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Update docs components
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kimrutherford committed Dec 11, 2024
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2 changes: 1 addition & 1 deletion src/app/config/docs.json
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"id" : "status/genome-overview"
},
{
"content" : "\n\n- -\n Genome overview Graphic and basic information about each chromosome\n Sequencing status Contig size, gap status and progress, including centromeres and telomeres\n Sequence updates Changes to the genome sequence since July 2003\n Sequence updates pending Pending changes, mainly from the Broad Institute, some supported by data from other sources\n Gene coordinate changes Changes to coordinates of individual genes since publication\n New and removed genes Genes identified or removed since publication\n Gene characterisation Current counts of protein coding gene status, as published in small scale experiments\n Genome statistics Information on the status of the genome (Note: Last updated January 2017)\n Priority unstudied genes Unstudied nuclear-encoded protein-coding genes conserved 1:1 in human\n Unmapped genes List of genes identified genetically but not cloned or physically mapped\n - -\n\nNote: Many older S. pombe sequence submissions to the DNA databases (International Nucleotide Sequence Database Collaboration databases, i.e. ENA, GenBank, DDBJ) contain one or more errors, and we do not have the resources to maintain past sequences or flag every error in PomBase.\n",
"content" : "\n\n- -\n Genome overview Graphic and basic information about each chromosome\n Sequencing status Contig size, gap status and progress, including centromeres and telomeres\n Sequence updates Changes to the genome sequence since July 2003\n Sequence updates pending Pending changes, mainly from the Broad Institute, some supported by data from other sources\n Protein coding gene coordinate changes Changes to coordinates of individual protein coding genes since publication\n RNA gene coordinate changes Changes to coordinates of RNA genes since publication\n New and removed genes Genes identified or removed since publication\n Gene characterisation Current counts of protein coding gene status, as published in small scale experiments\n Genome statistics Information on the status of the genome (Note: Last updated January 2017)\n Priority unstudied genes Unstudied nuclear-encoded protein-coding genes conserved 1:1 in human\n Unmapped genes List of genes identified genetically but not cloned or physically mapped\n - -\n\nNote: Many older S. pombe sequence submissions to the DNA databases (International Nucleotide Sequence Database Collaboration databases, i.e. ENA, GenBank, DDBJ) contain one or more errors, and we do not have the resources to maintain past sequences or flag every error in PomBase.\n",
"heading" : "Genome Status",
"id" : "status/index"
},
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24 changes: 15 additions & 9 deletions src/app/documentation/docs/docs.component.html
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Expand Up @@ -6907,7 +6907,7 @@ <h2 id="modification-data-bulk-upload-format">Modification data bulk upload form
<li>Gene names are optional</li>
<li>For help finding suitable ontology (PSI-MOD) terms to describe your phenotypes, see the <a href="https://curation.pombase.org/pombe/docs/modification_annotation">Canto protein modification documentation</a>. If you can’t find a term you need, email the <a href="mailto:[email protected]">helpdesk</a> for assistance; we can advise you, and request new terms as needed.</li>
<li>For the Evidence column, we use a small selection from the <a href="http://www.evidenceontology.org/">Evidence Ontology</a> (ECO). You are welcome to enquire with us in advance to find out which ECO terms/IDs fit your experiments, but we can accept files with brief descriptions, which curators will convert to ECO IDs.</li>
<li>The Residue column indicates the position modified. For protein modifications, use one-letter amino acid code. Multiple entries are allowed, but only for cases where two or more of the same modification are known to be present at the same time. Separate entries with commas (e.g. S72,T85). Position numbering should reflect the current sequence data in PomBase. Please refer to the <a routerLink="/status/gene-coordinate-changes">Gene Coordinate Changes</a> page to ensure that your residue position entries are up to date. Histones should be represented using the unprocessed protein sequence coordinates, not the processed coordinates conventionally used to describe histones. Histone modifications will be represented on the gene pages as K4(K5) processed(preprocessed), but our checking pipeline will expect unmodified forms.</li>
