Update docs components

src/app/config/docs.json

@@ -35,7 +35,7 @@
       "id" : "about/pombase-and-collaborative-publications"
    },
    {
-      "content" : "\n\nThe  (SAB) provides strategic scientific advice to the PomBase resource covering current and future priorities related to curation, tools provided and outreach. They will advise how can we better align S. pombe knowledge to human genetics and health. The SAB is an independent body, made up of leading experts in both fission yeast biology and Model Organism Databases from around the world. The SAB meets annually, but are also the first point of contact for intermittent feedback on resource reallocation that may affect the wider community.\n\nSAB Meeting reports\n\n-  October 2022 SAB meeting report\n\nCurrent members\n\nLi-Lin Du National Institute of Biological Sciences, Beijing, China\n\nKathleen Gould Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA\n\nDoug Howe The Zebrafish Information Network, University of Oregon, Eugene, OR, USA\n\nSabina Leonelli Exeter Centre for the Study of the Life Sciences & Department of Sociology, Philosophy and Anthropology, University of Exeter, Exeter, UK\n\nSamuel Marguerat UCL Cancer Institute, London, UK\n\nSophie Martin Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland\n\nRelated pages\n\nFission yeast gene naming committee\n",
+      "content" : "\n\nThe  (SAB) provides strategic scientific advice to the PomBase resource covering current and future priorities related to curation, tools provided and outreach. They will advise how can we better align S. pombe knowledge to human genetics and health. The SAB is an independent body, made up of leading experts in both fission yeast biology and Model Organism Databases from around the world. The SAB meets annually, but are also the first point of contact for intermittent feedback on resource reallocation that may affect the wider community.\n\nSAB Meeting reports\n\n-  October 2022 SAB meeting report\n\nCurrent members\n\nLi-Lin Du National Institute of Biological Sciences, Beijing, China\n\nKathleen Gould Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA\n\nSabina Leonelli Exeter Centre for the Study of the Life Sciences & Department of Sociology, Philosophy and Anthropology, University of Exeter, Exeter, UK\n\nSophie Martin Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland\n\nPast SAB members\n\nDoug Howe The Zebrafish Information Network, University of Oregon, Eugene, OR, USA\n\nSamuel Marguerat UCL Cancer Institute, London, UK\n\nRelated pages\n\nFission yeast gene naming committee\n",
       "heading" : "PomBase Scientific Advisory Board",
       "id" : "about/pombase-sab"
    },
@@ -140,7 +140,7 @@
       "id" : "community/internet-resources"
    },
    {
-      "content" : "\n\nNote that some of the links below go to pages listing subdirectories that are organised slightly differently from the links on this page. Your browser may prompt you to open or download files.\n\nIf you have trouble finding anything, please ask the helpdesk.\n\n-\n\nData download site\n\nMain directory for S. pombe data\n\n-\n\nGenome sequence and features\n\n-  Genome sequence (FASTA or enriched EMBL format for Artemis)\n-  Feature coordinates (coding regions, introns, exons, UTRs, etc.)\n-  Genomic regions (centromeres, telomeres, mating type)\n\n-\n\n displayed in the genome browser\n\nThe data files used for the tracks in the JBrowse genome browser are available from the external_datasets directory. The directory names are the either the publication details (PubMed ID) or the GEO/SRA dataset ID.\n\nFor detailed information about each genome browser track, please see the JBrowse configuration table. This file is a spreadsheet in comma separated value format. The columns are described on the dataset submission page.\n\n-\n\nAnnotation datasets\n\nAnnotation type  Description\n - -\n Protein datasets  Protein sequence FASTA database, peptide features, properties, etc.\n GO annotations  Gene Ontology annotation files\n Macromolecular complexes  Subunits of protein and ribonucleoprotein complexes (GO cellular component terms and annotated genes)\n Phenotype annotations  FYPO phenotype annotation files - complete annotation set (PHAF) or viability summary\n Human disease associations  Fission yeast orthologs of human disease associated genes with disease descriptions and Mondo ontology terms\n Modifications  Protein modification data file (RNA modifications to be added in future)\n Orthologs  Manually curated ortholog sets for human and S. cerevisiae; also see documentation\n\n-\n\nGene names and IDs\n\nMappings between PomBase systematic IDs, gene names, product descriptions, and UniProt accession numbers\n\n-\n\nGO slim\n\nCurrent GO slim IDs and term names:\n\n-  GO biological process slim\n-  GO molecular function slim\n-  GO cellular component slim\n\n-\n\nMondo slim\n\nCurrent fission yeast Mondo Disease Ontology slim IDs and term names\n\n-\n\nCurated inventories\n\n-  DNA binding sites\n-  Drug targets\n\n-\n\nNote: S. pombe files are no longer available from the old “pombase” FTP site within the EBI domain. If you have a link that contains ftp.ebi.ac.uk, please check these pages for a link using https://www.pombase.org/. Please contact the PomBase curators if you need help finding a file or directory.\n",
