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schema.json
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{
"$schema": "http://json-schema.org/draft-07/schema#",
"$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. <a href=\"https://orcid.org/0000-0002-1825-0097\" target=\"_blank\" rel=\"noopener noreferrer\">https://orcid.org/0000-0002-1825-0097</a> .",
"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., <a target=\"_blank\" rel=\"noopener noreferrer\" href=\"https://gnps.ucsd.edu/ProteoSAFe/result.jsp?task=a507232a787243a5afd69a6c6fa1e508&view=advanced_view\">https://gnps.ucsd.edu/ProteoSAFe/result.jsp?task=a507232a787243a5afd69a6c6fa1e508&view=advanced_view</a>. Warning, there cannot be spaces in the URI.",
"format": "uri"
},
"molecular_network": {
"type": "string",
"pattern": "^[0-9a-z]{32}$",
"title": "Molecular Network Task ID",
"description": "If you have run a Molecular Network on GNPS, please provide the task ID of the Molecular Network job. It can be found in the URL of the Molecular Networking job, e.g., in <a target=\"_blank\" rel=\"noopener noreferrer\" href=\"https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=c36f90ba29fe44c18e96db802de0c6b9\">https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=c36f90ba29fe44c18e96db802de0c6b9</a> the task ID is c36f90ba29fe44c18e96db802de0c6b9."
}
}
},
{
"type": "object",
"title": "MetaboLights",
"required": [
"metabolights_study_id"
],
"properties": {
"metabolights_study_id": {
"type": "string",
"title": "MetaboLights study identifier",
"pattern": "^MTBLS[0-9]{1,}$",
"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., <a href=\"https://www.ncbi.nlm.nih.gov/nuccore/AL645882\" target=\"_blank\" rel=\"noopener noreferrer\">AL645882</a>, 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: <a target=\"_blank\" rel=\"noopener noreferrer\" href=\"https://www.ncbi.nlm.nih.gov/nuccore/NC_003888.3\">NC_003888.3</a>"
},
"JGI_Genome_ID": {
"type": "string",
"title": "JGI IMG genome ID",
"description": "For example: <a target=\"_blank\" rel=\"noopener noreferrer\" href=\"https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=641228474\">641228474</a>"
}
}
},
{
"properties": {
"genome_type": {
"enum": [
"metagenome"
]
},
"ENA_NCBI_accession": {
"type": "string",
"title": "ENA/NCBI accession number",
"description": "For example: <a target=\"_blank\" rel=\"noopener noreferrer\" href=\"https://www.ebi.ac.uk/ena/browser/view/GCA_900283375.1\">GCA_900283375</a>"
},
"MGnify_accession": {
"type": "string",
"title": "MGnify accession number",
"description": "For example: <a target=\"_blank\" rel=\"noopener noreferrer\" href=\"https://www.ebi.ac.uk/metagenomics/studies/MGYS00001053\">MGYS00001053</a>"
},
"JGI_ID": {
"type": "string",
"title": "JGI IMG (meta)genome ID",
"description": "For example: <a target=\"_blank\" rel=\"noopener noreferrer\" href=\"https://img.jgi.doe.gov/cgi-bin/m/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=3300005805\">3300005805</a>"
}
}
}
]
}
}
},
"BioSample_accession": {
"type": "string",
"title": "BioSample accession number",
"description": "If publicly available metadata is available at <a href=\"https://www.ncbi.nlm.nih.gov/biosample/\" target=\"_blank\" rel=\"noopener noreferrer\">BioSamples</a>, please provide the BioSample accession number, e.g. <a target=\"_blank\" rel=\"noopener noreferrer\" href=\"https://www.ncbi.nlm.nih.gov/biosample/?term=SAMEA3648350\">SAMEA3648350</a>, 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",