Merge pull request #151 from joerivandervelde/main

Update resources

generated/art-decor/fair-genomes_en-US.xml

@@ -204160,6 +204160,15 @@ Options for Pre-filled, ready-to-use reagent cartridges intented to improve chem
 <concept code="https://w3id.org/fair-genomes/resource/FG_0000739" codeSystem="2.16.840.1.113883.2.4.3.11.60.120.5.12" codeSystemName="FG" displayName="ClearSeq Inherited Disease, 16, XT by Agilent Technologies" level="0" type="L">
 <designation language="en-US" type="preferred" displayName="ClearSeq Inherited Disease, 16, XT by Agilent Technologies sourced from https://www.biocompare.com, accessed May 2020."/>
 </concept>
+<concept code="https://w3id.org/fair-genomes/resource/FG_0000747" codeSystem="2.16.840.1.113883.2.4.3.11.60.120.5.12" codeSystemName="FG" displayName="Accel-Amplicon Plus Panel by Swift Biosciences" level="0" type="L">
+<designation language="en-US" type="preferred" displayName="Accel-Amplicon Plus Panel by Swift Biosciences"/>
+</concept>
+<concept code="https://w3id.org/fair-genomes/resource/FG_0000748" codeSystem="2.16.840.1.113883.2.4.3.11.60.120.5.12" codeSystemName="FG" displayName="TruSight Oncology 500 by Illumina" level="0" type="L">
+<designation language="en-US" type="preferred" displayName="TruSight Oncology 500 by Illumina"/>
+</concept>
+<concept code="https://w3id.org/fair-genomes/resource/FG_0000749" codeSystem="2.16.840.1.113883.2.4.3.11.60.120.5.12" codeSystemName="FG" displayName="SeqCap EZ Choice Library SR by Roche NimbleGen" level="0" type="L">
+<designation language="en-US" type="preferred" displayName="SeqCap EZ Choice Library SR by Roche NimbleGen"/>
+</concept>
 <concept code="https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-dna-pcr-free.html" codeSystem="2.16.840.1.113883.2.4.3.11.60.120.5.33" codeSystemName="Illumina" displayName="Illumina TruSeq DNA PCR-Free" level="0" type="L">
 <designation language="en-US" type="preferred" displayName="Illumina TruSeq DNA PCR-Free provides simple, all-inclusive library preparation for whole-genome sequencing applications."/>
 </concept>

generated/latex/fair-genomes.tex

@@ -6,7 +6,7 @@
 \textbf{FAIR Genomes metadata schema}
 \newline
 
-The FAIR Genomes semantic metadata schema to power reuse of NGS data in research and healthcare. Version 1.3-SNAPSHOT, 2022-02-28. This model consists of 9 modules that contain 112 metadata elements and 85361 lookups in total (excluding null flavors).
+The FAIR Genomes semantic metadata schema to power reuse of NGS data in research and healthcare. Version 1.3-SNAPSHOT, 2022-02-28. This model consists of 9 modules that contain 112 metadata elements and 85367 lookups in total (excluding null flavors).
 
 \begin{table}[htb]
 \begin{tabular}{lll}
@@ -167,9 +167,9 @@
 Sampleprep identifier & NCIT:C132299 & UniqueID \\
 Belongs to material & NCIT:C25683 & Reference to Material \\
 Input amount & AFRL:0000010 & Integer \\
-Library preparation kit & GENEPIO:0000085 & NGSKits lookup (616 choices) \\
+Library preparation kit & GENEPIO:0000085 & NGSKits lookup (619 choices) \\
 PCR free & NCIT:C17003 & Boolean \\
-Target enrichment kit & NCIT:C154307 & NGSKits lookup (616 choices) \\
+Target enrichment kit & NCIT:C154307 & NGSKits lookup (619 choices) \\
 UMIs present & EFO:0010199 & Boolean \\
 Intended insert size & FG:0000001 & Integer \\
 Intended read length & NCIT:C153362 & Integer \\

generated/markdown/fairgenomes-semantic-model.md

@@ -1,6 +1,6 @@
 # FAIR Genomes metadata schema
 
-The FAIR Genomes semantic metadata schema to power reuse of NGS data in research and healthcare. Version 1.3-SNAPSHOT, 2022-02-28. This model consists of __9 modules__ that contain __112 metadata elements__ and __85361 lookups__ in total (excluding null flavors).
+The FAIR Genomes semantic metadata schema to power reuse of NGS data in research and healthcare. Version 1.3-SNAPSHOT, 2022-02-28. This model consists of __9 modules__ that contain __112 metadata elements__ and __85367 lookups__ in total (excluding null flavors).
 
