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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
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ContextWork in laboratories or
core facilities
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ProteoWikiLIMS: Lab Information Management System
Proteomics Unit, CRG
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ProteoWiki
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ProteoWiki
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ProteoWikiForm input
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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
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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)
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User satisfaction tracking
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Lab operators extra inputWiki-way. Flexible. Some info structured, some not
DocumentationStandard Operation Procedures (SOP)Informal instrument queue
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Biocore WikiTask management system
Bioinformatics Unit, CRG
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Biocore Wiki
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Biocore WikiTask input
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Biocore WikiTask view
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Biocore WikiHour & costs list
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Example of biological dataContent Management
System (CMS)VastDB, Manuel Irimia's lab (CRG)
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Biological data CMSVastDB
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Biological data CMSVastDB
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VastDB overview
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Different data handling inMediaWiki as a CMS
User import via specific extensionsUsing modified External data extensionExtensions accessing file system
Mirror of PDB structures
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Semantic Data ImportData from CSV input
Output view handled withhandsontable.com
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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
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CouchDB + LuceneCoordinate search
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CouchDB + LuceneFull-text search
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Genome Annotation
Wiki frameworkAnnoWiki
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Genome AnnotationAnnoWiki
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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.
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Import and export formats
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Import and export formatsFASTA
http://www.nmpdr.org/FIG/wiki/view.cgi/FIG/FastaFormat
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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
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Integrating a genome browser
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Linking pages,
conceptual hierarchies
By using specific propertiesSMWParent extension
Quick retrieval of linked elementsParent, ancestorsChildren, descendantsNumber of hopsFilter by another property value
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Linking pages,
conceptual hierarchies
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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