The following are required:
Make sure that ontofetch is added to your PATH variable in order to run fetch.py. Please note that fetch.py will take about a half hour (or longer) to complete. Any ontologies not fetched will be logged at the end of the process. There are a handful of known missing ontologies, and PRo, NCBITaxon, and GAZ cannot currently be fetched due to their size (fix in progress). MONDO and DINTO also cannot be fetched due to their PURL redirect path (fix in progress).
Once you've run fetch.py, the owl:Ontology element from each ontology will be available in metadata/xml/.
To run extract.py, populate the metadata/md/ folder with the .md files here (to automate later). This will generate two TSVs in the main directory (see below for details).
obo_metadata.tsv contains extracted elements from the .md files available from the OBO Foundry repository. ont_metadata.tsv contains the same elements from the released ontology files. Currently, the script extracts the following elements:
- Title
- Description
- License
In the owl:Ontology elements from the released ontologies, these should be annotated with Dublin Core properties.
In either file, if an ontology's ID is followed by *, it means that the file does not exist.
In the ont_metadata.tsv file, columns with no headers are the rdfs:comment fields from the ontology metadata.