MetabolomicsHub Common Data Model Nodes - MHD MS Profile¶

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

Required Nodes & Relationships¶

Required MHD Nodes

Assay, Characteristic Definition, Metadata File, Organization, Parameter Definition, Person, Protocol, Sample, Sample Run, Study, Subject

Required MHD CV Terms

Characteristic Type, Characteristic Value, Data Provider, Descriptor, Parameter Type, Parameter Value, Protocol Type

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

graph LR
  Assay[Assay] ==>|embedded - metadata_file_ref| Metadata_File[Metadata File];
  Assay[Assay] ==>|embedded - technology_type_ref| Descriptor[Descriptor];
  Assay[Assay] ==>|embedded - assay_type_ref| Descriptor[Descriptor];
  Assay[Assay] ==>|embedded - measurement_type_ref| Descriptor[Descriptor];
  Assay[Assay] ==>|embedded - omics_type_ref| Descriptor[Descriptor];
  Assay[Assay] ==>|embedded - sample_run_refs| Sample_Run[Sample Run];
  Characteristic_Definition[Characteristic Definition] ==>|embedded - characteristic_type_ref| Characteristic_Type[Characteristic Type];
  Parameter_Definition[Parameter Definition] ==>|embedded - parameter_type_ref| Parameter_Type[Parameter Type];
  Protocol[Protocol] ==>|embedded - protocol_type_ref| Protocol_Type[Protocol Type];
  Sample_Run[Sample Run] ==>|embedded - sample_ref| Sample[Sample];
  Sample_Run[Sample Run] ==>|embedded - raw_data_file_refs| Raw_Data_File[Raw Data File];
  Study[Study] ==>|embedded - created_by_ref| Data_Provider[Data Provider];
  Study[Study] ==>|embedded - protocol_refs| Protocol[Protocol];
  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-instance| Characteristic_Value[Characteristic Value];
  Characteristic_Definition[Characteristic Definition] ==>|has-instance| Characteristic_Value[Characteristic Value];
  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];
  Metadata_File[Metadata File] ==>|describes| Study[Study];
  Parameter_Definition[Parameter Definition] ==>|has-type| Parameter_Type[Parameter Type];
  Parameter_Definition[Parameter Definition] ==>|used-in| Protocol[Protocol];
  Parameter_Definition[Parameter Definition] ==>|has-instance| Parameter_Value[Parameter Value];
  Parameter_Definition[Parameter Definition] ==>|has-instance| Parameter_Value[Parameter Value];
  Parameter_Definition[Parameter Definition] ==>|has-instance| Parameter_Value[Parameter Value];
  Person[Person] ==>|affiliated-with| Organization[Organization];
  Protocol[Protocol] ==>|used-in| Study[Study];
  Protocol[Protocol] ==>|has-type| Protocol_Type[Protocol Type];
  Raw_Data_File[Raw Data File] ==>|created-in| Study[Study];
  Sample[Sample] ==>|used-in| Study[Study];
  Sample[Sample] ==>|derived-from| Subject[Subject];
  Study[Study] ==>|provided-by| Data_Provider[Data Provider];
  Study[Study] ==>|has-assay| Assay[Assay];
  Study[Study] ==>|has-characteristic-definition| Characteristic_Definition[Characteristic Definition];
  Study[Study] ==>|has-metadata-file| Metadata_File[Metadata File];
  Study[Study] ==>|has-principal-investigator| Person[Person];
  Study[Study] ==>|submitted-by| Person[Person];
  Study[Study] ==>|has-protocol| Protocol[Protocol];
  Subject[Subject] ==>|has-characteristic-value| Characteristic_Value[Characteristic Value];
  Subject[Subject] ==>|source-of| Sample[Sample];
  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];
  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];

