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EBISPOT / ols4

Version 4 of the EMBL-EBI Ontology Lookup Service (OLS)
http://www.ebi.ac.uk/ols4/
Apache License 2.0
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Ontologies load failure - OLS4 #671

Closed deepananbu closed 5 months ago

deepananbu commented 5 months ago

We are facing multiple issues while loading ontologies through OLS4. Below are the issues

OntologyId Issue Exception
abcd Invalid URI org.apache.jena.riot.RiotException: Bad character in IRI (space): http://rs.tdwg.org/abcd/terms/Specimen[space]...
battinfo URL doesn't exist org.apache.jena.riot.RiotNotFoundException: Not found: https://w3id.org/emmo/domain/battery/0.8.0-beta/battery
bdsubj Content Type org.apache.jena.riot.RiotException: Failed to determine the content type: (URI=https://purl.org/fidbaudigital/subjects : stream=text/plain)
peco Content org.apache.jena.riot.RiotException: [line: 1, col: 1 ] Content is not allowed in prolog.
hoom Multiple Children org.apache.jena.riot.RiotException: [line: 21, col: 74] {E201} Multiple children of property element

These ontologies are loaded successfully in OLS3. Is there a way/approach we can follow to load these ontologies in OLS4?

haideriqbal commented 5 months ago

Hi @deepananbu, looking at the table you have provided I can see the majority of the issues you are facing are because of the format of the ontologies.

OLS4 only accepts ontologies which are in RDF/OWL format so this the ontology itself and all the imports need to be RDF format. If for example the ontology itself is not in RDF format or one of its import is not in RDF format then OLS would complain.

Just a note, PECO is already in OLS4 you can access it here: https://www.ebi.ac.uk/ols4/ontologies/peco

deepananbu commented 5 months ago

@haideriqbal - Do we have any workaround or temp solution to load these ontologies in OLS4? And what would be ideal solution to fix these kind of issues?

haideriqbal commented 5 months ago

@deepananbu possible fix would be to convert your ontologies to RDF format. You can do this using protoge (https://protege.stanford.edu/) or robot (https://robot.obolibrary.org/)

yangyangmiao2019 commented 5 months ago

http://www.ebi.ac.uk/efo/EFO_0009603 请问 这个数据如何下载？急，请求帮助。

henrietteharmse commented 5 months ago

@deepananbu I am closing this ticket for now as to the best of our knowledge this needs to be fixed on your side. Please feel free to open this again if this proves otherwise.