 ## Module overview
 
@@ -140,9 +140,9 @@ A sample preparation for a nucleic acids sequencing assay. Ontology: [OBI:000190
 | Sampleprep identifier | A unique proper name or character sequence that identifies this particular sample preparation. | [NCIT:C132299](http://purl.obolibrary.org/obo/NCIT_C132299) | UniqueID |
 | Belongs to material | Reference to the source material from which this sample was prepared. | [NCIT:C25683](http://purl.obolibrary.org/obo/NCIT_C25683) | Reference to instances of Material |
 | Input amount | Amount of input material in nanogram (ng). | [AFRL:0000010](http://purl.allotrope.org/ontologies/role#AFRL_0000010) | Integer |
-| Library preparation kit | Pre-filled, ready-to-use reagent cartridges intented to improve chemistry, cluster density and read length as well as improve quality (Q) scores for this sample. Reagent components are encoded to interact with the sequencing system to validate compatibility with user-defined applications. | [GENEPIO:0000085](http://purl.obolibrary.org/obo/GENEPIO_0000085) | [NGSKits](../../lookups/NGSKits.txt) lookup (616 choices [of type](http://purl.obolibrary.org/obo/GENEPIO_0000081)) |
+| Library preparation kit | Pre-filled, ready-to-use reagent cartridges intented to improve chemistry, cluster density and read length as well as improve quality (Q) scores for this sample. Reagent components are encoded to interact with the sequencing system to validate compatibility with user-defined applications. | [GENEPIO:0000085](http://purl.obolibrary.org/obo/GENEPIO_0000085) | [NGSKits](../../lookups/NGSKits.txt) lookup (619 choices [of type](http://purl.obolibrary.org/obo/GENEPIO_0000081)) |
 | PCR free | Indicates whether a polymerase chain reaction (PCR) was used to prepare this sample. PCR is a method for amplifying a DNA base sequence using multiple rounds of heat denaturation of the DNA and annealing of oligonucleotide primers complementary to flanking regions in the presence of a heat-stable polymerase. | [NCIT:C17003](http://purl.obolibrary.org/obo/NCIT_C17003) | Boolean |
-| Target enrichment kit | Indicates which target enrichment kit was used to prepare this sample. Target enrichment is a pre-sequencing DNA preparation step where DNA sequences are either directly amplified (amplicon or multiplex PCR-based) or captured (hybrid capture-based) in order to only focus on specific regions of a genome or DNA sample. | [NCIT:C154307](http://purl.obolibrary.org/obo/NCIT_C154307) | [NGSKits](../../lookups/NGSKits.txt) lookup (616 choices [of type](http://purl.obolibrary.org/obo/GENEPIO_0000081)) |
+| Target enrichment kit | Indicates which target enrichment kit was used to prepare this sample. Target enrichment is a pre-sequencing DNA preparation step where DNA sequences are either directly amplified (amplicon or multiplex PCR-based) or captured (hybrid capture-based) in order to only focus on specific regions of a genome or DNA sample. | [NCIT:C154307](http://purl.obolibrary.org/obo/NCIT_C154307) | [NGSKits](../../lookups/NGSKits.txt) lookup (619 choices [of type](http://purl.obolibrary.org/obo/GENEPIO_0000081)) |
 | UMIs present | Indicates whether any unique molecular identifiers (UMIs) are present. An UMI barcode is a short nucleotide sequence that is used to identify reads originating from an individual mRNA molecule. | [EFO:0010199](http://www.ebi.ac.uk/efo/EFO_0010199) | Boolean |
 | Intended insert size | In paired-end sequencing, the DNA between the adapter sequences is the insert. The length of this sequence is known as the insert size, not to be confused with the inner distance between reads. So, fragment length equals read adapter length (2x) plus insert size, and insert size equals read lenght (2x) plus inner distance. | [FG:0000001](https://w3id.org/fair-genomes/resource/FG_0000001) | Integer |
 | Intended read length | The number of nucleotides intended to be ordered from each side of a nucleic acid fragment obtained after the completion of a sequencing process. | [NCIT:C153362](http://purl.obolibrary.org/obo/NCIT_C153362) | Integer |

