Metabolomics Hub Common Data Model Nodes - MHD Legacy Profile¶

Profile Schema: https://metabolomicshub.github.io/mhd-model/schemas/v0_1/common-data-model-v0.1.legacy-profile.json

Required Nodes & Relationships¶

Required MHD Nodes

Characteristic Definition, Metadata File, Study

Required MHD CV Terms

Characteristic Type, Characteristic Value, Data Provider

The following graph shows only required nodes and required relationships. Relationships that start with 'embedded - ' show required node property.

graph LR
  Characteristic_Definition[Characteristic Definition] ==>|embedded - characteristic_type_ref| Characteristic_Type[Characteristic Type];
  Study[Study] ==>|embedded - created_by_ref| Data_Provider[Data Provider];
  Characteristic_Definition[Characteristic Definition] ==>|has-type| Characteristic_Type[Characteristic Type];
  Characteristic_Definition[Characteristic Definition] ==>|used-in| Study[Study];
  Metadata_File[Metadata File] ==>|describes| Study[Study];
  Study[Study] ==>|provided-by| Data_Provider[Data Provider];
  Study[Study] ==>|has-characteristic-definition| Characteristic_Definition[Characteristic Definition];
  Study[Study] ==>|has-metadata-file| Metadata_File[Metadata File];
  Characteristic_Type[Characteristic Type] ==>|type-of| Characteristic_Definition[Characteristic Definition];
  Characteristic_Value[Characteristic Value] ==>|instance-of| Characteristic_Definition[Characteristic Definition];
  Data_Provider[Data Provider] ==>|provides| Study[Study];

Required Relationships

Source Node	Relationship	Target Node	Min	Max
Characteristic Definition	[embedded] - characteristic_type_ref	Characteristic Type	1	1
Characteristic Definition	has-type	Characteristic Type	1	1
Characteristic Definition	used-in	Study	1	N (unbounded)
Characteristic Type	type-of	Characteristic Definition	1	N (unbounded)
Characteristic Value	instance-of	Characteristic Definition	1	N (unbounded)
Data Provider	provides	Study	1	1
Metadata File	describes	Study	1	1
Study	[embedded] - created_by_ref	Data Provider	1	1
Study	has-characteristic-definition	Characteristic Definition	1	N (unbounded)
Study	has-metadata-file	Metadata File	1	N (unbounded)
Study	provided-by	Data Provider	1	1

Required Node Properties

Source Node	Property Name
characteristic-definition	characteristic_type_ref
characteristic-definition	name
characteristic-type	name
data-provider	value
metadata-file	name
metadata-file	url_list
study	created_by_ref
study	dataset_url_list
study	description
study	mhd_identifier
study	public_release_date
study	repository_identifier
study	submission_date
study	title

Model Graph¶

The following graph shows all (required and optional) nodes and relationships.

graph LR
  Assay[Assay] ==>|described-as| Descriptor[Descriptor];
  Assay[Assay] ==>|part-of| Study[Study];
  Assay[Assay] ==>|follows| Protocol[Protocol];
  Characteristic_Definition[Characteristic Definition] ==>|has-instance| Characteristic_Value[Characteristic Value];
  Characteristic_Definition[Characteristic Definition] ==>|has-type| Characteristic_Type[Characteristic Type];
  Characteristic_Definition[Characteristic Definition] ==>|used-in| Study[Study];
  Derived_Data_File[Derived Data File] ==>|referenced-in| Metadata_File[Metadata File];
  Derived_Data_File[Derived Data File] ==>|created-in| Study[Study];
  Derived_Data_File[Derived Data File] ==>|described-as| Descriptor[Descriptor];
  Factor_Definition[Factor Definition] ==>|has-type| Factor_Type[Factor Type];
  Factor_Definition[Factor Definition] ==>|has-instance| Factor_Value[Factor Value];
  Factor_Definition[Factor Definition] ==>|used-in| Study[Study];
  Metabolite[Metabolite] ==>|identified-as| Metabolite_Identifier[Metabolite Identifier];
  Metabolite[Metabolite] ==>|described-as| Descriptor[Descriptor];
  Metabolite[Metabolite] ==>|reported-in| Study[Study];
  Metadata_File[Metadata File] ==>|described-as| Descriptor[Descriptor];
  Metadata_File[Metadata File] ==>|referenced-in| Metadata_File[Metadata File];
  Metadata_File[Metadata File] ==>|describes| Study[Study];
  Metadata_File[Metadata File] ==>|references| Derived_Data_File[Derived Data File];
  Metadata_File[Metadata File] ==>|references| Raw_Data_File[Raw Data File];
  Metadata_File[Metadata File] ==>|references| Result_File[Result File];
  Metadata_File[Metadata File] ==>|references| Supplementary_File[Supplementary File];
  Organization[Organization] ==>|funds| Project[Project];
  Organization[Organization] ==>|funds| Study[Study];
  Organization[Organization] ==>|manages| Project[Project];
  Organization[Organization] ==>|coordinates| Project[Project];
  Organization[Organization] ==>|affiliates| Person[Person];
  Organization[Organization] ==>|described-as| Descriptor[Descriptor];
  Parameter_Definition[Parameter Definition] ==>|has-instance| Parameter_Value[Parameter Value];
  Parameter_Definition[Parameter Definition] ==>|has-type| Parameter_Type[Parameter Type];
  Parameter_Definition[Parameter Definition] ==>|defined-in| Protocol[Protocol];
  Person[Person] ==>|described-as| Descriptor[Descriptor];
  Person[Person] ==>|affiliated-with| Organization[Organization];
  Person[Person] ==>|contributes| Project[Project];
  Person[Person] ==>|contributes| Study[Study];
  Person[Person] ==>|principal-investigator-of| Study[Study];
  Person[Person] ==>|submits| Study[Study];
  Person[Person] ==>|author-of| Publication[Publication];
  Project[Project] ==>|described-as| Descriptor[Descriptor];
  Project[Project] ==>|funded-by| Organization[Organization];
  Project[Project] ==>|managed-by| Organization[Organization];
  Project[Project] ==>|coordinated-by| Organization[Organization];
  Project[Project] ==>|has-contributor| Person[Person];
  Project[Project] ==>|has-publication| Publication[Publication];
  Project[Project] ==>|has-study| Study[Study];
  Protocol[Protocol] ==>|described-as| Descriptor[Descriptor];
  Protocol[Protocol] ==>|used-in| Assay[Assay];
  Protocol[Protocol] ==>|has-parameter-definition| Parameter_Definition[Parameter Definition];
  Protocol[Protocol] ==>|used-in| Study[Study];
  Protocol[Protocol] ==>|has-type| Protocol_Type[Protocol Type];
  Publication[Publication] ==>|described-as| Descriptor[Descriptor];
  Publication[Publication] ==>|describes| Project[Project];
  Publication[Publication] ==>|describes| Study[Study];
  Publication[Publication] ==>|has-author| Person[Person];
  Raw_Data_File[Raw Data File] ==>|described-as| Descriptor[Descriptor];
  Raw_Data_File[Raw Data File] ==>|created-in| Study[Study];
  Raw_Data_File[Raw Data File] ==>|referenced-in| Metadata_File[Metadata File];
  Result_File[Result File] ==>|described-as| Descriptor[Descriptor];
  Result_File[Result File] ==>|created-in| Study[Study];
  Result_File[Result File] ==>|referenced-in| Metadata_File[Metadata File];
  Sample[Sample] ==>|described-as| Descriptor[Descriptor];
  Sample[Sample] ==>|has-factor-value| Factor_Value[Factor Value];
  Sample[Sample] ==>|used-in| Study[Study];
  Sample[Sample] ==>|derived-from| Subject[Subject];
  Sample[Sample] ==>|derived-from| Specimen[Specimen];
  Sample[Sample] ==>|has-characteristic-value| Characteristic_Value[Characteristic Value];
  Sample_Run[Sample Run] ==>|described-as| Descriptor[Descriptor];
  Sample_Run_Configuration[Sample Run Configuration] ==>|described-as| Descriptor[Descriptor];
  Specimen[Specimen] ==>|described-as| Descriptor[Descriptor];
  Specimen[Specimen] ==>|has-characteristic-value| Characteristic_Value[Characteristic Value];
  Specimen[Specimen] ==>|source-of| Sample[Sample];
  Specimen[Specimen] ==>|derived-from| Subject[Subject];
  Study[Study] ==>|provided-by| Data_Provider[Data Provider];
  Study[Study] ==>|has-assay| Assay[Assay];
  Study[Study] ==>|funded-by| Organization[Organization];
  Study[Study] ==>|has-characteristic-definition| Characteristic_Definition[Characteristic Definition];
  Study[Study] ==>|has-derived-data-file| Derived_Data_File[Derived Data File];
  Study[Study] ==>|described-as| Descriptor[Descriptor];
  Study[Study] ==>|has-factor-definition| Factor_Definition[Factor Definition];
  Study[Study] ==>|has-repository-keyword| Descriptor[Descriptor];
  Study[Study] ==>|has-submitter-keyword| Descriptor[Descriptor];
  Study[Study] ==>|reports| Metabolite[Metabolite];
  Study[Study] ==>|has-metadata-file| Metadata_File[Metadata File];
  Study[Study] ==>|has-contributor| Person[Person];
  Study[Study] ==>|has-principal-investigator| Person[Person];
  Study[Study] ==>|submitted-by| Person[Person];
  Study[Study] ==>|part-of| Project[Project];
  Study[Study] ==>|has-protocol| Protocol[Protocol];
  Study[Study] ==>|has-publication| Publication[Publication];
  Study[Study] ==>|has-raw-data-file| Raw_Data_File[Raw Data File];
  Study[Study] ==>|has-result-file| Result_File[Result File];
  Study[Study] ==>|has-sample| Sample[Sample];
  Study[Study] ==>|has-supplementary-file| Supplementary_File[Supplementary File];
  Subject[Subject] ==>|described-as| Descriptor[Descriptor];
  Subject[Subject] ==>|has-characteristic-value| Characteristic_Value[Characteristic Value];
  Subject[Subject] ==>|source-of| Sample[Sample];
  Subject[Subject] ==>|has-factor-value| Factor_Value[Factor Value];
  Subject[Subject] ==>|source-of| Specimen[Specimen];
  Supplementary_File[Supplementary File] ==>|described-as| Descriptor[Descriptor];
  Supplementary_File[Supplementary File] ==>|created-in| Study[Study];
  Supplementary_File[Supplementary File] ==>|referenced-in| Metadata_File[Metadata File];
  Characteristic_Type[Characteristic Type] ==>|type-of| Characteristic_Definition[Characteristic Definition];
  Characteristic_Value[Characteristic Value] ==>|instance-of| Characteristic_Definition[Characteristic Definition];
  Characteristic_Value[Characteristic Value] ==>|value-of| Subject[Subject];
  Characteristic_Value[Characteristic Value] ==>|value-of| Specimen[Specimen];
  Characteristic_Value[Characteristic Value] ==>|value-of| Sample[Sample];
  Data_Provider[Data Provider] ==>|provides| Study[Study];
  Descriptor[Descriptor] ==>|describes| Assay[Assay];
  Descriptor[Descriptor] ==>|describes| Study[Study];
  Descriptor[Descriptor] ==>|describes| Metadata_File[Metadata File];
  Descriptor[Descriptor] ==>|describes| Raw_Data_File[Raw Data File];
  Descriptor[Descriptor] ==>|describes| Derived_Data_File[Derived Data File];
  Descriptor[Descriptor] ==>|describes| Supplementary_File[Supplementary File];
  Descriptor[Descriptor] ==>|describes| Result_File[Result File];
  Descriptor[Descriptor] ==>|describes| Metabolite[Metabolite];
  Descriptor[Descriptor] ==>|describes| Organization[Organization];
  Descriptor[Descriptor] ==>|describes| Person[Person];
  Descriptor[Descriptor] ==>|describes| Project[Project];
  Descriptor[Descriptor] ==>|describes| Publication[Publication];
  Descriptor[Descriptor] ==>|describes| Protocol[Protocol];
  Descriptor[Descriptor] ==>|describes| Sample[Sample];
  Descriptor[Descriptor] ==>|describes| Subject[Subject];
  Descriptor[Descriptor] ==>|describes| Sample_Run[Sample Run];
  Descriptor[Descriptor] ==>|describes| Sample_Run_Configuration[Sample Run Configuration];
  Descriptor[Descriptor] ==>|describes| Metabolite[Metabolite];
  Descriptor[Descriptor] ==>|keyword-of| Study[Study];
  Descriptor[Descriptor] ==>|keyword-of| Study[Study];
  Descriptor[Descriptor] ==>|keyword-of| Specimen[Specimen];
  Factor_Type[Factor Type] ==>|type-of| Factor_Definition[Factor Definition];
  Factor_Value[Factor Value] ==>|instance-of| Factor_Definition[Factor Definition];
  Factor_Value[Factor Value] ==>|value-of| Sample[Sample];
  Factor_Value[Factor Value] ==>|value-of| Specimen[Specimen];
  Factor_Value[Factor Value] ==>|value-of| Subject[Subject];
  Metabolite_Identifier[Metabolite Identifier] ==>|reported-identifier-of| Metabolite[Metabolite];
  Parameter_Type[Parameter Type] ==>|type-of| Parameter_Definition[Parameter Definition];
  Parameter_Value[Parameter Value] ==>|instance-of| Parameter_Definition[Parameter Definition];
  Protocol_Type[Protocol Type] ==>|type-of| Protocol[Protocol];