<li>The Residue column indicates the position modified. For protein modifications, use one-letter amino acid code. Multiple entries are allowed, but only for cases where two or more of the same modification are known to be present at the same time. Separate entries with commas (e.g. S72,T85). Position numbering should reflect the current sequence data in PomBase. Please refer to the <a routerLink="/status/gene-coordinate-changes-protein-coding">Gene Coordinate Changes</a> page to ensure that your residue position entries are up to date. Histones should be represented using the unprocessed protein sequence coordinates, not the processed coordinates conventionally used to describe histones. Histone modifications will be represented on the gene pages as K4(K5) processed(preprocessed), but our checking pipeline will expect unmodified forms.</li>
<li>See the table below for allowed annotation extensions. Multiple extensions can be included for a modification if they combine to form a “compound” extension (all parts apply together) Separate extensions with a comma (,)</li>
<li>Use PubMed IDs (e.g. “PMID:1234567”) in the Reference column</li>
<li>The taxon will usually be 4896 (the NCBI taxon ID for <em>Schizosaccharomyces pombe</em>), although if you have an NCBI taxon ID for a specific <em>S. pombe</em> strain you are welcome to use it</li>
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<li>We can currently capture only haploid and homozygous diploid datasets via PHAF files. Allowed values for this column are “haploid” and “homozygous diploid”. If the column is empty the dataset is assumed to be haploid. If you have a phenotype dataset for non-homozygous diploids please contact the <a href="mailto:[email protected]">Helpdesk</a></li>
</ol>
<p><strong>Details for allele types and descriptions:</strong></p>
<p>General note: Nucleotide and amino acid positions should reflect the current sequence data in PomBase. Please refer to the <a routerLink="/status/gene-coordinate-changes">Gene Coordinate Changes</a> page to ensure that your residue position entries are up to date.</p>
<p>General note: Nucleotide and amino acid positions should reflect the current sequence data in PomBase. Please refer to the <a routerLink="/status/gene-coordinate-changes-protein-coding">Gene Coordinate Changes</a> page to ensure that your residue position entries are up to date.</p>
<p>For protein-coding genes, number nucleotide residues from 1 starting with the A of the initiator ATG.</p>
<p>For histones, amino acid residue numbering assumes that the initiator methionine is removed.</p>
<table>
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<div class="left-menu-part left-sub-menu-item"><a routerLink="/status/telomeres">Telomeres</a></div>
<div class="left-menu-part left-menu-item"><a routerLink="/status/sequencing-updates">Sequence updates</a></div>
<div class="left-menu-part left-menu-item"><a routerLink="/status/sequence-updates-pending">Sequence updates pending</a></div>
<div class="left-menu-part left-menu-item"><a routerLink="/status/gene-coordinate-changes">Gene coordinate changes</a></div>
<div class="left-menu-part left-menu-item"><span>Gene coordinate changes</span></div>
<div class="left-menu-part left-sub-menu-item"><a routerLink="/status/gene-coordinate-changes-protein-coding">Protein coding genes</a></div>
<div class="left-menu-part left-sub-menu-item"><a routerLink="/status/gene-coordinate-changes-RNA">RNA genes</a></div>
<div class="left-menu-part left-menu-item"><a routerLink="/status/new-and-removed-genes">New and removed genes</a></div>
<div class="left-menu-part left-menu-item"><a routerLink="/status/gene-characterisation">Gene characterisation</a></div>
<div class="left-menu-part left-menu-item"><a routerLink="/status/priority-unstudied-genes">Priority unstudied genes</a></div>
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<td>Pending changes, mainly from the Broad Institute, some supported by data from other sources</td>
</tr>
<tr class="odd">
<td><a routerLink="/status/gene-coordinate-changes">Gene coordinate changes</a></td>
<td>Changes to coordinates of individual genes since publication</td>
<td><a routerLink="/status/gene-coordinate-changes-protein-coding">Protein coding gene coordinate changes</a></td>
<td>Changes to coordinates of individual protein coding genes since publication</td>
</tr>
<tr class="even">
<td><a routerLink="/status/gene-coordinate-changes-RNA">RNA gene coordinate changes</a></td>
<td>Changes to coordinates of RNA genes since publication</td>
</tr>
<tr class="odd">
<td><a routerLink="/status/new-and-removed-genes">New and removed genes</a></td>
<td>Genes identified or removed since publication</td>
</tr>
<tr class="odd">
<tr class="even">
<td><a routerLink="/status/gene-characterisation">Gene characterisation</a></td>
<td>Current counts of protein coding gene status, as published in small scale experiments</td>
</tr>
<tr class="even">
<tr class="odd">
<td><a routerLink="/status/statistics">Genome statistics</a></td>
<td>Information on the status of the genome (Note: Last updated January 2017)</td>
</tr>
<tr class="odd">
<tr class="even">
<td><a routerLink="/status/priority-unstudied-genes">Priority unstudied genes</a></td>
<td>Unstudied nuclear-encoded protein-coding genes conserved 1:1 in human</td>
</tr>
<tr class="even">
<tr class="odd">
<td><a routerLink="/status/unmapped_genes">Unmapped genes</a></td>
<td>List of genes identified genetically but not cloned or physically mapped</td>
</tr>
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