Required Relationships

Source Node	Relationship	Target Node	Min	Max
Assay	[embedded] - assay_type_ref	Descriptor	1	1
Assay	[embedded] - measurement_type_ref	Descriptor	1	1
Assay	[embedded] - metadata_file_ref	Metadata File	1	1
Assay	[embedded] - omics_type_ref	Descriptor	1	1
Assay	[embedded] - sample_run_refs	Sample Run	1	N (unbounded)
Assay	[embedded] - technology_type_ref	Descriptor	1	1
Assay	follows	Protocol	1	N (unbounded)
Assay	part-of	Study	1	1
Characteristic Definition	[embedded] - characteristic_type_ref	Characteristic Type	1	1
Characteristic Definition (characteristic_type_ref.name = organism)	has-instance	Characteristic Value	1	N (unbounded)
Characteristic Definition (characteristic_type_ref.name = organism part)	has-instance	Characteristic Value	1	N (unbounded)
Characteristic Definition (characteristic_type_ref.name = cell type)	has-instance	Characteristic Value	1	N (unbounded)
Characteristic Definition (characteristic_type_ref.name = disease)	has-instance	Characteristic Value	1	N (unbounded)
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
Parameter Definition	[embedded] - parameter_type_ref	Parameter Type	1	1
Parameter Definition (parameter_type_ref.name = mass spectrometry instrument)	has-instance	Parameter Value	1	N (unbounded)
Parameter Definition (parameter_type_ref.name = acquisition polarity)	has-instance	Parameter Value	1	N (unbounded)
Parameter Definition (parameter_type_ref.name = acquisition polarity)	has-instance	Parameter Value	1	N (unbounded)
Parameter Definition	has-type	Parameter Type	1	1
Parameter Definition	used-in	Protocol	1	N (unbounded)
Parameter Type	type-of	Parameter Definition	1	N (unbounded)
Parameter Value	instance-of	Parameter Definition	1	N (unbounded)
Person	affiliated-with	Organization	1	N (unbounded)
Protocol	[embedded] - protocol_type_ref	Protocol Type	1	1
Protocol	has-type	Protocol Type	1	1
Protocol	used-in	Study	1	N (unbounded)
Protocol Type	type-of	Protocol	1	N (unbounded)
Raw Data File	created-in	Study	1	N (unbounded)
Sample	derived-from	Subject	1	N (unbounded)
Sample	used-in	Study	1	1
Sample Run	[embedded] - raw_data_file_refs	Raw Data File	1	N (unbounded)
Sample Run	[embedded] - sample_ref	Sample	1	1
Study	[embedded] - created_by_ref	Data Provider	1	1
Study	[embedded] - protocol_refs	Protocol	1	N (unbounded)
Study	has-assay	Assay	1	N (unbounded)
Study	has-characteristic-definition	Characteristic Definition	2	N (unbounded)
Study	has-metadata-file	Metadata File	1	N (unbounded)
Study	has-principal-investigator	Person	1	N (unbounded)
Study	has-protocol	Protocol	1	N (unbounded)
Study	provided-by	Data Provider	1	1
Study	submitted-by	Person	1	N (unbounded)
Subject	has-characteristic-value	Characteristic Value	1	N (unbounded)
Subject	source-of	Sample	1	N (unbounded)

Required Node Properties

Source Node	Property Name
assay	assay_type_ref
assay	measurement_type_ref
assay	metadata_file_ref
assay	name
assay	omics_type_ref
assay	repository_identifier
assay	sample_run_refs
assay	technology_type_ref
characteristic-definition	characteristic_type_ref
characteristic-definition	name
characteristic-type	name
data-provider	value
metadata-file	extension
metadata-file	name
metadata-file	url_list
organization	name
parameter-definition	name
parameter-definition	parameter_type_ref
parameter-type	name
person	email_list
person	full_name
protocol	name
protocol	protocol_type_ref
protocol-type	name
raw-data-file	extension
raw-data-file	name
raw-data-file	url_list
sample	name
sample-run	raw_data_file_refs
sample-run	sample_ref
study	created_by_ref
study	dataset_url_list
study	description
study	license
study	mhd_identifier
study	protocol_refs
study	public_release_date
study	repository_identifier
study	submission_date
study	title
subject	name

Additional Requirements

The following nodes are required with the specified value.

Source Node	Minimum Node Count	Property / Relationship	Value
characteristic-value	1	[instance-of].characteristic_type_ref.name	[EFO, EFO:0000324, cell type]
characteristic-value	1	[instance-of].characteristic_type_ref.name	[EFO, MONDO:0000001, disease]
characteristic-value	1	[instance-of].characteristic_type_ref.name	[NCIT, NCIT:C14250, Organism]
characteristic-value	1	[instance-of].characteristic_type_ref.name	[NCIT, NCIT:C103199, Organism Part]
parameter-definition	1	[used-in].protocol_type_ref.name	[CHMO, CHMO:0000470, mass spectrometry]
parameter-value	1	[instance-of].parameter_type_ref.name	[MS, MS:1003776, acquisition polarity]
parameter-value	1	[instance-of].parameter_type_ref.name	[MSIO, MSIO:0000171, mass spectrometry instrument]

MHD Domain Objects¶

Assay¶

Assay node is required in the MHD MS 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`	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`
tag_list	optional	`list[KeyValue]`	Key-value tags related to the object
external_reference_list	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	required	`MhdObjectId`	Reference ID to the metadata file describing the assay Target node type: `metadata-file` Validation Rule: `Target node type: metadata-file`
technology_type_ref	required	`CvTermObjectId`	Reference ID to the technology type CV term object Target CV term type: `descriptor` Validation Rules: `Target node type: descriptor Allowed CV Terms: * [OBI, OBI:0000470, mass spectrometry assay]`
assay_type_ref	required	`CvTermObjectId`	Reference ID to the assay type CV term object 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:0003741, capillary electrophoresis mass spectrometry assay], * [OBI, OBI:0000470, mass spectrometry assay]`
measurement_type_ref	required	`CvTermObjectId`	Reference ID to the measurement type CV term object Target CV term type: `descriptor` Validation Rules: `Target node type: descriptor Allowed CV Terms: * [MS, MS:1003904, untargeted analysis], * [MS, MS:1003905, targeted analysis], * [MS, MS:1003906, semi-targeted analysis]`
omics_type_ref	required	`CvTermObjectId`	Reference ID to the omics type CV term object Target CV term type: `descriptor` Validation Rules: `Target node type: descriptor Allowed CV Terms: * [EDAM, EDAM:topic_3172, Metabolomics], * [EDAM, EDAM:topic_0153, Lipidomics], * [EDAM, EDAM:topic_3955, Fluxomics], * [wikidata, wikidata:Q115452339, exposomics]`
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	required	`list[MhdObjectId]`	List of sample run object IDs associated with the assay 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	1	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 Required min count in the dataset: 1.

