UPD docs, FIX tests

client/src/components/home/HomeFeatures.vue

@@ -14,15 +14,23 @@
           </span>
           <div class="text-900 text-xl mb-3 font-medium dark:text-white/80">Data format</div>
           <span class="text-700 line-height-3 dark:text-white/80">
-            Support and promote the bedRMod format. This format is similar to the
+            Support and promote the
+            <a
+              class="text-primary-500 hover:text-secondary-500"
+              href="https://dieterich-lab.github.io/scimodom/bedrmod.html"
+              target="_blank"
+              rel="noopener noreferrer"
+              >bedRMod</a
+            >
+            format. This format is similar to the
             <a
               class="text-primary-500 hover:text-secondary-500"
               href="https://www.encodeproject.org/data-standards/wgbs/"
               target="_blank"
               rel="noopener noreferrer"
               >ENCODE bedMethyl</a
             >
-            format (BED9+2), but includes a header.
+            format (BED9+2).
           </span>
         </div>
         <div class="col-12 md:col-4 mb-4 px-5">
@@ -31,8 +39,8 @@
           </span>
           <div class="text-900 text-xl mb-3 font-medium dark:text-white/80">Database</div>
           <span class="text-700 line-height-3 dark:text-white/80">
-            Starting with m6A and Ψ, we continuously add new data encompassing a wide range of
-            modifications, RNA types (mRNA, tRNA, rRNA), technologies, and species.
+            Starting with m6A, m5C, and Ψ (whole-transcriptome), we continuously add new data
+            encompassing a wide range of modifications, RNA types, technologies, and species.
           </span>
         </div>
         <div class="col-12 md:col-4 mb-4 px-5">
@@ -41,7 +49,7 @@
           </span>
           <div class="text-900 text-xl mb-3 font-medium dark:text-white/80">Tools</div>
           <span class="text-700 line-height-3 dark:text-white/80">
-            Search and compare modifications across dataset. More tools coming: genome browser,
+            Search and compare modifications across datasets. More tools coming: genome browser,
             visualization.
           </span>
         </div>
@@ -51,7 +59,8 @@
           </span>
           <div class="text-900 text-xl mb-3 font-medium dark:text-white/80">Access</div>
           <span class="text-700 line-height-3 dark:text-white/80">
-            Login with data upload, access management, sharing, and more.</span
+            Registration and login is optional. Login with data upload, access management, and
+            more.</span
           >
         </div>
         <div class="col-12 md:col-4 mb-4 px-5">

client/src/components/home/HomeViews.vue

@@ -17,7 +17,7 @@ import CardLink from '@/components/ui/CardLink.vue'
       <div>
         <CardLink icon="pi pi-list dark:text-white/80" route="browse">
           <template v-slot:title> Data repository </template>
-          <template v-slot:content> Browse through or search the available dataset. </template>
+          <template v-slot:content> Browse through or search the available datasets. </template>
           <template v-slot:link> Browse </template>
         </CardLink>
       </div>

