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obophenotype / provisional_cell_ontology

Draft cell type definitions from data - candidates for inclusion in CL

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Change component #8

Closed shawntanzk closed 2 years ago

shawntanzk commented 2 years ago

Currently there is some error:

robot --catalog catalog-v001.xml annotate -I "https://raw.githubusercontent.com/obophenotype/brain_data_standards_ontologies/pcl_migration/bdso-base-ext.owl" --ontology-iri http://purl.obolibrary.org/obo/pcl/components/bdso-base-ext.owl -o components/bdso-base-ext.owl 2021-12-02 14:28:06,467 ERROR org.obolibrary.robot.IOHelper - Input ontology contains 557 triple(s) that could not be parsed:

http://purl.obolibrary.org/obo/PCL_0011564 http://www.w3.org/1999/02/22-rdf-syntax-ns#type _:genid2147495839.
http://purl.obolibrary.org/obo/PCL_0011428 http://www.w3.org/1999/02/22-rdf-syntax-ns#type _:genid2147495737.
http://purl.obolibrary.org/obo/PCL_0012570 http://www.w3.org/1999/02/22-rdf-syntax-ns#type _:genid2147496043.
http://purl.obolibrary.org/obo/PCL_0011570 http://www.w3.org/1999/02/22-rdf-syntax-ns#type _:genid2147495841.
http://purl.obolibrary.org/obo/PCL_0013487 http://www.w3.org/1999/02/22-rdf-syntax-ns#type _:genid2147496140.
http://purl.obolibrary.org/obo/PCL_0013525 http://www.w3.org/1999/02/22-rdf-syntax-ns#type _:genid2147496168.
http://purl.obolibrary.org/obo/PCL_0011434 http://www.w3.org/1999/02/22-rdf-syntax-ns#type _:genid2147495743.

shawntanzk commented 2 years ago

Currently fixing issues by using sh run.sh make components/bdso-base-ext.owl prepare_release to run a release which forces make to build bdso-base-ext first - this allows the importing of terms to work properly (sh run.sh make all_components prepare_release should work too) - Nico mentioned that there are some technical issues that are more tricky to solve, but we can use this as a workaround for now