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

Reverse Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max	Description
descriptor	describes	described-as	assay	0	N
protocol	used-in	follows	assay	0	N
study	has-assay	part-of	assay	1	N	Required min count in the dataset: 1.

Characteristic Definition¶

Characteristic Definition node is required in the MHD MS Profile. Minimum: 4, 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`
tag_list	optional	`list[KeyValue]`	Key-value tags related to the object
external_reference_list	optional	`list[KeyValue]`	External references related to the object
url_list	optional	`list[AnyUrl]`	URL list related to the object
repository_identifier	required	`str`	Unique identifier assigned to the characteristic definition in the repository
name	required	`str`	Name of the characteristic attribute Minimum length: `2` Validation Rule: `Min Length: 2, Required`
characteristic_type_ref	required	`CvTermObjectId`	Reference ID to the characteristic type CV term object 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, MONDO:0000001, disease], * [EFO, EFO:0000324, cell type]`

Node Relationships

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

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	Required min count in the dataset: 2.
characteristic-value	instance-of	has-instance	characteristic-definition	1	N	Required min count in the dataset: 2.
study	has-characteristic-definition	used-in	characteristic-definition	2	N	Required min count in the dataset: 2.

Derived Data File¶

Derived Data File node is optional in the MHD MS 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`
tag_list	optional	`list[KeyValue]`	Key-value tags related to the object
external_reference_list	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`
repository_identifier	required	`str`	Unique identifier assigned to the file in the source repository
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 Rules: `Target node type: descriptor Allowed Parent CV Terms: * [EDAM, EDAM:format_1915, Format] Allow parent (root) CV Term: No, * [MS, MS:1001459, file format] Allow parent (root) CV Term: No Exceptions: Allowed Placeholder Values: source='' accession=''`
compression_format_refs	optional	`list[CvTermObjectId]`	The structure or encoding used to compress the contents of the file, typically indicated by its extension (e.g., .zip, .tar, .gz, etc.). List item order shows order of compressions. e.g. [tar format, gzip format] for tar.gz Target CV term type: `descriptor` Validation Rules: `Target node type: descriptor Allowed Parent CV Terms: * [EDAM, EDAM:format_1915, Format] Allow parent (root) CV Term: No, * [MS, MS:1001459, file format] Allow parent (root) CV Term: No Exceptions: Allowed Placeholder Values: source='' accession=''`
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

Embedded Relationships: descriptor

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 MS 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`
tag_list	optional	`list[KeyValue]`	Key-value tags related to the object
external_reference_list	optional	`list[KeyValue]`	External references related to the object
url_list	optional	`list[AnyUrl]`	URL list related to the object
repository_identifier	required	`str`	Unique identifier assigned to the factor definition in the repository
name	required	`str`	Name of the factor (e.g. dose, time point) Minimum length: `2` Validation Rule: `Min Length: 2, Required`
factor_type_ref	required	`CvTermObjectId`	Reference ID to the factor type CV term object Target CV term type: `factor-type` Validation Rules: `Target node type: factor-type Allowed CV Terms: * [EFO, MONDO:0000001, disease]`

Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max
factor-definition	has-instance	instance-of	factor-value	0	N
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 MS 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`
tag_list	optional	`list[KeyValue]`	Key-value tags related to the object
external_reference_list	optional	`list[KeyValue]`	External references related to the object
url_list	optional	`list[AnyUrl]`	URL list related to the object
name	required	`str`	Name or chemical label of the metabolite 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 (root) CV Term: No, * [EDAM, EDAM:data_2894, Compound accession] Allow parent (root) CV Term: No Exceptions: Allowed Other Sources: REFMET` -----
metabolite	measured-in	measures	raw-data-file	0	N
metabolite	reported-in	reports	study	1	N
metabolite	reported-in	reports	metadata-file	0	N
metabolite	reported-in	reports	result-file	0	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
metadata-file	reports	reported-in	metabolite	0	N
raw-data-file	measures	measured-in	metabolite	0	N
result-file	reports	reported-in	metabolite	0	N
study	reports	reported-in	metabolite	0	N