MHD Domain Objects¶

Assay¶

Assay node is optional in the MHD Legacy Profile. Minimum: 0, Maximum: N (unbounded)

Properties

Property Name	Necessity	Type	Description
id	optional	`MhdObjectId`	The id property uniquely identifies the object
type	optional	`MhdObjectType`	Its value MUST be `assay`
created_by_ref	optional	`CvTermValueObjectId`	The id property of the data-provider who created the object Target CV term type: `data-provider` Validation Rule: `Allow any valid CV Term Exceptions: Allowed Other Sources: wikidata, ILX`
tags	optional	`list[KeyValue]`	Key-value tags related to the object
descriptors	optional	`list[CvTerm]`	Descriptors of the object
external_references	optional	`list[KeyValue]`	External references related to the object
url_list	optional	`list[AnyUrl]`	URL list related to the object
repository_identifier	required	`str`	An assay identifier that uniquely identifies the assay in repository Minimum length: `2` Validation Rule: `Min Length: 2, Required`
name	required	`str`	Name of the assay. It SHOULD be unique in a study Minimum length: `2` Validation Rule: `Min Length: 2, Required`
metadata_file_ref	optional	`MhdObjectId`	Target node type: `metadata-file` Validation Rule: `Target node type: metadata-file`
technology_type_ref	optional	`CvTermObjectId`	Target CV term type: `descriptor` Validation Rules: `Target node type: descriptor Allowed CV Terms: * [OBI, OBI:0000470, mass spectrometry assay], * [OBI, OBI:0000623, NMR spectroscopy assay]`
assay_type_ref	optional	`CvTermObjectId`	Target CV term type: `descriptor` Validation Rules: `Target node type: descriptor Allowed CV Terms: * [OBI, OBI:0003097, liquid chromatography mass spectrometry assay], * [OBI, OBI:0003110, gas chromatography mass spectrometry assay], * [OBI, OBI:0000470, mass spectrometry assay], * [OBI, OBI:0000623, NMR spectroscopy assay]`
measurement_type_ref	optional	`CvTermObjectId`	Target CV term type: `descriptor` Validation Rules: `Target node type: descriptor Allowed CV Terms: * [MSIO, MSIO:0000100, targeted metabolite profiling], * [MSIO, MSIO:0000101, untargeted metabolite profiling], * [OBI, OBI:0000366, metabolite profiling assay]`
omics_type_ref	optional	`CvTermObjectId`	Target CV term type: `descriptor` Validation Rules: `Target node type: descriptor Allowed CV Terms: * [EDAM, EDAM:3172, Metabolomics], * [EDAM, EDAM:0153, Lipidomics], * [EDAM, EDAM:3955, Fluxomics]`
protocol_refs	optional	`list[MhdObjectId]`	The id properties of protocols used in assay. A protocol is a defined and standardized procedure followed to collect, prepare, or analyze biological samples Target node type: `protocol` Validation Rule: `Target node type: protocol`
sample_run_refs	optional	`list[MhdObjectId]`	Target node type: `sample-run` Validation Rule: `Target node type: sample-run`

Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max	Description
assay	described-as	describes	descriptor	0	N	A link to a descriptor that describes the assay.
assay	follows	used-in	protocol	0	N	A link to a protocol conducted in assay.
assay	part-of	has-assay	study	1	1	A link to a study that the assay was conducted as part of it to generate data addressing study objectives

Embedded Relationships: descriptor, metadata-file, protocol, sample-run

Reverse Node Relationships

Source	Relationship	Reverse Name	Target	Max
descriptor	describes	described-as	assay	N
protocol	used-in	follows	assay	N
study	has-assay	part-of	assay	N

Characteristic Definition¶

Characteristic Definition node is required in the MHD Legacy Profile. Minimum: 1, Maximum: N (unbounded)

