",
"title": "Peptide labelling",
"enum": [
"iTRAQ",
"ICPL",
"Dimethyl",
"Custom",
"None"
],
"default": "None"
}
},
"dependencies": {
"analysis_mode": {
"oneOf": [{
"properties": {
"analysis_mode": {
"enum": ["Data-dependent acquisition (DDA)"]
},
"genome_database": {
"title": "Genome database",
"description": "The genome from which the predicted proteome database was generated, used to guide the parent ion selection. If no genome was used then keep field unselected.",
"type":"string"
},
"transcriptomics_database": {
"title": "Transcriptomics database",
"description": "The transcriptome from which the predicted proteome database was generated, used to guide the parent ion selection. Please input a NCBI GEO database accession. For example GSE171784. If no transcriptome was used then keep field empty.",
"type":"string"
}
}
}, {
"properties": {
"analysis_mode": {
"enum": ["Data-independent acquisition (DIA)"]
}
}
}]
},
"peptide_labelling": {
"oneOf": [{
"properties": {
"peptide_labelling": {
"enum": ["Custom"]
},
"custom_peptide_labelling": {
"type": "string",
"title": "Description of custom labelling"
}
}
}, {
"properties": {
"peptide_labelling": {
"enum": ["Dimethyl"]
},
"peptide_labelling_dimethyl_specification": {
"type": "string",
"title": "Dimethyl specification"
}
}
}, {
"properties": {
"peptide_labelling": {
"enum": [
"iTRAQ",
"ICPL",
"None"]
}
}
}]
}
}
},
"identification": {
"title": "Identification",
"type": "object",
"properties": {
"genome_database": {
"title": "Genome database",
"description": "The genome from which the predicted proteome database was generated, used in your protein identification process. If no genome was used then keep field unselected.",
"type":"string"
},
"transcriptomics_database": {
"title": "Transcriptomics database",
"description": "The transcriptome from which the predicted proteome database was generated, used in your protein identification process. Please input a NCBI GEO database accession. For example GSE171784. If no transcriptome was used then keep field empty.",
"type":"string"
}
},
"additionalProperties": false
},
"experimental_details": {
"type": "object",
"title": "Experimental details",
"description": "A proteome can have different experimental details than a metabolomics data file. If different add experimental details in section 4 and pick from list here.",
"properties": {
"sample_preparation_label": {
"type": "string",
"title": "Sample Growth Conditions",
"description": "Please select the Sample Growth Conditions Label for this proteome."
},
"instrumentation_method_label": {
"type": "string",
"title": "Instrumentation Method",
"description": "Please select the Instrumentation Method Label for this proteome."
}
},
"additionalProperties": false
},
"more_info": {
"type": "object",
"title": "Info",
"properties": {
"publications": {
"type": "string",
"pattern": "[0-9]{1,}",
"title": "Key publications",
"description": "Publications describing the proteomics experiment. Please input PubMed IDs (PMIDs, not PMCIDs!), separated by commas: e.g., '12000953,8843436'. Only enter numeric characters and commas. If a PMID is not available, a DOI can be entered instead (without the designation 'DOI' itself, e.g. '10.1039/c4sc01927j')"
},
"notes": {
"type": "string",
"title": "Additional notes",
"description": "If you have used a method that is in some aspects novel to the community, please specify here."
}
},
"additionalProperties": false
},
"proteome_label": {
"type": "string",
"title": "Proteome label",
"description": "Please assign a unique proteome Label for this proteome to help you recall it during the linking step.",
"minLength": 1
}
}
}
},
"genome_metabolome_links": {
"type": "array",
"title": "6. Genome - Proteome - Metabolome Links",
"description": "Create a linked pair by selecting the Genome Label and optional Proteome label as provided earlier. Subsequently links to the metabolomics data file belonging to that genome/proteome with appropriate experimental methods.",
"items": {
"type": "object",
"required": [
"genome_label",
"metabolomics_file",
"sample_preparation_label",
"extraction_method_label",
"instrumentation_method_label"
],
"properties": {
"genome_label": {
"type": "string",
"title": "Genome/Metagenome",
"description": "Please select the Genome Label to be linked to a metabolomics data file."
},
"proteome_label": {
"type": "string",
"title": "Proteome",
"description": "Please select the Proteome Label to be linked to a metabolomics data file."
