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Update docs components
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@kimrutherford
kimrutherford committed Jan 23, 2025
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9 changes: 9 additions & 0 deletions src/app/config/doc-config.json
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"faq/can-i-view-nucleotide-sequence-genome-browser" : "Can I view nucleotide sequence in the genome browser?",
"faq/can-i-view-variation-data-pombase" : "Can I view variation data in PomBase?",
"faq/can-i-visualise-networks-pombase" : "Can I visualise networks in PomBase?",
"faq/community" : "Category: Community",
"faq/data-submission-and-formats" : "Category: Data submission and formats",
"faq/do-i-need-password-download-ftp-site" : "Do I need a password to download from the FTP site?",
"faq/do-you-have-polyadenylation-data-fission-yeast" : "Do you have polyadenylation data for fission yeast?",
"faq/finding-data" : "Category: Finding data",
"faq/gene-page" : "Category: Gene page",
"faq/genome-browser" : "Category: Genome browser",
"faq/genome-statistics-and-lists" : "Category: Genome statistics and lists",
"faq/help-canto-isn-t-working-me.-do-you-have-any-suggestions" : "Help! Canto isn't working for me. Do you have any suggestions?",
"faq/how-are-mating-type-specific-gene-pages-organized" : "How are the mating type specific gene pages organized?",
"faq/how-are-non-coding-rna-genes-identified" : "How are non-coding RNA genes identified?",
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"faq/how-many-conserved-unstudied-proteins-are-there-how-list-generated" : "How many conserved unstudied proteins are there? How is the list generated?",
"faq/i-found-discrepancy-between-genbank-embl-ena-or-ddbj-entry-and-sequence-pombase.-what-should-i-do" : "I found a discrepancy between a GenBank (EMBL/ENA or DDBJ) entry and a sequence in PomBase. What should I do?",
"faq/index" : "Frequently asked questions",
"faq/orthology" : "Category: Orthology",
"faq/s.-pombe-transcriptome-available-fasta-format" : "Is the *S. pombe* transcriptome available in FASTA format?",
"faq/there-any-programmatic-access-pombase-data" : "Is there any programmatic access to PomBase data?",
"faq/there-any-rdna-repeat-sequences-pombase" : "Are there any rDNA repeat sequences in PomBase?",
"faq/there-equivalent-artemis-java-applet-pombase" : "Is there an equivalent to the Artemis java applet in PomBase?",
"faq/there-list-drug-targets-s.-pombe" : "Is there a list of drug targets in *S. pombe*?",
"faq/there-list-protein-complexes-s.-pombe-and-their-subunits" : "Is there a list of protein complexes in *S. pombe*, and their subunits?",
"faq/tools-and-resources" : "Category: Tools and resources",
"faq/using-ontologies" : "Category: Using ontologies",
"faq/what-annotation-extension" : "What is an annotation extension?",
"faq/what-bam-format" : "What is BAM format?",
"faq/what-bed-format" : "What is BED format?",
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6 changes: 6 additions & 0 deletions src/app/documentation/docs/docs.component.html
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<div class="docs">
<app-social-contact></app-social-contact>

<div class="docs-404" *ngIf="pageName == '404'">
<div>
<app-not-found></app-not-found>
</div>
</div>
<div *ngIf="section == 'about'">
<app-page-contents-menu title="About" titleRoute="/about">

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56 changes: 32 additions & 24 deletions src/app/front-panel-content/front-panel-content.component.html
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</div>
<div *ngIf="panelId == 357">
<p><app-recent-community-pubs></app-recent-community-pubs></p>
<p>Cbf11 and Mga2 function together to activate transcription of lipid metabolism genes and promote mitotic fidelity in fission yeast.</p>



<p>Originally published in <a href='https://doi.org/10.1371/journal.pgen.1011509'>PLoS Genet</a>.</p>

</div>
<div *ngIf="panelId == 358">
<p>Browse PomBase’s inventory of conserved proteins with no known biological role</p>
<p><app-recent-community-pubs></app-recent-community-pubs></p>

</div>
<div *ngIf="panelId == 359">
<p>The fission yeast <a routerLink="/browse-curation/fission-yeast-go-slim-terms">GO slim</a> provides a summary of genes annotated to broad biological processes</p>
<p>Browse PomBase’s inventory of conserved proteins with no known biological role</p>

</div>
<div *ngIf="panelId == 360">
<p>Use the <a routerLink="/query">Advanced Search</a> to construct complex queries (GO, phenotypes, taxonomic distribution, domain, chromosomal location).</p>
<p>The fission yeast <a routerLink="/browse-curation/fission-yeast-go-slim-terms">GO slim</a> provides a summary of genes annotated to broad biological processes</p>

</div>
<div *ngIf="panelId == 361">
<p>PomBase has integrated over 200,000 manually curated gene-specific annotations. See our <a routerLink="/about/resource-metrics">Resource Metrics</a> page for more literature curation progress reports.</p>
<p>Use the <a routerLink="/query">Advanced Search</a> to construct complex queries (GO, phenotypes, taxonomic distribution, domain, chromosomal location).</p>