Properties

Property Name	Necessity	Type	Description
id	optional	`MhdObjectId`	The id property uniquely identifies the object
type	optional	`MhdObjectType`	The type property identifies type of the object Its value MUST be `characteristic-definition`
created_by_ref	optional	`CvTermValueObjectId`	The id property of the data-provider who created the object Target CV term type: `data-provider` Validation Rule: `Allow any valid CV Term Exceptions: Allowed Other Sources: wikidata, ILX`
tags	optional	`list[KeyValue]`	Key-value tags related to the object
descriptors	optional	`list[CvTerm]`	Descriptors of the object
external_references	optional	`list[KeyValue]`	External references related to the object
url_list	optional	`list[AnyUrl]`	URL list related to the object
name	required	`str`	Minimum length: `2` Validation Rule: `Min Length: 2, Required`
characteristic_type_ref	required	`CvTermObjectId`	Target CV term type: `characteristic-type` Validation Rules: `Target node type: characteristic-type Allowed CV Terms: * [NCIT, NCIT:C14250, organism], * [NCIT, NCIT:C103199, organism part], * [EFO, EFO:0000408, disease], * [EFO, EFO:0000324, cell type]`

Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max	Description
characteristic-definition	has-instance	instance-of	characteristic-value	0	N	Target Validation Rule: `----- Conditional - (Organism) [Source characteristic_type_ref.accession = NCIT:C14250] Allow any valid CV Term Exceptions: Allowed Placeholder Values: source='' accession='' Allowed Other Sources: wikidata, ILX` -----
characteristic-definition	has-type	type-of	characteristic-type	1	1
characteristic-definition	used-in	has-characteristic-definition	study	1	N

Embedded Relationships: characteristic-type

Reverse Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max	Description
characteristic-type	type-of	has-type	characteristic-definition	1	N
characteristic-value	instance-of	has-instance	characteristic-definition	1	N
study	has-characteristic-definition	used-in	characteristic-definition	1	N	Required min count in the dataset: 1.

Derived Data File¶

Derived Data File node is optional in the MHD Legacy Profile. Minimum: 0, Maximum: N (unbounded)

Properties

Property Name	Necessity	Type	Description
id	optional	`MhdObjectId`	The id property uniquely identifies the object
type	optional	`MhdObjectType`	The type property identifies type of the object Its value MUST be `derived-data-file`
created_by_ref	optional	`CvTermValueObjectId`	The id property of the data-provider who created the object Target CV term type: `data-provider` Validation Rule: `Allow any valid CV Term Exceptions: Allowed Other Sources: wikidata, ILX`
tags	optional	`list[KeyValue]`	Key-value tags related to the object
descriptors	optional	`list[CvTerm]`	Descriptors of the object
external_references	optional	`list[KeyValue]`	External references related to the object
url_list	required	`list[AnyUrl]`	URL list related to the object Minimum length: `1` Validation Rule: `Min Length: 1, Required`
name	required	`str`	Name of the file. File MUST be a file (not folder or link).It MAY be relative path (e.g., FILES/study.txt) or a file in a compressed file (e.g., FILES/study.zip#data/metadata.tsv) Minimum length: `2` Validation Rule: `Min Length: 2, Required`
size	optional	`int`	The size of the file in bytes, representing the total amount of data contained in the file
hash_sha256	optional	`str`	The SHA-256 cryptographic hash of the file content, used to verify file integrity and ensure that the file has not been altered
format_ref	optional	`CvTermObjectId`	The structure or encoding used to store the contents of the file, typically indicated by its extension (e.g., .txt, .csv, .mzML, .raw, etc.) Target CV term type: `descriptor` Validation Rule: `Allowed Parent CV Terms: * [EDAM, EDAM:1915, Format] Allow parent CV Term: No Allow only leaf CV Terms: No`
compression_format_ref	optional	`CvTermObjectId`	The structure or encoding used to compress the contents of the file, typically indicated by its extension (e.g., .zip, .tar, .gz, etc.) Target CV term type: `descriptor` Validation Rule: `Allowed Parent CV Terms: * [EDAM, EDAM:1915, Format] Allow parent CV Term: No Allow only leaf CV Terms: No`
extension	required	`str`	The extension of file. It MUST contain all extensions (e.g., .raw, .mzML, .d.zip, .raw.zip, etc.) Minimum length: `2` Validation Rule: `Min Length: 2, Required`

Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max	Description
derived-data-file	created-in	has-derived-data-file	study	1	1
derived-data-file	described-as	describes	descriptor	0	N	A link to a descriptor that describes the derived data file.
derived-data-file	referenced-in	references	metadata-file	0	N

Reverse Node Relationships

Source	Relationship	Reverse Name	Target	Max
descriptor	describes	described-as	derived-data-file	N
metadata-file	references	referenced-in	derived-data-file	N
study	has-derived-data-file	created-in	derived-data-file	N

Factor Definition¶

Factor Definition node is optional in the MHD Legacy Profile. Minimum: 0, Maximum: N (unbounded)

Properties

Property Name	Necessity	Type	Description
id	optional	`MhdObjectId`	The id property uniquely identifies the object
type	optional	`MhdObjectType`	The type property identifies type of the object Its value MUST be `factor-definition`
created_by_ref	optional	`CvTermValueObjectId`	The id property of the data-provider who created the object Target CV term type: `data-provider` Validation Rule: `Allow any valid CV Term Exceptions: Allowed Other Sources: wikidata, ILX`
tags	optional	`list[KeyValue]`	Key-value tags related to the object
descriptors	optional	`list[CvTerm]`	Descriptors of the object
external_references	optional	`list[KeyValue]`	External references related to the object
url_list	optional	`list[AnyUrl]`	URL list related to the object
name	required	`str`	Minimum length: `2` Validation Rule: `Min Length: 2, Required`
factor_type_ref	required	`CvTermObjectId`	Target node type: `factor-type` Validation Rule: `Target node type: factor-type`

Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max	Description
factor-definition	has-instance	instance-of	factor-value	0	N	Target Validation Rule: `----- Conditional - (Disease) [Source factor_type_ref.accession = EFO:0000408] Ontology Sources:DOID, HP, MP, SNOMED Exceptions: Allowed Other Sources: wikidata, ILX` -----
factor-definition	has-type	type-of	factor-type	1	1
factor-definition	used-in	has-factor-definition	study	1	N

Embedded Relationships: factor-type

Reverse Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max
factor-type	type-of	has-type	factor-definition	1	N
factor-value	instance-of	has-instance	factor-definition	1	N
study	has-factor-definition	used-in	factor-definition	0	N

Metabolite¶

Metabolite node is optional in the MHD Legacy Profile. Minimum: 0, Maximum: N (unbounded)

Properties

Property Name	Necessity	Type	Description
id	optional	`MhdObjectId`	The id property uniquely identifies the object
type	optional	`MhdObjectType`	The type property identifies type of the object Its value MUST be `metabolite`
created_by_ref	optional	`CvTermValueObjectId`	The id property of the data-provider who created the object Target CV term type: `data-provider` Validation Rule: `Allow any valid CV Term Exceptions: Allowed Other Sources: wikidata, ILX`
tags	optional	`list[KeyValue]`	Key-value tags related to the object
descriptors	optional	`list[CvTerm]`	Descriptors of the object
external_references	optional	`list[KeyValue]`	External references related to the object
url_list	optional	`list[AnyUrl]`	URL list related to the object
name	required	`str`	Minimum length: `2` Validation Rule: `Min Length: 2, Required`

Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max	Description
metabolite	described-as	describes	descriptor	0	N
metabolite	identified-as	reported-identifier-of	metabolite-identifier	0	N	Target Validation Rule: `----- Allowed Parent CV Terms: * [CHEMINF, CHEMINF:000464, chemical database identifier] Allow parent CV Term: No Allow only leaf CV Terms: No` -----
metabolite	reported-in	reports	study	1	N

Reverse Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max
descriptor	describes	described-as	metabolite	0	N
metabolite-identifier	reported-identifier-of	identified-as	metabolite	1	N
study	reports	reported-in	metabolite	0	N

Metadata File¶

Metadata File node is required in the MHD Legacy Profile. Minimum: 1, Maximum: N (unbounded)