},
"metabolomics_file": {
"type": "string",
"title": "Location of metabolomics data file",
"description": "Please provide a direct link to the metabolomics data file location, e.g. ftp://massive.ucsd.edu/MSV000078839/spectrum/R5/CNB091_R5_M.mzXML found in the FTP download of a MassIVE dataset or https://www.ebi.ac.uk/metabolights/MTBLS307/files/Urine_44_fullscan1_pos.mzXML found in the Files section of a MetaboLights study. Warning, there cannot be spaces in the URI.",
"format": "uri"
},
"sample_preparation_label": {
"type": "string",
"title": "Sample Growth Conditions",
"description": "Please select the Sample Growth Conditions Label for this linked metabolomics dataset."
},
"extraction_method_label": {
"type": "string",
"title": "Extraction Method",
"description": "Please select the Extraction Method Label for this linked metabolomics dataset."
},
"instrumentation_method_label": {
"type": "string",
"title": "Instrumentation Method",
"description": "Please select the Instrumentation Method Label for this linked metabolomics dataset."
}
},
"additionalProperties": false
}
},
"BGC_MS2_links": {
"type": "array",
"title": "7. Biosynthetic Gene Cluster - MS/MS Links",
"description": "If you already know of a biosynthetic gene cluster or biosynthetic gene cluster family that can be linked to a molecule or molecular family, please provide details in this section. Biosynthetic gene clusters can be found in MIBiG.",
"items": {
"type": "object",
"required": [
"BGC_ID",
"verification"
],
"properties": {
"known_link": {
"type": "string",
"title": "Known linked gene cluster and molecule",
"description": "Please provide a brief description of the known linked molecule(s) and gene cluster(s), including the name of the molecule(s)."
},
"verification": {
"type": "array",
"title": "Link verification",
"description": "Please indicate if verification of the link between BGC and MS2 is experimentally validated or bioinformatically inferred.",
"items": {
"type": "string",
"enum": [
"Experimentally validated with knockouts, heterologous expression, or other gene cluster manipulation",
"Bioinformatically inferred through comparative analysis with another experimentally defined gene cluster",
"Experimentally validated with NMR and/or detailed MS/MS analysis",
"Evidence as indicated in MIBiG"
]
},
"uniqueItems": true
},
"omics_based_evidence": {
"type": "object",
"title": "Verified with additional experimental omics-based evidence",
"required": ["omics_based_evidence_type"],
"properties": {
"omics_based_evidence_type": {
"type": "string",
"title": "Type",
"enum": ["Quantitative proteomics experiment", "Nonquantitative proteomics experiment", "Not available"],
"default": "Not available",
"description": "Select which omics-based experiment type has given evidence of link between BGC cluster and molecule."
}
},
"dependencies": {
"omics_based_evidence_type": {
"oneOf": [{
"properties": {
"omics_based_evidence_type": {
"enum": ["Not available"]
}
}
},{
"properties": {
"omics_based_evidence_type": {
"enum": ["Nonquantitative proteomics experiment"]
},
"nonquantitative_proteomics_experiment": {
"type": "object",
"title": "Nonquantitative proteomics experiment",
"required": ["evidences"],
"additionalProperties": false,
"properties": {
"evidences": {
"type": "string",
"title": "Nonquantitative evidences",
"description": "Describe evidences."
}
}
}
}
},{
"properties": {
"omics_based_evidence_type": {
"enum": ["Quantitative proteomics experiment"]
},
"quantitative_proteomics_experiment": {
"type": "object",
"title": "Quantitative proteomics experiment",
"required": ["evidences", "comparison_groups"],
"additionalProperties": false,
"properties": {
"evidences": {
"type": "string",
"title": "Quantitative evidences",
"description": "Describe quantitative evidences between control and experimental."
},
"comparison_groups": {
"type": "array",
"title": "Comparison groups",
"minItems": 1,
"items": {
"type": "object",
"required": [
"control_group",
"experimental_group",
"metabolite_concentration",
"protein_id",
"protein_fold"
],
"additionalProperties": false,
"properties": {
"control_group": {
"type": "string",
"title":" Control group",
"description": "Please select the proteome label for the control group."
},
"experimental_group": {
"type": "string",
"title": "Experimental group",
"description": "Please select the proteome label for the experimental group."
},
"metabolite_concentration": {
"type": "string",
"title": "Change in metabolite concentration",
"description": "Change in metabolite concentration between control and experimental group",
"enum": [
"increased",
"decreased"
]
},
"protein_id": {
"type": "object",
"title": "Protein",
"required": ["protein_database", "protein_identifier"],
"properties": {
"genome": {
"type": "string",
"title": "Source genome",
"description": "Select the genome label from which the protein was translated."
