Import mondo owl file into neo4j

Integrations Linked Data, RDF, Ontology
1

Hi everyone,

My name is Jordi Valls, and I'm really new in neo4j and I have some questions about to import ontologies using the mondo.owl file...
I download this file from this web page:
http://obofoundry.org/ontology/mondo.html

I followed the instructions form:
https://neo4j.com/docs/labs/nsmntx/current/import/#actual-rdf-import

And I'm able to generate the graph example following the command:
CALL n10s.rdf.import.fetch("https://github.com/neo4j-labs/neosemantics/raw/3.5/docs/rdf/nsmntx.ttl","Turtle");

So I understand that the installation has been done correctly.

Then I import the mondo.owl using this command:
CALL n10s.onto.import.fetch("file://mondo.owl", "Turtle")

obtaining this output:
terminationStatus triplesLoaded triplesParsed namespaces extraInfo callParams
"KO" 0 0 null "mondo.owl" { }

and obviously my graph is just one node empty.

So I dont understand why I cannot import correctly mondo.owl, I need to modify some parameter?? I suspect that the format of mondo.owl is not compatible with format of neo4j, if it is confirmed, How can I adapt mondo.owl to neo4j format?
Mondo is a semi-automatically constructed ontology that merges in multiple disease resources to yield a coherent merged ontology

Thanks for your time and consideration.

Jordi

2

Hola @jvallsma7 , looks like the mondo.owl file uses RDF/XML serialization format, not Turtle.
Give it another try but setting "RDF/XML" as the second param instead of "Turtle".

That should hopefully do the job.

You may need to also adjust the path to your file.

I'm on a mac and here's what my import statement (I downloaded the mondo.owl to my Downloads folder) looks like:

call n10s.rdf.import.fetch("file:///Users/jb/Downloads/mondo.owl","RDF/XML")

╒═══════════════════╤═══════════════╤═══════════════╤════════════╤═══════════╤════════════╕
│"terminationStatus"│"triplesLoaded"│"triplesParsed"│"namespaces"│"extraInfo"│"callParams"│
╞═══════════════════╪═══════════════╪═══════════════╪════════════╪═══════════╪════════════╡
│"OK"               │2316154        │2316154        │null        │""         │{}          │
└───────────────────┴───────────────┴───────────────┴────────────┴───────────┴────────────┘

Hope this helps.

Cheers,

JB.

1 Like
3

Really thanks Jesus, now it works! But my question now is how I can know if I've to put Turtle or RDF/XML? Besides, I've import the mondo.owl and other named doid.owl in same neo4j browser window, but they do not make different node colors, one for each dataset, how can I do it?

Besides, I want to differentiate the hierarchy in different nodes, but I dont know if I've to modify these owl files....

Again thanks for your time and patience.

Jordi

4

Hi again Jordi, well I'm afraid the only way to tell what format is your file in you have to be familiar with the different RDF serialization formats and their syntaxes: Turtle, RDF/XML, N-Triples, JSON-LD... there are specs from the W3C for all of them.

You can change the style of the nodes and rels in the neo4j browser following the instructions here.

Hope that helps, sorry for the delayed response sometimes we cannot be as reactive as we would like to.

Cheers,

JB

5

Thanks a lot Jesus for your reply. Don't trouble for delayed response, I'm appreciate your time to answer questions.

Jordi