Properties

Property Name	Necessity	Type	Description
id	optional	`MhdObjectId`	The id property uniquely identifies the object
type	optional	`MhdObjectType`	The type property identifies type of the object Its value MUST be `metadata-file`
created_by_ref	optional	`CvTermValueObjectId`	The id property of the data-provider who created the object Target CV term type: `data-provider` Validation Rule: `Allow any valid CV Term Exceptions: Allowed Other Sources: wikidata, ILX`
tags	optional	`list[KeyValue]`	Key-value tags related to the object
descriptors	optional	`list[CvTerm]`	Descriptors of the object
external_references	optional	`list[KeyValue]`	External references related to the object
url_list	required	`list[AnyUrl]`	URL list related to the object Minimum length: `1` Validation Rule: `Min Length: 1, Required`
name	required	`str`	Name of the file. File MUST be a file (not folder or link).It MAY be relative path (e.g., FILES/study.txt) or a file in a compressed file (e.g., FILES/study.zip#data/metadata.tsv) Minimum length: `2` Validation Rule: `Min Length: 2, Required`
size	optional	`int`	The size of the file in bytes, representing the total amount of data contained in the file
hash_sha256	optional	`str`	The SHA-256 cryptographic hash of the file content, used to verify file integrity and ensure that the file has not been altered
format_ref	optional	`CvTermObjectId`	The structure or encoding used to store the contents of the file, typically indicated by its extension (e.g., .txt, .csv, .mzML, .raw, etc.) Target CV term type: `descriptor` Validation Rule: `Allowed Parent CV Terms: * [EDAM, EDAM:1915, Format] Allow parent CV Term: No Allow only leaf CV Terms: No`
compression_format_ref	optional	`CvTermObjectId`	The structure or encoding used to compress the contents of the file, typically indicated by its extension (e.g., .zip, .tar, .gz, etc.) Target CV term type: `descriptor` Validation Rule: `Allowed Parent CV Terms: * [EDAM, EDAM:1915, Format] Allow parent CV Term: No Allow only leaf CV Terms: No`
extension	optional	`str`	The extension of file. It MUST contain all extensions (e.g., .raw, .mzML, .d.zip, .raw.zip, etc.)

Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max	Description
metadata-file	described-as	describes	descriptor	0	N
metadata-file	describes	has-metadata-file	study	1	1	Required min count in the dataset: 1.
metadata-file	referenced-in	references	metadata-file	0	N
metadata-file	references	referenced-in	derived-data-file	0	N
metadata-file	references	referenced-in	raw-data-file	0	N
metadata-file	references	referenced-in	result-file	0	N
metadata-file	references	referenced-in	supplementary-file	0	N

Reverse Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max
derived-data-file	referenced-in	references	metadata-file	0	N
descriptor	describes	described-as	metadata-file	0	N
metadata-file	referenced-in	references	metadata-file	0	N
raw-data-file	referenced-in	references	metadata-file	0	N
result-file	referenced-in	references	metadata-file	0	N
study	has-metadata-file	describes	metadata-file	1	N
supplementary-file	referenced-in	references	metadata-file	0	N

Organization¶

Organization node is optional in the MHD Legacy Profile. Minimum: 0, Maximum: N (unbounded)

Properties

Property Name	Necessity	Type	Description
id	optional	`MhdObjectId`	The id property uniquely identifies the object
type	optional	`MhdObjectType`	The type property identifies type of the object Its value MUST be `organization`
created_by_ref	optional	`CvTermValueObjectId`	The id property of the data-provider who created the object Target CV term type: `data-provider` Validation Rule: `Allow any valid CV Term Exceptions: Allowed Other Sources: wikidata, ILX`
tags	optional	`list[KeyValue]`	Key-value tags related to the object
descriptors	optional	`list[CvTerm]`	Descriptors of the object
external_references	optional	`list[KeyValue]`	External references related to the object
url_list	optional	`list[AnyUrl]`	URL list related to the object
repository_identifier	optional	`str`
name	required	`str`	Minimum length: `1` Validation Rule: `Min Length: 1, Required`
department	optional	`str`
unit	optional	`str`
address	optional	`str`

Node Relationships

Source	Relationship	Reverse Name	Target	Max
organization	affiliates	affiliated-with	person	N
organization	coordinates	coordinated-by	project	N
organization	described-as	describes	descriptor	N
organization	funds	funded-by	project	N
organization	funds	funded-by	study	N
organization	manages	managed-by	project	N

Reverse Node Relationships

Source	Relationship	Reverse Name	Target	Max
descriptor	describes	described-as	organization	N
person	affiliated-with	affiliates	organization	N
project	coordinated-by	coordinates	organization	N
project	funded-by	funds	organization	N
project	managed-by	manages	organization	N
study	funded-by	funds	organization	N

Parameter Definition¶

Parameter Definition node is optional in the MHD Legacy Profile. Minimum: 0, Maximum: N (unbounded)

Properties

Property Name	Necessity	Type	Description
id	optional	`MhdObjectId`	The id property uniquely identifies the object
type	optional	`MhdObjectType`	The type property identifies type of the object Its value MUST be `parameter-definition`
created_by_ref	optional	`CvTermValueObjectId`	The id property of the data-provider who created the object Target CV term type: `data-provider` Validation Rule: `Allow any valid CV Term Exceptions: Allowed Other Sources: wikidata, ILX`
tags	optional	`list[KeyValue]`	Key-value tags related to the object
descriptors	optional	`list[CvTerm]`	Descriptors of the object
external_references	optional	`list[KeyValue]`	External references related to the object
url_list	optional	`list[AnyUrl]`	URL list related to the object
name	required	`str`	Minimum length: `2` Validation Rule: `Min Length: 2, Required`
parameter_type_ref	required	`CvTermObjectId`	Target node type: `parameter-type` Validation Rule: `Target node type: parameter-type`

Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max	Description
parameter-definition	defined-in	has-parameter-definition	protocol	1	N
parameter-definition	has-instance	instance-of	parameter-value	0	N	Target Validation Rule: `----- Conditional - (Mass spectrometry instrument) [Source parameter_type_ref.accession = MSIO:0000171] Allow any valid CV Term Exceptions: Allowed Placeholder Values: source='' accession='' Allowed Other Sources: wikidata, ILX` -----
parameter-definition	has-type	type-of	parameter-type	1	1

Embedded Relationships: parameter-type

Reverse Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max
parameter-type	type-of	has-type	parameter-definition	1	N
parameter-value	instance-of	has-instance	parameter-definition	1	N
protocol	has-parameter-definition	defined-in	parameter-definition	0	N

Person¶

Person node is optional in the MHD Legacy Profile. Minimum: 0, Maximum: N (unbounded)

Properties

Property Name	Necessity	Type	Description
id	optional	`MhdObjectId`	The id property uniquely identifies the object
type	optional	`MhdObjectType`	The value of this property MUST be 'person' Its value MUST be `person`
created_by_ref	optional	`CvTermValueObjectId`	The id property of the data-provider who created the object Target CV term type: `data-provider` Validation Rule: `Allow any valid CV Term Exceptions: Allowed Other Sources: wikidata, ILX`
tags	optional	`list[KeyValue]`	Key-value tags related to the object
descriptors	optional	`list[CvTerm]`	Descriptors of the object
external_references	optional	`list[KeyValue]`	External references related to the object
url_list	optional	`list[AnyUrl]`	URL list related to the object
full_name	required	`str`	Full name of person Minimum length: `5` Validation Rule: `Min Length: 5, Required`
orcid	optional	`str`	ORCID identifier of person Example: `"1234-0001-8473-1713" "1234-0001-8473-171X"`
emails	optional	`list[EmailStr]`	Email addresses of person
phones	optional	`list[str]`	Phone number of person (with international country code) Example: `[ "+449340917271", "00449340917271" ]`
addresses	optional	`list[str]`

Node Relationships

Source	Relationship	Reverse Name	Target	Max
person	affiliated-with	affiliates	organization	N
person	author-of	has-author	publication	N
person	contributes	has-contributor	project	N
person	contributes	has-contributor	study	N
person	described-as	describes	descriptor	N
person	principal-investigator-of	has-principal-investigator	study	N
person	submits	submitted-by	study	N

Reverse Node Relationships

Source	Relationship	Reverse Name	Target	Max
descriptor	describes	described-as	person	N
organization	affiliates	affiliated-with	person	N
project	has-contributor	contributes	person	N
publication	has-author	author-of	person	N
study	has-contributor	contributes	person	N
study	has-principal-investigator	principal-investigator-of	person	N
study	submitted-by	submits	person	N

Project¶

Project node is optional in the MHD Legacy Profile. Minimum: 0, Maximum: N (unbounded)

Properties

Property Name	Necessity	Type	Description
id	optional	`MhdObjectId`	The id property uniquely identifies the object
type	optional	`MhdObjectType`	The type property identifies type of the object Its value MUST be `project`
created_by_ref	optional	`CvTermValueObjectId`	The id property of the data-provider who created the object Target CV term type: `data-provider` Validation Rule: `Allow any valid CV Term Exceptions: Allowed Other Sources: wikidata, ILX`
tags	optional	`list[KeyValue]`	Key-value tags related to the object
descriptors	optional	`list[CvTerm]`	Descriptors of the object
external_references	optional	`list[KeyValue]`	External references related to the object
url_list	optional	`list[AnyUrl]`	URL list related to the object
title	required	`str`	Minimum length: `25` Validation Rule: `Min Length: 25, Required`
description	optional	`str`
grant_identifiers	optional	`list[Annotated]`
doi	optional	`str`