Metadata File¶

Metadata File node is required in the MHD MS 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`
tag_list	optional	`list[KeyValue]`	Key-value tags related to the object
external_reference_list	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`
repository_identifier	required	`str`	Unique identifier assigned to the file in the source repository
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 Rules: `Target node type: descriptor Allowed Parent CV Terms: * [EDAM, EDAM:format_1915, Format] Allow parent (root) CV Term: No, * [MS, MS:1001459, file format] Allow parent (root) CV Term: No Exceptions: Allowed Placeholder Values: source='' accession=''`
compression_format_refs	optional	`list[CvTermObjectId]`	The structure or encoding used to compress the contents of the file, typically indicated by its extension (e.g., .zip, .tar, .gz, etc.). List item order shows order of compressions. e.g. [tar format, gzip format] for tar.gz Target CV term type: `descriptor` Validation Rules: `Target node type: descriptor Allowed Parent CV Terms: * [EDAM, EDAM:format_1915, Format] Allow parent (root) CV Term: No, * [MS, MS:1001459, file format] Allow parent (root) CV Term: No Exceptions: Allowed Placeholder Values: source='' accession=''`
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
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
metadata-file	reports	reported-in	metabolite	0	N

Embedded Relationships: descriptor

Reverse Node Relationships

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

Organization¶

Organization node is required in the MHD MS 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 `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`
tag_list	optional	`list[KeyValue]`	Key-value tags related to the object
external_reference_list	optional	`list[KeyValue]`	External references related to the object
url_list	optional	`list[AnyUrl]`	URL list related to the object
repository_identifier	optional	`str`	Unique identifier assigned to the organization in the source repository Validation Rule:
name	required	`str`	Name of the organization Minimum length: `10` Validation Rule: `Min Length: 10, Required`
ror_id	optional	`str`	Research Organization Registry (ROR) identifier
department	optional	`str`	Department within the organization
unit	optional	`str`	Sub-unit or division within the organization or department
address	optional	`str`	Postal address of the organization

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	Min	Max
descriptor	describes	described-as	organization	0	N
person	affiliated-with	affiliates	organization	1	N
project	coordinated-by	coordinates	organization	0	N
project	funded-by	funds	organization	0	N
project	managed-by	manages	organization	0	N
study	funded-by	funds	organization	0	N

Parameter Definition¶

Parameter Definition node is required in the MHD MS 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 `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`
tag_list	optional	`list[KeyValue]`	Key-value tags related to the object
external_reference_list	optional	`list[KeyValue]`	External references related to the object
url_list	optional	`list[AnyUrl]`	URL list related to the object
repository_identifier	required	`str`	Unique identifier assigned to the parameter definition in the repository
name	required	`str`	Name of the parameter Minimum length: `2` Validation Rule: `Min Length: 2, Required`
parameter_type_ref	required	`CvTermObjectId`	Reference ID to the parameter type CV term object Target node type: `parameter-type` Validation Rule: `Target node type: parameter-type`

Node Relationships

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

Embedded Relationships: parameter-type

Reverse Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max	Description
parameter-type	type-of	has-type	parameter-definition	1	N
parameter-value	instance-of	has-instance	parameter-definition	1	N	Required min count in the dataset: 1.
protocol	has-parameter-definition	used-in	parameter-definition	0	N	Required min count in the dataset: 1.

Person¶

Person node is required in the MHD MS 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 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`
tag_list	optional	`list[KeyValue]`	Key-value tags related to the object
external_reference_list	optional	`list[KeyValue]`	External references related to the object
url_list	optional	`list[AnyUrl]`	URL list related to the object
repository_identifier	required	`str`	Unique identifier assigned to the person in the source repository
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"`
email_list	required	`list[EmailStr]`	Email addresses of person Minimum length: `1` Validation Rule: `Min Length: 1, Required`
phone_list	optional	`list[str]`	Phone number of person (with international country code) Example: `"['+449340917271', '00449340917271']"`
address_list	optional	`list[str]`	Addresses of person

Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max	Description
person	affiliated-with	affiliates	organization	1	N
person	author-of	has-author	publication	0	N
person	contributes	has-contributor	project	0	N
person	contributes	has-contributor	study	0	N
person	described-as	describes	descriptor	0	N
person	principal-investigator-of	has-principal-investigator	study	0	N	Required min count in the dataset: 1.
person	submits	submitted-by	study	0	N	Required min count in the dataset: 1.

Reverse Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max	Description
descriptor	describes	described-as	person	0	N
organization	affiliates	affiliated-with	person	0	N
project	has-contributor	contributes	person	0	N
publication	has-author	author-of	person	0	N
study	has-contributor	contributes	person	0	N
study	has-principal-investigator	principal-investigator-of	person	1	N	Required min count in the dataset: 1.
study	submitted-by	submits	person	1	N	Required min count in the dataset: 1.

