UPD docs

client/src/components/documentation/DocAbout.vue

@@ -50,7 +50,7 @@ import img2 from '@/assets/images/docs/about2.png'
       </a>
       short name. The classification of detection technologies is based on the underlying assay,
       <span class="italic">e.g.</span>
-      chemical- or enzyme/protein-assisted sequencing (NGS 2nd generation), and Native RNA or cDNA
+      chemical- or enzyme/protein-assisted sequencing (NGS 2nd generation), and native RNA or cDNA
       sequencing (NGS 3rd generation).
     </p>
     <p class="indent-4 text-lg underline underline-offset-8 decoration-gb-4/25 font-semibold">
@@ -70,8 +70,9 @@ import img2 from '@/assets/images/docs/about2.png'
     </p>
     <p class="indent-4 text-lg leading-relaxed mt-2 mb-2">
       Projects are identified using a <span class="font-semibold">SMID</span> or
-      <span class="font-semibold">Sci-ModoM identifier</span>. Click on the
-      <i class="pi pi-plus -ml-3 mr-1" /> button to access this information and more:
+      <span class="font-semibold">Sci-ModoM identifier</span>. Click on the info (<i
+        class="pi pi-info -ml-4"
+      />) button to access this information and more:
       <img :src="img2" class="object-center mt-6 mb-6" alt="About: project" />
     </p>
     <p class="indent-4 text-lg underline underline-offset-8 decoration-gb-4/25 font-semibold">
@@ -97,6 +98,9 @@ import img2 from '@/assets/images/docs/about2.png'
       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.
+      <Message severity="info" :closable="false"
+        >Sci-ModoM currently uses human GRCh38 and mouse GRCm39</Message
+      >
     </p>
     <p class="indent-4 text-xl leading-relaxed mt-12 mb-2">
       For detailed documentation and development notes, consult the

client/src/components/documentation/DocBrowse.vue

@@ -14,29 +14,32 @@ import img4 from '@/assets/images/docs/browse4.png'
       Query and filters
     </p>
     <p class="indent-4 text-lg leading-relaxed mt-2 mb-2">
-      Query the database to find projects and/or datasets. You can refine your search using global
-      filters (top left of table <span class="italic">e.g.</span> search for datasets containing
-      "NSUN" in their metadata or title):
+      Query the database to find projects and/or datasets, and access metadata. You can refine your
+      search using global filters (top left of table <span class="italic">e.g.</span> search for
+      datasets containing "NSUN" in their metadata or title):
       <img :src="img1" class="object-center mt-6 mb-6" alt="Browse: global filter" />
       and/or table filters (RNA type and modification, organism, cell, tissue and/or organ, or
       technology, <span class="italic">e.g.</span> search for "mESC"):
       <img :src="img2" class="object-center mt-6 mb-6" alt="Browse: table filter" />
       Use "Match Any" to combine filters, <span class="italic">e.g.</span> search for different
       technologies:
       <img :src="img3" class="object-center mt-6 mb-6" alt="Browse: table filter" />
+      <Message severity="warn" :closable="false"
+        >Don't forget to clear filters when changing search parameters, this is not automatically
+        done</Message
+      >
     </p>
     <p class="indent-4 text-lg underline underline-offset-8 decoration-gb-4/25 font-semibold">
       Results table
     </p>
     <p class="indent-4 text-lg leading-relaxed mt-2 mb-2">
       <Message severity="success" :closable="false">Download datasets as bedRMod</Message>
       <Message severity="success" :closable="false">Access or export metadata and more</Message>
-      Click the
-      <i class="pi pi-plus -ml-3 mr-1" /> button to see project-related information and additional
-      attachments (BAM files):
+      Click the info (<i class="pi pi-info -ml-4" />) button to see project-related information and
+      additional attachments (BAM files):
       <img :src="img4" class="object-center mt-6 mb-6" alt="Browse: plus" />
       BAM file attachments (if available) allow to access read-level information before it is
-      aggregated site-wise into bedRMod. A dataset can be downloaded as a
+      aggregated site-wise into bedRMod. Each dataset can be downloaded as a
       <a
         class="text-primary-500 hover:text-secondary-500"
         href="https://dieterich-lab.github.io/scimodom/bedrmod.html"

