Fixes fairgenomes#119

joerivandervelde · Jan 24, 2022 · de715f6 · de715f6
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Showing 9 changed files with 19 additions and 19 deletions.
diff --git a/fair-genomes.yml b/fair-genomes.yml
@@ -466,8 +466,8 @@ modules:
             description: Method used to determine the order of bases in a nucleic acid sequence.
             ontology: FIX:0000704 [http://purl.obolibrary.org/obo/FIX_0000704]
             values: LookupOne [lookups/SequencingMethods.txt], ofType [http://purl.obolibrary.org/obo/NCIT_C17565]
-          - name: Average read depth
-            description: The average number of times a particular locus (site, nucleotide, amplicon, region) was sequenced.
+          - name: Median read depth
+            description: The median number of times a particular locus (site, nucleotide, amplicon, region) was sequenced.
             ontology: NCIT:C155320 [http://purl.obolibrary.org/obo/NCIT_C155320]
             values: Integer
           - name: Observed read length

diff --git a/generated/art-decor/fair-genomes_en-US.xml b/generated/art-decor/fair-genomes_en-US.xml
@@ -715,20 +715,20 @@ href="http://art-decor.org/ADAR/rv/DECOR.sch" type="application/xml" schematypes
 <name language="en-US">Sequencing</name>
 <desc language="en-US">The determination of complete (typically nucleotide) sequences, including those of genomes (full genome sequencing, de novo sequencing and resequencing), amplicons and transcriptomes.</desc>
 <property name="url">http://edamontology.org/topic_3168</property>
-<concept id="2.16.840.1.113883.2.4.3.11.60.120.2.101" statusCode="draft" effectiveDate="2021-07-20T24:00:00" type="item">
-<name language="en-US">Average read depth</name>
-<desc language="en-US">The average number of times a particular locus (site, nucleotide, amplicon, region) was sequenced.</desc>
-<property name="url">http://purl.obolibrary.org/obo/NCIT_C155320</property>
-<valueDomain type="count">
-</valueDomain>
-</concept>
 <concept id="2.16.840.1.113883.2.4.3.11.60.120.2.96" statusCode="draft" effectiveDate="2021-07-20T24:00:00" type="item">
 <name language="en-US">Belongs to sample</name>
 <desc language="en-US">Reference to the prepared sample, i.e. the source that was sequenced.</desc>
 <property name="url">http://purl.obolibrary.org/obo/NCIT_C25683</property>
 <valueDomain type="string">
 </valueDomain>
 </concept>
+<concept id="2.16.840.1.113883.2.4.3.11.60.120.2.101" statusCode="draft" effectiveDate="2021-07-20T24:00:00" type="item">
+<name language="en-US">Median read depth</name>
+<desc language="en-US">The median number of times a particular locus (site, nucleotide, amplicon, region) was sequenced.</desc>