Project¶

Project node is optional in the MHD MS 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`
tag_list	optional	`list[KeyValue]`	Key-value tags related to the object
external_reference_list	optional	`list[KeyValue]`	External references related to the object
url_list	optional	`list[AnyUrl]`	URL list related to the object
title	required	`str`	Title of the project Minimum length: `25` Validation Rule: `Min Length: 25, Required`
repository_identifier	required	`str`	Unique identifier assigned to the project in the source repository
description	optional	`str`	Summary description of the project goals and scope
grant_identifier_list	optional	`list[Annotated]`	List of grant identifiers funding the project
doi	optional	`str`	Digital Object Identifier (DOI) assigned to the project

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 required in the MHD MS 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 `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`
tag_list	optional	`list[KeyValue]`	Key-value tags related to the object
external_reference_list	optional	`list[KeyValue]`	External references related to the object
url_list	optional	`list[AnyUrl]`	URL list related to the object
repository_identifier	required	`str`	Unique identifier assigned to the protocol in the source repository
name	required	`str`	Name or title of the protocol
protocol_type_ref	required	`CvTermObjectId`	Reference ID to the protocol type CV term object Target CV term type: `protocol-type` Validation Rules: `Target node type: protocol-type Allowed CV Terms: * [CHMO, CHMO:0000470, mass spectrometry], * [CHMO, CHMO:0001000, chromatography], * [EFO, EFO:0005518, sample collection protocol], * [EFO, EFO:0003969, treatment protocol], * [MS, MS:1000831, sample preparation] Exceptions: Allowed Other Sources: wikidata, ILX`
description	optional	`str`	Detailed description of the protocol procedure Validation Rule:
parameter_definition_refs	optional	`list[MhdObjectId]`	List of parameter definition object IDs associated with the protocol Target node type: `parameter-definition`

Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max	Description
protocol	described-as	describes	descriptor	0	N
protocol	has-parameter-definition	used-in	parameter-definition	0	N	Required min count in the dataset: 1.
protocol	has-parameter-value	value-of	parameter-value	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	Required min count in the dataset: 1.

Embedded Relationships: protocol-type

Reverse Node Relationships

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

Publication¶

Publication node is optional in the MHD MS 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`
tag_list	optional	`list[KeyValue]`	Key-value tags related to the object
external_reference_list	optional	`list[KeyValue]`	External references related to the object
url_list	optional	`list[AnyUrl]`	URL list related to the object
title	required	`str`	Title of the publication
doi	required	`str`	Digital Object Identifier (DOI) for the publication
pubmed_id	optional	`str`	PubMed unique identifier (PMID) of the publication
author_list	optional	`list[Annotated]`	List of publication authors

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 MS 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`
tag_list	optional	`list[KeyValue]`	Key-value tags related to the object
external_reference_list	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`
repository_identifier	required	`str`	Unique identifier assigned to the file in the source repository
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 Rules: `Target node type: descriptor Allowed Parent CV Terms: * [EDAM, EDAM:format_1915, Format] Allow parent (root) CV Term: No, * [MS, MS:1001459, file format] Allow parent (root) CV Term: No Exceptions: Allowed Placeholder Values: source='' accession=''`
compression_format_refs	optional	`list[CvTermObjectId]`	The structure or encoding used to compress the contents of the file, typically indicated by its extension (e.g., .zip, .tar, .gz, etc.). List item order shows order of compressions. e.g. [tar format, gzip format] for tar.gz Target CV term type: `descriptor` Validation Rules: `Target node type: descriptor Allowed Parent CV Terms: * [EDAM, EDAM:format_1915, Format] Allow parent (root) CV Term: No, * [MS, MS:1001459, file format] Allow parent (root) CV Term: No Exceptions: Allowed Placeholder Values: source='' accession=''`
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	measures	measured-in	metabolite	0	N
raw-data-file	referenced-in	references	metadata-file	0	N

Embedded Relationships: descriptor

Reverse Node Relationships

Source	Relationship	Reverse Name	Target	Max
descriptor	describes	described-as	raw-data-file	N
metabolite	measured-in	measures	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 MS 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`
tag_list	optional	`list[KeyValue]`	Key-value tags related to the object
external_reference_list	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`
repository_identifier	required	`str`	Unique identifier assigned to the file in the source repository
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 Rules: `Target node type: descriptor Allowed Parent CV Terms: * [EDAM, EDAM:format_1915, Format] Allow parent (root) CV Term: No, * [MS, MS:1001459, file format] Allow parent (root) CV Term: No Exceptions: Allowed Placeholder Values: source='' accession=''`
compression_format_refs	optional	`list[CvTermObjectId]`	The structure or encoding used to compress the contents of the file, typically indicated by its extension (e.g., .zip, .tar, .gz, etc.). List item order shows order of compressions. e.g. [tar format, gzip format] for tar.gz Target CV term type: `descriptor` Validation Rules: `Target node type: descriptor Allowed Parent CV Terms: * [EDAM, EDAM:format_1915, Format] Allow parent (root) CV Term: No, * [MS, MS:1001459, file format] Allow parent (root) CV Term: No Exceptions: Allowed Placeholder Values: source='' accession=''`
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
result-file	reports	reported-in	metabolite	0	N

Embedded Relationships: descriptor

Reverse Node Relationships

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

Sample¶

Sample node is required in the MHD MS 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 `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`
tag_list	optional	`list[KeyValue]`	Key-value tags related to the object
external_reference_list	optional	`list[KeyValue]`	External references related to the object
url_list	optional	`list[AnyUrl]`	URL list related to the object
name	required	`str`	Name or identifier of the sample Minimum length: `1` Validation Rule: `Min Length: 1, Required`
repository_identifier	optional	`str`	Unique identifier assigned to the sample in the repository Validation Rule:
additional_identifier_list	optional	`list[CvTermValue]`	List of additional secondary identifiers for the sample

Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max
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
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 required in the MHD MS 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 `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`
tag_list	optional	`list[KeyValue]`	Key-value tags related to the object
external_reference_list	optional	`list[KeyValue]`	External references related to the object
url_list	optional	`list[AnyUrl]`	URL list related to the object
repository_identifier	required	`str`	Unique identifier assigned to the sample run in the repository
name	optional	`str`	Name or label of the sample run Validation Rule:
sample_ref	required	`MhdObjectId`	Reference ID to the sample object measured in this run Target node type: `sample` Validation Rule: `Target node type: sample`
sample_run_configuration_refs	optional	`list[MhdObjectId]`	List of configuration object IDs for the sample run Target node type: `sample-run-configuration` Validation Rule: `Target node type: sample-run-configuration`
raw_data_file_refs	required	`list[MhdObjectId]`	List of raw data file object IDs produced by the sample run Target node type: `raw-data-file` Validation Rule: `Target node type: raw-data-file`
derived_data_file_refs	optional	`list[MhdObjectId]`	List of derived data file object IDs generated from the sample run Target node type: `derived-data-file` Validation Rule: `Target node type: derived-data-file`
result_file_refs	optional	`list[MhdObjectId]`	List of result file object IDs produced from the sample run Target node type: `result-file` Validation Rule: `Target node type: result-file`
supplementary_file_refs	optional	`list[MhdObjectId]`	List of supplementary file object IDs associated with the sample run Target node type: `supplementary-file` Validation Rule: `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: derived-data-file, raw-data-file, result-file, sample, sample-run-configuration, supplementary-file

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 MS 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`
tag_list	optional	`list[KeyValue]`	Key-value tags related to the object
external_reference_list	optional	`list[KeyValue]`	External references related to the object
url_list	optional	`list[AnyUrl]`	URL list related to the object
repository_identifier	required	`str`	Unique identifier assigned to the sample run configuration in the repository
protocol_ref	required	`MhdObjectId`	Reference ID to the protocol object defining the run configuration Target node type: `protocol` Validation Rule: `Target node type: protocol`
parameter_value_refs	optional	`list[MhdObjectId or CvTermObjectId or CvTermValueObjectId]`	List of parameter value object IDs specifying run parameters Target node type: `parameter-value` Validation Rule: `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: parameter-value, 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 MS 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`
tag_list	optional	`list[KeyValue]`	Key-value tags related to the object
external_reference_list	optional	`list[KeyValue]`	External references related to the object
url_list	optional	`list[AnyUrl]`	URL list related to the object
name	required	`str`	Name or identifier of the specimen Minimum length: `1` Validation Rule: `Min Length: 1, Required`
repository_identifier	optional	`str`	Unique identifier assigned to the specimen in the repository Minimum length: `1` Validation Rule: `Min Length: 1`
additional_identifier_list	optional	`list[CvTermValue]`	List of additional secondary identifiers for the specimen

Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max
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
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 MS 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`
tag_list	optional	`list[KeyValue]`	Key-value tags related to the object
external_reference_list	optional	`list[KeyValue]`	External references related to the object
url_list	optional	`list[AnyUrl]`	URL list related to the object
mhd_identifier	required	`str`	Unique MetabolomicsHub Data (MHD) identifier for the study Minimum length: `8` Validation Rule: `Min Length: 8, Required`
repository_identifier	required	`str`	Accession number or identifier in the source repository Minimum length: `2` Validation Rule: `Min Length: 2, Required`
additional_identifier_list	optional	`list[CvTermValue]`	List of additional database or secondary identifiers for the study
title	required	`str`	Title of the study Minimum length: `25` Validation Rule: `Min Length: 25, Required`
description	required	`str`	Detailed abstract or summary description of the study Minimum length: `60` Validation Rule: `Min Length: 60, Required`
submission_date	required	`datetime`	Date and time when the study was submitted
public_release_date	required	`datetime`	Date and time when the study was publicly released
license	required	`HttpUrl`	Data license or URL defining usage rights for the study Example: `"https://creativecommons.org/publicdomain/zero/1.0/"`
grant_identifier_list	optional	`list[Annotated]`	List of grant identifiers funding the study
dataset_url_list	required	`list[AnyUrl]`	List of dataset access or repository URLs
related_dataset_list	optional	`list[KeyValue]`	List of related dataset key-value pairs
protocol_refs	required	`list[MhdObjectId]`	List of protocol object IDs used in the study Target node type: `protocol` Validation Rule: `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	1	N	Required min count in the dataset: 1.
study	has-characteristic-definition	used-in	characteristic-definition	2	N	Required min count in the dataset: 2.
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	Required min count in the dataset: 1.
study	has-principal-investigator	principal-investigator-of	person	1	N	Required min count in the dataset: 1.
study	has-protocol	used-in	protocol	1	N	Required min count in the dataset: 1.
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	Target Validation Rule: `----- Allow any valid CV Term Exceptions: Allowed Placeholder Values: source='' accession='' Allowed Other Sources: wikidata, ILX` -----
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	Target Validation Rule: `----- Allow any valid CV Term Exceptions: Allowed Placeholder Values: source='' accession='' Allowed Other Sources: wikidata, ILX` -----
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	1	N	Required min count in the dataset: 1.

