Skip to content

Commit

Permalink
Dendron workspace sync
Browse files Browse the repository at this point in the history 
## Synced vaults:
- dendron-dbgi

Dendron version: 0.124.0
Hostname: vpn-client-43-15.unifr.ch
  • Loading branch information
@oolonek
oolonek committed Sep 18, 2023
1 parent 2397883 commit f6b3d09
Show file tree
Hide file tree
Showing 2 changed files with 140 additions and 2 deletions.
136 changes: 135 additions & 1 deletion vault/emi-semantic-model.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
id: u3r5ovqpurmj36nsvmetsl8
title: Emi Semantic Model
desc: ''
updated: 1693574568667
updated: 1695045009288
created: 1693548771769
---

Expand Down Expand Up @@ -126,3 +126,137 @@ classDiagram
}
```


#### Schema of an EMI Observation procedure

```mermaid
graph TD
Smartphone -->|rdf:type|sosa:Sensor
Smartphone -->|sosa:madeObservation|Field_Observation["Field_Observation"]
Smartphone -->|sosa:observes|Pictures["Pictures"]
Field_Observation -->|rdf:type|sosa:Observation["sosa:Observation"]
Field_Observation -->|sosa:observedProperty|Pictures["Pictures"]
Pictures --> |rdf:type|sosa:Observable_property["sosa:Observable_property"]
Field_Observation -->|sosa:usedProcedure|Observation_Procedure["Observation_Procedure"]
Field_Observation -->|sosa:resultTime|xsd:dateTime
Field_Observation -->|"sosa:hasFeatureOfInterest"|Living_System["Living_System"]
Field_Observation -->|sosa:hasResult|iNaturalist_Observation["iNaturalist_Observation"]
Living_System -->|skos:narrower|t_a["ex:Taxon_a"]
Living_System -->|skos:narrower|t_b["ex:Taxon_b"]
t_a -->|rdf:type|w["<a href=http://www.wikidata.org/entity/Q16521>wikidata:Q16521</a>"]
t_b -->|rdf:type|w["<a href=http://www.wikidata.org/entity/Q16521>wikidata:Q16521</a>"]
t_a -->|"emi:isClassifiedWith (optional)"|w2["Specimen Type Vocabulary"]
t_b -->|"emi:isClassifiedWith (optional)"|w2["Specimen Type Vocabulary"]
```

#### Schema of an EMI Collection procedure

```mermaid
graph TD
Collector -->|rdf:type|sosa:Sampler
Collector -->|sosa:madeSampling|Field_Sampling["Field_Sampling"]
Field_Sampling -->|rdf:type|sosa:Sampling["sosa:Sampling"]
Field_Sampling -->|sosa:usedProcedure|Sampling_Procedure["Sampling_Procedure"]
Field_Sampling -->|sosa:resultTime|xsd:dateTime
Field_Sampling -->|"sosa:hasFeatureOfInterest"|Living_System["Living_System"]
Field_Sampling -->|sosa:hasResult|Field_Sample["Field_Sample"]
Living_System -->|skos:narrower|t_a["ex:Taxon_a"]
Living_System -->|skos:narrower|t_b["ex:Taxon_b"]
t_a -->|rdf:type|w["<a href=http://www.wikidata.org/entity/Q16521>wikidata:Q16521</a>"]
t_b -->|rdf:type|w["<a href=http://www.wikidata.org/entity/Q16521>wikidata:Q16521</a>"]
t_a -->|"emi:isClassifiedWith (optional)"|w2["Specimen Type Vocabulary"]
t_b -->|"emi:isClassifiedWith (optional)"|w2["Specimen Type Vocabulary"]
```

#### Schema of an EMI Extraction procedure

```mermaid
graph TD
Extractor -->|rdf:type|sosa:Actuator
Extractor -->|sosa:madeActuation|Lab_Extraction["Lab_Extraction"]
Lab_Extraction -->|rdf:type|sosa:Actuation["sosa:Actuation"]
Lab_Extraction -->|sosa:usedProcedure|Lab_Extraction_Procedure["Lab_Extraction_Procedure"]
Lab_Extraction -->|sosa:resultTime|xsd:dateTime
Lab_Extraction -->|"sosa:hasFeatureOfInterest"|Field_Sample["Field_Sample"]
Lab_Extraction -->|sosa:hasResult|Lab_Extract["Lab_Extract"]
```


#### Schema of an EMI Mass Spectrometry analysis procedure

```mermaid
graph TD
Mass_Spectrometer -->|rdf:type|MS_Actuator["sosa:Actuator"]
Mass_Spectrometer -->|rdf:type|MS_Sampler["sosa:Sampler"]
Mass_Spectrometer -->|sosa:madeActuation|Mass_Spectrometry_Analysis["Mass_Spectrometry_Analysis"]
Mass_Spectrometer -->|sosa:madeSampling|Mass_Spectrometry_Analysis["Mass_Spectrometry_Analysis"]
Mass_Spectrometry_Analysis -->|rdf:type|MS_Actuation["sosa:Actuation"]
Mass_Spectrometry_Analysis -->|sosa:usedProcedure|Mass_Spectrometry_Analysis_Procedure["Mass_Spectrometry_Analysis_Procedure"]
Mass_Spectrometry_Analysis -->|sosa:resultTime|ms_time["xsd:dateTime"]
Mass_Spectrometry_Analysis -->|"sosa:hasFeatureOfInterest"|Lab_Extract["Lab_Extract"]
Mass_Spectrometry_Analysis -->|sosa:hasResult|Mass_Spectrometry_Results["Mass_Spectrometry_Results"]
```


### Schema of an EMI overall procedure


