SIB COVID-19 Integrated Knowledgebase

Examples

  1. Get all steps in the pangenome build, with their start and end positionsSELECT ?step ?bp ?ep ?path WHERE {?step a vg:Step; faldo:begin ?bp ; faldo:end ?ep . ?bp a faldo:Position ; faldo:position ?begin . ?ep a faldo:Position ; faldo:reference ?path ; faldo:position ?end . }
  2. Get UniProt proteins linked to a vg:Path in this graphSELECT DISTINCT ?uniprot ?path WHERE { ?path a vg:Path . ?embl up:locatedOn/owl:sameAs ?path . ?uniprot rdfs:seeAlso ?embl . }
  3. For the exons annotated in the INDSC records show the nodes in the pangenome graph that overlapSELECT DISTINCT ?node ?annotation ?sbpValue ?bpValue ?sepValue ?epValue WHERE { ?path a vg:Path ; skos:closeMatch ?genome . ?uniprot rdfs:seeAlso ?emblcds . ?emblcds up:locatedOn/owl:sameAs ?genome . ?region faldo:begin ?bp ; faldo:end ?ep . ?bp faldo:reference ?p ; faldo:position ?bpValue . ?ep faldo:reference ?p ; faldo:position ?epValue . ?annotation faldo:location ?region ; a insdcschema:Exon MINUS {?region a vg:Step } ?step a vg:Step ; vg:path ?path ; vg:node ?node ; faldo:begin/faldo:position ?sbpValue ; faldo:end/faldo:position ?sepValue . FILTER((?bpValue <= ?sbpValue) && (?epValue >= ?sepValue)) }
  4. Find annotations that are annotated in CDS that differ by one in pangenome node space from a other CDS on the places where these mismatch.SELECT DISTINCT ?insdCDS #?insdCDSBegin ?insdCDSEnd ?step ?path ?node ?nextNode ?nextPath ?insdcStepBegin ?insdcStepEnd ?uniprotSequence ?uniprot ?stepBeginInProteinSpace ?stepEndInProteinSpace ?annotationText { # Find CDS annoted by INDSC that do not match a UniProt protein. ?insdCDS insdcschema:translation ?sequence ; a insdcschema:Coding_Sequence ; faldo:location ?insdCDSLocation . MINUS { ?uniprotSequence rdf:value ?sequence . } # Get the range of this CDS and make sure the coordinates are on the # path we need later ?insdCDSLocation faldo:begin [ faldo:reference ?path ; faldo:position ?insdCDSBegin] ; faldo:end [ faldo:reference ?path ; faldo:position ?insdCDSEnd] . ?step a vg:Step ; vg:path/skos:closeMatch ?path ; vg:node ?node ; faldo:begin [ faldo:reference/skos:closeMatch ?path ; faldo:position ?insdcStepBegin ] ; faldo:end [ faldo:reference/skos:closeMatch ?path ; faldo:position ?insdcStepEnd ] . ## I always forget how to interval ranges :( FILTER ( (?insdcStepBegin >= ?insdCDSBegin && ?insdcStepBegin <= ?insdCDSEnd) || (?insdCDSBegin >= ?insdcStepBegin && ?insdCDSBegin <= ?insdcStepEnd) || (?insdcStepEnd >= ?insdCDSEnd && ?insdcStepEnd <= ?insdCDSBegin) || (?insdCDSEnd >= ?insdcStepEnd && ?insdCDSEnd <= ?insdcStepBegin) ) ## Then we look for a node close to the ones in the CDS in genome graph space (one step) ?node vg:linksForwardToForward ?nextNode . ?step2 a vg:Step ; vg:path/skos:closeMatch ?nextPath ; vg:node ?nextNode . ## Where that node is on a uniprot matching sequence ?nextinsdCDS insdcschema:translation ?nextSequence ; a insdcschema:Coding_Sequence ; faldo:location/faldo:begin/faldo:reference ?nextPath . ?uniprot up:sequence/rdf:value ?nextSequence . BIND(IF(?insdCDSBegin > ?insdcStepBegin, ?insdCDSBegin, ?insdcStepBegin - ?insdCDSBegin)/3 AS ?stepBeginInProteinSpace) BIND(IF(?insdCDSEnd > ?insdcStepEnd, ?insdcStepEnd, ?insdCDSBegin - ?insdcStepEnd)/3 AS ?stepEndInProteinSpace) ?uniprot up:annotation ?annotation . ?annotation a up:Active_Site_Annotation . ?annotation up:range ?annotationRegion . ?annotation rdfs:comment ?annotationText . ?annotationRegion faldo:begin/faldo:position ?annotationBegin . ?annotationRegion faldo:end/faldo:position ?annotationEnd . FILTER (?annotationBegin >= ?stepBeginInProteinSpace && ?annotationEnd < ?stepEndInProteinSpace ) }
  5. Polymorphisms located on ACE2 and TMPRSS2 and affecting proteins’ activity, structure, PTM...SELECT DISTINCT (STR(?gn) AS ?genename) ?pos (STR(?snpac) AS ?varid) (str(?orgaa) AS ?orgAA) ?annot_type (STR(?txt) AS ?note) (STR(?varaa) AS ?varAA) ?freq WHERE { VALUES ?entry {nextprot:NX_Q9BYF1 nextprot:NX_O15393} # proteins of interest (ACE2, TMPRSS2) ?entry np:gene /np:name ?gn. ?entry np:isoform ?iso . ?iso np:swissprotDisplayed true; np:variant ?var . ?var np:start ?pos ; np:original ?orgaa; np:variation ?varaa . ?var np:evidence / np:allele-frequency ?freq . ?var np:evidence / np:reference ?xref . ?xref np:provenance <http://nextprot.org/rdf/db/dbSNP>; np:accession ?snpac . ?iso np:positionalAnnotation ?annot . optional {?annot rdfs:comment ?txt .} ?annot a ?annot_type . { ?annot np:start ?pos; np:end ?pos. filter (not exists {?annot a np:Variant. }) filter (not exists {?annot a np:SequenceConflict. }) } UNION { ?annot a np:DisulfideBond. {?annot np:start ?pos. } UNION {?annot np:end ?pos. } } } ORDER BY ?entry ?pos

SIB experts part of the fight against the COVID-19 pandemic

SIB experts and resources are taking part in the global effort to develop dedicated data services, analysis tools, training offer - and to improve knowledge sharing to fight the COVID-19 pandemic:

About

This knowledge graph combines data from various sources of interest in the research on SARS-CoV-2 and COVID-19:

It is free to access and supports the SPARQL 1.1 Standard.

There are 64,580,219 triples in this endpoint (2020-06-19). The query timeout is 45 minutes. All triples are available in the default graph. There are 9 named graphs.

The data in this knwledge graph is a combination of pre-release data and data from various sources that might be interesting for research on SARS-CoV-2,

The data in this knwledge graph is a combination of pre-release data and data from various sources that might be interesting for research on SARS-CoV-2,

Documentation

  1. Statistics and diagrams
  2. Example queries
  3. Classes and predicates defined by the UniProt consortium
  4. Classes and predicates used for the pangenome model
  5. Classes and predicates used for the harmonizing of locations