Embedded Relationships: data-provider, protocol

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 Required min count in the dataset: 1.
characteristic-definition	used-in	has-characteristic-definition	study	1	N	Required min count in the dataset: 1.
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	Required min count in the dataset: 1.
person	submits	submitted-by	study	0	N	Required min count in the dataset: 1.
project	has-study	part-of	study	0	N
protocol	used-in	has-protocol	study	1	N	Required min count in the dataset: 1.
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 required in the MHD MS 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 `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`
tag_list	optional	`list[KeyValue]`	Key-value tags related to the object
external_reference_list	optional	`list[KeyValue]`	External references related to the object
url_list	optional	`list[AnyUrl]`	URL list related to the object
name	required	`str`	Name or identifier of the subject Minimum length: `1` Validation Rule: `Min Length: 1, Required`
subject_type_ref	optional	`CvTermObjectId`	Reference ID to the subject type CV term object Validation Rule: `Target node type: descriptor`
repository_identifier	optional	`str`	Unique identifier assigned to the subject in the repository Minimum length: `1` Validation Rule: `Min Length: 1`
additional_identifier_list	optional	`list[CvTermValue]`	List of additional secondary identifiers for the subject

Node Relationships

Source	Relationship	Reverse Name	Target	Min	Max
subject	described-as	describes	descriptor	0	N
subject	has-characteristic-value	value-of	characteristic-value	1	N
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

Embedded Relationships: descriptor

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 MS 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`
tag_list	optional	`list[KeyValue]`	Key-value tags related to the object
external_reference_list	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`
repository_identifier	required	`str`	Unique identifier assigned to the file in the source repository
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 Rules: `Target node type: descriptor Allowed Parent CV Terms: * [EDAM, EDAM:format_1915, Format] Allow parent (root) CV Term: No, * [MS, MS:1001459, file format] Allow parent (root) CV Term: No Exceptions: Allowed Placeholder Values: source='' accession=''`
compression_format_refs	optional	`list[CvTermObjectId]`	The structure or encoding used to compress the contents of the file, typically indicated by its extension (e.g., .zip, .tar, .gz, etc.). List item order shows order of compressions. e.g. [tar format, gzip format] for tar.gz Target CV term type: `descriptor` Validation Rules: `Target node type: descriptor Allowed Parent CV Terms: * [EDAM, EDAM:format_1915, Format] Allow parent (root) CV Term: No, * [MS, MS:1001459, file format] Allow parent (root) CV Term: No Exceptions: Allowed Placeholder Values: source='' accession=''`
extension	optional	`str`	The extension of file. It MUST contain all extensions (e.g., .raw, .mzML, .d.zip, .raw.zip, etc.) Validation Rule:

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

Embedded Relationships: descriptor

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 MS Profile. Minimum: 2, 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	Required min count in the dataset: 2.