+<property name="url">http://purl.obolibrary.org/obo/NCIT_C155320</property>
+<valueDomain type="count">
+</valueDomain>
+</concept>
 <concept id="2.16.840.1.113883.2.4.3.11.60.120.2.103" statusCode="draft" effectiveDate="2021-07-20T24:00:00" type="item">
 <name language="en-US">Observed insert size</name>
 <desc language="en-US">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.</desc>
@@ -1052,7 +1052,7 @@ href="http://art-decor.org/ADAR/rv/DECOR.sch" type="application/xml" schematypes
 <terminologyAssociation conceptId="2.16.840.1.113883.2.4.3.11.60.120.2.98" conceptFlexibility="2021-07-20T24:00:00" code="0000071" codeSystem="2.16.840.1.113883.2.4.3.11.60.120.5.7" codeSystemName="GENEPIO" displayName="Sequencing platform" effectiveDate="2021-07-20T24:00:00"/>
 <terminologyAssociation conceptId="2.16.840.1.113883.2.4.3.11.60.120.2.99" conceptFlexibility="2021-07-20T24:00:00" code="0001921" codeSystem="2.16.840.1.113883.2.4.3.11.60.120.5.7" codeSystemName="GENEPIO" displayName="Sequencing instrument model" effectiveDate="2021-07-20T24:00:00"/>
 <terminologyAssociation conceptId="2.16.840.1.113883.2.4.3.11.60.120.2.100" conceptFlexibility="2021-07-20T24:00:00" code="0000704" codeSystem="2.16.840.1.113883.2.4.3.11.60.120.5.33" codeSystemName="FIX" displayName="Sequencing method" effectiveDate="2021-07-20T24:00:00"/>
-<terminologyAssociation conceptId="2.16.840.1.113883.2.4.3.11.60.120.2.101" conceptFlexibility="2021-07-20T24:00:00" code="C155320" codeSystem="2.16.840.1.113883.2.4.3.11.60.120.5.0" codeSystemName="NCIT" displayName="Average read depth" effectiveDate="2021-07-20T24:00:00"/>
+<terminologyAssociation conceptId="2.16.840.1.113883.2.4.3.11.60.120.2.101" conceptFlexibility="2021-07-20T24:00:00" code="C155320" codeSystem="2.16.840.1.113883.2.4.3.11.60.120.5.0" codeSystemName="NCIT" displayName="Median read depth" effectiveDate="2021-07-20T24:00:00"/>
 <terminologyAssociation conceptId="2.16.840.1.113883.2.4.3.11.60.120.2.102" conceptFlexibility="2021-07-20T24:00:00" code="C153362" codeSystem="2.16.840.1.113883.2.4.3.11.60.120.5.0" codeSystemName="NCIT" displayName="Observed read length" effectiveDate="2021-07-20T24:00:00"/>
 <terminologyAssociation conceptId="2.16.840.1.113883.2.4.3.11.60.120.2.103" conceptFlexibility="2021-07-20T24:00:00" code="0000002" codeSystem="2.16.840.1.113883.2.4.3.11.60.120.5.9" codeSystemName="FG" displayName="Observed insert size" effectiveDate="2021-07-20T24:00:00"/>
 <terminologyAssociation conceptId="2.16.840.1.113883.2.4.3.11.60.120.2.104" conceptFlexibility="2021-07-20T24:00:00" code="0000089" codeSystem="2.16.840.1.113883.2.4.3.11.60.120.5.7" codeSystemName="GENEPIO" displayName="Percentage Q30" effectiveDate="2021-07-20T24:00:00"/>