```mermaid
graph TD
subgraph field
subgraph collection
Collector -->|rdf:type|sosa:Sampler
Collector -->|sosa:madeSampling|Field_Sampling["Field_Sampling"]
Field_Sampling -->|rdf:type|sosa:Sampling["sosa:Sampling"]
Field_Sampling -->|sosa:usedProcedure|Sampling_Procedure["Sampling_Procedure"]
Field_Sampling -->|sosa:resultTime|fs_time["xsd:dateTime"]
end
subgraph observation
Smartphone -->|rdf:type|sosa:Sensor
Smartphone -->|sosa:madeObservation|Field_Observation["Field_Observation"]
Smartphone -->|sosa:observes|Pictures["Pictures"]
Field_Observation -->|rdf:type|sosa:Observation["sosa:Observation"]
Field_Observation -->|sosa:observedProperty|Pictures["Pictures"]
Pictures --> |rdf:type|sosa:Observable_property["sosa:Observable_property"]
Field_Observation -->|sosa:usedProcedure|Observation_Procedure["Observation_Procedure"]
Field_Observation -->|sosa:resultTime|fo_time["xsd:dateTime"]
Field_Observation -->|sosa:hasResult|iNaturalist_Observation["iNaturalist_Observation"]
end
Field_Observation -->|"sosa:hasFeatureOfInterest"|Living_System["Living_System"]
Field_Sampling -->|"sosa:hasFeatureOfInterest"|Living_System["Living_System"]
Living_System -->|skos:narrower|t_a["ex:Taxon_a"]
Living_System -->|skos:narrower|t_b["ex:Taxon_b"]
end
Lab_Extraction -->|"sosa:hasFeatureOfInterest"|Field_Sample["Field_Sample"]
t_a -->|rdf:type|w["<a href=http://www.wikidata.org/entity/Q16521>wikidata:Q16521</a>"]
t_b -->|rdf:type|w["<a href=http://www.wikidata.org/entity/Q16521>wikidata:Q16521</a>"]
t_a -->|"emi:isClassifiedWith (optional)"|w2["Specimen Type Vocabulary"]
t_b -->|"emi:isClassifiedWith (optional)"|w2["Specimen Type Vocabulary"]
Field_Sampling -->|sosa:hasResult|Field_Sample["Field_Sample"]
subgraph lab
direction TB
subgraph mass_spectrometry
Mass_Spectrometer -->|rdf:type|MS_Actuator["sosa:Actuator"]
Mass_Spectrometer -->|rdf:type|MS_Sampler["sosa:Sampler"]
Mass_Spectrometer -->|sosa:madeActuation|Mass_Spectrometry_Analysis["Mass_Spectrometry_Analysis"]
Mass_Spectrometer -->|sosa:madeSampling|Mass_Spectrometry_Analysis["Mass_Spectrometry_Analysis"]
Mass_Spectrometry_Analysis -->|rdf:type|MS_Actuation["sosa:Actuation"]
Mass_Spectrometry_Analysis -->|sosa:usedProcedure|Mass_Spectrometry_Analysis_Procedure["Mass_Spectrometry_Analysis_Procedure"]
Mass_Spectrometry_Analysis -->|sosa:resultTime|ms_time["xsd:dateTime"]
Mass_Spectrometry_Analysis -->|sosa:hasResult|Mass_Spectrometry_Results["Mass_Spectrometry_Results"]
end
subgraph extraction
Extractor -->|rdf:type|sosa:Actuator
Extractor -->|sosa:madeActuation|Lab_Extraction["Lab_Extraction"]
Lab_Extraction -->|rdf:type|sosa:Actuation["sosa:Actuation"]
Lab_Extraction -->|sosa:usedProcedure|Lab_Extraction_Procedure["Lab_Extraction_Procedure"]
Lab_Extraction -->|sosa:resultTime|xsd:dateTime
Lab_Extraction -->|sosa:resultTime|le_time["xsd:dateTime"]
end
Lab_Extraction -->|sosa:hasResult|Lab_Extract["Lab_Extract"]
Mass_Spectrometry_Analysis -->|"sosa:hasFeatureOfInterest"|Lab_Extract["Lab_Extract"]
end
```

6 changes: 5 additions & 1 deletion vault/open-notebook.dbgi.pmallard.2023.09.17.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
id: uchpm4tt1enj34vr209qauc
title: '2023-09-17'
desc: ''
updated: 1694932520626
updated: 1694935574463
created: 1694932202779
traitIds:
- open-notebook-dbgi-pmallard
Expand Down Expand Up @@ -53,6 +53,10 @@ https://www.idigbio.org/content/biodigicon-2023-0

## Notes

https://github.com/bio-guoda/preston/issues/250
https://linker.bio/hash://sha256/f849c870565f608899f183ca261365dce9c9f1c5441b1c779e0db49df9c2a19d


## Todo tomorrow, one day ... or never

###
Expand Down

0 comments on commit f6b3d09

Please sign in to comment.