Node Relationships

Source	Relationship	Reverse Name	Target	Max
project	coordinated-by	coordinates	organization	N
project	described-as	describes	descriptor	N
project	funded-by	funds	organization	N
project	has-contributor	contributes	person	N
project	has-publication	describes	publication	N
project	has-study	part-of	study	N
project	managed-by	manages	organization	N

Reverse Node Relationships

Source	Relationship	Reverse Name	Target	Max
descriptor	describes	described-as	project	N
organization	coordinates	coordinated-by	project	N
organization	funds	funded-by	project	N
organization	manages	managed-by	project	N
person	contributes	has-contributor	project	N
publication	describes	has-publication	project	N
study	part-of	has-study	project	N

Protocol¶

Protocol node is optional in the MHD Legacy Profile. Minimum: 0, Maximum: N (unbounded)

Properties

Property Name	Necessity	Type	Description
id	optional	`MhdObjectId`	The id property uniquely identifies the object
type	optional	`MhdObjectType`	The type property identifies type of the object Its value MUST be `protocol`
created_by_ref	optional	`CvTermValueObjectId`	The id property of the data-provider who created the object Target CV term type: `data-provider` Validation Rule: `Allow any valid CV Term Exceptions: Allowed Other Sources: wikidata, ILX`
tags	optional	`list[KeyValue]`	Key-value tags related to the object
descriptors	optional	`list[CvTerm]`	Descriptors of the object
external_references	optional	`list[KeyValue]`	External references related to the object
url_list	optional	`list[AnyUrl]`	URL list related to the object
name	required	`str`
protocol_type_ref	required	`CvTermObjectId`	Target CV term type: `protocol-type` Validation Rules: `Target node type: protocol-type Allowed CV Terms: * [EFO, EFO:0005518, sample collection protocol], * [MS, MS:1000831, sample preparation], * [CHMO, CHMO:0000470, mass spectrometry], * [OBI, OBI:0200000, data transform], * [MI, MI:2131, metabolite identification], * [CHMO, CHMO:0001000, chromatography], * [EFO, EFO:0003969, treatment protocol], * [CHMO, CHMO:0001024, capillary electrophoresis], * [MS, MS:1000058, flow injection analysis] Exceptions: Allowed Other Sources: wikidata, ILX`
description	required	`str`
parameter_definition_refs	optional	`list[MhdObjectId]`	Target node type: `parameter-definition`

Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max
protocol	described-as	describes	descriptor	0	N
protocol	has-parameter-definition	defined-in	parameter-definition	0	N
protocol	has-type	type-of	protocol-type	1	1
protocol	used-in	follows	assay	0	N
protocol	used-in	has-protocol	study	1	N

Embedded Relationships: protocol-type

Reverse Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max	Description
assay	follows	used-in	protocol	0	N	A link to a protocol conducted in assay.
descriptor	describes	described-as	protocol	0	N
parameter-definition	defined-in	has-parameter-definition	protocol	1	N
protocol-type	type-of	has-type	protocol	1	N
study	has-protocol	used-in	protocol	0	N

Publication¶

Publication node is optional in the MHD Legacy Profile. Minimum: 0, Maximum: N (unbounded)

Properties

Property Name	Necessity	Type	Description
id	optional	`MhdObjectId`	The id property uniquely identifies the object
type	optional	`MhdObjectType`	The type property identifies type of the object Its value MUST be `publication`
created_by_ref	optional	`CvTermValueObjectId`	The id property of the data-provider who created the object Target CV term type: `data-provider` Validation Rule: `Allow any valid CV Term Exceptions: Allowed Other Sources: wikidata, ILX`
tags	optional	`list[KeyValue]`	Key-value tags related to the object
descriptors	optional	`list[CvTerm]`	Descriptors of the object
external_references	optional	`list[KeyValue]`	External references related to the object
url_list	optional	`list[AnyUrl]`	URL list related to the object
title	required	`str`
doi	required	`str`
pub_med_id	optional	`str`
authors	optional	`list[Annotated]`

Node Relationships

Source	Relationship	Reverse Name	Target	Max
publication	described-as	describes	descriptor	N
publication	describes	has-publication	project	N
publication	describes	has-publication	study	1
publication	has-author	author-of	person	N

Reverse Node Relationships

Source	Relationship	Reverse Name	Target	Max
descriptor	describes	described-as	publication	N
person	author-of	has-author	publication	N
project	has-publication	describes	publication	N
study	has-publication	describes	publication	N

Raw Data File¶

Raw Data File node is optional in the MHD Legacy Profile. Minimum: 0, Maximum: N (unbounded)

Properties

Property Name	Necessity	Type	Description
id	optional	`MhdObjectId`	The id property uniquely identifies the object
type	optional	`MhdObjectType`	The type property identifies type of the object Its value MUST be `raw-data-file`
created_by_ref	optional	`CvTermValueObjectId`	The id property of the data-provider who created the object Target CV term type: `data-provider` Validation Rule: `Allow any valid CV Term Exceptions: Allowed Other Sources: wikidata, ILX`
tags	optional	`list[KeyValue]`	Key-value tags related to the object
descriptors	optional	`list[CvTerm]`	Descriptors of the object
external_references	optional	`list[KeyValue]`	External references related to the object
url_list	required	`list[AnyUrl]`	URL list related to the object Minimum length: `1` Validation Rule: `Min Length: 1, Required`
name	required	`str`	Name of the file. File MUST be a file (not folder or link).It MAY be relative path (e.g., FILES/study.txt) or a file in a compressed file (e.g., FILES/study.zip#data/metadata.tsv) Minimum length: `2` Validation Rule: `Min Length: 2, Required`
size	optional	`int`	The size of the file in bytes, representing the total amount of data contained in the file
hash_sha256	optional	`str`	The SHA-256 cryptographic hash of the file content, used to verify file integrity and ensure that the file has not been altered
format_ref	optional	`CvTermObjectId`	The structure or encoding used to store the contents of the file, typically indicated by its extension (e.g., .txt, .csv, .mzML, .raw, etc.) Target CV term type: `descriptor` Validation Rule: `Allowed Parent CV Terms: * [EDAM, EDAM:1915, Format] Allow parent CV Term: No Allow only leaf CV Terms: No`
compression_format_ref	optional	`CvTermObjectId`	The structure or encoding used to compress the contents of the file, typically indicated by its extension (e.g., .zip, .tar, .gz, etc.) Target CV term type: `descriptor` Validation Rule: `Allowed Parent CV Terms: * [EDAM, EDAM:1915, Format] Allow parent CV Term: No Allow only leaf CV Terms: No`
extension	required	`str`	The extension of file. It MUST contain all extensions (e.g., .raw, .mzML, .d.zip, .raw.zip, etc.) Minimum length: `2` Validation Rule: `Min Length: 2, Required`

Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max
raw-data-file	created-in	has-raw-data-file	study	1	N
raw-data-file	described-as	describes	descriptor	0	N
raw-data-file	referenced-in	references	metadata-file	0	N

Reverse Node Relationships

Source	Relationship	Reverse Name	Target	Max
descriptor	describes	described-as	raw-data-file	N
metadata-file	references	referenced-in	raw-data-file	N
study	has-raw-data-file	created-in	raw-data-file	N

Result File¶

Result File node is optional in the MHD Legacy Profile. Minimum: 0, Maximum: N (unbounded)

Properties

Property Name	Necessity	Type	Description
id	optional	`MhdObjectId`	The id property uniquely identifies the object
type	optional	`MhdObjectType`	The type property identifies type of the object Its value MUST be `result-file`
created_by_ref	optional	`CvTermValueObjectId`	The id property of the data-provider who created the object Target CV term type: `data-provider` Validation Rule: `Allow any valid CV Term Exceptions: Allowed Other Sources: wikidata, ILX`
tags	optional	`list[KeyValue]`	Key-value tags related to the object
descriptors	optional	`list[CvTerm]`	Descriptors of the object
external_references	optional	`list[KeyValue]`	External references related to the object
url_list	required	`list[AnyUrl]`	URL list related to the object Minimum length: `1` Validation Rule: `Min Length: 1, Required`
name	required	`str`	Name of the file. File MUST be a file (not folder or link).It MAY be relative path (e.g., FILES/study.txt) or a file in a compressed file (e.g., FILES/study.zip#data/metadata.tsv) Minimum length: `2` Validation Rule: `Min Length: 2, Required`
size	optional	`int`	The size of the file in bytes, representing the total amount of data contained in the file
hash_sha256	optional	`str`	The SHA-256 cryptographic hash of the file content, used to verify file integrity and ensure that the file has not been altered
format_ref	optional	`CvTermObjectId`	The structure or encoding used to store the contents of the file, typically indicated by its extension (e.g., .txt, .csv, .mzML, .raw, etc.) Target CV term type: `descriptor` Validation Rule: `Allowed Parent CV Terms: * [EDAM, EDAM:1915, Format] Allow parent CV Term: No Allow only leaf CV Terms: No`
compression_format_ref	optional	`CvTermObjectId`	The structure or encoding used to compress the contents of the file, typically indicated by its extension (e.g., .zip, .tar, .gz, etc.) Target CV term type: `descriptor` Validation Rule: `Allowed Parent CV Terms: * [EDAM, EDAM:1915, Format] Allow parent CV Term: No Allow only leaf CV Terms: No`
extension	required	`str`	The extension of file. It MUST contain all extensions (e.g., .raw, .mzML, .d.zip, .raw.zip, etc.) Minimum length: `2` Validation Rule: `Min Length: 2, Required`

Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max
result-file	created-in	has-result-file	study	1	N
result-file	described-as	describes	descriptor	0	N
result-file	referenced-in	references	metadata-file	0	N

Reverse Node Relationships

Source	Relationship	Reverse Name	Target	Max
descriptor	describes	described-as	result-file	N
metadata-file	references	referenced-in	result-file	N
study	has-result-file	created-in	result-file	N

Sample¶

Sample node is optional in the MHD Legacy Profile. Minimum: 0, Maximum: N (unbounded)

Properties

Property Name	Necessity	Type	Description
id	optional	`MhdObjectId`	The id property uniquely identifies the object
type	optional	`MhdObjectType`	The type property identifies type of the object Its value MUST be `sample`
created_by_ref	optional	`CvTermValueObjectId`	The id property of the data-provider who created the object Target CV term type: `data-provider` Validation Rule: `Allow any valid CV Term Exceptions: Allowed Other Sources: wikidata, ILX`
tags	optional	`list[KeyValue]`	Key-value tags related to the object
descriptors	optional	`list[CvTerm]`	Descriptors of the object
external_references	optional	`list[KeyValue]`	External references related to the object
url_list	optional	`list[AnyUrl]`	URL list related to the object
name	required	`str`	Minimum length: `1` Validation Rule: `Min Length: 1, Required`
repository_identifier	required	`str`
additional_identifiers	optional	`list[CvTermValue]`

Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max	Description
sample	derived-from	source-of	subject	1	N
sample	derived-from	source-of	specimen	0	N
sample	described-as	describes	descriptor	0	N
sample	has-characteristic-value	value-of	characteristic-value	0	N	Target Validation Rule: `----- Ontology Sources:ENVO Exceptions: Allowed Other Sources: wikidata, ILX` -----
sample	has-factor-value	value-of	factor-value	0	N
sample	used-in	has-sample	study	1	1

Reverse Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max
characteristic-value	value-of	has-characteristic-value	sample	0	N
descriptor	describes	described-as	sample	0	N
factor-value	value-of	has-factor-value	sample	1	N
specimen	source-of	derived-from	sample	1	N
study	has-sample	used-in	sample	0	N
subject	source-of	derived-from	sample	1	N

Sample Run¶

Sample Run node is optional in the MHD Legacy Profile. Minimum: 0, Maximum: N (unbounded)

Properties

Property Name	Necessity	Type	Description
id	optional	`MhdObjectId`	The id property uniquely identifies the object
type	optional	`MhdObjectType`	The type property identifies type of the object Its value MUST be `sample-run`
created_by_ref	optional	`CvTermValueObjectId`	The id property of the data-provider who created the object Target CV term type: `data-provider` Validation Rule: `Allow any valid CV Term Exceptions: Allowed Other Sources: wikidata, ILX`
tags	optional	`list[KeyValue]`	Key-value tags related to the object
descriptors	optional	`list[CvTerm]`	Descriptors of the object
external_references	optional	`list[KeyValue]`	External references related to the object
url_list	optional	`list[AnyUrl]`	URL list related to the object
name	optional	`str`
sample_ref	optional	`MhdObjectId`	Target node type: `sample` Validation Rule: `Target node type: sample`
sample_run_configuration_refs	optional	`list[MhdObjectId]`	Target node type: `sample-run-configuration`
raw_data_file_refs	optional	`list[MhdObjectId]`	Target node type: `raw-data-file` Validation Rule: `Target node type: raw-data-file`
derived_data_file_refs	optional	`list[MhdObjectId]`	Target node type: `derived-data-file`
result_file_refs	optional	`list[MhdObjectId]`	Target node type: `result-file`
supplementary_file_refs	optional	`list[MhdObjectId]`	Target node type: `supplementary-file`

Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max	Description
sample-run	described-as	describes	descriptor	0	N

Embedded Relationships: raw-data-file, sample

Reverse Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max	Description
descriptor	describes	described-as	sample-run	0	N

Sample Run Configuration¶

Sample Run Configuration node is optional in the MHD Legacy Profile. Minimum: 0, Maximum: N (unbounded)

Properties

Property Name	Necessity	Type	Description
id	optional	`MhdObjectId`	The id property uniquely identifies the object
type	optional	`MhdObjectType`	The type property identifies type of the object Its value MUST be `sample-run-configuration`
created_by_ref	optional	`CvTermValueObjectId`	The id property of the data-provider who created the object Target CV term type: `data-provider` Validation Rule: `Allow any valid CV Term Exceptions: Allowed Other Sources: wikidata, ILX`
tags	optional	`list[KeyValue]`	Key-value tags related to the object
descriptors	optional	`list[CvTerm]`	Descriptors of the object
external_references	optional	`list[KeyValue]`	External references related to the object
url_list	optional	`list[AnyUrl]`	URL list related to the object
protocol_ref	required	`MhdObjectId`	Target node type: `protocol` Validation Rule: `Target node type: protocol`
parameter_value_refs	optional	`list[MhdObjectId or CvTermObjectId or CvTermValueObjectId]`	Target node type: `parameter-value`

Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max	Description
sample-run-configuration	described-as	describes	descriptor	0	N

Embedded Relationships: protocol

Reverse Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max	Description
descriptor	describes	described-as	sample-run-configuration	0	N

Specimen¶

Specimen node is optional in the MHD Legacy Profile. Minimum: 0, Maximum: N (unbounded)

Properties

Property Name	Necessity	Type	Description
id	optional	`MhdObjectId`	The id property uniquely identifies the object
type	optional	`MhdObjectType`	The type property identifies type of the object Its value MUST be `specimen`
created_by_ref	optional	`CvTermValueObjectId`	The id property of the data-provider who created the object Target CV term type: `data-provider` Validation Rule: `Allow any valid CV Term Exceptions: Allowed Other Sources: wikidata, ILX`
tags	optional	`list[KeyValue]`	Key-value tags related to the object
descriptors	optional	`list[CvTerm]`	Descriptors of the object
external_references	optional	`list[KeyValue]`	External references related to the object
url_list	optional	`list[AnyUrl]`	URL list related to the object
name	required	`str`	Minimum length: `1` Validation Rule: `Min Length: 1, Required`
repository_identifier	required	`str`	Minimum length: `1` Validation Rule: `Min Length: 1, Required`
additional_identifiers	optional	`list[CvTermValue]`

Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max	Description
specimen	derived-from	source-of	subject	1	N
specimen	described-as	describes	descriptor	0	N
specimen	has-characteristic-value	value-of	characteristic-value	0	N	Target Validation Rule: `----- Ontology Sources:ENVO Exceptions: Allowed Other Sources: wikidata, ILX` -----
specimen	source-of	derived-from	sample	1	N

Reverse Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max
characteristic-value	value-of	has-characteristic-value	specimen	0	N
descriptor	keyword-of	has-repository-keyword	specimen	0	N
factor-value	value-of	has-factor-value	specimen	1	N
sample	derived-from	source-of	specimen	0	N
subject	source-of	derived-from	specimen	0	N