},
"protein_database": {
"type": "string",
"title": "Protein database",
"enum": ["uniprot", "refseq", "de novo"],
"default": "de novo",
"description": "Database in which protein identifier of protein can be found."
},
"protein_identifier": {
"type": "string",
"title": "Protein identifier",
"description": "Identifier of protein which changed between control and experiment. When public identifier (Uniprot or RefSeq) is available then please fill in the public identifier. When public identifier is not available then please fill in a custom identifier."
}
}
},
"protein_fold": {
"type": "object",
"title": "Protein fold",
"description": "Change seen in protein between control and experimental group",
"required": ["protein_fold_change"],
"properties": {
"protein_fold_change": {
"type": "number",
"title": "Log2 fold change",
"description": "Protein log2 transformed fold change: experiment group / control group."
},
"quantitation_type": {
"type": "string",
"enum": ["None", "Peak intensity", "Peak area"],
"title": "Quantitation type",
"default": "None",
"description": "What quantiation was used for the protein fold change"
}
},
"additionalProperties": false
}
}
}
}
}
}
}
}]
}
}
},
"SMILES": {
"type": "string",
"title": "Simplified molecular-input line-entry system (SMILES)",
"description": "Please provide the SMILES notation for the known molecule."
},
"IUPAC": {
"type": "string",
"title": "International union of pure and applied chemistry (IUPAC) name",
"description": "Please provide the IUPAC name for the known molecule,"
},
"BGC_ID": {
"type": "object",
"title": "MIBiG BGC accession",
"properties": {
"BGC": {
"type": "string",
"enum": [
"MIBiG number associated with this exact BGC",
"MIBiG number of a similar BGC from a closely related strain"
],
"default": "MIBiG number associated with this exact BGC"
}
},
"dependencies": {
"BGC": {
"oneOf": [
{
"properties": {
"BGC": {
"enum": [
"MIBiG number associated with this exact BGC"
]
},
"MIBiG_number": {
"type": "string",
"title": "MIBiG accession for exact BGC",
"description": "For example 'BGC0000259'.",
"pattern": "^BGC[0-9]{7}$"
}
},
"required": [
"BGC",
"MIBiG_number"
]
},
{
"properties": {
"BGC": {
"enum": [
"MIBiG number of a similar BGC from a closely related strain"
]
},
"similar_MIBiG_number": {
"type": "string",
"title": "MIBiG accession for similar BGC",
"description": "For example 'BGC0000259'.",
"pattern": "^BGC[0-9]{7}$"
},
"strain": {
"type": "string",
"title": "Strain accession number",
"description": "Please provide the strain accession number of the genome containing the similar BGC."
},
"coordinates": {
"type": "string",
"title": "BGC Coordinates",
"description": "Please provide the beginning and end coordinates of the similar BGC from the genome specified above."
}
},
"required": [
"BGC",
"similar_MIBiG_number"
]
}
]
}
}
},
"link": {
"type": "string",
"title": "What would you like to link?",
"enum": [
"GNPS molecular family",
"single molecule"
],
"default": "single molecule"
}
},
"dependencies": {
"link": {
"oneOf": [
{
"properties": {
"link": {
"enum": [
"GNPS molecular family"
]
},
"network_nodes_URL": {
"type": "string",
"title": "GNPS network nodes URL",
"description": "Please provide the URL from GNPS for the network nodes page: first click 'View Spectral Families (In Browser Network Visualizer)' and then click 'Network Nodes' and copy this URL, e.g. https://gnps.ucsd.edu/ProteoSAFe/result.jsp?view=cluster_info_sliced&componentindex=290&show=true&task=c36f90ba29fe44c18e96db802de0c6b9#%7B%7D"
}
},
"required": [
"link",
"network_nodes_URL"
]
},
{
"properties": {
"link": {
"enum": [
"single molecule"
]
},
"MS2_URL": {
"type": "string",
"title": "Mass spectrometry fragmentation file",
"description": "Please provide the URL to a mzML/mzXML/MGF/MSP file for the mass spectrum with the molecule to link. Warning, there cannot be spaces in the URI.",
"format": "uri"
},
"MS2_scan": {
"type": "string",
"title": "Mass spectrometry fragmentation scan number",
"description": "Please provide the MS2 scan number for the molecule to link."
}
},
"required": [
"link",
"MS2_URL",
"MS2_scan"
]
}
]
}
}
}
}
},
"additionalProperties": false
}