From 63a20df7c5848ace9878e09543ce01b412151694 Mon Sep 17 00:00:00 2001
From: bedroesb <bedro@psb.vib-ugent.be>
Date: Tue, 16 Nov 2021 20:14:41 +0100
Subject: [PATCH] nicer listing

---
 pages/your_domain/plant_sciences.md | 56 ++++++++++++++++++-----------
 1 file changed, 35 insertions(+), 21 deletions(-)

diff --git a/pages/your_domain/plant_sciences.md b/pages/your_domain/plant_sciences.md
index 5eb009f61..76b7f1661 100644
--- a/pages/your_domain/plant_sciences.md
+++ b/pages/your_domain/plant_sciences.md
@@ -83,36 +83,50 @@ For managers of plant phenotyping data repositories that support a project or in
 ### Solutions
 In order to ensure interoperability of VCF files, the following VCF meta-information lines should be used:
 * Obligatory meta-information line :  
-  * ##fileformat : file format.  
-    Examples:  
+  * **`##fileformat`** : file format.  
+    Examples:
+    ```
     ##fileformat=VCFv4.3  
-    ##fileformat=VCFv4.1  
+    ##fileformat=VCFv4.1
+    ```
 * Recommended meta-information lines :  
-  * ##bioinformatics_source (URL or URI): Analytic approach usually consisting of chains of bioinformatics tools for creating the VCF file specified as the DOI of a publication, or more generally as URL/URI, like a public repository for the scripts used.  
-    Examples:  
+  * **`##bioinformatics_source (URL or URI)`**: Analytic approach usually consisting of chains of bioinformatics tools for creating the VCF file specified as the DOI of a publication, or more generally as URL/URI, like a public repository for the scripts used.  
+    Examples:
+    ```
     ##bioinformatics_source=”doi.org/10.1038/s41588-018-0266-x”  
-    ##bioinformatics_source=”doi.org/10.3389/fpls.2021.628439”  
-  * ##reference_ac (assembly_accession): accession number, including the version, of the reference sequence on which the variation data of the present VCF is based.  
-    Examples:  
+    ##bioinformatics_source=”doi.org/10.3389/fpls.2021.628439”
+    ```
+  * **`##reference_ac (assembly_accession)`**: accession number, including the version, of the reference sequence on which the variation data of the present VCF is based.  
+    Examples:
+    ```
     ##reference_ac=GCA_902498975.1  
-    ##reference_ac=GCA_000005005.5  
-  * ##reference_url (DOI): a DOI (or URL/URI) for downloading of this reference genome, preferably from one INSDC archive.  
-    Examples:  
+    ##reference_ac=GCA_000005005.5 
+    ```
+  * **`##reference_url (DOI)`**: a DOI (or URL/URI) for downloading of this reference genome, preferably from one INSDC archive.  
+    Examples: 
+    ```
     ##reference_url=”ftp.ncbi.nlm.nih.gov/genomes/all/GCA/902/498/975/GCA_902498975.1_Morex_v2.0/GCA_902498975.1_Morex_v2.0_genomic.fna.gz”  
-    ##reference_url=”ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/005/005/GCA_000005005.5_B73_RefGen_v3/GCA_000005005.5_B73_RefGen_v3_genomic.fna.gz”  
-  * ##contig (<ID=ctg1, length=sequence_length, assembly=gca_accession, md5=md5_hash, species=species_of_interest>) : The individual sequence(s) of the reference genome  
-    Examples:  
+    ##reference_url=”ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/005/005/GCA_000005005.5_B73_RefGen_v3/GCA_000005005.5_B73_RefGen_v3_genomic.fna.gz”
+    ```
+  * **`##contig (<ID=ctg1, length=sequence_length, assembly=gca_accession, md5=md5_hash, species=species_of_interest>)`** : The individual sequence(s) of the reference genome  
+    Examples:
+    ```
     ##contig=<ID=chr1H,length=522466905,assembly=GCA_902498975.1,md5=8d21a35cc68340ecf40e2a8dec9428fa,species="Hordeum vulgare">  
-    ##contig=<ID=GK000031.3,length=301433382,assembly=GCA_000005005.5,md5=74dfe85ad898416814fa98e8d7048f76,species=”Zea mays”>  
-  * ##SAMPLE(<ID=BioSample_accession, DOI=url, Original=Accession_number, Name=Genotype_name>) : Describe the material whose variants are given in the genotype call columns in greater detail and can be extended using the specifications of the VCF format.  
-    Examples:  
+    ##contig=<ID=GK000031.3,length=301433382,assembly=GCA_000005005.5,md5=74dfe85ad898416814fa98e8d7048f76,species=”Zea mays”>
+    ```
+  * **`##SAMPLE(<ID=BioSample_accession, DOI=url, Original=Accession_number, Name=Genotype_name>)`** : Describe the material whose variants are given in the genotype call columns in greater detail and can be extended using the specifications of the VCF format.  
+    Examples: 
+    ```
     ##SAMPLE=<ID=SAMEA7836897,DOI="doi.org/10.25642/IPK/GBIS/17527",Original="HOR 1361 BRG",Name="Hordeum vulgare L. convar. vulgare var. densum Sér.">  
-    ##SAMPLE=<ID=SAMEA9111398,DOI=”www.ipk-gatersleben.de”,Original=”CAPFRU07”,Name=”RCAT077650”>  
+    ##SAMPLE=<ID=SAMEA9111398,DOI=”www.ipk-gatersleben.de”,Original=”CAPFRU07”,Name=”RCAT077650”>
+    ```
 * Optional meta-information lines :  
-  * ##fileDate: creation date of the VCF in the basic form without separator: YYYYMMDD  
-    Examples:  
+  * **`##fileDate`**: creation date of the VCF in the basic form without separator: YYYYMMDD  
+    Examples:
+    ```
     ##fileDate=20211028  
-    ##fileDate=20120316  
+    ##fileDate=20120316
+    ```
   * In case of adding new fields : Please check the official format specifications to avoid redundancy and possible incompatibilities.