</div>
<div *ngIf="panelId == 362">
<p>PomBase uses manually curated Gene Ontology annotation to generate biological process-specific networks, such as the cytokinesis network excerpted above. Currently available networks are linked to the <a routerLink="/browse-curation/fission-yeast-go-slim-terms">GO slim</a> page.</p>
<p>PomBase has integrated over 200,000 manually curated gene-specific annotations. See our <a routerLink="/about/resource-metrics">Resource Metrics</a> page for more literature curation progress reports.</p>

</div>
<div *ngIf="panelId == 363">
<p>PomBase provides extensive documentation and answers many questions in the <a routerLink="/faq">FAQ</a>. For any information you can’t find there, please <app-contact-email [linkName]="'contact the helpdesk'" [subject]="'PomBase question'"></app-contact-email>.</p>
<p>PomBase uses manually curated Gene Ontology annotation to generate biological process-specific networks, such as the cytokinesis network excerpted above. Currently available networks are linked to the <a routerLink="/browse-curation/fission-yeast-go-slim-terms">GO slim</a> page.</p>

</div>
<div *ngIf="panelId == 364">
<p>PomBase has pioneered a community curation system that enables researchers to contribute publication-based annotations directly to database curators. To participate, search for the PubMed ID of your paper <a href="https://curation.pombase.org/pombe">in Canto</a> or <app-contact-email [linkName]="'contact the helpdesk'" [subject]="'PomBase question'"></app-contact-email>.</p>
<p>PomBase provides extensive documentation and answers many questions in the <a routerLink="/faq">FAQ</a>. For any information you can’t find there, please <app-contact-email [linkName]="'contact the helpdesk'" [subject]="'PomBase question'"></app-contact-email>.</p>

</div>
<div *ngIf="panelId == 365">
<p>4020 of the 5070 fission yeast protein-coding genes now have assigned standard names. We encourage all authors and reviewers to ensure that gene names are registered prior to publication. Visit our <a routerLink="/gene-names">gene registry page</a> and the <a routerLink="/gene-names/gene-naming-guidelines"><em>S. pombe</em> gene naming guidelines</a> for more information.</p>
<p>PomBase has pioneered a community curation system that enables researchers to contribute publication-based annotations directly to database curators. To participate, search for the PubMed ID of your paper <a href="https://curation.pombase.org/pombe">in Canto</a> or <app-contact-email [linkName]="'contact the helpdesk'" [subject]="'PomBase question'"></app-contact-email>.</p>

</div>
<div *ngIf="panelId == 366">
<p>Of the 3526 <em>S. pombe</em> with identified human orthologs, over 500 have been implicated in disease. These are manually annotated with terms from a small in-house vocabulary, and can be searched as described in the <a routerLink="/faq/how-can-i-find-s.-pombe-genes-associated-human-disease">disease gene FAQ</a>.</p>
<p>4020 of the 5070 fission yeast protein-coding genes now have assigned standard names. We encourage all authors and reviewers to ensure that gene names are registered prior to publication. Visit our <a routerLink="/gene-names">gene registry page</a> and the <a routerLink="/gene-names/gene-naming-guidelines"><em>S. pombe</em> gene naming guidelines</a> for more information.</p>

</div>
<div *ngIf="panelId == 367">
<p>Of the 3526 <em>S. pombe</em> with identified human orthologs, over 500 have been implicated in disease. These are manually annotated with terms from a small in-house vocabulary, and can be searched as described in the <a routerLink="/faq/how-can-i-find-s.-pombe-genes-associated-human-disease">disease gene FAQ</a>.</p>

</div>
<div *ngIf="panelId == 368">
<p>A guide to getting the most from PomBase, and to its curation philosophy and data organization. <a href="https://link.springer.com/protocol/10.1007/978-1-4939-7737-6_4">Free download</a> thanks to the <a href="https://wellcome.ac.uk/">Wellcome Trust</a>.</p>



<p><a href="https://link.springer.com/protocol/10.1007/978-1-4939-7737-6_4">View chapter …</a></p>

</div>
<div *ngIf="panelId == 368">
<div *ngIf="panelId == 369">
<p>Unknown process now down to 696, <a routerLink="/gene_subset/characterisation_status_conserved_unknown">conserved unknowns 410</a>.</p>

<p>Our “Unknowns” manuscript is now available on bioRxiv: <a href="https://www.biorxiv.org/content/early/2018/11/16/469569">DOI: 10.1101/469569</a>.</p>

</div>
<div *ngIf="panelId == 369">
<div *ngIf="panelId == 370">
<p>Access <a routerLink="/term/MONDO:0000001">Disease associations</a> for 907 pombe genes (up from 610), includes new associations derived from MalaCards. This number will increase as work is still in progress…</p>

