URI Namespace - EMO-BON Data Workflow Handbook

This section provides a comprehensive overview of the URI namespaces used within the EMO-BON ecosystem.

URI Design Principles¶

EMO-BON URI patterns are designed for:

Consistency: Predictable structure across entity types
Dereferenceability: URIs can be resolved to get information about entities
Interoperability: Compatible with linked data standards
Publication: Suitable for static content hosting without requiring a triple store

Overview - URI Path Patterns¶

Base URI: https://data.emobon.embrc.eu

Each URI is further extended with a path specific to the entity type:

Entity type	`/repository`	`/path-to/file.extension`	`#fragment-identifier`
RO-Profiles
ro-profiles	`/{name}-profile`	`/{version}`
RO-Crates
governance-crate	`/governance-crate`
observatory-crate	`/observatory-{obsid}-crate`
analysis-results-crate	`/analysis-results-{cluster}-crate`
sequencing-logistics-crate	`/sequencing-logistics-crate`
Data Entities
Observatory	`/observatory-{obs_id}-crate`	`/{env_package}/observatory/{obs_id}`
Sampling event	`/observatory-{obs_id}-crate`	`/{env_package}/sampling-event/{sampling_event}`
Sample	`/observatory-{obs_id}-crate`	`/{env_package}/sample/{source_mat_id}`
Observation	`/observatory-{obs_id}-crate`	`/{env_package}/observation/{source_mat_id}`	`#{observedProperty}`

Taxon summary	`/analysis-results-{cluster}-crate`	`{source_mat_id}-ro-crate/taxonomy-summary-{geneticMarker}`	`#{OTU-ID}`
Functional annotation	`/analysis-results-{cluster}-crate`	`{source_mat_id}-ro-crate/functional-annotation`	`#{rowID}`

batch	`/sequencing-logistics-crate`	`/shipment/batch/{batchID}`
sequence-run	`/sequencing-logistics-crate`	`/shipment/batch/{batchID}`	`#SequenceAnalysis`

Detailed Specifications - URI Path Patterns¶

RO-Profiles¶

URI pattern: {base}/{name}-profile/{version}

Parameter	Description	Allowed Values	Example URI
`{name}`	Name of the profile	observatory, sequencing, analysis-results	observatory
`{version}`	Profile version	`latest` or specific version (`vM.m.p`)	latest, v1.0.0

Examples:

Governance Crate¶

URI: {base}/governance-crate

Example: https://data.emobon.embrc.eu/governance-crate/

Observatory Crate¶

URI pattern: {base}/observatory-{obsid}-crate

Parameter	Description	Allowed Values	Example(s)
`{obsid}`	Unique observatory ID	free-text IDs	hcmr-1, BPNS

Example: https://data.emobon.embrc.eu/observatory-hcmr-1-crate

Analysis-Results Crate¶

URI pattern:

{base}/analysis-results-{cluster}-crate

Parameter	Description	Allowed Values	Example
`{cluster}`	Unique analysis cluster ID	free-text IDs	cluster-01

Example: https://data.emobon.embrc.eu/analysis-results-cluster-01-crate

Sequencing Logistics Crate¶

URI: {base}/sequencing-logistics-crate

Observatory¶

URI pattern: {base}/observatory-{obs_id}-crate/{env_package}/observatory/{obs_id}

Parameter	Description	Allowed Values	Example
`{obs_id}`	Unique observatory ID	free-text IDs	hcmr-1, BPNS
`{env_package}`	Environment package	water / sediment / soil	water, sediment

Example: http://data.emobon.embrc.eu/observatory-hcmr-1-crate/water/observatory/HCMR-1

Sampling Event¶

URI pattern: {base}/observatory-{obs_id}-crate/{env_package}/sampling-event/{sampling_event}

Parameter	Description	Allowed Values	Example
`{obs_id}`	Unique observatory ID	free-text IDs	hcmr-1, BPNS
`{env_package}`	Environment package	water, sediment	water, sediment
`{sampling_event}`	Unique sampling event ID	free-text IDs	HCMR-1_Wa_221027

Example: http://data.emobon.embrc.eu/observatory-hcmr-1-crate/water/sampling-event/HCMR-1_Wa_221027

Sample¶

URI pattern: {base}/observatory-{obs_id}-crate/{env_package}/sample/{source_mat_id}

Parameter	Description	Allowed Values	Example
`{obs_id}`	Unique observatory ID	free-text IDs	hcmr-1, BPNS
`{env_package}`	Environment package	water, sediment	water, sediment
`{source_mat_id}`	Unique sample ID	free-text IDs	EMOBON_HCMR-1_Wa_1

Example: http://data.emobon.embrc.eu/observatory-hcmr-1-crate/water/sample/EMOBON_HCMR-1_Wa_1

Observation¶

URI pattern: {base}/observatory-{obs_id}-crate/{env_package}/observation/{source_mat_id}#{observedProperty}

Parameter	Description	Allowed Values	Example
`{obs_id}`	Unique observatory ID	free-text IDs	hcmr-1, BPNS
`{env_package}`	Environment package	water, sediment	water, sediment
`{source_mat_id}`	Unique sample ID	free-text IDs	EMOBON_HCMR-1_Wa_1
`{observedProperty}`	Name of the observed property	temperature, pH	chlorophyll, sea_subsurf_salinity

Example: http://data.emobon.embrc.eu/observatory-hcmr-1-crate/water/observation/EMOBON_HCMR-1_Wa_1#chlorophyll

Taxononmy Annotation¶

URI pattern: {base}/analysis-results-{cluster}-crate/{source_mat_id}-ro-crate/taxonomy-summary/{geneticMarker}/{geneticMarker}-taxonomy-summary#{OTU-ID}

Parameter	Description	Allowed Values	Example
`{cluster}`	Unique analysis cluster ID	free-text IDs	cluster-01
`{source_mat_id}`	Unique sample ID	free-text IDs	EMOBON_AAOT_Wa_42
`{geneticMarker}`	Genetic marker used during analysis	SLU / SSU	SSU
`{OTU-ID}`	OTU ID	integer IDs	2157

Example: https://data.emobon.embrc.eu/analysis-results-cluster-01-crate/EMOBON_AAOT_Wa_42-ro-crate/taxonomy-summary/SSU/SSU-taxonomy-summary#2157

Functional Annotation¶

URI pattern: {base}/analysis-results-{cluster}-crate/{source_mat_id}-ro-crate/functional-annotation/functional-annotation#{rowID}

Parameter	Description	Allowed Values	Example
`{cluster}`	Unique analysis cluster ID	free-text IDs	cluster-01
`{source_mat_id}`	Unique sample ID	free-text IDs	EMOBON_AAOT_Wa_42
`{rowID}`	An identifier for the functional annotation	row index	0055085

Example: https://data.emobon.embrc.eu/analysis-results-cluster-01-crate/EMOBON_AAOT_Wa_42-ro-crate/functional-annotation/functional-annotation#GO:0055085

Batch¶

URI pattern: {base}/sequencing-logistics-crate/shipment/batch/{batchID}

Parameter	Description	Allowed Values
`{batchID}`	Unique batch identifier	free-text IDs

Sequence Run¶

URI pattern: {base}/sequencing-logistics-crate/shipment/batch/{batchID}#SequenceAnalysis

Parameter	Description	Allowed Values
`{batchID}`	Batch ID for sequence run	free-text IDs