2023-02-13

This is PMAS's COMMONS Lab daily Open Notebook.

Today is 2023.02.13

Todo today

SWAT4HCLS

Tutorials can be found here https://www.swat4ls.org/workshops/basel2023/tutorials/

Those which are organized as interactive you can find the zoom links here. Track A https://zoom.us/j/98544172437 Track B https://us02web.zoom.us/j/85986933013 Track C https://zoom.us/j/99286755590

The other sessions will be streamed on the website. For Q&A please use Discord channel https://discord.gg/WC6qanWj

The final programme of the conference days can be found here https://www.swat4ls.org/workshops/basel2023/scientific-programme-2023/ All sessions will be streamed at the conference website. For Q&A please use Discord channel https://discord.gg/BRwbWWjDaE

Information about BioHackathon can be found here https://www.swat4ls.org/workshops/basel2023/scientific-programme-2023/

We work at https://cocalc.com/projects/

Ontology at the Topo Data on the bottom (instances of the ontology)

Prefix is simply a declaration of an IRI abbreviation

Remember that in the turtle data above we can see:

'ttr:John a dbo:Person'

'a' can also be used instead of 'rdf:type'

'a' is a synonym of 'rdf:type'

If you dont know what is your data. Dont fill it in

https://sparql.rhea-db.org/

Put your code here

chebi = '18059'

#endpoint:https://sparql.rhea-db.org/sparql
#query Q9: Select Rhea reactions using CHEBI:31488 (N-acylsphinganine) or one of its descendant as reaction participant

PREFIX rh:<http://rdf.rhea-db.org/>
PREFIX CHEBI:<http://purl.obolibrary.org/obo/CHEBI_>
PREFIX up:<http://purl.uniprot.org/core/>

SELECT distinct ?chebi ?chebiUniprotName ?rhea ?equation 
WHERE {
  ?rhea rdfs:subClassOf rh:Reaction .
  ?rhea rh:equation ?equation .
  ?rhea rh:side/rh:contains/rh:compound/rh:chebi ?chebi .
  ?chebi rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf CHEBI:""" + chebi + """ .
  ?chebi up:name ?chebiUniprotName .
}
ORDER BY ?chebi

Note :

To fetch exactly one level: ?chebi rdfs:subClassOf CHEBI:""" + chebi + """ .

To fetch exactly all level: ?chebi rdfs:subClassOf* CHEBI:""" + chebi + """ .

To fetch exactly one to three levels: ?chebi rdfs:subClassOf/rdfs:subClassOf/rdfs:subClassOf CHEBI:""" + chebi + """ .

print(sparql_QEx4)

SPARQL is 1 based

When one queries the Uniprot KB (or other massive source) one can work 2step wise.

1 get a subset of the graph


P05067ttl = """base <http://purl.uniprot.org/uniprot/>  
prefix up: <http://purl.uniprot.org/core/>
prefix taxon: <http://purl.uniprot.org/taxonomy/>

<P05067> a up:Protein ;
         up:organism taxon:9606 .
"""

P05067=Graph().parse(format='ttl', data=P05067ttl)

for subj, pred, obj in P05067:
   print(subj, pred, obj)

And then query this subgraph

qres=P05067.query("""
PREFIX up: <http://purl.uniprot.org/core/> 
PREFIX uniprotkb: <http://purl.uniprot.org/uniprot/>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>

SELECT ?protein ?taxon
WHERE {
  ?protein a up:Protein ;
           up:organism ?taxon .
}""")

for row in qres:
    print("The taxon (organism id) of %s is %s" % row)