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Translating GXA data to agrischemas

Experiment, general description

This is similar to the MIAPPE use case.

bkr:exp_E-MTAB-3103 a bioschema:Study;
	schema:identifier "E-MTAB-3103";
	dc:title "Tissue layers from developing wheat grain at 12 days post-anthesis";
	schema:description "Inner pericarp, outer pericarp and endosperm layers from...";
	schema:datePublished "2015-04-24";
	schema:subjectOf bkr:pmid_26044828;
	schema:additionalProperty [
		a schema:PropertyValue;
		schema:propertyID "organism";
		schema:value "triticum aestivum";
		# See MIAPPE, TODO: move the MIAPPE documentation to a general doc
		dc:type <http://purl.bioontology.org/ontology/NCBITAXON/4565>
	]
.

bkr:pmid_26044828 a agri:ScholarlyPublication;
	dc:title "Heterologous expression and transcript analysis of gibberellin biosynthetic genes..."
	agri:pmedId "26044828";
	agri:authorsList "Pearce S, Huttly AK, Prosser IM, Li YD, Vaughan SP, ...";
	# Other possible properties: schema:datePublished
	# other proposed property are: pmedId, doiId (which could also be managed via PropertyValue) 
.

Gene expression levels, differential expression experiments

# For quick access, you might redundantly state it without attributes
bkr:gene_traescs7d02g431500 bioschema:expressedIn cond_4_week_0x3B_cold_temperature_regimen.

# Then, add attributes via reification
bkr:gxaexp_E-GEOD-58805_traescs7d02g431500_4_week_0x3B_cold_temperature_regimen_vs_2_week_0x3B_control a rdf:Statement;
  rdf:subject bkr:gene_traescs7d02g431500;
	rdf:predicate bioschema:expressedIn;
	rdf:object bkr:cond_4_week_0x3B_cold_temperature_regimen;

	# We propose a set of specific properties to indicate these sequencing technology details.
	#
	# TODO: there is an alternative representation, based on property values, 
	# see the MIAPPE use case. That is, the expressedIn statement becomes a ComputedValue too, 
	# so that we have a uniform representation of experimental results.
	agri:log2FoldChange 1.9;
	agri:pvalue 3.129E-29;
	agri:evidence bkr:exp_E-GEOD-38344;
.

Gene expression levels, NGS experiments

# As above, first the base statement.
bkr:gene_traescs1d02g156000 bioschema:expressedIn bkr:cond_14_day_post_anthesis_0x2C_aleurone_layer.

# Then, add attributes via reification
bkr:gxaexp_E-GEOD-38344_traescs1d02g156000_14_day_post_anthesis_0x2C_aleurone_layer a rdf:Statement;
  rdf:subject bkr:gene_traescs1d02g156000;
	rdf:predicate bioschema:expressedIn;
	rdf:object bkr:cond_14_day_post_anthesis_0x2C_aleurone_layer;
	# We propose a set of specific properties to indicate these sequencing technology details
	# TODO: again, could be based on the agri:StudyComputedValue proposed for MIAPPE.
	agri:tpmCount 32;
	# Based on common thresholds used for TPM, but this is a very specific detail
	agri:ordinalTpm "medium"; 
	agri:evidence bkr:exp_E-GEOD-38344;
.

Genes and experimental factors

These are the entities involved in the gene expression level statements above.

# The genes
bkr:gene_traescs1d02g156000 a bioschema:Gene;
	schema:identifier "TRAESCS1D02G156000";
	# other properties, see the biomolecular biology case
.

# The reference conditions
#  
bkr:cond_14_day_post_anthesis_0x2C_aleurone_layer a agri:ExperimentalFactorValue; 
  schema:name "14 day post anthesis, aleurone layer";
  # These can come from eg, manual curation or auto-annotation
  # (of course multiple terms are possible)
  dc:type
    <http://purl.obolibrary.org/obo/PO_0005360>, # aleurone layer
		<http://www.cropontology.org/rdf/CO_321:0000434>; # day 
.

Real data and Sample Queries

In the Knetminer group we publish data from the EBI's Gene Expression Atlas as RDF data, using the modelling approach shown above. You can find the data and sample queries on our SPARQL endpoint.

Here you can find the scripts that do the GXA/RDF conversion. These are part of our DFW dataset.

Base conditions and time points

In the GXA conversion above, we modelled details like base conditions and time points:

bkr:gxaexp_E-GEOD-16333_at5g02540_pif4_0x3B_pif5_vs_wild_type_in_far-red_light_1h a rdf:Statement;
  rdf:subject bkr:gene_at5g02540;
	rdf:predicate bioschema:expressedIn;
	rdf:object bkr:cond_pif4_0x3B_pif5;
	
	# Both base conditions and time points are conditions, so they're modelled as shown above
	agri:baseCondition 
		bkr:cond_wild_type, bkr:cond_far-red_light; 
	
	agri:timePoint bkr:cond_1_hours;

	agri:log2FoldChange -1.1;
	agri:pvalue 0.02169;
	agri:evidence bkr:exp_E-GEOD-16333;
.