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ebi-chebi / ChEBI

Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds.
https://www.ebi.ac.uk/chebi
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Is there a tutorial to parse ChEBI owl/obo files? #4300

Closed wanglu2014 closed 1 year ago

wanglu2014 commented 2 years ago

To parse full file in this link, and extract relationship. https://ftp.ebi.ac.uk/pub/databases/chebi/ontology/nightly/ I do know ChEBI provides csv files in another link, however, the direct parsing of owl files might be important task for our study. Thank you for your attention.

amalik01 commented 1 year ago

Hi,

ChEBI provides the ChEBI ontology in the W3C standard web ontology language (OWL) format. Tools such as Protégé, TopBraid, the NeOn toolkit and the OWL-API can be used with this ontology.

wanglu2014 commented 1 year ago

Hi,

ChEBI provides the ChEBI ontology in the W3C standard web ontology language (OWL) format. Tools such as Protégé, TopBraid, the NeOn toolkit and the OWL-API can be used with this ontology.

Thank you for your reply. I do know those tools. However, by my knwoledge, there is no direct function to read owl as a tree or formated data frame, so we can extract information form chebi files . There is a great effort to processing readed files. Could you kindly suggest an example on how to process chebi data?

amalik01 commented 1 year ago

There is LibChEBI which is available to access ChEBI data (further info: https://jcheminf.biomedcentral.com/articles/10.1186/s13321-016-0123-9).

sorenwacker commented 1 year ago

You can also read obo files with obonet (Python) and turn them into a NetworkX graph.