Map data from the open streetmap project [4].
The FAIR datastation? A solution for Aspergillus research?
Where do you look up or share (research) data?
there is a poll here
ASPAR_KR
project again?Standardising research data.
Improve datasharing.
ASPAR_KR
Introducing an existing standard.
Easy to understand and use.
No standards are fully ready yet.
Standards are impossible to develop without cooperation.
The FAIRDS
[2] platform may be useful here.
FAIRDS
, what is it for?Standardisation of omics data.
Users register their study, and make it FAIR from the start.
For standardised data management.
Automated analysis pipelines.
Made by the friendly folks at the WUR’s synthetic system biology:
WEB app.
Distributed as open source.
Excel based.
FAIRDS
, how does it work?Experimental design is part of the dataset.
Minimum information standards are used.
New templates can be introduced.
excel
templates.FAIRDS
makes RDF.Investigation class
Study class, sub question of Investigation.
Observation class, what a study observed.
Sample class, what a study observed.
Assay class, what was measured.
That’s all well and good, but how does it work?
Imagine the following situation.
The data set to be FAIRified.
Our FAIRification programme.
The FAIR data, how can we use this?
We need an
To explain linked data concepts
RDF
files are plain text of various formats.
The basis is the triple.
RDF
statement.This…
@base <http://example.org/> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix rel: <http://www.perceive.net/schemas/relationship/> .
<#green-goblin>
rel:enemyOf <#spiderman> ;
a foaf:Person ; # in the context of the Marvel universe
foaf:name "Green Goblin" .
<#spiderman>
rel:enemyOf <#green-goblin> ;
a foaf:Person ;
foaf:name "Spiderman", "Человек-паук"@ru .
Turns into this …
SPARQL
is a programming language for analysis of RDF
.@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix rel: <http://www.perceive.net/schemas/relationship/> .
PREFIX ex: <http//example.org/>
SELECT ?person ?enemy
WHERE
{
?person a foaf:Person ;
foaf:name ?name ;
rel:enemyOf ?enemy .
FILTER(STRSTARTS(?name, "Green")) .
}
should return: “Green goblin” ex:spiderman
RDF
data.# read in the RDF file.
rdf <- rdflib::rdf_parse("hylke_air_method_example/data.ttl",
format = "turtle")
rdf
Total of 425 triples, stored in hashes
-------------------------------
<http://fairbydesign.nl/ontology/inv_arnhemVsNijmegenComparison/stu_arnhemVsNijmegen/obs_nijmegenAirSamples/sam_CultureNijmegenStation2> <http://schema.org/description> "A two layer culture made from the delta trap taken from the station square in Nijmegen" .
<http://fairbydesign.nl/ontology/inv_arnhemVsNijmegenComparison/stu_arnhemVsNijmegen/obs_nijmegenAirSamples/sam_CultureNijmegenStation2> <http://fairbydesign.nl/ontology/biosafety_level> "2"^^<http://www.w3.org/2001/XMLSchema#integer> .
<http://fairbydesign.nl/ontology/inv_arnhemVsNijmegenComparison/stu_arnhemVsNijmegen> <http://schema.org/identifier> "arnhemVsNijmegen" .
<http://fairbydesign.nl/ontology/selection_medium> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/1999/02/22-rdf-syntax-ns#Property> .
<http://fairbydesign.nl/ontology/inv_arnhemVsNijmegenComparison/stu_arnhemVsNijmegen/obs_nijmegenAirSamples/sam_CultureNijmegenPark1> <http://fairbydesign.nl/ontology/antibiotics> "CHEMBL1835949" .
<http://fairbydesign.nl/ontology/inv_arnhemVsNijmegenComparison/stu_arnhemVsNijmegen/obs_arnhemAirSamples/sam_CultureArnhemStation2> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://jermontology.org/ontology/JERMOntology#Sample> .
<http://fairbydesign.nl/ontology/biosafety_level> <http://schema.org/valueRequired> "true"^^<http://www.w3.org/2001/XMLSchema#boolean> .
<http://fairbydesign.nl/ontology/inv_arnhemVsNijmegenComparison/stu_arnhemVsNijmegen/obs_nijmegenAirSamples/sam_CultureNijmegenStation2> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://jermontology.org/ontology/JERMOntology#Sample> .
<http://fairbydesign.nl/ontology/inv_arnhemVsNijmegenComparison/stu_arnhemVsNijmegen/obs_nijmegenAirSamples/sam_CultureNijmegenStation2> <http://fairbydesign.nl/ontology/medium_type> "flamingo medium" .
<http://fairbydesign.nl/ontology/inv_arnhemVsNijmegenComparison/stu_arnhemVsNijmegen/obs_arnhemAirSamples/sam_arnhem2> <http://fairbydesign.nl/ontology/packageName> "DeltaTrap" .
... with 415 more triples
sparql_query <-
'
prefix ppeo: <http://purl.org/ppeo/PPEO.owl#>
prefix jerm: <http://jermontology.org/ontology/JERMOntology#>
prefix fair: <http://fairbydesign.nl/ontology/>
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
prefix schema: <http://schema.org/>
SELECT
?observation_label ?sample_label
?total_cfu
?selection_cfu
WHERE {
# Get the samples of interest
?observation_unit a ppeo:observation_unit .
?observation_unit jerm:hasPart ?parts .
?parts a jerm:Sample .
?parts fair:packageName "DeltaTrap" .
?parts fair:derives ?cultures .
?observation_unit schema:name ?observation_label .
?parts schema:name ?sample_label .
# Experimental data
?cultures fair:total_cfu ?total_cfu .
?cultures fair:selection_cfu ?selection_cfu .
}
'
result <- rdflib::rdf_query(rdf, sparql_query)
result
# A tibble: 8 × 4
observation_label sample_label total_cfu selection_cfu
<chr> <chr> <dbl> <dbl>
1 The city of Nijmegen Nijmegen Station plein 2 57 21
2 The city of Nijmegen Nijmegen Station plein 1 53 24
3 The city of Nijmegen Kronenburger park 2 61 26
4 The city of Nijmegen Kronenburger park 1 70 30
5 The city of Arnhem Arnhem Centraal 2 66 28
6 The city of Arnhem Arnhem Centraal 1 55 18
7 The city of Arnhem Sonsbeek park 2 51 23
8 The city of Arnhem Sonsbeek park 1 52 20
FAIRDS
.And…
ASPAR_KR
.FAIRDS
.Extra slides for extra questions
ASPAR_KR
alternativesalternative | + | - |
---|---|---|
seek4science | * Supports ISA * Sharing of templates online. |
* A bit more complicated to contribute to. * Not available locally via excel sheets. |
FAIRshare | * Locally available |
* Limited in scope to genomics or immunology. * Not clear how to expand it. |
Does not want to share his likeness
II azole resistance international meeting
Source code of this presentation here