generated/molgenis-emx/samplepreparation_librarypreparationkit.tsv

@@ -615,6 +615,9 @@ ClearSeq Inherited Disease Plus, 96, XT by Agilent Technologies	ClearSeq Inherit
 ClearSeq Inherited Disease Plus, 96, XT2 by Agilent Technologies	ClearSeq Inherited Disease Plus, 96, XT2 by Agilent Technologies sourced from https://www.biocompare.com, accessed May 2020.	FG	0000738	https://w3id.org/fair-genomes/resource/FG_0000738
 ClearSeq Inherited Disease, 16, XT by Agilent Technologies	ClearSeq Inherited Disease, 16, XT by Agilent Technologies sourced from https://www.biocompare.com, accessed May 2020.	FG	0000739	https://w3id.org/fair-genomes/resource/FG_0000739
 Illumina TruSeq DNA PCR-Free	Illumina TruSeq DNA PCR-Free provides simple, all-inclusive library preparation for whole-genome sequencing applications.	Illumina	truseq-dna-pcr-free	https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-dna-pcr-free.html
+Accel-Amplicon Plus Panel by Swift Biosciences	Accel-Amplicon Plus Panel by Swift Biosciences	FG	0000747	https://w3id.org/fair-genomes/resource/FG_0000747
+TruSight Oncology 500 by Illumina	TruSight Oncology 500 by Illumina	FG	0000748	https://w3id.org/fair-genomes/resource/FG_0000748
+SeqCap EZ Choice Library SR by Roche NimbleGen	SeqCap EZ Choice Library SR by Roche NimbleGen	FG	0000749	https://w3id.org/fair-genomes/resource/FG_0000749
 NoInformation (NI, nullflavor)	The value is exceptional (missing, omitted, incomplete, improper). No information as to the reason for being an exceptional value is provided. This is the most general exceptional value. It is also the default exceptional value.	HL7	NI	http://terminology.hl7.org/CodeSystem/v3-NullFlavor#NI
 Invalid (INV, nullflavor)	The value as represented in the instance is not a member of the set of permitted data values in the constrained value domain of a variable.	HL7	INV	http://terminology.hl7.org/CodeSystem/v3-NullFlavor#INV
 Derived (DER, nullflavor)	An actual value may exist, but it must be derived from the provided information (usually an EXPR generic data type extension will be used to convey the derivation expression .	HL7	DER	http://terminology.hl7.org/CodeSystem/v3-NullFlavor#DER

generated/molgenis-emx/samplepreparation_targetenrichmentkit.tsv

@@ -615,6 +615,9 @@ ClearSeq Inherited Disease Plus, 96, XT by Agilent Technologies	ClearSeq Inherit
 ClearSeq Inherited Disease Plus, 96, XT2 by Agilent Technologies	ClearSeq Inherited Disease Plus, 96, XT2 by Agilent Technologies sourced from https://www.biocompare.com, accessed May 2020.	FG	0000738	https://w3id.org/fair-genomes/resource/FG_0000738
 ClearSeq Inherited Disease, 16, XT by Agilent Technologies	ClearSeq Inherited Disease, 16, XT by Agilent Technologies sourced from https://www.biocompare.com, accessed May 2020.	FG	0000739	https://w3id.org/fair-genomes/resource/FG_0000739
 Illumina TruSeq DNA PCR-Free	Illumina TruSeq DNA PCR-Free provides simple, all-inclusive library preparation for whole-genome sequencing applications.	Illumina	truseq-dna-pcr-free	https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-dna-pcr-free.html
+Accel-Amplicon Plus Panel by Swift Biosciences	Accel-Amplicon Plus Panel by Swift Biosciences	FG	0000747	https://w3id.org/fair-genomes/resource/FG_0000747
+TruSight Oncology 500 by Illumina	TruSight Oncology 500 by Illumina	FG	0000748	https://w3id.org/fair-genomes/resource/FG_0000748
+SeqCap EZ Choice Library SR by Roche NimbleGen	SeqCap EZ Choice Library SR by Roche NimbleGen	FG	0000749	https://w3id.org/fair-genomes/resource/FG_0000749
 NoInformation (NI, nullflavor)	The value is exceptional (missing, omitted, incomplete, improper). No information as to the reason for being an exceptional value is provided. This is the most general exceptional value. It is also the default exceptional value.	HL7	NI	http://terminology.hl7.org/CodeSystem/v3-NullFlavor#NI
 Invalid (INV, nullflavor)	The value as represented in the instance is not a member of the set of permitted data values in the constrained value domain of a variable.	HL7	INV	http://terminology.hl7.org/CodeSystem/v3-NullFlavor#INV
 Derived (DER, nullflavor)	An actual value may exist, but it must be derived from the provided information (usually an EXPR generic data type extension will be used to convey the derivation expression .	HL7	DER	http://terminology.hl7.org/CodeSystem/v3-NullFlavor#DER