client/src/components/documentation/DocCompare.vue

@@ -17,8 +17,11 @@ import img4 from '@/assets/images/docs/compare4.png'
       Compare datasets to one another by finding modification sites common to multiple datasets
       (intersection) or those only found in a group of datasets (difference), or find modification
       sites in a given dataset that are close to, but not intersecting with sites in other datasets
-      (closest). Perform these operations strand-aware or unaware. Use available datasets, or upload
-      your own data to compare it against database records, without registration or login.
+      (closest). Perform these operations strand-aware or unaware.
+      <span class="font-semibold"
+        >Use available datasets, or upload your own data to compare it against database records,
+        without registration or login</span
+      >.
     </p>
     <p class="indent-4 text-lg leading-relaxed mt-2 mb-2">
       First select a given organism, then select up to 3 reference datasets. Use the search bar
@@ -33,7 +36,8 @@ import img4 from '@/assets/images/docs/compare4.png'
       to BED6.
       <Message severity="warn" :closable="false"
         >Data coming from a different assembly or an inconsistent choice of reference dataset will
-        lead to spurious comparison results</Message
+        lead to spurious comparison results. Liftover is not yet available for data
+        comparison!</Message
       >
       Finally, select the operation you want to perform on the datasets selected in previous steps:
       <img :src="img3" class="object-center mt-6 mb-6" alt="Compare: filter 3" />

client/src/components/documentation/DocSearch.vue

@@ -6,6 +6,7 @@ import img4 from '@/assets/images/docs/search4.png'
 import img5 from '@/assets/images/docs/search5.png'
 import img6 from '@/assets/images/docs/search6.png'
 import img7 from '@/assets/images/docs/search7.png'
+import img8 from '@/assets/images/docs/search8.png'
 </script>
 
 <template>
@@ -17,8 +18,9 @@ import img7 from '@/assets/images/docs/search7.png'
       Query and filters
     </p>
     <p class="indent-4 text-lg leading-relaxed mt-2 mb-2">
-      Search modifications site-wise across whole transcriptomes. To query the database, first
-      select a modification and species:
+      Search modifications site-wise across whole transcriptomes, by organism and technology, or by
+      gene or genomic region. To query the database for a given modification, first select a
+      modification and species:
       <img :src="img1" class="object-center mt-6 mb-6" alt="Search: filter species" />
       Available cell types, tissues, and/or organisms are shown for a given modification. A standard
       nomenclature is used to describe cell strains, faithful to published data
@@ -39,6 +41,9 @@ import img7 from '@/assets/images/docs/search7.png'
       <Message severity="info" :closable="false"
         >Gene and genomic (chromosome) selection are mutually exclusive</Message
       >
+      To query the database for all modifications in a particular gene or genomic region, use the
+      toggle button, and select a gene or a genomic region:
+      <img :src="img8" class="object-center mt-6 mb-6" alt="Search: gene or chrom" />
     </p>
     <p class="indent-4 text-lg underline underline-offset-8 decoration-gb-4/25 font-semibold">
       Results table
@@ -61,10 +66,14 @@ import img7 from '@/assets/images/docs/search7.png'
         format</Message
       >
       <Message severity="success" :closable="false"
-        >Click on <i class="pi pi-plus -ml-3 mr-1" /> to retrieve site-specific information</Message
+        >Click on "Gene" to access gene table information on Ensembl</Message
+      >
+      <Message severity="success" :closable="false"
+        >Click on <i class="pi pi-info -ml-3 mr-1" /> to retrieve site-specific information</Message
       >
       Query results are shown in tabular format where sites are recorded per dataset, allowing to
-      organize data and prioritize sites with high stoichiometry, coverage, and/or score.
+      organize data and prioritize sites with high stoichiometry, coverage, and/or score. Export all
+      results to a CSV file.
       <img :src="img5" class="object-center mt-6 mb-6" alt="Search: results table" />
       All columns with arrow signs can be sorted. Multiple columns can be sorted at once, this
       requires a metaKey (<span class="italic">e.g.</span> ⌘ or Ctrl) to be pressed when clicking a
@@ -76,7 +85,7 @@ import img7 from '@/assets/images/docs/search7.png'
       <img :src="img7" class="object-center mt-6 mb-6" alt="Search: plus bottom" />
     </p>
     <p class="indent-4 text-lg leading-relaxed mt-2 mb-2">
-      Selected records can be exported to CSV, including site-specific information. To download all
+      These tables can also be exported to CSV, including site-specific information. To download
       records for a given dataset, click on the EUFID; the <span class="italic">Browse</span> view
       allows to download bedRMod-formatted records.
     </p>