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 MS 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`	Value of CV term
unit	optional	`UnitCvTerm`	Unit CV term if value has a unit
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
characteristic-value	instance-of	has-instance	characteristic-definition	1	N	Required min count in the dataset: 2. Target Validation Rules: ----- Conditional - (organism) [Source * [instance-of].characteristic_type_ref.name = organism] Ontology Sources:NCBITAXON, ENVO, CHEBI Exceptions: Allowed Other Sources: wikidata, ILX ----- Conditional - (organism part) [Source * [instance-of].characteristic_type_ref.name = organism part] Ontology Sources:UBERON, BTO, NCIT, CHEBI Exceptions: Allowed Other Sources: wikidata, ILX ----- Conditional - (cell type) [Source * [instance-of].characteristic_type_ref.name = cell type] Ontology Sources:CL, CLO Exceptions: Allowed Missing CV Terms: * [NCIT, NCIT:C48660, Not Applicable], * [NCIT, NCIT:C126101, Not Available], * [NCIT, NCIT:C150904, Masked Data] Allowed Other Sources: wikidata, ILX ----- Conditional - (disease) [Source * [instance-of].characteristic_type_ref.name = disease] Ontology Sources:MONDO, MP, SNOMED, PATO Exceptions: Allowed Missing CV Terms: * [NCIT, NCIT:C48660, Not Applicable], * [NCIT, NCIT:C126101, Not Available], * [NCIT, NCIT:C150904, Masked Data] Allowed Other Sources: wikidata, ILX -----
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	1	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 MS 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 `data-provider`
value	required	`str`	Value of CV term
unit	optional	`UnitCvTerm`	Unit CV term if value has a unit
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 required in the MHD MS 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 `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 MS 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 MS 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`	Value of CV term
unit	optional	`UnitCvTerm`	Unit CV term if value has a unit
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
factor-value	instance-of	has-instance	factor-definition	1	N	Target Validation Rule: `----- Conditional - (disease) [Source * [instance-of].factor_type_ref.name = disease] Ontology Sources:MONDO, MP, SNOMED, PATO Exceptions: Allowed Missing CV Terms: * [NCIT, NCIT:C48660, Not Applicable], * [NCIT, NCIT:C126101, Not Available], * [NCIT, NCIT:C150904, Masked Data] Allowed Other Sources: wikidata, ILX` -----
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 MS 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 `metabolite-identifier`
value	required	`str or int or float or Decimal`	Value of CV term
unit	optional	`UnitCvTerm`	Unit CV term if value has a unit
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 required in the MHD MS 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 `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 required in the MHD MS 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 `parameter-value`
value	optional	`str or int or float or Decimal`	Value of CV term
unit	optional	`UnitCvTerm`	Unit CV term if value has a unit
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	Required min count in the dataset: 1. Target Validation Rules: ----- Conditional - (mass spectrometry instrument) [Source * [instance-of].parameter_type_ref.name = mass spectrometry instrument] Allowed Parent CV Terms: * [MS, MS:1000031, instrument model] Allow parent (root) CV Term: No Excluded CV Terms: ^.instrument model Exceptions: Allowed Other Sources: wikidata, ILX ----- Conditional - (acquisition polarity) [Source [instance-of].parameter_type_ref.name = acquisition polarity] Allowed CV Terms: * [MS, MS:1000076, negative polarity acquisition], * [MS, MS:1000077, positive polarity acquisition], * [MS, MS:1002833, alternating polarity acquisition], * [MS, MS:1003774, mixed polarity acquisition] Exceptions: Allowed Other Sources: wikidata, ILX ----- Conditional - (ionization type) [Source * [instance-of].parameter_type_ref.name = ionization type] Allowed Parent CV Terms: * [MS, MS:1000008, ionization type] Allow parent (root) CV Term: No Exceptions: Allowed Other Sources: wikidata, ILX ----- Conditional - (instrument class) [Source * [instance-of].parameter_type_ref.name = instrument class] Allowed Parent CV Terms: * [MS, MS:1003761, instrument class] Allow parent (root) CV Term: No Exceptions: Allowed Other Sources: wikidata, ILX ----- Conditional - (inlet type) [Source * [instance-of].parameter_type_ref.name = inlet type] Allowed Parent CV Terms: * [MS, MS:1000007, inlet type] Allow parent (root) CV Term: No Exceptions: Allowed Other Sources: wikidata, ILX ----- Conditional - (chromatography instrument) [Source * [instance-of].parameter_type_ref.name = chromatography instrument] Allowed Parent CV Terms: * [MS, MS:1003737, separation system] Allow parent (root) CV Term: No Exceptions: Allowed Other Sources: wikidata, ILX ----- Conditional - (chromatography column) [Source * [instance-of].parameter_type_ref.name = chromatography column] Allow any valid CV Term Exceptions: Allowed Placeholder Values: source='' accession='' Allowed Other Sources: wikidata, ILX ----- Conditional - (chromatography separation) [Source * [instance-of].parameter_type_ref.name = chromatography separation] Allowed Parent CV Terms: * [MS, MS:1002270, chromatography separation] Allow parent (root) CV Term: No Exceptions: Allowed Other Sources: wikidata, ILX -----
parameter-value	value-of	has-parameter-value	protocol	0	N

Reverse Node Relationships

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

Protocol Type¶

Protocol Type node is required in the MHD MS 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 `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

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-instance| Characteristic_Value[Characteristic Value];
  Characteristic_Definition[Characteristic Definition] ==>|has-instance| Characteristic_Value[Characteristic Value];
  Characteristic_Definition[Characteristic Definition] ==>|has-instance| Characteristic_Value[Characteristic Value];
  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];
  Metabolite[Metabolite] ==>|reported-in| Metadata_File[Metadata File];
  Metabolite[Metabolite] ==>|reported-in| Result_File[Result File];
  Metabolite[Metabolite] ==>|measured-in| Raw_Data_File[Raw Data File];
  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];
  Metadata_File[Metadata File] ==>|reports| Metabolite[Metabolite];
  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] ==>|used-in| Protocol[Protocol];
  Parameter_Definition[Parameter Definition] ==>|has-instance| Parameter_Value[Parameter Value];
  Parameter_Definition[Parameter Definition] ==>|has-instance| Parameter_Value[Parameter Value];
  Parameter_Definition[Parameter Definition] ==>|has-instance| Parameter_Value[Parameter Value];
  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] ==>|has-parameter-value| Parameter_Value[Parameter Value];
  Protocol[Protocol] ==>|used-in| Study[Study];
  Protocol[Protocol] ==>|has-type| Protocol_Type[Protocol Type];
  Protocol[Protocol] ==>|has-parameter-definition| Parameter_Definition[Parameter Definition];
  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];
  Raw_Data_File[Raw Data File] ==>|measures| Metabolite[Metabolite];
  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];
  Result_File[Result File] ==>|reports| Metabolite[Metabolite];
  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];
  Parameter_Value[Parameter Value] ==>|value-of| Protocol[Protocol];
  Protocol_Type[Protocol Type] ==>|type-of| Protocol[Protocol];