diff --git a/generated/java/org/fairgenomes/generated/Sequencing.java b/generated/java/org/fairgenomes/generated/Sequencing.java
@@ -9,7 +9,7 @@ public class Sequencing {
 	public String sequencingplatform;
 	public String sequencinginstrumentmodel;
 	public String sequencingmethod;
-	public int averagereaddepth;
+	public int medianreaddepth;
 	public int observedreadlength;
 	public int observedinsertsize;
 	public double percentageq30;

diff --git a/generated/latex/fair-genomes.tex b/generated/latex/fair-genomes.tex
@@ -186,7 +186,7 @@
 Sequencing platform & GENEPIO:0000071 & SequencingPlatform lookup (7 choices) \\
 Sequencing instrument model & GENEPIO:0001921 & SequencingInstrumentModels lookup (39 choices) \\
 Sequencing method & FIX:0000704 & SequencingMethods lookup (35 choices) \\
-Average read depth & NCIT:C155320 & Integer \\
+Median read depth & NCIT:C155320 & Integer \\
 Observed read length & NCIT:C153362 & Integer \\
 Observed insert size & FG:0000002 & Integer \\
 Percentage Q30 & GENEPIO:0000089 & Decimal \\

diff --git a/generated/markdown/fairgenomes-semantic-model.md b/generated/markdown/fairgenomes-semantic-model.md
@@ -156,7 +156,7 @@ The determination of complete (typically nucleotide) sequences, including those
 | Sequencing platform | The used sequencing platform (i.e. brand, name of a company that produces sequencer equipment). | [GENEPIO:0000071](http://purl.obolibrary.org/obo/GENEPIO_0000071) | [SequencingPlatform](../../lookups/SequencingPlatform.txt) lookup (7 choices [of type](http://purl.obolibrary.org/obo/GENEPIO_0000071)) |
 | Sequencing instrument model | The used product name and model number of a manufacturer's genomic (dna) sequencer. | [GENEPIO:0001921](http://purl.obolibrary.org/obo/GENEPIO_0001921) | [SequencingInstrumentModels](../../lookups/SequencingInstrumentModels.txt) lookup (39 choices [of type](http://purl.obolibrary.org/obo/GENEPIO_0001921)) |
 | Sequencing method | Method used to determine the order of bases in a nucleic acid sequence. | [FIX:0000704](http://purl.obolibrary.org/obo/FIX_0000704) | [SequencingMethods](../../lookups/SequencingMethods.txt) lookup (35 choices [of type](http://purl.obolibrary.org/obo/NCIT_C17565)) |
-| Average read depth | The average number of times a particular locus (site, nucleotide, amplicon, region) was sequenced. | [NCIT:C155320](http://purl.obolibrary.org/obo/NCIT_C155320) | Integer |
+| Median read depth | The median number of times a particular locus (site, nucleotide, amplicon, region) was sequenced. | [NCIT:C155320](http://purl.obolibrary.org/obo/NCIT_C155320) | Integer |
 | Observed read length | The number of nucleotides successfully 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 |
 | Observed 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:0000002](https://w3id.org/fair-genomes/resource/FG_0000002) | Integer |
 | Percentage Q30 | Percentage of reads with a Phred quality score over 30, which indicates less than a 1/1000 chance that the base was called incorrectly. | [GENEPIO:0000089](http://purl.obolibrary.org/obo/GENEPIO_0000089) | Decimal |

diff --git a/generated/molgenis-emx/sequencing_attributes.tsv b/generated/molgenis-emx/sequencing_attributes.tsv
@@ -5,7 +5,7 @@ sequencingdate	Sequencing date	Date on which this sequencing assay was performed
 sequencingplatform	Sequencing platform	The used sequencing platform (i.e. brand, name of a company that produces sequencer equipment). (GENEPIO:0000071)	sequencing	xref	FALSE	FALSE	TRUE	TRUE	fair-genomes_sequencing_sequencingplatform
 sequencinginstrumentmodel	Sequencing instrument model	The used product name and model number of a manufacturer's genomic (dna) sequencer. (GENEPIO:0001921)	sequencing	xref	FALSE	FALSE	TRUE	TRUE	fair-genomes_sequencing_sequencinginstrumentmodel
 sequencingmethod	Sequencing method	Method used to determine the order of bases in a nucleic acid sequence. (FIX:0000704)	sequencing	xref	FALSE	FALSE	TRUE	TRUE	fair-genomes_sequencing_sequencingmethod
-averagereaddepth	Average read depth	The average number of times a particular locus (site, nucleotide, amplicon, region) was sequenced. (NCIT:C155320)	sequencing	int	FALSE	FALSE	TRUE	TRUE	
+medianreaddepth	Median read depth	The median number of times a particular locus (site, nucleotide, amplicon, region) was sequenced. (NCIT:C155320)	sequencing	int	FALSE	FALSE	TRUE	TRUE	
 observedreadlength	Observed read length	The number of nucleotides successfully ordered from each side of a nucleic acid fragment obtained after the completion of a sequencing process. (NCIT:C153362)	sequencing	int	FALSE	FALSE	TRUE	TRUE	
 observedinsertsize	Observed 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:0000002)	sequencing	int	FALSE	FALSE	TRUE	TRUE	
 percentageq30	Percentage Q30	Percentage of reads with a Phred quality score over 30, which indicates less than a 1/1000 chance that the base was called incorrectly. (GENEPIO:0000089)	sequencing	decimal	FALSE	FALSE	TRUE	TRUE	

