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This repository contains code for the AOP-Wiki XML-to-RDF conversion and guidance to deploy a Virtuoso SPARQL endpoint Docker image that is loaded with the AOP-Wiki RDF
License: MIT License
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Log with date and numbers (e.g. add rows to a table)
A GH action to
Additionally, add automatic push to Zenodo of the new RDF
e.g. Zenodo
Frequency should be defined, as a daily push might be overkill -- @egonw what are your thoughts?
if not che .find ('{http://www.aopkb.org/aop-xml}jchem-inchi-key' )== None :
chedict [che .get ('id' )]['jchem-inchi-key' ]= 'http://identifiers.org/inchikey/' + str (che .find ('{http://www.aopkb.org/aop-xml}jchem-inchi-key' ).text )
if not che .find ('{http://www.aopkb.org/aop-xml}indigo-inchi-key' )== None :
chedict [che .get ('id' )]['indigo-inchi-key' ]= 'http://identifiers.org/inchikey/' + che .find ('{http://www.aopkb.org/aop-xml}indigo-inchi-key' ).text [:- 1 ]
We need a proper link for the inchi-keys that are present in the AOP Wiki.
Please let me know if it is applicable.
Describe in void file the promapping and hgncmapping data
AOP Wiki PR.txt
Where do these PR ontology IDs map to? Not all use regular expression pattern. This was taken from the AOP Wiki XML of July 1st 2018.
Notebook to execute SPARQL queries on the RDF
Ontologies that are not currently marked with a URI for biological objects
Ontologies that are not currently marked with a URI for biological processes
For cell terms, organ terms and biological action, WIKI is used (meaning AOP-wiki), for which a URI should be minted.
if not che .find ('{http://www.aopkb.org/aop-xml}dsstox-id' )== None :
chedict [che .get ('id' )]['dsstox-id' ]= che .find ('{http://www.aopkb.org/aop-xml}dsstox-id' ).text [:- 1 ]
DSStox IDs are not registered on identifiers.org. Need to find another way to link to the right URLs.
Now it is basically a script. To make the code and procedure more informative, the blocks of code should give some output