generated/molgenis-emx2/librarypreparationkit.csv

@@ -615,6 +615,9 @@ name,definition,codesystem,code,ontologyTermURI
 "ClearSeq Inherited Disease Plus, 96, XT2 by Agilent Technologies","ClearSeq Inherited Disease Plus, 96, XT2 by Agilent Technologies sourced from https://www.biocompare.com, accessed May 2020.","FG","0000738","https://w3id.org/fair-genomes/resource/FG_0000738"
 "ClearSeq Inherited Disease, 16, XT by Agilent Technologies","ClearSeq Inherited Disease, 16, XT by Agilent Technologies sourced from https://www.biocompare.com, accessed May 2020.","FG","0000739","https://w3id.org/fair-genomes/resource/FG_0000739"
 "Illumina TruSeq DNA PCR-Free","Illumina TruSeq DNA PCR-Free provides simple, all-inclusive library preparation for whole-genome sequencing applications.","Illumina","truseq-dna-pcr-free","https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-dna-pcr-free.html"
+"Accel-Amplicon Plus Panel by Swift Biosciences","Accel-Amplicon Plus Panel by Swift Biosciences","FG","0000747","https://w3id.org/fair-genomes/resource/FG_0000747"
+"TruSight Oncology 500 by Illumina","TruSight Oncology 500 by Illumina","FG","0000748","https://w3id.org/fair-genomes/resource/FG_0000748"
+"SeqCap EZ Choice Library SR by Roche NimbleGen","SeqCap EZ Choice Library SR by Roche NimbleGen","FG","0000749","https://w3id.org/fair-genomes/resource/FG_0000749"
 "NoInformation (NI, nullflavor)","The value is exceptional (missing, omitted, incomplete, improper). No information as to the reason for being an exceptional value is provided. This is the most general exceptional value. It is also the default exceptional value.","HL7","NI","http://terminology.hl7.org/CodeSystem/v3-NullFlavor#NI"
 "Invalid (INV, nullflavor)","The value as represented in the instance is not a member of the set of permitted data values in the constrained value domain of a variable.","HL7","INV","http://terminology.hl7.org/CodeSystem/v3-NullFlavor#INV"
 "Derived (DER, nullflavor)","An actual value may exist, but it must be derived from the provided information (usually an EXPR generic data type extension will be used to convey the derivation expression .","HL7","DER","http://terminology.hl7.org/CodeSystem/v3-NullFlavor#DER"

generated/molgenis-emx2/targetenrichmentkit.csv

@@ -615,6 +615,9 @@ name,definition,codesystem,code,ontologyTermURI
 "ClearSeq Inherited Disease Plus, 96, XT2 by Agilent Technologies","ClearSeq Inherited Disease Plus, 96, XT2 by Agilent Technologies sourced from https://www.biocompare.com, accessed May 2020.","FG","0000738","https://w3id.org/fair-genomes/resource/FG_0000738"
 "ClearSeq Inherited Disease, 16, XT by Agilent Technologies","ClearSeq Inherited Disease, 16, XT by Agilent Technologies sourced from https://www.biocompare.com, accessed May 2020.","FG","0000739","https://w3id.org/fair-genomes/resource/FG_0000739"
 "Illumina TruSeq DNA PCR-Free","Illumina TruSeq DNA PCR-Free provides simple, all-inclusive library preparation for whole-genome sequencing applications.","Illumina","truseq-dna-pcr-free","https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-dna-pcr-free.html"
+"Accel-Amplicon Plus Panel by Swift Biosciences","Accel-Amplicon Plus Panel by Swift Biosciences","FG","0000747","https://w3id.org/fair-genomes/resource/FG_0000747"
+"TruSight Oncology 500 by Illumina","TruSight Oncology 500 by Illumina","FG","0000748","https://w3id.org/fair-genomes/resource/FG_0000748"
+"SeqCap EZ Choice Library SR by Roche NimbleGen","SeqCap EZ Choice Library SR by Roche NimbleGen","FG","0000749","https://w3id.org/fair-genomes/resource/FG_0000749"
 "NoInformation (NI, nullflavor)","The value is exceptional (missing, omitted, incomplete, improper). No information as to the reason for being an exceptional value is provided. This is the most general exceptional value. It is also the default exceptional value.","HL7","NI","http://terminology.hl7.org/CodeSystem/v3-NullFlavor#NI"
 "Invalid (INV, nullflavor)","The value as represented in the instance is not a member of the set of permitted data values in the constrained value domain of a variable.","HL7","INV","http://terminology.hl7.org/CodeSystem/v3-NullFlavor#INV"
 "Derived (DER, nullflavor)","An actual value may exist, but it must be derived from the provided information (usually an EXPR generic data type extension will be used to convey the derivation expression .","HL7","DER","http://terminology.hl7.org/CodeSystem/v3-NullFlavor#DER"

