Post on 22-May-2022
Semantic MediaWiki as a platform forlab management and biological
annotation
Toni Hermoso Pulido ( )Bioinformatics Core Facility
Centre for Genomic Regulation (BCN)
@toniher
https://biocore.crg.eu
ContextWork in laboratories or
core facilities
ProteoWikiLIMS: Lab Information Management System
Proteomics Unit, CRG
ProteoWiki
ProteoWiki
ProteoWikiForm input
Mail communication
Based on Semantic Tasks extensionAsking user for action (bring samples to the lab)Informing user about request statusUsers can opt out verbose communication
User satisfaction tracking
When request closedEmail sent. User directed to a Special Page formValid for a limited time (e. g., 2 weeks max)Only editable a few times (or only once)
User satisfaction tracking
Lab operators extra inputWiki-way. Flexible. Some info structured, some not
DocumentationStandard Operation Procedures (SOP)Informal instrument queue
Biocore WikiTask management system
Bioinformatics Unit, CRG
Biocore Wiki
Biocore WikiTask input
Biocore WikiTask view
Biocore WikiHour & costs list
Example of biological dataContent Management
System (CMS)VastDB, Manuel Irimia's lab (CRG)
Biological data CMSVastDB
Biological data CMSVastDB
VastDB overview
Different data handling inMediaWiki as a CMS
User import via specific extensionsUsing modified External data extensionExtensions accessing file system
Mirror of PDB structures
Semantic Data ImportData from CSV input
Output view handled withhandsontable.com
CouchDB + LuceneMaking search faster
CouchDB: NoSQL Document DBMSLucene: Information retrieve library.ElasticSearch or Solr based on itMapping SMW Templates to JSONdocumentsIndexing for coordinates and full-textsearchIt might be ported to ElasticSearch
CouchDB + LuceneCoordinate search
CouchDB + LuceneFull-text search
Genome Annotation
Wiki frameworkAnnoWiki
Genome AnnotationAnnoWiki
Import and export formats
FASTA files (sequences)GFF or GTF (feature, relationship, location)Others: chromosome sizes, etc.Raw text filesWhen convenient external tools:
NCBI-BlastSAMToolsetc.
Import and export formats
Import and export formatsFASTA
http://www.nmpdr.org/FIG/wiki/view.cgi/FIG/FastaFormat
Import and export formatsGFF
##gff-version 3
##sequence-region ctg123 1 1497228
ctg123 . gene 1000 9000 . + . ID=gene00001;Name=EDEN
ctg123 . TF_binding_site 1000 1012 . + . ID=tfbs00001;Parent=gene00001
ctg123 . mRNA 1050 9000 . + . ID=mRNA00001;Parent=gene00001;Name=EDEN.1
https://bioinf.comav.upv.es/courses/sequence_analysis/snp_calling.html
Integrating a genome browser
Linking pages,
conceptual hierarchies
By using specific propertiesSMWParent extension
Quick retrieval of linked elementsParent, ancestorsChildren, descendantsNumber of hopsFilter by another property value
Linking pages,
conceptual hierarchies
Acknowledgements
Biocore WikiCarlos Company
Julia PonomarenkoLuca CozzutoSarah Bonnin
Guglielmo Romaet al.
ProteoWikiEduard Sabidó
Francesco MancusoCristina Chiva
Eva BorràsGuadalupe Espadas
et al.
VastDBManuel IrimiaJavier Tapial
Luca Cozzuto
AnnoWikiLuca Cozzuto
Carlos Company
... and all involved open-source community