diff --git a/generated/molgenis-emx2/molgenis.csv b/generated/molgenis-emx2/molgenis.csv
@@ -310,7 +310,7 @@ sequencing,sequencingdate,date,,,,"Date on which this sequencing assay was perfo
 sequencing,sequencingplatform,ref,,,sequencingplatform,"The used sequencing platform (i.e. brand, name of a company that produces sequencer equipment).",http://purl.obolibrary.org/obo/GENEPIO_0000071
 sequencing,sequencinginstrumentmodel,ref,,,sequencinginstrumentmodel,"The used product name and model number of a manufacturer's genomic (dna) sequencer.",http://purl.obolibrary.org/obo/GENEPIO_0001921
 sequencing,sequencingmethod,ref,,,sequencingmethod,"Method used to determine the order of bases in a nucleic acid sequence.",http://purl.obolibrary.org/obo/FIX_0000704
-sequencing,averagereaddepth,int,,,,"The average number of times a particular locus (site, nucleotide, amplicon, region) was sequenced.",http://purl.obolibrary.org/obo/NCIT_C155320
+sequencing,medianreaddepth,int,,,,"The median number of times a particular locus (site, nucleotide, amplicon, region) was sequenced.",http://purl.obolibrary.org/obo/NCIT_C155320
 sequencing,observedreadlength,int,,,,"The number of nucleotides successfully ordered from each side of a nucleic acid fragment obtained after the completion of a sequencing process.",http://purl.obolibrary.org/obo/NCIT_C153362
 sequencing,observedinsertsize,int,,,,"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.",https://w3id.org/fair-genomes/resource/FG_0000002
 sequencing,percentageq30,decimal,,,,"Percentage of reads with a Phred quality score over 30, which indicates less than a 1/1000 chance that the base was called incorrectly.",http://purl.obolibrary.org/obo/GENEPIO_0000089

diff --git a/generated/ontology/fair-genomes.ttl b/generated/ontology/fair-genomes.ttl
@@ -688,11 +688,11 @@ fg:Sequencing_Sequencing_method a owl:ObjectProperty;
   dc:description "Method used to determine the order of bases in a nucleic acid sequence.";
   rdfs:range obo:NCIT_C17565 .
 
-fg:Sequencing_Average_read_depth a owl:DatatypeProperty;
-  rdfs:label "Average read depth";
+fg:Sequencing_Median_read_depth a owl:DatatypeProperty;
+  rdfs:label "Median read depth";
   rdfs:domain fg:Sequencing;
   rdfs:isDefinedBy obo:NCIT_C155320;
-  dc:description "The average number of times a particular locus (site, nucleotide, amplicon, region) was sequenced." .
+  dc:description "The median number of times a particular locus (site, nucleotide, amplicon, region) was sequenced." .
 
 fg:Sequencing_Observed_read_length a owl:DatatypeProperty;
   rdfs:label "Observed read length";

diff --git a/generated/palga-codebook/CODEBOOK.tsv b/generated/palga-codebook/CODEBOOK.tsv
@@ -100,7 +100,7 @@ Sequencing date	Date on which this sequencing assay was performed.	GENEPIO	00000
 Sequencing platform	The used sequencing platform (i.e. brand, name of a company that produces sequencer equipment).	GENEPIO	0000071	ST	Sequencing platform	SequencingPlatform	single-select	{url=http://purl.obolibrary.org/obo/GENEPIO_0000071}	Sequencing	
 Sequencing instrument model	The used product name and model number of a manufacturer's genomic (dna) sequencer.	GENEPIO	0001921	ST	Sequencing instrument model	SequencingInstrumentModels	single-select	{url=http://purl.obolibrary.org/obo/GENEPIO_0001921}	Sequencing	
 Sequencing method	Method used to determine the order of bases in a nucleic acid sequence.	FIX	0000704	ST	Sequencing method	SequencingMethods	single-select	{url=http://purl.obolibrary.org/obo/FIX_0000704}	Sequencing	
-Average read depth	The average number of times a particular locus (site, nucleotide, amplicon, region) was sequenced.	NCIT	C155320	INT	Average read depth		text	{url=http://purl.obolibrary.org/obo/NCIT_C155320}	Sequencing	
+Median read depth	The median number of times a particular locus (site, nucleotide, amplicon, region) was sequenced.	NCIT	C155320	INT	Median read depth		text	{url=http://purl.obolibrary.org/obo/NCIT_C155320}	Sequencing	
 Observed read length	The number of nucleotides successfully ordered from each side of a nucleic acid fragment obtained after the completion of a sequencing process.	NCIT	C153362	INT	Observed read length		text	{url=http://purl.obolibrary.org/obo/NCIT_C153362}	Sequencing	
 Observed 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	0000002	INT	Observed insert size		text	{url=https://w3id.org/fair-genomes/resource/FG_0000002}	Sequencing	
 Percentage Q30	Percentage of reads with a Phred quality score over 30, which indicates less than a 1/1000 chance that the base was called incorrectly.	GENEPIO	0000089	DECIMAL	Percentage Q30		text	{url=http://purl.obolibrary.org/obo/GENEPIO_0000089}	Sequencing