Study¶

Study node is required in the MHD Legacy Profile. Minimum: 1, Maximum: 1

Properties

Property Name	Necessity	Type	Description
id	optional	`MhdObjectId`	The id property uniquely identifies the object
type	optional	`MhdObjectType`	The type property identifies type of the object Its value MUST be `study`
created_by_ref	required	`CvTermValueObjectId`	The id property of the data-provider who created the object Target CV term type: `data-provider` Validation Rules: `Target node type: data-provider Allow any valid CV Term Exceptions: Allowed Other Sources: wikidata, ILX`
tags	optional	`list[KeyValue]`	Key-value tags related to the object
descriptors	optional	`list[CvTerm]`	Descriptors of the object
external_references	optional	`list[KeyValue]`	External references related to the object
url_list	optional	`list[AnyUrl]`	URL list related to the object
mhd_identifier	required	`str`	Minimum length: `8` Validation Rule: `Min Length: 8, Required`
repository_identifier	required	`str`	Minimum length: `2` Validation Rule: `Min Length: 2, Required`
additional_identifiers	optional	`list[KeyValue]`
title	required	`str`	Minimum length: `25` Validation Rule: `Min Length: 25, Required`
description	required	`str`	Minimum length: `60` Validation Rule: `Min Length: 60, Required`
submission_date	required	`datetime`
public_release_date	required	`datetime`
license	optional	`HttpUrl`	Example: `"https://creativecommons.org/publicdomain/zero/1.0/"`
grant_identifiers	optional	`list[Annotated]`
dataset_url_list	required	`list[AnyUrl]`
related_datasets	optional	`list[KeyValue]`
protocol_refs	optional	`list[MhdObjectId]`	Target node type: `protocol`

Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max	Description
study	described-as	describes	descriptor	0	N
study	funded-by	funds	organization	0	N
study	has-assay	part-of	assay	0	N
study	has-characteristic-definition	used-in	characteristic-definition	1	N	Required min count in the dataset: 1.
study	has-contributor	contributes	person	0	N
study	has-derived-data-file	created-in	derived-data-file	0	N
study	has-factor-definition	used-in	factor-definition	0	N
study	has-metadata-file	describes	metadata-file	1	N
study	has-principal-investigator	principal-investigator-of	person	0	N
study	has-protocol	used-in	protocol	0	N
study	has-publication	describes	publication	0	N
study	has-raw-data-file	created-in	raw-data-file	0	N
study	has-repository-keyword	keyword-of	descriptor	0	N
study	has-result-file	created-in	result-file	0	N
study	has-sample	used-in	sample	0	N
study	has-submitter-keyword	keyword-of	descriptor	0	N
study	has-supplementary-file	created-in	supplementary-file	0	N
study	part-of	has-study	project	0	N
study	provided-by	provides	data-provider	1	1
study	reports	reported-in	metabolite	0	N
study	submitted-by	submits	person	0	N

Embedded Relationships: data-provider

Reverse Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max	Description
assay	part-of	has-assay	study	1	1	A link to a study that the assay was conducted as part of it to generate data addressing study objectives
characteristic-definition	used-in	has-characteristic-definition	study	1	N
data-provider	provides	provided-by	study	1	1
derived-data-file	created-in	has-derived-data-file	study	1	1
descriptor	describes	described-as	study	0	N
descriptor	keyword-of	has-repository-keyword	study	0	N
factor-definition	used-in	has-factor-definition	study	1	N
metabolite	reported-in	reports	study	1	N
metadata-file	describes	has-metadata-file	study	1	1	Required min count in the dataset: 1.
organization	funds	funded-by	study	0	N
person	contributes	has-contributor	study	0	N
person	principal-investigator-of	has-principal-investigator	study	0	N
person	submits	submitted-by	study	0	N
project	has-study	part-of	study	0	N
protocol	used-in	has-protocol	study	1	N
publication	describes	has-publication	study	0	1
raw-data-file	created-in	has-raw-data-file	study	1	N
result-file	created-in	has-result-file	study	1	N
sample	used-in	has-sample	study	1	1
supplementary-file	created-in	has-supplementary-file	study	1	N

Subject¶

Subject node is optional in the MHD Legacy Profile. Minimum: 0, Maximum: N (unbounded)

Properties

Property Name	Necessity	Type	Description
id	optional	`MhdObjectId`	The id property uniquely identifies the object
type	optional	`MhdObjectType`	The type property identifies type of the object Its value MUST be `subject`
created_by_ref	optional	`CvTermValueObjectId`	The id property of the data-provider who created the object Target CV term type: `data-provider` Validation Rule: `Allow any valid CV Term Exceptions: Allowed Other Sources: wikidata, ILX`
tags	optional	`list[KeyValue]`	Key-value tags related to the object
descriptors	optional	`list[CvTerm]`	Descriptors of the object
external_references	optional	`list[KeyValue]`	External references related to the object
url_list	optional	`list[AnyUrl]`	URL list related to the object
name	required	`str`	Minimum length: `1` Validation Rule: `Min Length: 1, Required`
subject_type	optional	`CvTerm`
repository_identifier	required	`str`	Minimum length: `1` Validation Rule: `Min Length: 1, Required`
additional_identifiers	optional	`list[CvTermValue]`

Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max	Description
subject	described-as	describes	descriptor	0	N
subject	has-characteristic-value	value-of	characteristic-value	1	N	Target Validation Rule: `----- Ontology Sources:ENVO Exceptions: Allowed Other Sources: wikidata, ILX` -----
subject	has-factor-value	value-of	factor-value	0	N
subject	source-of	derived-from	sample	1	N
subject	source-of	derived-from	specimen	0	N

Reverse Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max
characteristic-value	value-of	has-characteristic-value	subject	0	N
descriptor	describes	described-as	subject	0	N
factor-value	value-of	has-factor-value	subject	0	N
sample	derived-from	source-of	subject	1	N
specimen	derived-from	source-of	subject	1	N

Supplementary File¶

Supplementary File node is optional in the MHD Legacy Profile. Minimum: 0, Maximum: N (unbounded)

Properties

Property Name	Necessity	Type	Description
id	optional	`MhdObjectId`	The id property uniquely identifies the object
type	optional	`MhdObjectType`	The type property identifies type of the object Its value MUST be `supplementary-file`
created_by_ref	optional	`CvTermValueObjectId`	The id property of the data-provider who created the object Target CV term type: `data-provider` Validation Rule: `Allow any valid CV Term Exceptions: Allowed Other Sources: wikidata, ILX`
tags	optional	`list[KeyValue]`	Key-value tags related to the object
descriptors	optional	`list[CvTerm]`	Descriptors of the object
external_references	optional	`list[KeyValue]`	External references related to the object
url_list	required	`list[AnyUrl]`	URL list related to the object Minimum length: `1` Validation Rule: `Min Length: 1, Required`
name	required	`str`	Name of the file. File MUST be a file (not folder or link).It MAY be relative path (e.g., FILES/study.txt) or a file in a compressed file (e.g., FILES/study.zip#data/metadata.tsv) Minimum length: `2` Validation Rule: `Min Length: 2, Required`
size	optional	`int`	The size of the file in bytes, representing the total amount of data contained in the file
hash_sha256	optional	`str`	The SHA-256 cryptographic hash of the file content, used to verify file integrity and ensure that the file has not been altered
format_ref	optional	`CvTermObjectId`	The structure or encoding used to store the contents of the file, typically indicated by its extension (e.g., .txt, .csv, .mzML, .raw, etc.) Target CV term type: `descriptor` Validation Rule: `Allowed Parent CV Terms: * [EDAM, EDAM:1915, Format] Allow parent CV Term: No Allow only leaf CV Terms: No`
compression_format_ref	optional	`CvTermObjectId`	The structure or encoding used to compress the contents of the file, typically indicated by its extension (e.g., .zip, .tar, .gz, etc.) Target CV term type: `descriptor` Validation Rule: `Allowed Parent CV Terms: * [EDAM, EDAM:1915, Format] Allow parent CV Term: No Allow only leaf CV Terms: No`
extension	optional	`str`	The extension of file. It MUST contain all extensions (e.g., .raw, .mzML, .d.zip, .raw.zip, etc.)

Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max
supplementary-file	created-in	has-supplementary-file	study	1	N
supplementary-file	described-as	describes	descriptor	0	N
supplementary-file	referenced-in	references	metadata-file	0	N

Reverse Node Relationships

Source	Relationship	Reverse Name	Target	Max
descriptor	describes	described-as	supplementary-file	N
metadata-file	references	referenced-in	supplementary-file	N
study	has-supplementary-file	created-in	supplementary-file	N

MHD CV Term Objects¶

Characteristic Type¶

Characteristic Type node is required in the MHD Legacy Profile. Minimum: 1, Maximum: N (unbounded)

Properties

Property Name	Necessity	Type	Description
id	optional	`CvTermObjectId`	The id property uniquely identifies the object
type	optional	`MhdObjectType`	The type property identifies type of the CV Term object Its value MUST be `characteristic-type`
source	optional	`str`	Ontology source name
accession	optional	`str`	Accession number of CV term in compact URI format
name	required	`str`	Label of CV term

Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max	Description
characteristic-type	type-of	has-type	characteristic-definition	1	N

Reverse Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max	Description
characteristic-definition	has-type	type-of	characteristic-type	1	1

Characteristic Value¶

Characteristic Value node is required in the MHD Legacy Profile. Minimum: 1, Maximum: N (unbounded)