generated/ontology/fair-genomes-ngskits.ttl

@@ -3692,6 +3692,24 @@ fg:Sample_preparation_Library_preparation_kit_Illumina_TruSeq_DNA_PCR-Free a obo
   dc:description "Illumina TruSeq DNA PCR-Free provides simple, all-inclusive library preparation for whole-genome sequencing applications.";
   rdfs:isDefinedBy <https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-dna-pcr-free.html> .
 
+fg:Sample_preparation_Library_preparation_kit_Accel-Amplicon_Plus_Panel_by_Swift_Biosciences
+  a obo:GENEPIO_0000081;
+  rdfs:label "Accel-Amplicon Plus Panel by Swift Biosciences";
+  dc:description "Accel-Amplicon Plus Panel by Swift Biosciences";
+  rdfs:isDefinedBy <https://w3id.org/fair-genomes/resource/FG_0000747> .
+
+fg:Sample_preparation_Library_preparation_kit_TruSight_Oncology_500_by_Illumina a
+    obo:GENEPIO_0000081;
+  rdfs:label "TruSight Oncology 500 by Illumina";
+  dc:description "TruSight Oncology 500 by Illumina";
+  rdfs:isDefinedBy <https://w3id.org/fair-genomes/resource/FG_0000748> .
+
+fg:Sample_preparation_Library_preparation_kit_SeqCap_EZ_Choice_Library_SR_by_Roche_NimbleGen
+  a obo:GENEPIO_0000081;
+  rdfs:label "SeqCap EZ Choice Library SR by Roche NimbleGen";
+  dc:description "SeqCap EZ Choice Library SR by Roche NimbleGen";
+  rdfs:isDefinedBy <https://w3id.org/fair-genomes/resource/FG_0000749> .
+
 <https://w3id.org/fair-genomes/ontology/Sample_preparation_Library_preparation_kit_NoInformation_(NI,_nullflavor)>
   a obo:GENEPIO_0000081;
   rdfs:label "NoInformation (NI, nullflavor)";
@@ -7470,6 +7488,23 @@ fg:Sample_preparation_Target_enrichment_kit_Illumina_TruSeq_DNA_PCR-Free a obo:G
   dc:description "Illumina TruSeq DNA PCR-Free provides simple, all-inclusive library preparation for whole-genome sequencing applications.";
   rdfs:isDefinedBy <https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-dna-pcr-free.html> .
 
+fg:Sample_preparation_Target_enrichment_kit_Accel-Amplicon_Plus_Panel_by_Swift_Biosciences
+  a obo:GENEPIO_0000081;
+  rdfs:label "Accel-Amplicon Plus Panel by Swift Biosciences";
+  dc:description "Accel-Amplicon Plus Panel by Swift Biosciences";
+  rdfs:isDefinedBy <https://w3id.org/fair-genomes/resource/FG_0000747> .
+
+fg:Sample_preparation_Target_enrichment_kit_TruSight_Oncology_500_by_Illumina a obo:GENEPIO_0000081;
+  rdfs:label "TruSight Oncology 500 by Illumina";
+  dc:description "TruSight Oncology 500 by Illumina";
+  rdfs:isDefinedBy <https://w3id.org/fair-genomes/resource/FG_0000748> .
+
+fg:Sample_preparation_Target_enrichment_kit_SeqCap_EZ_Choice_Library_SR_by_Roche_NimbleGen
+  a obo:GENEPIO_0000081;
+  rdfs:label "SeqCap EZ Choice Library SR by Roche NimbleGen";
+  dc:description "SeqCap EZ Choice Library SR by Roche NimbleGen";
+  rdfs:isDefinedBy <https://w3id.org/fair-genomes/resource/FG_0000749> .
+
 <https://w3id.org/fair-genomes/ontology/Sample_preparation_Target_enrichment_kit_NoInformation_(NI,_nullflavor)>
   a obo:GENEPIO_0000081;
   rdfs:label "NoInformation (NI, nullflavor)";