+      "content" : "\n\nNote that some of the links below go to pages listing subdirectories that are organised slightly differently from the links on this page. Your browser may prompt you to open or download files.\n\nIf you have trouble finding anything, please ask the helpdesk.\n\n-\n\nData download site\n\nMain directory for S. pombe data\n\n-\n\nDataset and ontology versions\n\nThe versions page is updated each night.\n\n-\n\nGenome sequence and features\n\n-  Genome sequence (FASTA or enriched EMBL format for Artemis)\n-  Feature coordinates (coding regions, introns, exons, UTRs, etc.)\n-  Genomic regions (centromeres, telomeres, mating type)\n\n-\n\n displayed in the genome browser\n\nThe data files used for the tracks in the JBrowse genome browser are available from the external_datasets directory. The directory names are the either the publication details (PubMed ID) or the GEO/SRA dataset ID.\n\nFor detailed information about each genome browser track, please see the JBrowse configuration table. This file is a spreadsheet in comma separated value format. The columns are described on the dataset submission page.\n\n-\n\nAnnotation datasets\n\nAnnotation type  Description\n - -\n Protein datasets  Protein sequence FASTA database, peptide features, properties, etc.\n GO annotations  Gene Ontology annotation files\n Macromolecular complexes  Subunits of protein and ribonucleoprotein complexes (GO cellular component terms and annotated genes)\n Phenotype annotations  FYPO phenotype annotation files - complete annotation set (PHAF) or viability summary\n Human disease associations  Fission yeast orthologs of human disease associated genes with disease descriptions and Mondo ontology terms\n Modifications  Protein modification data file (RNA modifications to be added in future)\n Orthologs  Manually curated ortholog sets for human and S. cerevisiae; also see documentation\n\n-\n\nGene names and IDs\n\nMappings between PomBase systematic IDs, gene names, product descriptions, and UniProt accession numbers\n\n-\n\nGO slim\n\nCurrent GO slim IDs and term names:\n\n-  GO biological process slim\n-  GO molecular function slim\n-  GO cellular component slim\n\n-\n\nMondo slim\n\nCurrent fission yeast Mondo Disease Ontology slim IDs and term names\n\n-\n\nCurated inventories\n\n-  DNA binding sites\n-  Drug targets\n\n-\n\nNote: S. pombe files are no longer available from the old “pombase” FTP site within the EBI domain. If you have a link that contains ftp.ebi.ac.uk, please check these pages for a link using https://www.pombase.org/. Please contact the PomBase curators if you need help finding a file or directory.\n",
       "heading" : "Datasets",
       "id" : "datasets/index"
    },
@@ -210,7 +210,7 @@
       "id" : "documentation/gene-page-gene-structure-history"
    },
    {
-      "content" : "\n\nThe Literature section of a gene page lists the papers that have curated data for the gene or its product.\n\nAt the top of the section, there is a link to search PubMed for any papers on the gene. This may retrieve papers not on the gene page Literature list, if there are papers not yet curated (or spurious matches to the search criteria).\n\nFor each paper, the full citation and the number of genes curated from the paper are shown, and a “Details” link goes to the publication page.\n\nBy default, the list is sorted alphabetically by first author. Use the “Sort by” links to change the order.\n",
+      "content" : "\n\nThe Literature section of a gene page lists the papers that have curated data for the gene or its product, and papers which mention the gene in keywords.\n\nAt the top of the section, there is a link to search PubMed for any papers on the gene. This may retrieve papers not on the gene page Literature list, if there are papers not yet curated (or spurious matches to the search criteria).\n\nFor each paper, the full citation and the number of genes curated from the paper are shown, and a “Details” link goes to the publication page.\n\nBy default, the list is sorted alphabetically by first author. Use the “Sort by” links to change the order.\n",
       "heading" : "Gene page: Literature",
       "id" : "documentation/gene-page-literature"
    },
@@ -385,7 +385,7 @@
       "id" : "downloads/phenotype-annotations"
    },
    {
-      "content" : "\n\nThe full protein dataset is available in FASTA format (link downloads gzipped file from PomBase).\n\nThe protein data directory contains assorted data (see the README for file formats):\n\n-  PeptideStats.tsv - Predicted molecular weight (kDa), predicted pI, charge, length (residues), codon adaptation index (CAI)\n-  Protein_Features.tsv - Protein features such as domains and family assignments\n-  aa_composition.tsv - Amino acid composition\n-  transmembrane_domain_coords_and_seqs.tsv - Sequences and coordinates for transmembrane domains\n\nAlso see the protein modification annotations directory.\n",
+      "content" : "\n\nThe full protein dataset is available in FASTA format (link downloads gzipped file from PomBase).\n\nThe protein data directory contains assorted data (see the README for file formats):\n\n-  PeptideStats.tsv - Predicted molecular weight (kDa), predicted pI, charge, length (residues), codon adaptation index (CAI)\n-  protein_domains_and_features.tsv - Protein features such as domains and family assignments\n-  aa_composition.tsv - Amino acid composition\n-  transmembrane_domain_coords_and_seqs.tsv - Sequences and coordinates for transmembrane domains\n\nAlso see the protein modification annotations directory.\n",
       "heading" : "Protein datasets",
       "id" : "downloads/protein-datasets"
    },