Properties

Property Name	Necessity	Type	Description
id	optional	`CvTermValueObjectId`	The id property uniquely identifies the object
type	optional	`MhdObjectType`	The type property identifies type of the CV Term Value object Its value MUST be `characteristic-value`
value	optional	`str or int or float or Decimal`
unit	optional	`UnitCvTerm`
source	optional	`str`	Ontology source name
accession	optional	`str`	Accession number of CV term in compact URI format
name	optional	`str`	Label of CV term

Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max
characteristic-value	instance-of	has-instance	characteristic-definition	1	N
characteristic-value	value-of	has-characteristic-value	subject	0	N
characteristic-value	value-of	has-characteristic-value	specimen	0	N
characteristic-value	value-of	has-characteristic-value	sample	0	N

Reverse Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max
characteristic-definition	has-instance	instance-of	characteristic-value	0	N
sample	has-characteristic-value	value-of	characteristic-value	0	N
specimen	has-characteristic-value	value-of	characteristic-value	0	N
subject	has-characteristic-value	value-of	characteristic-value	1	N

Data Provider¶

Data Provider node is required in the MHD Legacy Profile. Minimum: 1, Maximum: 1

Properties

Property Name	Necessity	Type	Description
id	optional	`CvTermValueObjectId`	The id property uniquely identifies the object
type	optional	`MhdObjectType`	The type property identifies type of the CV Term Value object Its value MUST be `data-provider`
value	required	`str`
unit	optional	`UnitCvTerm`
source	optional	`str`	Ontology source name
accession	optional	`str`	Accession number of CV term in compact URI format
name	optional	`str`	Label of CV term

Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max	Description
data-provider	provides	provided-by	study	1	1

Reverse Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max	Description
study	provided-by	provides	data-provider	1	1

Descriptor¶

Descriptor node is optional in the MHD Legacy Profile. Minimum: 0, Maximum: N (unbounded)

Properties

Property Name	Necessity	Type	Description
id	optional	`CvTermObjectId`	The id property uniquely identifies the object
type	optional	`MhdObjectType`	The type property identifies type of the CV Term object Its value MUST be `descriptor`
source	optional	`str`	Ontology source name
accession	optional	`str`	Accession number of CV term in compact URI format
name	optional	`str`	Label of CV term

Node Relationships

Source	Relationship	Reverse Name	Target	Max
descriptor	describes	described-as	assay	N
descriptor	describes	described-as	study	N
descriptor	describes	described-as	metadata-file	N
descriptor	describes	described-as	raw-data-file	N
descriptor	describes	described-as	derived-data-file	N
descriptor	describes	described-as	supplementary-file	N
descriptor	describes	described-as	result-file	N
descriptor	describes	described-as	metabolite	N
descriptor	describes	described-as	organization	N
descriptor	describes	described-as	person	N
descriptor	describes	described-as	project	N
descriptor	describes	described-as	publication	N
descriptor	describes	described-as	protocol	N
descriptor	describes	described-as	sample	N
descriptor	describes	described-as	subject	N
descriptor	describes	described-as	sample-run	N
descriptor	describes	described-as	sample-run-configuration	N
descriptor	keyword-of	has-repository-keyword	study	N
descriptor	keyword-of	has-repository-keyword	specimen	N

Reverse Node Relationships

Source	Relationship	Reverse Name	Target	Max	Description
assay	described-as	describes	descriptor	N	A link to a descriptor that describes the assay.
derived-data-file	described-as	describes	descriptor	N	A link to a descriptor that describes the derived data file.
metabolite	described-as	describes	descriptor	N
metadata-file	described-as	describes	descriptor	N
organization	described-as	describes	descriptor	N
person	described-as	describes	descriptor	N
project	described-as	describes	descriptor	N
protocol	described-as	describes	descriptor	N
publication	described-as	describes	descriptor	N
raw-data-file	described-as	describes	descriptor	N
result-file	described-as	describes	descriptor	N
sample	described-as	describes	descriptor	N
sample-run	described-as	describes	descriptor	N
sample-run-configuration	described-as	describes	descriptor	N
specimen	described-as	describes	descriptor	N
study	described-as	describes	descriptor	N
study	has-repository-keyword	keyword-of	descriptor	N
study	has-submitter-keyword	keyword-of	descriptor	N
subject	described-as	describes	descriptor	N
supplementary-file	described-as	describes	descriptor	N

Factor Type¶

Factor Type node is optional in the MHD Legacy Profile. Minimum: 0, Maximum: N (unbounded)

Properties

Property Name	Necessity	Type	Description
id	optional	`CvTermObjectId`	The id property uniquely identifies the object
type	optional	`MhdObjectType`	The type property identifies type of the CV Term object Its value MUST be `factor-type`
source	optional	`str`	Ontology source name
accession	optional	`str`	Accession number of CV term in compact URI format
name	required	`str`	Label of CV term

Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max	Description
factor-type	type-of	has-type	factor-definition	1	N

Reverse Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max	Description
factor-definition	has-type	type-of	factor-type	1	1

Factor Value¶

Factor Value node is optional in the MHD Legacy Profile. Minimum: 0, Maximum: N (unbounded)

Properties

Property Name	Necessity	Type	Description
id	optional	`CvTermValueObjectId`	The id property uniquely identifies the object
type	optional	`MhdObjectType`	The type property identifies type of the CV Term Value object Its value MUST be `factor-value`
value	optional	`str or int or float or Decimal`
unit	optional	`UnitCvTerm`
source	optional	`str`	Ontology source name
accession	optional	`str`	Accession number of CV term in compact URI format
name	optional	`str`	Label of CV term

Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max
factor-value	instance-of	has-instance	factor-definition	1	N
factor-value	value-of	has-factor-value	sample	1	N
factor-value	value-of	has-factor-value	specimen	1	N
factor-value	value-of	has-factor-value	subject	0	N

Reverse Node Relationships

Source	Relationship	Reverse Name	Target	Max
factor-definition	has-instance	instance-of	factor-value	N
sample	has-factor-value	value-of	factor-value	N
subject	has-factor-value	value-of	factor-value	N

Metabolite Identifier¶

Metabolite Identifier node is optional in the MHD Legacy Profile. Minimum: 0, Maximum: N (unbounded)

Properties

Property Name	Necessity	Type	Description
id	optional	`CvTermObjectId`	The id property uniquely identifies the object
type	optional	`MhdObjectType`	The type property identifies type of the CV Term object Its value MUST be `metabolite-identifier`
source	optional	`str`	Ontology source name
accession	optional	`str`	Accession number of CV term in compact URI format
name	optional	`str`	Label of CV term

Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max	Description
metabolite-identifier	reported-identifier-of	identified-as	metabolite	1	N

Reverse Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max	Description
metabolite	identified-as	reported-identifier-of	metabolite-identifier	0	N

Parameter Type¶

Parameter Type node is optional in the MHD Legacy Profile. Minimum: 0, Maximum: N (unbounded)

Properties

Property Name	Necessity	Type	Description
id	optional	`CvTermObjectId`	The id property uniquely identifies the object
type	optional	`MhdObjectType`	The type property identifies type of the CV Term object Its value MUST be `parameter-type`
source	optional	`str`	Ontology source name
accession	optional	`str`	Accession number of CV term in compact URI format
name	required	`str`	Label of CV term

Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max	Description
parameter-type	type-of	has-type	parameter-definition	1	N

Reverse Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max	Description
parameter-definition	has-type	type-of	parameter-type	1	1

Parameter Value¶

Parameter Value node is optional in the MHD Legacy Profile. Minimum: 0, Maximum: N (unbounded)

Properties

Property Name	Necessity	Type	Description
id	optional	`CvTermValueObjectId`	The id property uniquely identifies the object
type	optional	`MhdObjectType`	The type property identifies type of the CV Term Value object Its value MUST be `parameter-value`
value	optional	`str or int or float or Decimal`
unit	optional	`UnitCvTerm`
source	optional	`str`	Ontology source name
accession	optional	`str`	Accession number of CV term in compact URI format
name	optional	`str`	Label of CV term

Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max	Description
parameter-value	instance-of	has-instance	parameter-definition	1	N

Reverse Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max	Description
parameter-definition	has-instance	instance-of	parameter-value	0	N

Protocol Type¶

Protocol Type node is optional in the MHD Legacy Profile. Minimum: 0, Maximum: N (unbounded)

Properties

Property Name	Necessity	Type	Description
id	optional	`CvTermObjectId`	The id property uniquely identifies the object
type	optional	`MhdObjectType`	The type property identifies type of the CV Term object Its value MUST be `protocol-type`
source	optional	`str`	Ontology source name
accession	optional	`str`	Accession number of CV term in compact URI format
name	required	`str`	Label of CV term

Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max	Description
protocol-type	type-of	has-type	protocol	1	N

Reverse Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max	Description
protocol	has-type	type-of	protocol-type	1	1