</div>
<div *ngIf="panelId == 370">
<div *ngIf="panelId == 371">
<p>Our “unknowns” analysis is now published in <a href="https://royalsocietypublishing.org/doi/10.1098/rsob.180241">Open Biology</a>. You can browse the <a routerLink="/status/priority-unstudied-genes">list of fission yeast unknown proteins</a>, and use the “Visualise” button to explore the data interactively in QuiLT, the new tool inspired by <a href="https://royalsocietypublishing.org/doi/10.1098/rsob.180241#RSOB180241F4">Figure 4</a>.</p>

</div>
<div *ngIf="panelId == 371">
<div *ngIf="panelId == 372">
<p>PomBase’s advanced search now allows you to retrieve <a routerLink="/documentation/pombase-go-slim-documentation">GO slim</a> annotations for any set of search results. Combine with the “Gene IDs” query option to find GO slim annotations for your own list of genes.</p>

</div>
<div *ngIf="panelId == 372">
<div *ngIf="panelId == 373">
<p>The PomBase <a routerLink="/motif_search">Protein Motif Search Tool</a> allows you to search for any user-defined amino acid sequence, supporting exact matches, wildcards, gaps, and ambiguity codes. This search is now fully integrated into PomBase, allowing results to be sent directly to the <a routerLink="/query">advanced search</a>.</p>

</div>
<div *ngIf="panelId == 373">
<div *ngIf="panelId == 374">
<p>The PomBase <a href="https://www.pombase.org/jbrowse/">JBrowse instance</a> provides a responsive online environment in which to visualise published genomic datasets. For more information please see our <a href="https://www.pombase.org/documentation/JBrowse_quick_start">JBrowse documentation page</a>. Authors are welcome to submit their published data to PomBase for hosting.</p>

</div>
<div *ngIf="panelId == 374">
<div *ngIf="panelId == 375">
<p>Authors now contribute curation to PomBase for almost all new fission yeast publications. Find out how you can benefit in our <a href="https://academic.oup.com/database/article/doi/10.1093/database/baaa028/5827230">new paper on community curation</a>, and visit the <a href="https://curation.pombase.org/pombe"><em>S. pombe</em> Canto home</a> to participate.</p>

</div>
<div *ngIf="panelId == 375">
<div *ngIf="panelId == 376">
<p>Access <a routerLink="/term/MONDO:0000001">Disease associations</a> for 1239 of the 3540 pombe genes with human orthologs (up from 987 in 2019), using the MONDO disease ontology. Or browse the <a href="https://www.pombase.org/browse-curation/disease-slim">disease slim set here</a>.</p>

</div>
<div *ngIf="panelId == 376">
<div *ngIf="panelId == 377">
<p><a href="https://www.micropublication.org/journals/biology/species/s-pombe/"><em>S. pombe</em> microPublications</a> describe brief, novel findings, negative and/or reproduced results, and results which may lack a broader scientific narrative. Find microPublications in the PomBase simple search, or <a href="https://www.micropublication.org/submit-new-article/">submit your own</a>.</p>

</div>
<div *ngIf="panelId == 377">
<div *ngIf="panelId == 378">
<p>Browse <a routerLink="/term/MONDO:0000001">Disease associations</a>, annotated using the Mondo disease ontology, for 1401 (up from 907 in 2019 and 1239 in 2020) of the 3560 <em>S. pombe</em> genes that have human orthologs. See the <a routerLink="/browse-curation/disease-slim">disease slim set</a> for a summary view.</p>

</div>
<div *ngIf="panelId == 378">
<div *ngIf="panelId == 379">
<p>Browse <a routerLink="/term/MONDO:0000001">Disease associations</a>, annotated using the Mondo disease ontology, for 1471 (up from 1401 in August 2021) of the 3597 <em>S. pombe</em> genes that have human orthologs. See the <a routerLink="/browse-curation/disease-slim">disease slim set</a> for a summary view.</p>

</div>
<div *ngIf="panelId == 379">
<div *ngIf="panelId == 380">
<p>We cloned PomBase to create a fully community-maintained resource for the <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3789812/">emerging model S. japonicus</a>; providing genome browser, literature curation, and query tools.</p>



<p><a href="https://www.japonicusdb.org/">Visit JaponicusDB</a></p>

</div>
<div *ngIf="panelId == 380">
<div *ngIf="panelId == 381">
<p><a href="https://pombase.github.io/canto_tutorial/">A new website</a> with videos and documentation for <a href="https://curation.pombase.org/">Canto</a>, our community curation tool. The website includes short step-by-step text and video guides on how to make annotations in Canto.</p>



<p><a href="https://pombase.github.io/canto_tutorial/">Visit the new Canto documentation</a></p>

</div>
<div *ngIf="panelId == 381">
<div *ngIf="panelId == 382">
<p>Although over half of fission yeast proteins are now published in small-scale experiments, and the roles of a further &gt;1900 can be inferred, there are still 616 of unknown process, of these 356 are conserved outside the fission yeast, 126 as far as human.</p>


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