client/src/views/DocumentationView.vue

@@ -15,40 +15,36 @@ import SubTitle from '@/components/ui/SubTitle.vue'
           <span>Introduction</span>
         </h1>
         <p class="indent-4 text-xl leading-relaxed mt-2 mb-4">
-          Sci-ModoM is under active development. Consult our roadmap for 2024
-          <!-- <div class="flex justify-center mt-4 animate-pulse"> -->
-          <RouterLink class="pl-2 animate-pulse" :to="{ name: 'roadmap' }">
-            <!-- <a class="pl-2 animate-pulse" href="https://www.trr319-rmap.de" target="_blank" rel="noopener noreferrer"> -->
-            <Button icon="pi pi-arrow-right" size="small" label="Learn more" rounded />
-          </RouterLink>
-          <!-- </a> -->
-          <!-- </div> -->
+          Sci-ModoM is a quantitative database of RNA modification sites derived from
+          high-throughput sequencing experiments. It is dedicated to novel assays that provide
+          transcriptome-wide information at single-base resolution. An intuitive user–interface
+          allows to <span class="italic">Search</span> and
+          <span class="italic">Compare</span> modifications site-wise or across whole datasets, and
+          to <span class="italic">Browse</span> through or download datasets and retrieve the
+          associated metadata.
         </p>
         <p class="indent-4 text-lg underline underline-offset-8 decoration-gb-4/25 font-semibold">
           Query nomenclature
         </p>
         <p class="indent-4 text-lg leading-relaxed mt-2 mb-2">
           Sci-ModoM allows to query RNA modification sites according to RNA type, species,
           technology, and genomic features (<span class="italic">Search</span>). The classification
-          of detection technologies is based on
-          <a
-            class="text-primary-500 hover:text-secondary-500"
-            href="https://www.nature.com/articles/s12276-022-00821-0"
-            target="_blank"
-            rel="noopener noreferrer"
-            >Detection technologies for RNA modifications</a
-          >.
+          of detection technologies is based on the underlying assay,
+          <span class="italic">e.g.</span>
+          antibody-based, chemically- or enzymatically-treated, or direct read-out (Nanopore).
         </p>
         <p class="indent-4 text-lg underline underline-offset-8 decoration-gb-4/25 font-semibold">
           Project and dataset
         </p>
         <p class="indent-4 text-lg leading-relaxed mt-2 mb-2">
           Data is also accessible at the study- or dataset-level (<span class="italic">Browse</span
-          >). Each dataset is assigned a <span class="font-semibold">EUFID</span> or
-          <span class="font-semibold">EUF identifier</span>. One or more dataset can belong to a
-          study or project, <span class="italic">e.g.</span> dataset "Wildtype HEK293T" and
-          "Wildtype mESC" belong to the "GLORI" project. Projects are identified using a
-          <span class="font-semibold">SMID</span> or
+          >). One or more dataset can belong to a study or project,
+          <span class="italic">e.g.</span> dataset "Wildtype HEK293T" and "Wildtype mESC" belong to
+          the "GLORI" project. Each dataset is assigned a
+          <span class="font-semibold">EUFID</span> or
+          <span class="font-semibold"
+            >Epitranscriptome Unified exchange Format (EUF) identifier</span
+          >. Projects are identified using a <span class="font-semibold">SMID</span> or
           <span class="font-semibold">Sci-ModoM identifier</span>. A dataset can include one or more
           modification, but is uniquely associated with a given species (including cell type,
           tissue, or organ) and technology.
@@ -58,7 +54,8 @@ import SubTitle from '@/components/ui/SubTitle.vue'
         </p>
         <p class="indent-4 text-lg leading-relaxed mt-2 mb-2">
           Simply put, a dataset consists of per-site records of RNA modifications stored in a given
-          bedRMod file. For more information, consult the
+          bedRMod file. This file contains a formatted header with metadata, followed by distinct
+          RNA modification sites, one per line. For more information, consult the
           <a
             class="text-primary-500 hover:text-secondary-500"
             href="https://dieterich-lab.github.io/scimodom/bedrmod.html"
@@ -71,16 +68,16 @@ import SubTitle from '@/components/ui/SubTitle.vue'
           Assembly
         </p>
         <p class="indent-4 text-lg leading-relaxed mt-2 mb-2">
-          Available assemblies for different organisms define the assembly version used in
-          Sci-ModoM. Dataset that do not match the database assembly version are lifted over. Only
-          chromosomes are considered.
+          Only one genome assembly version per species is used in Sci-ModoM. Dataset that do not
+          match the database assembly version are lifted over. Only chromosome-level information is
+          considered; unassigned contigs or scaffolds are discarded.
         </p>
         <p class="indent-4 text-lg underline underline-offset-8 decoration-gb-4/25 font-semibold">
           Annotation
         </p>
         <p class="indent-4 text-lg leading-relaxed mt-2 mb-2">
-          Annotation are created by intersecting dataset records with features (UTRs, CDS, ...)
-          merged across transcripts extracted from a given Ensembl GTF file.
+          Datasets are annotated with gene informations and genomic features (UTRs, CDS, ...) using
+          a fixed version of Ensembl.
         </p>
         <p class="indent-4 text-xl leading-relaxed mt-4 mb-2">
           For detailed documentation and development notes, consult the
@@ -92,18 +89,26 @@ import SubTitle from '@/components/ui/SubTitle.vue'
             >server documentation</a
           >.
         </p>
+        <p class="indent-4 text-xl leading-relaxed mt-4 mb-2">
+          Consult our development plan for 2024
+          <RouterLink class="pl-2 animate-pulse" :to="{ name: 'roadmap' }">
+            <!-- <a class="pl-2 animate-pulse" href="https://www.trr319-rmap.de" target="_blank" rel="noopener noreferrer"> -->
+            <Button icon="pi pi-arrow-right" size="small" label="Learn more" rounded />
+          </RouterLink>
+        </p>
       </div>
       <!-- HOW TO -->
       <div class="text-justify m-6 dark:text-white/80">
         <h1 class="font-ham text-4xl font-semibold m-auto pt-4 pb-4">
           <span>Search</span>
         </h1>
         <p class="indent-4 text-lg leading-relaxed mt-2 mb-2">