client/src/components/home/HomeIntro.vue

@@ -14,7 +14,7 @@
       </p>
     </div>
     <div class="flex justify-center mt-4 animate-pulse">
-      <a href="https://www.trr319-rmap.de" target="_blank" rel="noopener noreferrer">
+      <a href="https://humanrnomeproject.org" target="_blank" rel="noopener noreferrer">
         <Button icon="pi pi-arrow-right" label="Learn more" rounded />
       </a>
     </div>

client/src/components/home/HomeRelease.vue

@@ -26,9 +26,10 @@ onMounted(() => {
         <h1 class="font-ham text-4xl font-semibold m-auto p-4 dark:text-white/80">
           <span>Release</span>
         </h1>
-        <p class="text-xl font-medium text-gray-600 pt-4 pb-2 dark:text-surface-400">
+        <p class="leading-loose text-xl font-medium text-gray-600 pt-4 pb-2 dark:text-surface-400">
           Sci-ModoM contains {{ sites }} reported sites with stoichiometric information across
-          {{ datasets }} datasets, annotated using Ensembl release 110.
+          {{ datasets }} datasets, for genome assemblies <br />
+          GRCh38 (human) and GRCm39 (mouse), annotated using Ensembl release 110.
         </p>
         <div class="flex flex-row pt-12">
           <div class="basis-1/2">

server/docs/source/bedrmod.rst

@@ -71,7 +71,7 @@ As bedRMod contains data for only one organism, only one reference to organism,
 
 
 While all tags are required, ``sequencing_platform``, ``basecalling``, ``bioinformatics_workflow``, ``experiment`` or ``external_source`` can be left
-empty *e.g.*
+empty, although it is strongly advised to provide as much information as possible, *e.g.*
 
 ::
 
@@ -89,8 +89,7 @@ empty *e.g.*
 
 .. attention::
 
-    For data upload to Sci-ModoM, ``fileformat``, ``organism``, and ``assembly`` are validated. Only the latest specifications are used, and only ``modification_type=RNA`` is allowed. The ``assembly`` tag entry must match exactly the chosen assembly and must follow the Ensembl nomenclature.
-    Additional user-defined tags or extra header lines starting with ``#`` are ignored during upload.
+    For data upload to Sci-ModoM, ``fileformat``, ``organism``, and ``assembly`` are validated. Only the latest specifications are used, and only ``modification_type=RNA`` is allowed. The ``assembly`` tag entry must match exactly the assembly chosen from the dropdown menu during upload, and it must follow the Ensembl nomenclature. Data does not have to be for a specific genome assembly, Sci-ModoM will take care of lifting over all records to the most recent assembly for each organism. Additional user-defined tags or extra header lines starting with ``#`` are ignored during upload.
 
 
 The data section

server/docs/source/flask.rst

@@ -98,3 +98,9 @@ If required, a project and all associated data can be removed with
 .. code-block:: bash
 
     flask delete [OPTIONS] SMID
+
+To force update the charts, run
+
+.. code-block:: bash
+
+    flask sunburst-update [OPTIONS]