-          To query the database for RNA modifications, first select a modification and species, then
-          available technologies. Sci-ModoM contains a large amount of records; selecting a
-          particular gene or genomic region can significantly reduce the query time. The search can
-          also be narrowed down by selecting a biotype or a genomic feature. Selected records can be
-          exported to CSV. To download all records for a given dataset, use
+          Search modifications site-wise across whole transcriptomes. To query the database, first
+          select a modification and species, then available technologies. Some dataset may contain a
+          large amount of records; selecting a particular gene of interest or a genomic region can
+          significantly reduce the query time. The search can also be narrowed down by selecting a
+          biotype or a genomic feature. Selected records can be exported to CSV. To download all
+          records for a given dataset, use
           <span class="italic">Browse</span>.
         </p>
         <p class="indent-4 text-lg leading-relaxed mt-2 mb-2">
@@ -115,22 +120,31 @@ import SubTitle from '@/components/ui/SubTitle.vue'
           <span>Browse</span>
         </h1>
         <p class="indent-4 text-lg leading-relaxed mt-2 mb-2">
-          Query the database to find projects, studies and/or dataset. You can refine your search
-          using global filters (top left of table), or table filters (RNA type and modification,
-          organism, cell, tissue and/or organ, or technology). Click the
+          Query the database to find projects and/or datasets. You can refine your search using
+          global filters (top left of table), or table filters (RNA type and modification, organism,
+          cell, tissue and/or organ, or technology). Click the
           <i class="pi pi-plus -ml-3 mr-1" /> button to see project-related information and
-          additional attachments. A dataset can be downloaded as a bedRMod file. Records can be
-          exported to CSV.
+          additional attachments. A dataset can be downloaded as a
+          <a
+            class="text-primary-500 hover:text-secondary-500"
+            href="https://dieterich-lab.github.io/scimodom/bedrmod.html"
+            target="_blank"
+            rel="noopener noreferrer"
+            >bedRMod</a
+          >
+          file. The list of datasets and their metadata can be exported to CSV.
         </p>
         <h1 class="font-ham text-4xl font-semibold m-auto pt-4 pb-4">
           <span>Compare</span>
         </h1>
         <p class="indent-4 text-lg leading-relaxed mt-2 mb-2">
-          Compare dataset by finding modification sites common to multiple dataset (intersection) or
-          those only found in a group of dataset (difference). You can also find modification sites
-          in a given dataset that are close to, but not intersecting with sites in other dataset
-          (closest). You can perform these operations using available dataset, but you can also
-          compare dataset with your own data.
+          Compare datasets site-wise, including your own, without registration or login. You can
+          compare datasets to one another by finding modification sites common to multiple datasets
+          (intersection) or those only found in a group of datasets (difference). You can also find
+          modification sites in a given dataset that are close to, but not intersecting with sites
+          in other datasets (closest). You can perform these operations strand-aware or unaware. You
+          can use available datasets, or upload your own data to compare it against database
+          records. You data is securely handled and is automatically deleted afterwards.
         </p>
         <p class="indent-4 text-lg leading-relaxed mt-2 mb-2">
           <span class="font-bold">1.</span> First select a given organism, then select up to 3
@@ -162,7 +176,7 @@ import SubTitle from '@/components/ui/SubTitle.vue'
           <span class="font-bold"
             >Sci-ModoM is freely available, and does not require login or registration</span
           >. Interested users can however register to propose new projects, and eventually upload
-          dataset and attachments that are made publicly available to all users.
+          datasets and attachments that are made publicly available to all users.
         </p>
         <p class="indent-4 text-lg underline underline-offset-8 decoration-gb-4/25 font-semibold">
           Project template
@@ -205,6 +219,17 @@ import SubTitle from '@/components/ui/SubTitle.vue'
           Use the Attach BAM files form to upload attachments. Attaching BAM files to a given
           dataset allow users to access read-level information.
         </p>
+        <p class="indent-4 text-lg leading-relaxed mt-2 mb-2">
+          <a
+            class="text-primary-500 hover:text-secondary-500"
+            href="https://dieterich-lab.github.io/scimodom/bedrmod.html"
+            target="_blank"
+            rel="noopener noreferrer"
+            >bedRMod</a
+          >
+          uses a 0-based, half-open coordinate system. If you use a 1-based index, all your
+          modification sites will be <span class="italic">off-by-one</span>!
+        </p>
         <p class="indent-4 text-lg underline underline-offset-8 decoration-gb-4/25 font-semibold">
           Dataset upload errors
         </p>

server/docs/source/bedrmod.rst

@@ -98,6 +98,11 @@ The data section
 
 The first nine columns generally follow the standard `BED specification <https://samtools.github.io/hts-specs/BEDv1.pdf>`_, but the name (4th column) must conform to the `MODOMICS <https://www.genesilico.pl/modomics/modifications>`_ nomenclature for the modification short name, and the score (5th column) is a site-specific measure of confidence. The last two columns contain the coverage (10th column), or number of reads at this position, and the frequency (11th column), or the integer value capped at 100 representing the precentage of reads that are modified at this position. These columns must be separated by tabs and each row must have the same number of columns.
 
+
+.. attention::
+
+    bedRMod is essentially a BED-formatted file, it uses a 0-based, half-open coordinate system. If you use a 1-based index, all your modification sites will be *off-by-one*!
+
 .. attention::
 
     For data upload to Sci-ModoM, chromosomes (1st column) must be formatted following the Ensembl short format *e.g.* 1 and not chr1, or MT and not chrM.